BCH final (test 1 and 2)

All cells have a cytoplasmic membrane ("plasma membrane") true or false

true

Utilize the following equations: Kw = [H+][OH-] = 1.01e-14 at 25 degrees Celsius (Kw is temperature dependent!) Kw = (Ka)(Kb) ; pKw = pKa + pKb pH = -log[H+] ; pOH = -log[OH-] [H+] = 10-pH ; [OH-] = 10-pOH pH + pOH = pKw = 14 pH = pKa + log([A-]/[HA]) = pKa + log(base/acid) [base] + [acid] = [buffer]

temp dependent the extra heat. That means that the forward reaction will be favoured, and more hydrogen ions and hydroxide ions will be formed.

Steroids are a very important class of -------- based ------- that perform many different jobs in the body.

terpene based lipids

chromosomal dna is coiled hierarchially

tertiary is folding and supercoiling that packs the dna molecule into small space

Determine why carbon plays a large role in diversity and functionality of biomolecules.

tetrahedral shape and ability to bond to itself allows versatility in molecular bonding - 4 bonds through electron pair sharing Carbon atoms can form linear chains, branched chains, and cyclic structures

molecular recognition

the molecular recognition that takes place in an enzyme substrate complex is based on structural complementarity but not actual binding events - The complementarity is quite specific (lock and key) but not permanent which supports the enzyme's function, allowing enzymes to recognize, convert, and detach from substrates (ligands) and their products. - in molecular recognitions, biomolecules interact specifically with one another (structural complementarity) - mediated by weak chemical forces (reversible) - allows for conservation and reduction of waste if unnecessary

How would titrating a base with an acid look

the opposite starting from the top and a half eq point u can find the pH at eq point the same way as a traditional buffer

since the A carbon is assymetric

there are two possible, non-superimposable,mirror images of the amino acids, Or enantiomers

plasma membrane is thick or thin delicate or not permeable or impermeable Permeability of cell membrane depends on the ------

thin, (4-10nm), delicate (held together by hydrophobic interactions with phospholipids), Permeable, semi-porous, barrier to outside environment physiological state (polar/nonpolar, charged/uncharged) of the cell and size and nature of molecules

Substituents on the left in the Fischer Projection are drawn ----- the ring in a Haworth Projection and the substituents on the right are drawn below the ring.

above

before doing buffer problem on test tryto understand it conceptually

ok

The extracellular matrix proteins contain -----------, including the ------------(shown above in abbreviated form).

several proteoglycans cartilage matrix proteoglycan

· Understand and describe the phase transition and the characteristics associated with it. The overall order of a Lipid bilayer is diverse. It can undergo a ----------------------------- phase transitions, somewhat like a solid to liquid phase transition. At cold ------- the bilayer is highly -------- and ------ --------- phase that is --------like. At higher ----------- the membrane is much more -------. This phase transition is a ---- transition and is based on a ------- -----. The more fluid phase is called the ----------- or ---------- It is characterized by --------- --------- ------, subsequently a ---- surface area and -------- bilayer than in the lower temperature "gel" phase.

The overall order of a Lipid bilayer is diverse. It can undergo a temperature-dependent phase transitions, somewhat like a solid to liquid phase transition. At cold temperatures the bilayer is highly ordered and densely packed phase that is gel-like. At higher temperatures the membrane is much more fluid. This phase transition is a sharp transition and is based on a TM (Melting temperature). The more fluid phase is called the liquid crystalline or liquid disordered state. It is characterized by less well-packed phospholipids, subsequently a larger surface area and thinner bilayer than in the lower temperature "gel" phase. The characteristics of increasing surface area and thinner bilayer are a consequence of the disruption of the packing of the hydrocarbon tails (heat energy disrupts the van der Waals interactions between them).

how can peptide bonds be linked? what is 2 or 3 linked called? 12-20? more than 20?

The peptide bond is a form of amide linkage and are linked together as dipeptides, tripeptides and up to about 12. 12-20 amino acids linked together is called oligopeptide More than 20 amino acids is called a polypeptide and//or a protein

Understand the secondary structure of proteins. Where do they arise from?

The structure of a protein starts begins with a primary sequence - The order of the amino acids in the primary structure allows secondary structures to arise. - Rotation in the backbone is allowed at linkages between the alpha carbon and the carbonyl carbon as well as between the alpha carbon and the nitrogen The secondary protein structure is a formed coil held together by hydrogen bonds.

use of mass spectrometry

Mass spectrometry (MS) is a commonly used, high-throughput tool for studying proteins. The procedure of MS-based protein identification involves digesting proteins into peptides, which are then separated, fragmented, ionised, and captured by mass spectrometers.Jan 21, 2013

identify the factors that make equilibria more complex.

Metal Ion effects ATP has phosphate groups on it that also bind to metal cations: Mg2+, Ca2+, Na+, K+. This binding stabilizes the phosphate groups, reducing the value of the free energy. For instance, Mg2+ is normally found in concentrations of 5 mM or greater in biological systems. At this concentration, the value of the free energy is 3-0.5 kJ/mol. At zero magnesium ion, the value increases to -35.7 kJ/mol. The binding of metal cations to ATP has a far greater effect than changes in pH.

There are 3 general groups of carbohydrates:

Monosaccharides, oligosaccharides and Polysaccharides.

What are common terpenes?

Monoterpenes (2 isoprene units) occur in all higher plants, and are the building blocks of cholesterol and other steroids, and carotenoids (photosynthetic pigments). Aldehydes and alcohols of monoterpenes are aromatic compounds in plants (e.g. menthol and citronella). Rubber is a terpene polymer.

Identify, structurally, the 5 different classified groups of high energy molecules. this slide (name them)

Most all of them include a phosphate group

positives of weak imf

Most biochemical reactions are reversible Weak bonds of biomolecules allow for reversibility Especially for enzyme functionality - - If all interactions were covalent bonds, enzymes would be unable to recognize, convert, and detach from substrates (ligands) and their product

What are the four structural classes of globular proteins?

Most globular structures belong to one of 4 structural classes All alpha - structure is dominated by all alpha helices All beta - structure is dominated by all beta sheets a/b - structure has intermingled helices and sheets A + b - structure has the helices and sheets separated

backbone of protein

N-C-C-N-C-C-etc, polypeptide chain

purines add the osine in dna deoxy(ex. adenosine) for pyrimidines idine cytidine deoxy for dna very little differences with ribose sugar for thymidine and uridine, no need to add deoxy because only in dna or rna IF THERE ARE 2 RINGS IN THE BASE IT IS A -------------, WHICH IS EITHER ----- OR -------

PURINE, ADENOSINE OR GUANINE

polysacs, Also known of as ------ , they are synthesized from monosaccharides and their derivatives.

"glycans"

If all 3 are the same fatty acid the triglyceride is called ------- if they are different it is called --------

"simple" "mixed"

In order for hydrogen bonds to have its max strength, ------, C=O and N-H groups must

(25 kJ/mol) arranged in space so O, H, and N atoms lie along a straight line

O-glycosylation

(O-linkage) In O- glycosylation, the addition of sugar chains can happen on the hydroxyl oxygen on the side- chain of hydroxy lysine, hydroxy proline, serine, or Threonine

What are the "Ramachandran angles"?

(Torsion angles) Rotation or dihedral angles - Alpha carbon to the nitrogen angle - Alpha carbon to the carboxyl angle - Two structures dihedral angle Start with the fully extended protein structure Rotate counter-clockwise start at +180 deg and decrease angle Rotate clockwise start at -180 increase angle

native state

(lowest energy point) 3-D folded tertiary structure

What is a prosthetic group?

(signal sequences). If the constituents are participants in the protein's function they are called the prosthetic group (ex. Iron in hemoglobin) any prosthetic groups that are incorporated into the complete protein structure. Hydrophobic residues INTERNALIZED

aliphatic amino acids, RANK HYDROPHOBICNESS

- Alkane chains (hydrophobic) hydrocarbons - Pink portion is the constant in all of the amino acids - Other part is side chain (gives personalities) Proline - cyclic Glycine - H Alanine - methyl Valine - V Leucine - V with one additional, butyl Isoleucine - variation of leucine, methyl brought down 1 , butyl group Internalized in various protein structures Exception is glycine because only has hydrogen, no carbons (NOT HYDROPHOBIC)

Ionic/dipole interactions

- stronger than other IMFs - Depend on type of dipole - permanent or induced - can created dipoles in other molecules or in their actual molecules - bonding can be layered or bonding side to side

Understand amino acid reactions. How is a peptide bond formed? What kind of reaction is this?

Peptide bond formation - a condensation reaction. Two amino acids are joined together by a removal of a water molecule, forming a peptide bond

Once you have isolated the protein out of the cell, you still have a bunch of other crap in the cell. You need to get rid of the other cellular items

Precipitation - Precipitate the protein with Ammonium sulfate (NH4)2SO4 You just keep precipitating out the precipitate protein and once you have isolated the ammonium sulfate precipitate (with protein), you can remove the ammonium sulfate by dialysis to remove the chemical you don't want You can visualize the protein because it aggregates (hydrophobic groups) and you will end up with a visible amount of protein. If you do a large prep you can do this all at once because it can handle large volumes

What amino acid has a secondary alpha-carbon?

Proline

What amino acid(s) are considered helix breakers - what does this mean?

Proline (and glycine)- considered a helix breaker because of the limited rotation around the phi bond - Glycine - small and disrupts regularity - Proline - Proline also destabilizes α-helices because of its irregular geometry; its R-group bonds back to the nitrogen of the amide group, which causes steric hindrance. "helix breakers" because they disrupt the regularity of the α helical backbone conformation; however, both have unusual conformational abilities and are commonly found in turns.

The linkages between the glyproteins and carbs can be

-O- or -N-

which 2 phenomena help to stabilize the protein in its conformation

1 - Formation of lots of hydrogen bonds 2 - reduction of surface area accessible to the aqueous solvent

differences between protein helices in a-keratin (alpha helices) and keratin types

Protein helices are stretchy and can elongate. When keratin is stretched it can form a more sheet like structure B-keratin - of feather and nails are extended and have a more rigid and stiff consistency. More rigid and stiff due to the b-keratin angle with coils with alpha helices so a little stiffer.

Proteins

Proteins - also known as peptides (chain of aa) Most important function in the cell are enzymes. Catalysts that catalyze metabolic reactions Made of monomer amino acids Linked amino acids by peptide bonds to create long polypeptide chains Functions of structure, catalyze cellular processes

What are the general trends in folding?

Proteins can fold reversibly. How do they know how to fold to begin with? TRENDS - secondary structure folds first - Nonpolar residues aggregate to form a hydrophobic collapse - Long range interactions form between secondary structures and via hydrophobic interactions - There may be intermediate states in the process

Another factor that is going to determine the energy of a system, that is the order of the system. What is the molecular information going to do.

2^N equally probable ways that N molecules can be distributed in the bulb - This increase of randomness of the gas is entropy - Configurations Entropy = boltzmann constant (given quantity) - takes the number of ordered states and convert that value into an energy value ie. joules times the Ln W (W = maximum number of probable states/configurations)

mRNA methylated cap

7-methyl guanosine triphosphate cap

------ -------- dictates structure/function

AA sequence

Know the essential versus non-essential amino acids. What does it mean to be essential? What does it mean to be non-essential?

AA's are also classified if they are essential, (not created in the body, consumed) or nonessential (synthesized by your metabolism) Essential (PVT TIM HALL)- phenylalanine, valine, tryptophan, threonine, isoleucine, methionine, histidine, arginine, lysine, leucine . Bodies cannot make essential amino acids so we need to consume them

Compare

ATP -> to adp + Pi is much less delta G than expected Phosphoenol pyruvate (recharge molecule for ATP) is nearly double which is why they are coupled to it can recharge generate amounts of Free energy

Cells depend on energy to stay alive which can be obtained from either

ATP, Light, NADPH through simple lysis reactions.

Pyrophosphates

Acid anhydride bonding as part of ATP molecule

what type of formation is peptide bond formation

Actual bond formation is dehydration synthesis, removing of water between the two - creates the peptide bond between the carbonyl and amine group on two different peptides, forming dipeptides.

What are chaperones and what do they do? 2 types?

Also known as "heat shock" proteins. proteins that Interact with partially folded or improperly folded polypeptides, helping facilitating correct folding pathways or providing micro environments in which folding can occur - prevents inappropriate aggregation - they bind transiently (not permanent) Hsp70 and chaperonins (Hsp60)

How water deals with hydrophobic molecules

Another portion of water is the formation of hydrophobic spheres of hydrophobic molecules in water. Basically they don't share polarity like the ionic structures do , this is more minimization of surface area in atere. Form circular micellar structures to internalize the surface area of interaction between water and oil . Micelles are spherical amphiphilic structures that have a hydrophobic core and a hydrophilic shell. This is negative entropy that drives the nonpolar molecules. This is a negative entropy driven process that creates, we want positive entropy normally Formation of micelles - lipid molecules that arrange themselves in a spherical form in aqueous solutions

What reaction creates the ester linkage?

Attachment to fatty acids that occurs - waxes that are esters basically Monohydric (1 hydroxyl group) alcohol and it gets bound through a dehydration synthesis to the carboxyl group on a fatty acid and forms a fatty acid

Proteoglycans can contain repeating units of--------- that span over ---- residues.

Ser-Gly amino acids 200

Prokaryotes -

Simple Less complex Single cell Cell wall Cell membrane Area of DNA called a nucleoid Cytoplasm that everything resides in Ribosomes where protein translation takes place Bacteria is a simple prokaryotic structure that resembles what cells looked like

What is a beta-turn?

B-turns allow the strand to fold back on itself or reverse the direction of the peptide chain. Glycine and proline are two amino acids commonly found in these turns.

Proteins with Multiple Transmembrane Segments The number of transmembrane segments for most proteins is between 1 and 12 regions but some are known to have up to 33. An example of this multiple transmembrane style of protein is -------------

Bacteriorhodopsin has 7 transmembrane alphaα-helices connected by short loops. It is nearly fully embedded in the membrane. A retinal chromophore (purple) lies approximately parallel to the membrane and a proline residue causes a kink in one of the helical segments.

basic amino acids,

Basic amino acids - Histidine, Arginine, and Lysine Hydrophilic, like water Amine groups on each Positively charged at physiological pH Almost always see arginine as being protonated

Enol Phosphates

Basically substituted what was a hydroxyl is now attached to a phosphate group. Double bond nearby which will create that instability creating the higher energy bond/ electron withdrawing and the electron repulsion giving more energy

Reproduction allowed by

Basics of DNA and RNA allows for reproduction to occur and allows for the ability to reproduce in almost exactly the same form (fidelity in the next gen - from genetic code). If genetic code mutates - there are 2 possible outcomes due to evolution If it leads to a stronger, heartier, then the organism will live on to reproduce If it makes it less likely for an organism to survive, it will not move on and die.

where is the amide bond (peptide bond located)? Double bond character?

Between amine group and carboxyl groups of two separate amino acids Note that this bond has 40% double bond character, importance?

Mannose

C2 epimer of glucose

Galactose

C4 epimer of glucose

To relax the muscle, the Ca2+ has to be pumped back into the SR vesicles. This is accomplished by use of a similar to ---- --- -- --- Ca2+ ions are transported into the SR for every ATP hydrolyzed.

Ca2+-ATPase. The process is done very similarly to the sodium-potassium Pump. 2 Ca2+ ions are transported into the SR for every ATP hydrolyzed.

cell surface carbohydrates role

Cell surface carbohydrates are basically molecular recognition molecules and there are many types. carbohydrates that are actually stuck to internal membrane bound proteins. These carbohydrates recognize various toxins, bacterias, all of these and act as signals/signal receptors for cells.

Distinguish between D and L amino-acids. What is the name of the molecule used to determine the D versus L enantiomer structure?

D and L designations which are only made by comparison to Glyceraldehyde

DNA and RNA as we know them are polymers of nucleotides linked by -------------- bonds. Nucleotides are added to the ----- group of the next nucleotide on the polymer chain. The NTP (or dNTP) is incorporated as a ------------. The phosphodiester bond forms between the ---' and -----' carbons of the adjacent pentose sugar groups: At the --------- end of polynucleotides there is usually a monophosphate. At the ------- end there is typically a hydroxyl. Strands of DNA or RNA are always written --- to ------regardless of length.

DNA and RNA as we know them are polymers of nucleotides linked by phosphodiester bonds. Nucleotides are added to the 3'-OH group of the next nucleotide on the polymer chain. The NTP (or dNTP) is incorporated as a monophosphate. The phosphodiester bond forms between the 3' and 5' carbons of the adjacent pentose sugar groups: At the 5' end of polynucleotides there is usually a monophosphate. At the 3' end there is typically a hydroxyl. Strands of DNA or RNA are always written 5' to 3' regardless of length.

there are several different types of RNA that do the majority of work with respect to using our DNA. DNA gets -------------- into RNA (-------) and ------- gets ----------into protein DNA can also -------- itself into other --------

DNA gets transcribed into RNA (mRNA) and mRNA gets translated into protein DNA can also replicate itself into other DNA's

Deoxy Sugars -

Deoxy sugars have one or more -OH group replaced by hydrogen. Found in DNA and many polysaccharides and glycoproteins.

Dimer of keratin to macrofibril

Dimer of the keratin molecule (coiled coil rod structure)(N terminal head, C-terminal tail) → protofilament (dimers aligned in a linear fashion one after another) → Mircofibril (same idea) → macrofibril (microfibrils wound around) Coiled coil with linear structure gives protofilament strands that allow molecules to have some stretch, pull hair, and elongate because in lines with gaps. Neat structural features Protein helices are stretchy and can elongate. When keratin is stretched it can form a more sheet like structure

What is an example of a restriction endonuclease? ----- ------------ -------------- (see figure 11) is an restriction endonuclease that was isolated from the bacteria ------ This endonuclease recognizes the pallindromic sequence "---------" The enzyme cuts the sequence between the G and A leaving a -----OH on the G and a -----P on the A (i.e. a type A nuclease). This results in sticky ends that are 5' overhangs

EcoR1 Restriction Endonuclease (see figure 11) is an restriction endonuclease that was isolated from the bacteria E. coli. This endonuclease recognizes the pallindromic sequence "GAATTC". The enzyme cuts the sequence between the G and A leaving a 3'-OH on the G and a 5'-P on the A (i.e. a type A nuclease). This results in sticky ends that are 5' overhangs

how to remember

Ehalf cell poxidizing agent

Acyl phosphates

Electron repulsion Electron withdrawing Stabilization would take place with the separation of the phosphate group

exo or endo nucleases type a

Endo and Exonucleases can cleave the bond in two places: Type a cleaves at the 3' end of the phosphodiester bond.

exo or endo nucleases type b

Endo and Exonucleases can cleave the bond in two places: Type b cleaves at the 5' end of the phosphodiester bond.

Enzymes (not)

Enzyme catalysis - responsibility of cell metabolism (important) - highly regulated through feedback inhibition or substrate concentration dependence - depends on cellular environment because weak imf limit optimum pH and temp ranges where enzymes can function or exist.

same things about fatty acids

Fatty Acids Have a molecular organization consisting of a hydrocarbon "tail" and carboxyl group "head" The carboxyl group is ionized under normal conditions, giving a negative charge to one end of the molecule. Hydrocarbon tail usually contains an even number of carbons, with typical lengths of 14-24 carbons. Odd numbered hydrocarbon tails are found in some marine organisms. Single bonds are free to rotate, and therefore, saturated fatty acids are quite flexible.

What are forces that stabilize proteins structure?

Forces that stabilize protein structure: - Interactions between atoms in the protein chain - Interactions between the protein and the solvent Hydrogen bonds Stabilizes alpha helical structure and beta sheet structure The alpha helix and beta sheets - their presence creates added stability Disulfide bonds add to the stability Hydrophobic interactions (although mainly try to avoid water) - actually compact the protein and stabilize it in that fashion Hydrogen bonds between side chains not only in main chain and that stabilizes Electrostatic interactions between side chains, or even between the two ends of the side chain based on pH Having metal ions coordinate with portions of the protein (example iron with hemoglobin)

What is electrophoresis based upon? At a charge of #, which pole (+ or -) would an amino acid be drawn?

Gel electrophoresis - separation based on charge , (ISOELECTRIC FOCUSING) - at a pH of about 7 many of the amino acids have a Isoelectric point very close to 7 and therefore they are neutral at that pH - but other amino acids that have ionizable side chains have Isoelectric points considerably further away from 7 and therefore are charged at that pH - if we run electrophoresis based on charge, we can separate amino acids based on their Isoelectric points. Also called isoelectric focusing. Idea is to separate them out based on their charges - we can adjust what is or not charged by varying the pH of the buffer solution in which we have the amino acids

What is the only amino acid that is achiral?

Glycine

Proteoglycans are also thought to be involved in

Growth Mediation.

What interactions are present at the tertiary level?

Hydrogen bonding Protein tertiary structure is due to interactions between R groups in the protein. Note that these R groups MUST be facing each other to interact. determined by a variety of interactions (that produce folding of the R groups and between R groups Interactions include - Hydrogen bonds (polar and/or charged areas) Ionic bonds - between charged R groups and Disulfide bridges Hydrophobic interactions (causing the folding) Van der waals interactions - among hydrophobic R groups (throughout the protein stabilizing it)

At constant pressure, there are changes in qp (Enthalpy) and changes in order - disorder (entropy)

If G is neg that means that either enthalpy given off is negative and entropy is positive or temperature is going to give it for us

Water molecules also stabilize the tertiary structure of the globular protein through hydrogen bonding

If an alpha helix is partially at the surface of the protein, the helix is generally found to have a hydrophobic face on one side and a hydrophilic face on the other. (ex. Flavodoxin)

If fully saturated, they tend to be -------- at room temperature.

If fully saturated, they tend to be solids at room temperature.

What does it mean to saturated or unsaturated?

If the hydrocarbon tail is composed exclusively with carbons having single bonds, it is saturated. Unsaturated fatty acids have one or more double bonds

N-glycosylation

In N-glycosylation, the addition of sugar chains can happen at the amide nitrogen on the side-chain of the asparagine. They can be of 2 types: 1. Complex oligosaccharide- diverse group of sugar like GIcNac, L-fucose, NANA are present 2. High mannose oligosaccharide- contain primarily Mannose

difference in terms of prokaryotes/plants and animals

In the prokaryotic cells and plant cells they have a cell wall, but they do have a membrane just below it in animal cells there is only plasma membrane

How does glycosylation influence the specification of blood type?

Individuals of all blood types possess red blood cells that express an oligosaccharide foundation called the O antigen. The addition of extra glycosyl units to this antigen results in either type A, type B, or type AB blood. Individuals with type A blood express a glycosyltransferase enzyme that catalyzes the addition of N-acetylgalactosamine to the O antigen. Individuals with type B blood express a glycosyltransferase enzyme that catalyzes the addition of galactose to the O antigen. Individuals with type AB blood express both glycosyl transferases and, thus, will possess O antigens modified with both galactose and N-acetylgalactosamine. Finally, individuals who express neither glycosyltransferase enzyme have unglycosylated O antigens, which results in type O blood.

transmembrane proteins

Integral proteins that span the membrane.

· Recall the functions of the following: UTP

drives carbohydrate metabolism

· Recall the functions of the following: CTP

drives lipid synthesis

· Recall the functions of the following: GTP

drives protein synthesis

All active transport reactions are ---------------- reactions

endergonic coupled with exergonic

fatty acid carboxyl head groups are generally found --------- to glycerol or another type of backbone.

esterified

A variety of polar groups can be --------- to the phosphate of phosphatidic acid. This phosphate ester structure is referred to as the ------ -------- of the phospholipid. Phosphatidylcholine (lecithin) and phosphatidylethanolamine are two phosphatides that represent the most common components of cellular membranes

esterified "head group"

Proteins have unique sequences based on

evolutionary relatedness

physical properties of triglycerides depend on

fatty acid components Physical properties Liquid or solid at RT based on if oils and fats (saturated) Melting point increases with more carbons and less double bonds Hydrocarbons are so long with strong dispersion forces (saturated) when can lay parallel and pack tightly making solid

Be able to read Fischer projections correctly - which bonds are coming out of the plane and which bonds are behind the plane?

fischer projection - top and bottom going away from you, middle coming towards you

Saturated Fatty acids are very ---------- with -------- ------- ---- ------ ------------ They are generally found in a ----------- conformation. This formation allows for ------------------- between the molecules. When double bonds are added this adds ------------- that prevent this ----------- and the fatty acids become more -------

flexible free rotation of their single bond. trans (zig-zag closed packing cis "kinks" to the chains close packing fluid.

· Know the different lipid nomenclature methods. o Omega-Reference

focus on this : Indicates the number of carbons, the number of double bonds, and the position of the double bond closest to the omega carbon --------------------- The omega reference system - Tells us how many carbons there are - Number of double bonds and the position of the double bond closest to the omega carbon - Omega 3 and 6 cant be converted in the human body and are important in the human body

Describe the major different types of RNA: messenger RNA,

function as messengers carrying the info in a gene to the protein synthesizing machinery ------------------ the transcript that you get from dna that then is transferred to the ribosome to be read into protein about 5% of rna in cell heterogenous in size and base sequence based on genes

-OH caused differences rna vs dna

functions differ dna is the cookbook rna cooks dna provides genetic info, rna does too (viruses, etc.) rna has a lot of activity compared to dna

Monosaccharides are

generally 3-7 carbons long and exist as either Ketose or Aldose forms:

waxes

generally solids at room temp and low melting.

which type of protein makes up the majority of proteins in nature The diversity of protein structure arises from 2 features?

globular make up the majority of proteins in nature The diversity of protein structure arises from 2 features - The ability to fold into a large number of distinct structures - The varied chemistry provided by the side chains of the 20 different amino acids.

If carbon is attached to two oxygens (hydroxyl and ether) and those oxygens are attached to a carbon and a hydrogen 2 ethers

hemiacetal 1 ether, 1 oh r, and h

Protein folding doesn't happen all at once - it is a Protein folding doesn't happen all at once - it is a --------------- --------------

hierarchical process

Most of the high energy compounds have a phosphate group (except acetyl CoA) hence they are also called --- The bonds in the high energy compounds that yield upon hydrolysis are called

high energy phosphates high energy bonds.

Ligand concentrations are normally much ------------ than the protein concentration so; units in molarity. A plot of ligand concentration versus ligand bound to protein creates a hyperbolic curve:

higher

Methods to find type by code

https://www.chegg.com/homework-help/questions-and-answers/consider-following-peptide-sequences--lsftvniqltwkfd-b-dqalnslienliqk-c-qqnwgglevidtlpvwfl-q40211217

All three disac sugars are important to human diet but none are directly absorbed. They are ----- first into their component sugars by both acid and bacteria in the digestive system.

hydrolyzed

major force that drives non-polar substances out of aqueous solutionz?

increased entropy of solvent (water)

FORMAtion of disulfide bonds ----- of a protein's secondary structure

is not a vital part

What amino acids have two chiral centers?

isoleucine and threonine

Patterns and principles of rna structure

it has a lot of different structures compared to dna with double helix rna has a lot of tertiary motifs

fluidity effects visual

lateral movement of phospholipids kinking increases fluidity

structure order in terms of functionality secondary is like -------- ----- The fully working protein is the ------- -------- Building finalization occurs ------

like building block tertiary structure cytosol

o What is the intermediate state of the membrane referred to as?

liquid crystal state

dna vs rna sugar

main difference is that ribose is found in RNA Deoxyribose is the sugar found in DNA

are all membranes (their structure) identical? if not what does it depend on

no , they are unique depending on the type of cell and the type of proteins that are embedded in the membrane

absorbances of different nucleotides, they have --------even without the phosphates in the wavelength of light UV allows you to determine ---------- of ------ and or -------- in a solution

absorbances of different nucleotides, they have differences even without the phosphates in the wavelength of light UV allows you to determine concentrations of nucleotides and or nucleosides in a solution

secondary structure of tRNA

acceptor arm is where the amino acid gets bound to the transfer RNA

Incorrect protein folding resulting in exposure of hydrophobic regions can result in (chaperon HSP70)

aggregation

terpene (recognizing)

all terpenes are derived from original skeleton which is isoprene or isoprenoids, they are units based on isopentane type structure things with this basic structure (isopentane) all get lumped into terpene kind of lipid

Rotation in the backbone is allowed at linkages between the

alpha carbon and the carbonyl carbon as well as between the alpha carbon and the nitrogen

Amide-linked myristoyl anchors.

amide linkage to N-terminal glycine

What are supersecondary structures?

are basically combinations of secondary structures as alpha-helices and beta sheets being the normal Ex. alpha/beta barrels (combination of 8 of alpha beta structures put together). Alpha in red and beta chains in blue. It kind of forms of barrels The connecting loop that connects all of these structures are in pink Hole in the center (barrel like)

these ceramides (secondary messengers) understand what a ceramide does overall and that it is a second messenger system

are specifically related to both cell growth and/or cell death (apoptosis) type of processes. There are a large number of ceramide molecules that act as secondary messengers depending on what the cell needs them to do at that point in time

In addition to their straight chain forms, all 5 and 6 carbon sugars can assume a cyclic structure that adds another -------------

asymmetric center

Describe the different levels of nucleic acid structure - secondary,

base pairing the double helix formed by 2 anti-parallel DNA strands bind together by hydrogen bonding between bases on opposite strands

Most all of these tend to be found in

bilayers that form cell membranes Not just fatty acids, but also phospholipids (phosphate group)

microRNAS

bind to mrna's and prevent translation

Glucose

c

o What are the two major pathways (terpene biosynthesis) ? Know the very basics.

can also come from glycolysis - basically sort of jump ship goes away from carb cycle into the lipid cycle by taking the glyceraldehyde-3-phosphate and adding 2 C atoms that come in from pyruvate. You can actually get it all the way down to IPP isopentyldiphosphate

· Recall the functions of the following: ATP

central to energy metabolism universally throughout the metabolism to provide energy for various reactions

What is the most common steroid in animals AND is a precursor for all other steroids in animals?

cholesterol

reaction that forms carbohydrates

dehydration synthesis

Which carbon atom do steroids differ at?

Vary by what is linked to C17

hsp70 Protects protein from ----- - with unfolded protein, residues are left open to solution makes them susceptible to --------, but chaperones attach and keep protein from being ---------

denaturation proteases denatured

Through both chemical and enzymatic reactions, sugars are modified into a number of ------- forms:

derivative Sugar Acids Sugar Alcohols Deoxy Sugars Sugar Esters Amino Sugars Acetals, Ketals and Glycosides (replacement of a hydroxyl group in the sugar molecule)

glucose and galactose are

diastereomers

Know the basic functions of the different RNA - transfer, ribosomal, messenger, small nuclear, small interfering, and micro ---------- are highly specific and usually synthesized to reduce the translation of specific messenger RNAs (mRNAs). This is done to reduce the synthesis of particular proteins. They form from double-stranded RNA transcribed and then cut to size in the nucleus before releasing into the cytoplasm. miRNAs are a more general suppressive tool, formed from single-stranded RNA precursors and characterized by their distinctive hairpin shape.

dna is just one type rna has more than one basically have to do with processing, removal of introns, blocking of production of some proteins sirna mirna

Variable or extra Arm of tRNA

doesnt do much but it's existent but differentiates the tRNA from being a class 1 (short arm) and type 2 (longer arm) differentiates trna's no real other function

large globular proteins are composed of multiple ------ or modules

domains

remember where the heads and tails

phosphate heads (polar) groups outside tails inside

Protein stability inside of the cell is talking about ------------ (--------)stability, not necessarily chemical stability.

physical (thermodynamic)

hydroxyl containing amino acids?

serine and threonine

polar amino acids,

serine, threonine, asparagine, glutamine, CSNQY cysteine

Once this happens different ------ ------- by different forms of attraction begin to move together via these longer range interactions

side chains

These carbohydrates recognize various toxins, bacterias, all of these and act as

signals/signal receptors for cells.

Topo

spatial arrangement only

What is a ceramide?

sphingosine + fatty acid core structure

How do you know if a reaction is exergonic

products formed (ADP and hydrogen phosphate/phosphate) have stronger covalent bonds (plus intermolecular forces with the surrounding solution and dissolved ions) than the starting materials. This is the case for any exothermic process.

colligative properties

properties that depend strictly on the number of solute particles and not their chemical nature

the Fluid mosaic model basically states that the membrane is a mosaic of ---------- that are ------ in a ---- (not ------, there is movement bilayer of phospholipids,

proteins bobbing fluid static

nitrogenous bases o Which are pyrimidines? Which are purines? ------------------------- What is the major difference between these two structurally? are they soluble, why

purines - adenine and guanine pyrimidines - cytosine, uracil, thymine ---------------- Structures: The pyrimidine ring systems is planar, whereas the purine rings have some pucker. G, A, T, C and U (single letter abbreviations are generally used) bases have moderate solubility due to their polar groups.

Domains

strong regions of secondary structure

If u run out of buffer there is a --------- drop in pH when adding acid if mmol of added acid is higher than mmol of buffer than you will run out of buffer take the -log of remainder of unbuffered acid to get pH

substantial

O-linked saccharides in glycoproteins are found on cell surfaces in two structural motifs:

(1) Highly extended above the membrane surface (possibly as a protection) or (2) as a support to push the active portion of the protein above the membrane to be able to interact with its substrate. Leukosialin is an example of motif 1, Low density lipoprotein receptor and decay accelerating factor are two proteins with motif 2. Antifreeze glycoproteins are those that allow fish to live in freezing waters. These glycoproteins have a peptide structure of [Ala-Ala-Thr]n - Ala-Ala where n can be 4, 5, 6,12, 17, 28, 45 or 50. Each threonine has a disaccharide with β-galactosyl-(1-3)-α-N-acetylglucosamine.

aromatic amino acids,

- Aromatic groups - All of these cyclic are pretty much hydrophobic, contain aromatic group, Tyrosine - OH ionizable, capable of participating in hydrogen bonds - pKa = 10.5, H-bonding Phenyalinine Tryptophan - bicyclic indole ring, hydrophobic Tryptophan is classified as nonpolar due to the hydrophobic and aromatic properties of the indole side chain."

Protein disulfide isomerase (PDI)

- Assist in protein folding. Chuffles (catalyzes interchange and shuffling of disulfide bonds) the disulfide bonds around until the proper native conformations are formed PDI - calalyzes elimination of folding intermediates with inappropriate disulfide crosslinks Peptide prolyl cis-trans-isomerase (PPI) - basically catalyzes flips cis/trans isomers proline peptide bonds

Groel Chaperonin (HSP 60)

- Basically take protein into cavity of the chaperonin and allow protein to fold inside of this GroEL - Provides favorable conditions for folding - Enhances and catalyzes protein folding - ATP driven

Most of the acids in biochem are in buffer systems in equilibria in the body which provide buffers to keep body pH constant what are some examples

- Phosphoric acid and carbonic acid are examples of acids found in buffer systems with pkas that vary because some are polyprotic (more than 1 proton to donate=more than 1 equilibrium that we are concerned with. Use ice table Do not include water, it is a liquid. Water is a pure substance and a solvent. The concentration won't change and it'll cancel out on both sides so there's no point in including it

Characteristics of polyprotic acid buffers

- Polyprotic acids have more than 1 dissociation (H2SO3) - each has a net ionic eq of H+ + -OH —-> H2O, one way due to low ionization of water in water - Sulfurous acid is a weak acid, which have a buffer region - region where acid and conjugate base are in equilibria and what is happening is as you are - adding strong base to the solution, instead of it simply negating a molecule of the acid, it is still neutralizing 1 proton but it is creating the conjugate base at the same time. And Because this has the potential to be an acid you will have 2 buffer regions and 2 equivalence points because it is a polyprotic acid with strong base- Anytime you titrate a polyprotic acid, you are going to have a - seperate equivalence point for each proton, your going to have difficulty visualizing the separate equivalence point - if there is not a good gap between the pKa values = -log of eq constants (ka) found on the on the pH , remember pH=pKA at the half equivalence points. IF pka Separated by more than three pk units then you are able to visualize, if not it is difficult to visualize. The loss of each mole of H+ shows up as separate equivalence point (but only if the two pKa's are separated by more than 3 pK units) The pH at the midpoint of the buffer region is equal to the pKa of that acid species - ½ eq point The same volume of added base is required to remove each mole of H+ - overall driving reaction is the formation of water, the neutralization of acid using base of some sort to create water. Because water is a covalent compound it is a one way reaction. If you know volume at a half eq point of eq point it helps find the rest.

Hydrophobic Interaction Chromatography

- Separates proteins according to their differences in their surface hydrophobicity - HIC utilizes a reversible interaction between the proteins and the hydrophobic ligand of a HIC resin. - The interaction between hydrophobic proteins and HIC resin is greatly enhanced by the running buffer - A high salt concentration enhances the interaction, lowering the salt concentration weakens it

L3: Thermodynamics Basic concepts Define thermodynamic terms: System, surroundings, isolated system, closed system, open system, enthalpy, entropy, Gibbs free energy, etc.

- System - portion of the universe we are studying - Surroundings - rest of the universe - rule that state what is done to the system has an equal and opposite reaction on surroundings (and vice versa) - isolated - no matter or energy exchange (not seen often in biochemistry ) - closed - no matter exchange, but energy can (ex. Folding of protein, changed energy but not matter) - open - both matter and energy exchange (most of biochemistry) 3 main properties that describe the thermodynamics of any chemical or biological system Enthalpy (H) - the heat content of a system Entropy (S) - the measure of "disorder" in a system or its energy dispersal. The sign of - ΔS can be determined by comparing the number of moles of gas on the reactant and product side. Since the number of moles of gas is decreasing, entropy is decreasing, and thus is negative. Gibbs free energy (G) - the amount of energy available to do work in a system. The Standard Gibbs free energy, ΔG°, is the energy required to convert one mole of reactants to one mole of products

GroEL/GroES (chaperonins) system in E. coli

- Unfolded proteins are bound into pockets in the GroEL complex - The pockets are capped transiently by the GroEs "lid" - GroEL undergoes substantial conformational changes, coupled to ATP hydrolysis and the binding and release of GroES - Which promote folding of the bound polypeptide The, isomerization

Dialysis

- Use of a semipermeable (dialysis bag) to contain a protein of interest. (pores made too small for it too leave)) - membrane placed into the dialysis then placed into a large container of water or buffer with lower concentration - Salt in the dialysis tubing moves from high concentration to low concentration via passive diffusion. As the volume of the solution in the dialysis tubing decreases, the protein concentration increases

Isoelectric focusing

- Zwitterionic molecules are separated according to their isoelectric point - Separation is achieved by initially establishing a pH gradient along a gel - The sample then travels through the pH gradient under an electric field until their individual charges reach 0, i.e., when they attain the pH corresponding to their isoelectric point.

Hydrogen bonds

- between electronegative atoms with lone pairs of electrons and attached hydrogens. In biochemistry this is H-O and H-N bonds, H-F not in living organisms

Effects on free energy

- conc of reactions increasing product reactions, increases spontaneity of the value (making it larger) - pH can also affect free energy. Problem with applying standard state pH (1.0) to biological stystems In a biological r Set the pH at 7 (1.0x10^(-7)) Because one of the most important energy molecules ATP, has a great dependence on the concentration on magnesium in the system, we set it to a standard state = [Mg2+]= 1.0mM so for a biological system we are still at 1 atm, but at 1.0x10-7 M = [H+], and Magnesium conc is [1.0mM], DENOTED WITH AN APOSTROPHE CALLED A PRIME

Explain the debate of whether a virus is a form of life or not. What are the characteristics of a virus? What are the major arguments against a virus being a life-form? What is the life cycle of a virus (the steps)?

- supramolecular complexes, DNA or RNA, Membrane envelope (protein coat), Parasitic Cell is smallest form of life Viruses do not meet all of the criteria - cannot reproduce independently without hijacking the host's repro system - are incapable of properly producing and utilizing energy from env. (lack machinery) - just membrane bound segments of DNA or RNA Mechanism of infection (virus) Utilizes their protein coat to help protect themselves and gain entry Hijacks metabolic machinery By hijacking the metabolic machinery, the virus is able to use it to reproduce its own dna. - It reproduces out of control, often causing lysis (cell death) of cells. - Can integrate in DNA, retroviruses embed their dna in the dna of the host cell. - Can even cause mutation that perpetuate, leading to uncontrolled cell growth (cancer) Viruses take over cell for the sole purpose of creating new viruses. Viruses are specific in the types of cells they infect depending on the protein receptors on the surface of the target cells Dna of virus is relatively simple, only what is needed to manufacture new virus parts Life cycle - Attachment to receptors -Entry - once inside the cell, - Replication (of viral dna) - instructions in dna are transcribed to rna - Biosynthesis - Protein building machinery of the host cell then translates these instructions (rna) into components of a new virus. - Assembly - these parts are assembled into new viruses within the host cell - Release - when ready, viruses emerge from the host cell, often killing it in the process Some viruses retain parts of the host's cell membrane, forming an envelope around the virus, giving protection from the immune system of the host organism. Each new virus is now able to infect a new cell, repeating the process. Antiviral drugs target point in life cycle to prevent replication

facilitated diffution deltaG needs to be less than ---- to transport Unlike passive diffusion, the transport proteins can become --------- if the substrate concentration is high enough.

0, negative "saturated" One important characteristic that is associated with facilitated diffusion is saturation. This process is saturable, which means, as the concentration gradient of the substance increases, it will go on increasing until it reaches a point where all the carrier molecules are occupied.

standard state conditions and how can you tell

1 M 298 K 1 atm Implied temp if not stated other wise 298.14 K (25 C) The standard state values are indicated by the inclusion of the degree symbol on any thermodynamic parameters

Proteins are formed as long polypeptide chains. what do you call 1, more than one chains that are identical chains that are different

1 chain - monomeric More than 1 chain - multimeric Chains that are identical - homomultimeric (ex - Hexokinase) Chains that are different - heteromultimer (ex - Hemoglobin) Most proteins are between 100 and 2000 amino acids long with exceptions to this general value (ex. Titin at 26,926 AA)

Determine the useful properties of water. 1. What gives rise to these unusual properties? 2. How does the presence of solute affect water molecules? (remember everything) including properties (what is the name of them)

1- the structure of water, particularly its polarity and ability to hydrogen bond with itself is what gives rise to most of its unusual properties. 2. Water can form hydration shells around ions (both positive and negative) The ion-dipole interaction with the solute is greater than the ions' attraction to each other This is a byproduct of water's high dielectric constant. The higher the dielectric constant the more competitive a solvent is with a polar or ionic solute. water has influence on solutes, solutes also have an influence on the properties of water. Solutes create order in water. By forcing water to form cage-like clathrate structures around non-polar molecules and ions water is no longer able to maintain its normal 4 hydrogen bond structure with itself. Polarity of water allows We have a dipole here and these will create clathrate cages around things like the sodium ions the partial negative charges of oxygen will surround, shell around the solute ion. The dielectric constant of water is much larger than other solvents allowing water to work better with ions than they do with themselves, allowing sodium chloride to break apart in water so easily, very important to our survival Colligative properties - properties that depend strictly on the number of solute particles and not their chemical nature. What does the addition of solutes, both covalent and ionic cause? increase boiling points lower freezing points affect both vapor pressure and osmotic pressure in aqueous solutions. Water is a unique polar solvent which allows it to interact with ions and all kinds of molecules that contain groups that have the potential of hydrogen bonds.

Sucrose

1-2 glycosidic linkage

What are the two basic types of integral proteins? Relate what we learned about protein structure here.

1. A soluble globular protein that has a relatively short hydrophobic amino acid sequence (typically at either the amino or carboxy terminus) that is inserted into the lipid bilayer and essentially keeps the soluble protein anchored to the lipid bilayer. 2. A protein that is almost entirely embedded in the lipid region of the bilayer, with only a small polar portion exposed to the aqueous face of the membrane. This type is predominantly alphaα-helix or betaβ-sheet in structure. This allows them to exist without the additional support of the aqueous environment as they can self-hydrogen bond. Proteins with a single transmembrane section are often anchored by a single \alphaα-helix.

Four types of lipid-linked anchors known that attach proteins to membranes

1. Amide-linked myristoyl anchors. 2. Thioester-linked fatty acid acyl anchors. 3. Thioether-linked prenyl anchors. 4. Glycosyl phosphatidylinositol anchors (GPI anchors).

What are the structural and functional advantages to quaternary association?

1. Stability - Reduction of the protein's surface to volume ratio stabilizes the protein. 2. Genetic economy and efficiency - less DNA is needed to create monomer subunits than a comparably sized single protein equal to the size of subunits summed 3. Combining catalytic sites on one protein - the product of one subunit may be the substrate of another subunit. 4. Cooperativity - allosteric binding can take place where the binding of substrate on one subunit up or down regulates the binding on another subunit

Lecture 11: Lipid Structure and Function · Recall the four major functions for lipids.

1. They serve as structural components of biological membranes. Form lipid bilayer for most cells 2. They provide energy reserves, predominantly in the form of Triacylglycerols. Store energy in fat cells 3. Both lipids and lipid derivatives serve as vitamins and hormones. 4. Lipophilic bile acids aid in lipid solubilization for digestion.

1. Understand buffer systems. What are the two components of a buffer? What is considered the "buffer zone"? 2. If a strong acid is added to an established buffer system, what happens to the concentrations of buffer components? 3. If a strong base is added to an established buffer system, what happens to the concentrations of the buffer components? Why?

1. are weak acid or base and the salt of their conjugate in equilibrium. - Biochemical systems are flush with buffers due to their need to maintain certain pHs. - Phosphate and carbonate acids are two prominent buffer systems used in the human body. - Both ions are readily available and have pKa values that allow them to be good buffers in the systems they maintain. A "good" buffer system is one that has a pKa value at or within 1 pH unit of the physiological pH that needs to be maintained. - The area +/- 1 pH unit from the pKa of an acid is called the buffer zone. This is the area in which the addition of strong acid or base has a minimal effect on the pH as the acid-conjugate base system absorbs the base or acid and simply shifts their equilibrium. The pH will then shift significantly once the titration reaches the equivalence point (where all of the protons or hydroxides in the titration are neutralized). ex. Because amino acids are weak acids they can be used as buffers as well. Anserine, an alanine-histidine dipeptide, is an example of use of amino acids as buffer systems. A buffer is created by preparing a solution of A- and HA The ratio of A- and HA, along with the pKa of HA, allows us to determine the solution pH 2. If you add some acid or base to the solution the ratio of A-/HA, THAT IS ALL THAT IS CHANGING Although the ratio changes, the log of the ratio does not change very much, as long as there is still A- in solution. This limits the pH change Again however If you add the strong base it will react with weak acid shifting eq to A- If you add strong acid it will react with A-, shifting the reaction to weak acid HA This prevents the pH of the solution from significantly rising, which it would if the buffer system was not present.

specificity

10^-7 Some concepts to remember - Binding assays measure the bound ligand, how we determine how much ligand is actually bound - The dissociation, Kd corresponds to the ligand concentration at which half the receptors are occupied. Can be used for drug design - Both affinity and specificity are important to protein function

Recall the three laws of thermodynamics.

1st law - total energy of the universe is constant. Cannot be created or destroyed only transferred or converted into different forms. - energy lost by system must be gained by the surroundings (and vice versa) - internal energy of system (E) - sum of KE and PE within system dE = E2 - E1 If deltaE is positive - energy has flown into system from surroundings If delta E is negative - it means that energy flowed out of the system into the surroundings. (think currency) 2nd law - more entropy is good. the natural processes of the universe move toward an increase in energy - IE the entropy of the universe is always increasing 3rd law - the entropy of a perfect crystal at 0K is 0. - When you drop temperature down, you are essentially stopping all processes. Idea if you could reach absolute zero everything comes to a standstill and everything is not moving there is no increase in entropy Breaking a glass cup stays that way entropy

Carbohydrates/sugars are what % of the membrane they are found attached to ----- and ------- as glycoproteins and glycolipids on the outside of membrane form glycolipids that help the cell to ------- other cells of the body

2-10% proteins and lipids act as signal recognizers

Stereochemistry is huge in sugars. Each aldose sugar with -- or more carbons and each ketose sugar with --- or more carbons has at least one chiral carbon. These structures are named as D,L enantiomers based on the highest numbered asymmetric carbon farthest from the carbonyl carbon.

3 , 4

Know the three classes of protein structure.

3 Basic classes protein structure - Fibrous, globular, or membrane. Fibrous - Simple, regular linear. Perform structural roles, generally insoluble in water (ex. collagen) Globular - Roughly spherical Has both hydrophobic and hydrophilic AA Most enzymes are globular Membrane Associated with cell membranes More hydrophobic than globular proteins

4 common naming systems

3 attempt to denote the chain length and the number and positions of any double bonding Trivial - historic names (ex. Oleic acid) IUPAC (explicit locations) Abbreviations (carboxyl reference, omega (w)-reference)

basic structure of a steroid, also of cholesterol · Recognize the structure of a steroid?

3 membered 6-ring structure with 1 5 membered ring numbering pretty much conservative structure with cholesterol, key differences take place at carbon 17 on the structure modifications

other end of mRNA

3' poly A tail polymer of adenylate

------ residues are

4 overall residues are required to form the turns with two of the residues forming a hydrogen bond to stabilize the turn.

How many residues are required to form the turns with ---- of the residues forming a hydrogen bond to stabilize the beta turn?

4,

1kcal

4.184 kJ Tells you the relationship

structural characteristics of tRNA. -2

5 arm overall each arm has its own particular purpose

Proteoglycans o Although the structures are not well known, what do they share in common? Where do they typically appear? What are their functions?

A type of glycoproteins. Glycosylated proteins with sugars attached to them but are attached to highly anionic (basic glycosaminoglycans (GAG sugars) A lot of proteoglycans that are involved in all the extracellular matrices of connective tissues (found in the connections between the bones and muscles and so forth) Provide hydration and swelling pressure to the tissue to allow it to withstand compressional forces, good thing for cartilage tissue and so forth The proteoglycans provide interaction between the protein component and other macromolecules.

how is free energy related to electrical potential in the cell

A voltaic cell converts the deltaG of a spontaneous redox reaction into the kinetic energy of electrons. The cell potential (Ecell) of a voltaic cell (spontaneous cell) - depends on the differences in electric potential between the two electrodes (2 ions or 2 metals involved in the reaction) Cell potential is also called the voltage of the cell or the electromotive forces (emf) (what is driving the electrons to move from one of the metals to the other) Anytime Ecell >0, this is going to be a spontaneous process

Buffers

A weak acid and the salt of its conj base A weak base and the salt of it's conj acid Buffers - A buffered solution is one that resists a change in its pH when either hydroxide ions or protons are added. Buffered solutions are simply solutions of weak acids and bases containing a common ion. When hydroxide ions are added to a buffer solution, they react with the acid and are replaced by the anions. If you know the ratio of acid to base and both amounts are large, the proton concentration can be easily be found using the equation: To find the pH easily, the Henderson-Hasselbalch equation can be used:

What is an alpha-helix?

A- helical structures in - Protein Has hydrogen bonding structure every 3.6 amino acids - Has a complete turn, turns have R groups external to the structure - Rotates around and there will be cyclic alpha helical structures inside the protein

Active transport systems require energy to operate. The most common types of energy used are:

ATP hydrolysis in a coupled reaction (most common) Light energy Energy stored in ion gradients. Coupled gradients. Transport Processes Driven by ATP

Other biological important anhydrides and their importance

Acetyl Phosphate and 1.3-Bisphosphoglycerate (1,3-BPG) are both Phosphoric-Carboxylic Anhydrides that play important roles in metabolism (as above). Enol phosphates (E.G. PEP) are another high energy molecule that acts as a phosphorylating agent as well.

What is a hemiacetal

Aldohexoses undergo cyclization to form hemiacetals referred to as pyranose forms (5 carbons + 1 Oxygen). This is an acid or base catalyzed reaction and is reversible.

What kind of light can nitrogenous bases absorb?

All of the pyrimidine and purine bases absorb U.V. light - so the concentration of DNA or RNA in a sample can be determined by measuring the UV absorbance.

Understand amino acid reactions. How is a peptide bond formed? What kind of reaction is this?

Amino acids are linked together by amide groups called peptide bonds When protein synthesis occurs, the carboxyl group of the amino acid at the end of the growing polypeptide chain reacts with the amino group of an incoming amino acid , releasing a molecule of water. The resulting bond between the amino acids is a peptide bond dehydration synthesis or reaction at a molecular level. This reaction is also known as a condensation reaction which usually occurs between amino acids

Amylose Can be ------- ------ If u put iodine with amylose it will form helical complex turn ------ ----------- solutions of amylose are very unstable due to Intermolecular -------- and association of neighboring ------- molecules this leads to -------- increase and --------------- of amylose

Amylose Can be very long If u put iodine with amylose it will turn blue aqueous solutions of amylose are very unstable due to Intermolecular attraction and association of neighboring amylose molecules this leads to viscocity increase and precipitation of amylose

Calculate the pI of a peptide's zwitterion. pI = 0.5(pKa1 + pKa2) How do you determine which pKa values you use?

As you would titrate this it would slowly move up until the neutral zwitterion would arise between pKa = 6.04 and pKa = 9.17 or the isoelectric point which would be the average. If the side chain is uncharged and doesn't have an ionizable hydrogen then you would take the pKa of the carboxyl group and the amine group, average them and this will give you the pH where the isoelectric point will occur (zwitterionic form) When you have a side chain the pI will depend on whether or not the side chain is isoelectric with carboxyl group or amine group. Can be low or high. We care about this because when we do separation of amino acids we need to know when and if the amino acid is going to be charged because our separation techniques depend on the charge on the amino acid to make it work. Average of the one that you went above its pka and the one you havent yet

Assays

Assays are run periodically throughout a purification to determine - Concentration of protein , how much have we retained throughout purification - Activity of protein - make sure protein is still functioning

Why are phosphate groups found on the outside of the helix in dna?

Because Like-charges repel, the acidic phosphate groups are on the outside (i.e. separated from each other as much as possible).

Denaturation is a two-state process - folded or unfolded. How does a protein become denatured?

Because Secondary and tertiary arise from weak IMF;s - They are susceptible to denaturation through temperature or chemical means - Denaturation is a 2-state process. Eg. FOLDED or NOT FOLDED . - If the conditions cause a breakdown of the intermolecular forces, the entire protein structure fall apart - Can be caused by pH, Temp, Chemicals (guanidine HCl or Urea for example)

Recall the properties of peptide bonds.

Because of the location of the carbonyl group near the peptide bond, the bond has a partial double bond character through resonance. - This resonance restricts the rotation at this bond - Creating a coplanar relationship between the alpha carbon of the two amino acids - In addition to having 40% double bond character, the peptide bond is also relatively polar. - This is because the resonance of the double bond of the carbonyl causes partial positive and negative charges to form on the carbonyl carbon and nitrogen respectively as it resonates.

How is water found in almost every biochemical structure and reaction?

Because water forms hydrogen bonds with both oxygen and nitrogen compounds.

what configurations do amino acids that participate in helices

Both D and L amino acids can participate in helices but they cannot be mixed.

really do your best to differentiate between proteoglycans and glycoproteins

Both glycoproteins and proteoglycans consist of proteins conjugated to sugars, but they are biochemically distinct entities. Proteoglycans consist of a protein core to which sulfated glycosaminoglycan chains covalently bond. These attachments always occur via O-glycosidic bonds because they are attached to serine residues. Proteoglycans are always localized to the cell surface and the extracellular matrix. Heparan sulfates are an example of proteoglycans that are associated with processes such as organismal development and blood coagulation. Glycoproteins are broadly defined as proteins that are conjugated to carbohydrates. This conjugation can occur at serine, threonine, or asparagine. As a result, glycoproteins can contain either N- or O-linked glycosidic bonds. Glycoproteins are found in the extracellular matrix and throughout the cell. Inside the cell, they are found in Golgi complexes, secretory granules, and lysosomes. Glycoprotein-bound lectins regulate basic processes such as cell adhesion and innate immunity.

features of N glycosilation

Bound together by large chains of enzymatic action and dolichol-P-P- oligosaccharide is reacted with protein transferase and this takes place in endoplasmic reticulum and so it gets processed after created and all these oligosaccharides (GIc3Man9(GIcNAc)2) are added to it. And something called high mannose form - which basically puts these mannosidases and glucosidases process this and add mannose sugars to it, it's called a high mannose forms if it stop, if doesnt stop it will continue to form complex glycans

pka's

COOH - around 2 , NH3 - 9.5-10 Arginine - 12.48 Aspartate - 3.65 Glutamate - 4.25 Cysteine - 8.18 Histidine - 6.00 Lysine - 10.53 Tyrosine - 10.07

o How are the Ca2+ ATPase and H+, K+ ATPase similar and different?

Ca+ ATPase: Ca2+ acts as cellular signal Muscle contraction: nerve impulse → SR → release of stores Ca2+ → [ Ca2+ ] increases Muscle relaxation: Ca2+ has to be pumped back into SR vesicles, this is done by Ca2+ ATPase pumps 2 Ca2+ ions INTO SR for each ATP hydrolyzes Gastric H+/K+ ATPase couples ATP hydrolysis to the pumping of H+ out of the cell and K+ into the cell electrically neutral because charge is +1 in both directions in another electrically neutral process the K+ ion is pumped out along with a Cl- ion using associated membrane transport system net result is maintenance of high [HCl ] in stomach bc pH of stomach is 0.8 to 1 and cells that form the lining have a preference of 7.4 so there is a concentration gradient across the mucosal cells this concentration difference is essential, BUT because of passive forces, the gradient wont be maintained structurally very similar to Na+/K+ ATPase

Calcium transport: Ca2+ -ATPase

Calcium is an ion that acts as a cellular signal in nearly all cells. In muscle cells the [Ca2+] is very low (~0.1mM). The ions are stored in sarcoplasmic (SR) reticulum (vesicles). When the muscle needs to contract, nerve impulses cause the SR to release Ca2+ ions and this causes the concentration to increase roughly 100 fold (10 mM).

cellulose Cellulose is a -------- of ---D-Glucose, which in contrast to starch, is oriented with CH2OH groups alternating ---- and ------- the plane of the cellulose molecule thus producing ------, ------- chains. The absence of --- ------- allows cellulose molecules to lie -------- together and form -------- structures. A Cellulose is the major structural material of -------. Wood is largely cellulose, and cotton is almost pure cellulose.

Can make a much more packed together due to gabs in betweeen. Makes it hard to degrade in the body. Body cannot break it down

Significance of branching of glycogen SIGNIFICANCE OF BRANCHING • Branched structure allows several ---- for simultaneous ---- and -------- • Branching speeds up ---------- • -------- glycogen phosphorylase cleaves one glucose as a time from a NON- reducing end of glycogen; each end can be attacked -------- by the enzyme at the same timel (Like picking grapes off of a bunch) * ---------- enzymes also play a part in -------- degradation Makes glycogen is an ------- way to store -------- • Structure makes it --------- and ----------- • Each glucose is readily accessible

Can only work on straight branches, need debranching enzymes for branches Enzymes for degrading can hydrolyze glucose from branches, speeds it up

· Describe the sodium potassium pump. What is the exchange Reactions within the cell that use K+ are inhibited by ----, thus, --------------- Ionic gradients of Na+ and K+ across the cell membrane are used to ---------- ----- ------ ---------- ----- ------- The ion concentration gradients are used to drive the ------------------- (Eg. Proteins or sugars etc.) Up to ----- of a cell's energy is use d in the maintenance of this pump.

Cells export Na+ and import K+ using a Na+-K+-ATPase. Reactions within the cell that use K+ are inhibited by Na+, thus, the [Na+] needs to be kept to a low in the cell. Ionic gradients of Na+ and K+ across the cell membrane are used to send signals down the length of a nerve cell. The ion concentration gradients are used to drive the transport processes for the compounds needing transport (Eg. Proteins or sugars etc.) Up to 40% of a cell's energy is used in the maintenance of this pump.

Recall the basics of each polysaccharide mentioned in the lecture. o Cellulose, What is the polysaccharide made from? What is the function? What bonds are present? Does it have a reducing end? § Be able to recognize the structures. Cellulose is the most ------ natural polymer in the world. Cellulose is made of ----glucose with ----------- -glycosidic linkages. Cellulose is resistant to ----------. The ------------- is needed to hydrolyze the glycosidic bond. Some bacteria make cellulase and can therefore "eat" cellulose.

Cellulose is the most abundant natural polymer in the world. Cellulose is made of D-glucose with \betaβ-1-4 glycosidic linkages. Cellulose is resistant to hydrolysis. The enzyme (cellulase) is needed to hydrolyze the glycosidic bond. Some bacteria make cellulase and can therefore "eat" cellulose. Cellulose is a repeating chain of cellobiose units, a non-reducing end, and a reducing end.

What is the difference between a carrier and channel protein (consider structure + active/passive transport)?

Channel - provide corridors that allow a specific molecule or ion to cross the membrane. literally channel/tunnel. Always passive transport (facilitated diffusion) Carrier - undergo a subtle change in shape that translocates the solute-binding site across the membrane. change in conformation can be passive or active if require energy most passive transport proteins are solute specific

Recall the basics of each polysaccharide mentioned in the lecture. o Chitin, major ones. What is the polysaccharide made from? What is the function? What bonds are present? Does it have a reducing end? § Be able to recognize the structures.

Chitin is in cell walls of fungi and exoskeletons of crustaceans, insects and spiders. Main difference between chitin and cellulose is the hydroxyl at the 2 position is replaced by -NHCOCH3. Chitin is composed of N-acetyl-D-glucosamine. α-chitin: all parallel 𝛃-chitin: antiparallel δ-Chitin : parallel separated by antiparallel structural supports.

Genetic testing has shown that there are a limited number of distinct domains in proteins. The Structural Classification of Proteins database (SCOP) organizes proteins into 5 classifications: Class, Fold, Superfamily, Family and Domain.

Class - is derived from secondary structure content in a domain Fold - describes the structure of the arrangement of the secondary structures in the domain A superfamily - includes domains of similar fold and function Family - A family includes domains with similar amino acid sequences. Domain - Larger globular proteins are often composed of multiple domains or modules. - These domains act as separate proteins with individual functions that add up to a cumulative overall functioning protein that retains the abilities of its individual domains. These domains are part of the tertiary structure of a protein. These domains were likely at one time individual proteins that have been "duplicated". There are many domains that are replicated in the same as well as different proteins.

Characteristics of globular proteins

Close packing is observed in most globular proteins with the packing densities being typically between 0.72 and 0.77. This is similar to the packing of solid spheres with only 25% being a void volume. These voids may provide "room' for conformational changes

how to find equivalence and half eq points

Close to vertical line - equivalence points Close to horizontal line - half equivalence point in the middle of buffer region. Also where pH=pKa equivalence points ( where moles of H+ = Moles of OH-) and multiple 1/2 equivalence points ( where [H3A] = [H2A-] and pH = pKa) The half equivalence point represents the point at which exactly half of the acid in the buffer solution has reacted with the titrant. The half equivalence point is relatively easy to determine because at the half equivalence point, the pKa of the acid is equal to the pH of the solution.

liposomes

Closed Lipid bilayer spheres that encapsulate ingredients, target their delivery to specific tissues of the skin, and control their release

Eukarya

Complex Multicellular (except protista) Have organelles All cells are coded by genes (organization of dna (made from nucleotides)) Dna is transcribed into rna -> translated into proteins that make up the structure of our cells and bodies. We are Complex organisms based on reading of genes. Unique genetic code, unique organisms Cytoplasmic membrane Cytoplasm (with structures inside) Ribosomes for protein production in rough ER (holds ribosomes in place) Golgi apparatus - package and delivery Chloroplasts - plants Mitochondria - power plant of the cell

Compound lipids1: phospholipids

Compound Lipids 1: phospholipids Fat derivatives - glycerol base, phosphate group attached as one of the three groups, Choline is a common group attached. Considered compound lipids

Compound Lipids

Compound lipids Most of compound lipids are esters of fatty acids containing groups in addition to an alcohol and fatty acid Phospholipids (phosphate groups), sphingolipids, glycolipids (sugars attached to lipids)

what is renaturation What is the amount of time required for renaturation directly related to? Renaturation experiments in which DNA from different species are mixed and allowed to --------- have shown similar sequences.

DNA Denaturation is Reversible Renaturation of duplex DNA means the two strands have to return to the correct base pairing order. The amount of time required for this renaturation to occur will be directly related to the complexity of the DNA sequence. Renaturation experiments in which DNA from different species are mixed and allowed to reanneal have shown similar sequences. This means there is some homology between species as different as humans and mice.

DNA and RNA are the informational molecules of life. Sequencing these molecules appears to be more ------- than sequencing proteins because of the larger ----- and ------ number of monomers, --- rather than ---. But the use of ---------- and ----- ------------- actually made the process simpler in the end.

DNA and RNA are the informational molecules of life. Sequencing these molecules appears to be more difficult than sequencing proteins because of the larger size and simpler number of monomers, 4 rather than 20. But the use of endonucleases and gel electrophoresis actually made the process simpler in the end.

Understand separation techniques. What is electrophoresis based upon? At a charge of #, which pole (+ or -) would an amino acid be drawn?

Diagnostics to determine amino acids in a protein - need to separate amino acids. General processes used to separate include Separation techniques take advantage of the ionization and solubility differences of amino acids. Partition properties - preference for one solvent over another Partition properties are used to separate the amino acids mostly by methods of chromatography like - ion exchange - high performance - Gas chromotographies Diagnostics to determine amino acids in a protein - need to separate amino acids. General processes used to separate include Gel E Paper choom

What is the importance of the double bond character

Dictates some of the properties of the bond and of the peptide chain in terms of rotation and ability to move because there is resonance due to the double bonding moves through from the carbonyl into C-N bond. There is double bond nature and resonance gives bond? Stability but also creates a planar structure in the bond.

Determine and explain the three major properties/patterns of biomolecules: Directional Informational 3-D Architecture

Directional - head and a tail, unsymmetrical unlike other smaller molecules. Structure that is sided - only organized in one direction. Use and produce energy Informational - Unique words or sentences. similar to sentences with monomers = alphabet (like DNA). dna proteins sugars Have 3-D architectures - Biomolecules are very Complex with unique tertiary and quaternary structures. Ex. complex Hemoglobin protein with embedded iron groups for transporting o2 but biomolecules are mainly held together by only the weakest IMF's : VDW and hydrogen bonds. BIOMOLECULES INTERACTIONS ARE CONTROLLED BY WEAK IMFS

How do intercalating agents affect structure of DNA? Intercalating agents are --------------------- -------- molecules that are --- and ---------. They are capable of -------- themselves into the ----- ----- causing ------- . This can cause -------- during the --------- of DNA, and the molecules are therefore, ---------. What are examples of intercalating agents?

Distortion of helical structure by intercalating agents Intercalating agents are organic aromatic macrocyclic molecules that are flat and hydrophobic. They are capable of inserting themselves into the DNA helix causing unwinding. This can cause errors during the replication of DNA, and the molecules are therefore, carcinogenic. Ethidium bromide, Acridine Orange and actinomycin D are some example agents.

Carbohydrates

Divided into 2 categories also called saccharides/sugars Mono /disaccharides are simple sugars (ex. glucose- mono, sucrose-di) Polysaccharides - complex sugars (ex: starch, glycogen, cellulose) These complex carbohydrates are formed by linking the simple sugars together (glycosidic bond) MAIN FUNCTION - energy and transport Carbohydrates - polymers are polysaccharides and disaccharides*; monomers are monosaccharides (simple sugars)

Do buffers participate in reactions

Do not usually participate in other reactions, other than fixing the PH We try to make buffers up that are "spectators" ex. Acetic acid and sodium acetate Ammonium chloride and ammonia Sodium carbonate and sodium hydrogen carbonate

energy changes in relation to q and w

Energy changes - energy of system factors (heat q and w work) Heat q - non mechanical transfer of energy lost or gained by a system Work w - force x distance in physics Work w for biological system (- P) x deltaV (change in volume))

Proteome/Proteomics

Entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time - It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. Proteomics is the study of and compilation of the proteome for an organism

Entropy and explain concept with bulb opening

Entropy is a State function determination of the degree of randomness or the number of states of a system. It depends only on the start and stop of degree of randomness of a system, (how many microstates did it start in how many did it end in). First entropy is 0. When you open the bulb and diffusion of gas occurs, entropy increases, you're basically looking at a constant energy process such that the energy of the system is still 0 but deltaS is greater than 0. Because it is a closed system so there is no loss of energy, all energy is constant (starting and ending energy of the system is 0) but there is an increase in entropy. The expansion however cools the gas, so there is an energy change. But the energy change is the entropy change, that is how you equate entropy with a change in energy. Basically equivalent to the decrease in thermal energy/kinetic energy.

Cis vs trans double bonds

Essentially two version as would be with any double bond structure - Cis - R groups basically near each other, strained (in most cases) because of electron-electron repulsion from two larger groups (R) Trans (MOST PEPTIDE BONDS) - opposite arrangement from each other. Preferred because less strain.

Organization and structure of cells

Eukarya (cell type) - animalia, protista (unicellular) , plantae, fungi - Prokarya - bacteria and archaea - Prokaryotes and eukaryotes have their unique structure however eukaryotes are far more complex.

· Explain the different forms of chromatin and the properties of histones. o What is euchromatin? What is heterochromatin?

Eukaryotic DNA is closely associated with proteins, creating chromatin. Two basic types of chromatin are euchromatin, which undergoes the normal process of condensation and decondensation in the cell cycle heterochromatin, which remains in a highly condensed state throughout the cell cycle, even during interphase --------------

· Describe the functions of exonucleases and endonucleases. o What is the difference between the two in terms of function? Exonucleases start at the ---- of ----------( ) and --------- -------- the ------------- bond in the ---------- Endonucleases cleave at an ------------ ---- within the ---------

Exonucleases start at the end of a polynucleotides (either the 3' or 5' end, depending on their specificity) and sequentially hydrolyze the phosphodiester bond in the polynucleotide. Endonucleases cleave at an internal site within the polynucleotide.

simple lipids 1: fatty acids

FATTY ACIDS Usually C16, C18, C20 (approx) A lot of hy drocarbon (end omega) with polar carboxyl group head (alpha end) Saturated (ex. Steric acid) If fully saturated, they tend to be solids at room temperature. As long chains, lipids can layer close together with compact density Are solids at room temperature

other type of fibrous protein

Fibroin and B-keratin are B-sheet proteins - composed of stacked antiparallel B-sheets. Found in spider silk B-keratin - of feather and nails are extended and have a more rigid and stiff consistency. More rigid and stiff due to the b-keratin angle with coils with alpha helices so a little stiffer.

what role do fibrous proteins play?

Fibrous proteins generally play structural roles (ex. A-Keratin) Contain multiple a-helical structures and they are arranged in a coiled structure. A-keratin is found in hair, nails, claws and horns. In some of these coils, covalent disulfide bonds form to make the structure more rigid. These bonds determine crying of hair and wool

2-D Gel electrophoresis

First step, protein separated into its charges with isoelectric focusing Second step - the protein is separated according to mass using SDS-PAGE

Know the four levels of protein structure. - Primary, secondary (super-secondary), tertiary, and quaternary.

For any given protein there are four levels of structure Primary (1o) - amino acid order, sequence Secondary (2o) - arrangement of amino acid backbone, meaning it's folding as it folds into shape. Hydrogen bonds interactions create coils (helices) and (sheets) Tertiary (3o) - Three dimensional structure (of entire protein) which includes any secondary structures and any prosthetic groups that are incorporated into the complete protein structure. Hydrophobic residues INTERNALIZED Quaternary (4o) - multiple subunits (arrangement), where a subunit would be a complete tertiary structure. 2 or more tertiary structures combined with each tertiary protein described as a subunit of the quaternary structure.

Use and understand the pH scale. What is considered acidic, basic, and neutral? What does a change of 1 unit of pH mean physically?

For p in pH - "power of hydrogen", the pH is the negative logarithm -log() of the [H+]. - The pH value determines the acidity of a solution. As the pH of pure water is 7, this is set as the "neutral" pH with the scale up or down from that point being considered basic (>7) or acidic (<7). - The pH scale is logarithmic which means that each change of a value of 1 unit is actually a 10x change in the concentration of [H+].

What reaction creates the ester linkage?t

Formation of triglycerides Dehydration synthesis Gives us ester linkage between fatty acids and glycerol

Amino Sugars - whaere is it commonly found some names

Found in oligosaccharides like chitin. Contain amino groups instead of hydroxyl groups at the C2 carbon. Muramic acid and neuraminic acid are other examples found in bacterial cell walls.

o What are the four basic types of interactions for peripheral proteins? What are the two basic types of integral proteins? Relate what we learned about protein structure here.

Four basic types of interactions attach the proteins to the surface of the membrane: 1. interaction by an amphipathic α-helix parallel to the membrane plane (in-plane membrane helix); 2. interaction by a hydrophobic loop; 3. interaction by a covalent link with a membrane lipid (lipidation); 4. interaction by direct or non-direct (e.g. with a calcium ion) electrostatic bonds with membrane lipids;

· Describe the double helix of DNA. What are the pairing rules? WHAt kind of bonding The basis of the complementarity is ------ -------, i.e. non-covalent interactions that can ------- be broken and re-formed.

G is always paired with C, and T always paired with A, ATGC The basis of the complementarity is hydrogen bonding, i.e. non-covalent interactions that can easily be broken and re-formed.

How many hydrogen bonds exist in dna? which pair of bases has stronger interactions

G-C base pairs are stabilized by three hydrogen bonds, whereas A-T base pairs are stabilized by two. This means that the G-C interaction is stronger than the A-T interaction

Gags are much much more ---------- or -------- carbohydrates than in glycoproteins Different stocks and different domains, proteoglycans

Gags are much much more branched or attachments carbohydrates than in glycoproteins Different stocks and different domains, proteoglycans

glycogen function GLYCOGEN FUNCTION: All cell types - -------- reserve, ATP from glycolysis Skeletal Muscle- Used to generate ATP during anaerobic muscle contraction Glycogenolysis (degrading glycogen) and glycolysis (degrading glucose) active together Liver: The 1 source of glucose for maintaining blood glucose Stored in ----- and ----------- as granules or particles Up to 10% of liver mass and 1-2% muscle mass

Glucose neogenesis - put things back together back to glucose and back to glycogenesis structure. GLYCOGEN FUNCTION: All cell types - Glucose reserve, ATP from glycolysis Skeletal Muscle- Used to generate ATP during anaerobic muscle contraction Glycogenolysis (degrading glycogen) and glycolysis (degrading glucose) active together Liver: The 1 source of glucose for maintaining blood glucose Stored in liver and muscle as granules or particles Up to 10% of liver mass and 1-2% muscle mass

Sugar Esters -

Glucose, Fructose and other monosaccharides with added phosphate groups. Found in many metabolic pathways as intermediates.Eg. ATP.

What are the nonpolar amino acids,

Glycine, Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Methionine, Proline

Glycogen PICTURE HOW IT LOOKS stored in ------ and ---------- ------ branches and more --------- (than amylopectin) Glycogen is the storage form of glucose in animals and humans which is analogous to the starch in plants. • Glycogen is synthesized and stored mainly in the ------ and the ---------. • Glycogen is a polymer of ----------- identical to ----------, but the branches in glycogen tend to be ------ (about 13 glucose units) and more ---------. • The glucose chains are organized ---------- like branches of a ----------- originating from a pair of molecules of elycogenin, a protein with a molecular weight of 38,000 that acts as a primer at the core of the structure. glycogen is easily converted back to glucose to provide energy

Glycogen - has shorter branches structure than amylopectin and more frequent Analogous to starch in plants, storage unit Each little dot glucose monomer stored in liver and muscles

Recall the basics of each polysaccharide mentioned in the lecture. o Glycogen, What is the polysaccharide made from? What is the function? What bonds are present? Does it have a reducing end? § Be able to recognize the structures. hyrolyzed by --- -- ---------------- to yield glucose and ----------------- (glucose-\alphaα-1-4-glucose disaccharide). It can also be hydrolyzed by ---------- -------- (in liver and muscle) to release glucose-----phosphate.

Glycogen is the major form of storage in animals. It is highly branched with \alphaα-1-6 branches. It is hydrolyzed by \alphaα- and \betaβ-amylases to yield glucose and maltose (glucose-\alphaα-1-4-glucose disaccharide). It can also be hydrolyzed by glycogen phosphorylase (in liver and muscle) to release glucose-1-phosphate. several nonreducing ends and one reducing end.

Glycolipids Glycolipids are composed of a ----------- with a --------- attached to the ------------- ----------. They are found in the --------- ---------- of some cells and, in addition to other functions, play a role in -------- -------- -------- ---------. The sugar residues of glycolipids are oriented toward the outside of the cell.

Glycolipids are composed of a sphingolipid with a carbohydrate attached to the sphingosine backbone. They are found in the outer membrane of some cells and, in addition to other functions, play a role in determining human blood type. The sugar residues of glycolipids are oriented toward the outside of the cell.

Glycopeptides, vs glyco-amino-acids and glycosyl-amino-acids

Glycopeptide Is carbohydrate linked to oligopeptide comp. of L- and/or D-amino acids A glyco-amino-acid is a saccharide attached to a single amino acid by any kind of covalent bond A glycosyl-amino-acid is a compound consisting of saccharide linked through a glycosyl linkage (O-, N-, or S-) to an amino acid (the hyphens are needed to avoid implying that the carbohydrate is necessarily linked to the amino acid.

Glucosyl / glycosyl group o What is a glucosyl group? How is it obtained?

Glycosyl groups that are part of these are essentially free radicals or substituents that are obtained from removing the hemiacetal hydroxyl group from glucose or other sugar molecules. Glycosyltransferase takes the monosaccharide and takes it from a nucleotide linked sugar and attaches it to the nonreducing end of an oligosaccharide chain Makes this long stretched out structures that is attached to the core protein as below Does Not have to be the same can be alternating.

What is the difference between glycosylation and glycation?

Glycosylation - enzymatic attachment of sugar to protein (more common) Glycation - non-enzymatic attachment of sugar to protein

Phosphagens

Guanidine group Electron withdrawing, high energy

The basic monomeric units that are used to build up complex oligosaccharides are essentially limited to:

Hexoses. Glucose, mannose, galactose (all aldoses), and fructose (ketose) Pentoses. Ribose, xylose (both aldoses)

o What is the difference between positive and negative supercoiling? most common is

Higher Complexity Structures in DNA Supercoiling Supercoiling can occur in two manners - Negative or Positive. Negative supercoiling - left-handed - strands are underwound. Positive supercoiling - right-handed - strands are overwound Negative supercoiling is most common in the cell.

o What are histones? What are the major types? What are most abundant amino acids found here? Why?

Histones Proteins in chromatin are the histones, which are relatively small, positively charged proteins of five major types: H1, H2A, H2B, H3, and H4. All histones have a high percentage of arginine and lysine, positively charged amino acids that give them a net positive charge The positive charges attract the negative charges on the phosphates of DNA and holds the DNA in contact with the histones. -------------------- proteins whose major use is to act as scaffolding for this winding of dna around them for that purpose a lot of there percentage of the amino acids are things like arg and lys which are pos charge at phys pH's, that attract the phosphate backbone of the dna(nucleic acids) allowing them to wind around the histones to compact

Packing up DNA Histones Histones are small, ----------charged proteins (rich in -------and ------- amino acids) that interact with ---------- via the oppositely charged ----------------------------- Histone proteins known as -----, ----, --- and ---- assemble in ------ to form an -------- structure around which DNA (---------) will wrap in a --------- manner (like a phone cord). This complex of core ------- octamer plus externally ------ DNA duplex is called the --------. ------- bp of DNA wrap around the histone octamer. The histone protein ------ is found at the end of the nucleosome and --------- the assembly and the --------------- of DNA between ------. The space between sequential ---------------- is 40-60 bp of DNA ---------- structures are spaced along the DNA duplex in a regular arrangement (and appear like -------- on a ---------- under high magnification).

Histones are small, positively charged proteins (rich in arginine and lysine amino acids) that interact with nucleic acids via the oppositely charged phosphate backbone. Histone proteins known as H2A, H2B, H3 and H4 assemble in pairs to form an octameric structure around which DNA (chromosomes) will wrap in a helical manner (like a phone cord). This complex of core histone octamer plus externally wound DNA duplex is called the nucleosome. 146 bp of DNA wrap around the histone octamer. The histone protein H1 is found at the end of the nucleosome and stabilizes the assembly and the segments of DNA between nucleosomes. The space between sequential nucleosomes is 40-60 bp of DNA Nucleosome structures are spaced along the DNA duplex in a regular arrangement (and appear like beads on a string under high magnification).

Prochiral centers and ----- system of naming chiral centers The C-2 of glycerol is not . The mirror image can be rotated to overlay the original:

However, if either of the CH2OH groups is modified, then the C2 atom in glycerol becomes chiral. Thus, the C2 carbon is said to be prochiral. A prochiral center is indicated by the prefix sn-

What are the two classes of chaperones?

Hsp70 and chaperonins (Hsp60)

Chromosome Structure Human DNA consists of ---- pairs of chromosomes, which are ------ and --------- ------ DNA molecules. Total number of nucleotides is about - billion bp long and this means they are 0.34 x 10-9m/bp * 3 x 109bp = 1m long for one pair of our chromosomes Since DNA is -------- stranded there is actually 2m of these linear molecules that have to fit into a cell that is only 20 μm in diameter. Obviously, the DNA is folded up in some way.

Human DNA consists of 23 pairs of chromosomes, which are linear double stranded DNA molecules. Total number of nucleotides is about 3 billion bp long and this means they are 0.34 x 10-9m/bp * 3 x 109bp = 1m long! Since DNA is double stranded there is actually 2m of these linear molecules that have to fit into a cell that is only 20 \muμm in diameter. Obviously, the DNA is folded up in some way.

Hydrogen bonds that run in ---------- 5' to 3' and 3' to 5' with --------- groups on the exterior the -------- are being bound in center A and T form --- H bonds G and C form ----- H bonds this has to do with --------- of the double helix , the more -- - -- rich regions are more stable because have more ------- than -- - -- the melting temps of the double helix with a --------- number of -- - -- are going to be a -------- temp helpful with PCR because you have to calculate these things know how much temp need to rise the apparatus to the cycle tube in order to completely separate double helix forming the polymerase chain reaction

Hydrogen bonds that run in antiparallel 5' to 3' and 3' to 5' with phosphate groups on the exterior the bases are being bound in center A and T form 2 H bonds G and C form 3 H bonds this has to do with stability of the double helix , the more G-C rich regions are more stable because have more H-bonds than A-T the melting temps of the double helix with a greater number of G-C are going to be a higher temp helpful with PCR because you have to calculate these things know how much temp need to rise the apparatus to the cycle tube in order to completely separate double helix forming the polymerase chain reaction

The process continues, -------- - ------------ and others produce formation of the complete protein structure into a --- -------, or ------- ------- (complete domains form and the entire polypeptide is folded)

Hydrophobic forces 3-D structure tertiary structure

beta bulges

If you have extra residues between hydrogen bonds, pleating would bulge out, called beta bulges The pleating in each case allows for the best alignment of h-bonded groups

Understand the concept of water's amphoteric behavior.

In addition to forming - hydrogen bonds and - clathrate structures to interact with solutes - water also has acid-base abilities. Water is in fact amphoteric-able to react both as a base and as an acid. Water is the conjugate base for the hydronium ion and as the conjugate acid to the hydroxide ion, water can react with acids or bases added to its solution. In addition to water being a solvent and being able to hydrogen bond which makes it very vital to livelihood, it can also act as an acid or base. Can dissociate into hydroxide and hydronium ions . Because of this hydroxide is the conjugate base to water and water is the conjugate base to the hydronium - amphipathic. Water is the fundamental underpinning of the pH system. Ionization constant of water

What does it mean to be parallel or anti-parallel? how does the hydrophobic and hydrophilic sidechains work? How are the side-chains affected by this distinction?

In the parallel B-sheet the peptide strands If amine and carboxylic of both strands are aligned, it is called parallel strand where the strands are traveling in the same direction - If antiparallel, essentially turned around and bonding in an opposite direction, this provides a linear, alignment with straight hydrogen bonds As in the alpha-Helix, the sheets are held together by hydrogen bonds In antiparallel sheets all of the hydrophobic side chains form on one side of the sheet - Means that the hydrophobic and hydrophilic amino acids alternate in these sheets. In parallel sheets this is not the case. - These antiparallel sheets are found in silk - Alpha helices provide flexibility and b-sheets give strength to the silk fibers composed predominantly of the keratin protein

· Determine major differences between peripheral and integral membrane proteins. INTEGRAL o What are they? do they penetrate the hydrophobic region What is the distribution of polarity? Where are they found? Can they be separated/detached from the membrane - is it easy or difficult? Why?

Integral Membrane Proteins. These proteins have both hydrophobic and hydrophilic regions that are integrated both in and out of the lipid bilayer. Integral membrane proteins may extend partly into the hydrophobic region, or may span the entire bilayer. Because of their integration with the bilayer, integral proteins are harder to separate from the bilayer, and require the addition of detergents to remove them.

Features of O-glycosylation

Involves a battery (whole bunch) of membrane-bound glycoprotein glycosyltransferases acting in a stepwise manner; each transferase is generally specific for a particular type of Linkage. • The enzymes involved are located in various subcompartments of the Golgi apparatus. • Each glycosylation reaction involves the appropriate Nucleotide-sugar. • O-Glycosylation occurs post translationally (after the protein has been translated by a ribosome) at certain Ser and Thr residues Has a bunch of glycoprotein glycosyltransferases that basically do the transfer of glycoprotein to the polypeptide. These enzymes are part of the golgi apparatus. Glycosylation rxn puts these 2 things together

types of isomers and what is there subcategories

Isomers Constitutional (structural) - completely different structures, different properties Stereoisomers - spatial isomers (different chemical properties) - enantiomers - diastereomers - rotated bonds but not mirror images, different chemical properties based . - cis/trans, conformers rotamers

The self ionization of water plays an underpinning role in our understanding and description of acid-base systems. what is it at equilibrium

It is 1.8e-16 at equilibrium, HOWEVER Generally ,because water is a liquid, it's concentration is not placed in an equilibrium molarity of water in water is 55.5M. The concentration of both ions of water when dissociated is 1e-7M each. If you plug these values into the equation above you find the more familiar value for the self ionization of water: [Kw] = [OH-][H+] = 1e-14

Key points to understand

KEY POINTS to understand about - protein sequences Proteins have unique sequences based upon evolutionary relatedness - Proteins that perform the same function have similar sequences. They are said to be homologous. - If the proteins are from different organisms they are called orthologous and if in the same organism paralogous. - Related proteins share common origins (E.g - Hemoglobin and myoglobin or the serine proteases: Trypsin, chymotrypsin, and elastase. - A mutant protein is a protein with a slightly different AA sequence (ex. Sickle cell hemoglobin)

Memorize and recognize the strong acids and strong bases. What does it mean to be a strong electrolyte or weak electrolyte?

Ka AND kb of strong acids because they are so large Strong electrolytes - Salts Strong acids and bases Complete dissociation - completely dissociate in water and water makes a very good solvent for the ionic compounds. Ions are caged by water by ion dipole interactions. KCl and weak electrolytes Strong acids and bases The conc of these is equivalent to the overall acid concentration. If 2M perchloric acid it would be 2M [H+] concentration.

Hsp70 chaperone Keep the protein from --------- or ----------- the hydrophobic residues too soon

Keep the protein from misfolding or conglomerating the hydrophobic residues too soon

quick recap of fibrous (structural proteins a-keratin

Keratin , Long stretched out fibrous protein 2 alpha helical structures interwoven together - coiled-coil Inside is then in a hair that form micro and macro fibrils Forms a macro structure of these proteins Medulla and cuticle, core Cortex. keratin has a and beta (more harder to stretch) forms

· Be able to recognize/draw the following sugars: o Glucose, Galactose, Mannose, Fructose, and Sucrose. Know the isomeric relationships (structural isomer, enantiomer, diastereomer but not epimer, epimer) between each of the monosaccharides (i.e. if you know the structure of glucose and know that galactose is an epimer at C4, then you don't have to memorize that structure).

Know the ones in red and and D-ribose, know where hydroxyls are in each one of these

What is the largest energy contribution in protein folding? Is protein folding enthalpically driven or entropically driven? How?

LARGEST energy contributions in protein folding comes from - liberation of water molecules involved in the hydrophobic interactions (effect) with non-polar residues in the protein - The release of these water molecules provides enough positive entropy that the overall free energy of folding is between -20 to -40 kJ/mol. Not a large value of energy so the folded protein is only "marginally stable". This lack of absolute stability is what makes proteins flexible.

Recall the most common disaccharides: o Lactose What two monosaccharides compose the disaccharide? What kind of bond is created between the monosaccharides (i.e. alpha-1,2 - be more specific than "glycosidic")? Are they reducing sugars? What does it mean to be a reducing sugar?

Lactose is comprised of a galactose linked to glucose via a \ betaβ-1-4 glycosidic bond. "Milk sugar" - it is the principle carbohydrate of milk. Must be broken down into galactose and glucose by the enzyme lactase. For the same reason lactose is a reducing sugar.

When is the membrane more rigid (gel-like) for each of these factors? Why is this the case? Explain. THIS STUFF IS ALL MOVING

Length and saturation of hydrocarbons, - more saturated, longer chain temperature - At low temperature, the fatty acid tails of the phospholipids move less and become more rigid. This decreases the overall fluidity of the membrane presence of cholesterol. at high temps, the cholesterol keeps the membrane from being too fluid and makes it more rigid allow the membrane to be not as susceptible to temp fluctuations as it might be otherwise

plane polarized

Light beam - composed of em waves that vibrate in all possible directions perpendicular to its path. Materials such as plastic polaroid film can absorb waves except ones that vibrate in a particular plane. Light that consists of waves by berating in only one plane - plane polarized light Chiral compounds interact with plane polarized light, rotating its vibration to the left or to the right. Therefore they are optically active, 2 enantiomers will rotate the plane of polarization through the same angle, but opposite directions

o What is the linking number? How does this relate to the twist and writhe?

Linking Number (L) - This is the basic parameter used to characterize supercoiling. number of times the two DNA strands are intertwined. In a relaxed(no supercoiling) B form DNA there are 10 bp per turn. The linking number can be calculated as the number of bp divided by the number of bp per turn so a strand of 500 bp would have a linking number of 50 if relaxed.

Membranes are Asymmetric and Heterogeneous Structures

Lipid bilayers are typically heterogeneous in their lipid content. This heterogeneity is in both the types and the locations of the lipids. Lateral heterogeneity is when clusters of single types of proteins or lipids form in the bilayer. Clustering arises due to ionic interactions with metal cations: Lateral Phase Separation. This can also be caused through other associations like protein interactions with either the hydrocarbon or head group of specific phospholipids in the bilayer.

Lipid nomenclature 1

Lipid nomenclature Naming of fatty acids can be done in one of three ways: The systematic name The common name Shorthand notation Shorthand notation: - The number of carbons (including carboxyl carbon) followed by a colon(:) and then the number of double bonds. Delta system tells you the location of the double bonds - Sometimes the location of the double bond(s) is specified in parentheses after this. - The carbonyl is carbon 1.

· Understand the polarity of lipids. Lipids are amphipathic - what does this mean? o Why aren't lipids soluble in water?

Lipids - amphipathic bust vast majority is hydrocarbon

· Determine the four major components to the plasma membrane's fluid mosaic model. o What is the major role of each of these components? How can these broad components be broken down further (i.e. the carbohydrates can be found mainly as glycolipids and glycoproteins)?

Lipids - form the bilayer that is the main component of membrane Small amount of carbs (sugars) - glycolipids or glycoproteins Cholesterol - stabilizing agent in the membrane - depending on the type of cell, cholesterol content varies (bacteria vs nerve) Proteins - major component of cell membranes - help stabilize and give membrane its strength - related or completely in charge of transport of molecules in and out of the cell

· Further explain how a membrane is fluid through the concept of movement.

Lipids and Proteins can MOVE in membranes These movements range from vibrations to undulations to complete transverse motions. Lateral movements are rapid but transverse movements take longer.

Lipids are generally long chains of

Lipids are generally long chains of hydrocarbons that are non-polar and may contain a polar motif (fatty acids) that allow them to be amphipathic.

B-DNA --------- conformation of DNA in solution ------- (---------) antiparallel helix --------- bp (base pairs) per turn of the helix Each base pair extends the helical length by -----Å e.g. the helix is -------- Å long per turn. This is the pitch of B DNA. Complementary bases -------- bond with each other. The ------rings of the -------- stack on top of each other up the helix. This provides ------------ interactions (van der Waals) also. Has a ------ and a -------- groove in the duplex.

Major conformation of DNA in solution Duplex (two chain) antiparallel helix 10 bp (base pairs) per turn of the helix Each base pair extends the helical length by 3.4Å e.g. the helix is 34Å long per turn. This is the pitch of B DNA. Complementary bases hydrogen bond with each other. The aromatic rings of the bases stack on top of each other up the helix. This provides hydrophobic interactions (van der Waals) also. Has a minor and a major groove in the duplex.

Determining unknown E half cell

Meaning of a measurement - having an anode and cathode, anode (-) and cathode (+), electrons travel from anode to cathode. Typical cell structure - salt bridge allows circuit to be completed. Whatever is at the cathode is being reduced Anode is where things are being oxidized What is being oxidized is acting as a reducing agent What is being reduced is acting as a oxidizing agent

MaLDI TOF

Measure the masses of various components using mass spectrophotometer The amino acid sequence can then be determined by mass spectrometry.

Hydrolysis of Nucleic Acids Modification of nucleic acids requires the ability to ------------the ---------- bonds that hold them together. This hydrolysis can be performed by several methodologies in the cell: --------------- ---------------

Modification of nucleic acids requires the ability to hydrolyze the phosphodiester bonds that hold them together. This hydrolysis can be performed by several methodologies in the cell: Acid/Base hydrolysis Enzymatic hydrolysis - Nucleases

Some of the function of the JUST the oligosaccharide chain in the glycoprotein functons that don't include cell signaling, or cell receptor

Modulate physicochemical properties like solubility, viscosity, charge, conformation, denaturation, and provides binding sites for bacteria and viruses. • Protect against proteolysis (basically like a barbed wire fence on the surface of the cell membrane, things can't get to it, branching of sugar sticking out keeps things away from cell membrane ), from inside and outside of cell Affect proteolytic processing of precursor proteins to smaller products (sugar can act as a guard or aid Are involved in biologic activity, eg, of human chorionic gonadotropin (hCG) (hormone) •Affect insertion into membranes, intracellular migration, sorting and Secretion (can be a guide or inhibitor) Affect embryonic development and differentiation May affect sites of metastases selected by cancer cells

Molecules like ATP than contain phosphoric anhydride linkages readily undergo hydrolysis of these bonds - why?

Molecules like ATP contain phosphoric anhydride linkages (shown below), readily undergo hydrolysis of these bonds due to: - Strain caused by electrostatic electrostatic repulsion in the bonds (oxygens create destabilizing partial positive charges on the phosphorus atom due to oxygens electron withdrawing) - Stabilization of the products by both ionization and resonance (products are negatively charged at physiological pH helping offset the partial positive charge on the phosphorus and the resonance in the product is not competitive - Increase in particles (entropic effects) - The bonds of the atp have electron withdrawing - Unstable enol form to stable keto form AMP does not have an anhydride structure and thus generates a much lower delta G

most high energy compounds have what group and what is the bond the yield upon hydrolysis

Most of the high energy compounds have a phosphate group (except acetyl CoA) hence they are also called high energy phosphates The bonds in the high energy compounds that yield upon hydrolysis are called high energy bonds.

N-linked

N-linkages are formed through the amide group on Asparagine to N-acetylgalactosamine but also have a mannose branched triad involved.

Are the amino acids found in nature typically D or L? How is the +/- system unrelated to D/L system?

Nature is L amino acids found in nature and proteins in the body The amino acids found in nature are L enantiomers as this is the form that is synthesized in the body. The + or -, Dextrorotary or levorotary designation is unrelated to the D and L designations which are only made by comparison to Glyceraldehyde. The + or -, Dextrorotary or levorotary terms come from the fact that enantiomers can rotate plane polarized light. Configuration vs optical activity The D-L system corresponds to the configuration of the molecule: spatial arrangement of its atoms around the chirality center.

Type 2 Requires ATP? Y or N Methylate DNA? Y or N Cut specifically? Y or N

No, Does not require ATP for hydrolysis No, Does not methylate DNA Yes, Cuts at specific sites

simple lipids 2: fats and oils

Normally talking about things like triglycerides: glycerol bound to a fatty acid through an ester bond - These fatty acids or other totally different groups attached to glycerol

Nucleic acids

Nucleic acids Made of nucleotides - cytosine, guanine, adenine , and uracil (RNA), thymine (DNA) DNA - heredity RNA - using heredity into functional groups of molecules that eventually produce our proteins

Nucleosomes can form a --------handed helical structure: ----- nucleosomes per turn ( ~--------- basepairs of DNA) helical diameter of 30nm. This molecular assembly is called a "----------" The -------- "fiber" forms looping structures (like a carpet pile) These can further assemble into the macro structures known as -------------

Nucleosomes can form a left-handed helical structure: six nucleosomes per turn ( ~1200 basepairs of DNA) helical diameter of 30nm. This molecular assembly is called a "Solenoid" The solenoid "fiber" forms looping structures (like a carpet pile) These can further assemble into the macro structures known as chromosomes

How are glycoproteins oriented in cell membranes?

O-linked (1) Highly extended above the membrane surface (possibly as a protection) or (2) as a support to push the active portion of the protein above the membrane to be able to interact with its substrate. towards the outside of the cell

testing knowledge

ON TEST above In nature aa - L In nature carbs -D

N-linked oligosaccharides

Oligosaccharides covalently linked to asparagine residues of proteins. N-linked immunoglobulins G and M,ribonuclease B and ovalbumin as well as some peptide hormones.

Omega is the end of the greek alphabet

Omega is the end of the greek alphabet If we count all of the carbons from carboxyl group If the double bond was at the 3rd carbon from the omega it would be omega 3

tertiary structure of tRNA

Once all bound together, has this double helical stem areas that forms this L shape and so you have reading at one end and the other end at the top gives amino acids

Lecture 9: Carbohydrate Structure and Nomenclature of Monosaccharides · Recall the key features that allow carbohydrates to be involved in energy production, cell structure, and recognition processes.

One or more asymmetric center in their structures Existence as either a ring or linear structure as needed Ability to form polymers through glycosidic bonds Ability to hydrogen bond via numerous -OH components in their structure

· Describe the different types of membrane transport in detail. what are they ---------------- All cells maintain --------- ------- of various --------- ions across their membranes. This is either required for -------- or is used in --------- --------, or as a source of -------------- ------. A key point to membrane transport is that most of the molecules that must be transported are----- or ------but their transport across the cell membrane requires them to pass through a hydrophobic environment. This is why transport is accomplished by specific integral membrane proteins.

Osmosis o Simple Diffusion. o Facilitated Diffusion. o Active Transport. o Bulk Flow. ---------------- Concentration Gradients inorganic survival, signal transduction, potential energy polar or ionic

other secondary structures that form more structural types of protein silk fibroin a almost ----- extended ----- -----

Other types of secondary structural that form more structural types of proteins Silk fibroin (B-pleated sheet instead of alpha helix protein) - silks in spiders and insect webs, caccons, insects Silk fibers are really strong but not really stretchy. Sewing hard Almost fully extended beta sheet meaning that it is stretched to the max not going to stretch any further and very strong so the fibroin and sericin (gummy protein stuff that sticks to the fibroin are components) Adult moths dissolve their cocoons and human cloths (enzyme cacconase) dissolves by hydrolysis cloths Also remove sericin by boiling it or hydrolysis (weak interaction)

Highest energy compound why are they usrful even though they have steep activation energies and low comparable energy release

PEP Phosphoenolpyruvate (very high energy) Although many phosphoryl group transfer reactions have high/steep activation energies (200-400 kj/mol) and only release about 30 - 40 kj/mol of energy, they are still useful due the the fact that enzymes catalyze the reactions and easily deal with the large activation energies

What is TLC based upon?

Paper chromatography or thin layer chromatography (based on polarity) Generally have a slightly polar solvent that is used (mobile phase) Amino acids will either bind to the paper or be carried along by the mobile phase. most polar binding to paper towards bottom and least polar being pushed along by the mobile phase. There is also a molecular weight component. Allows us to separate amino acids both by polarity and molar mass and make a determination amino acid content for a protein.

what characteristic do peptide bonds have and what is it similar to

Peptide bonds are planar Reason is the same reason ethene structure is planar due to partial double bond structure. Double bond nature creates it into a planar structure

peptidoglycan parts

Peptidoglycan structure Unique structure that forms as part of the A peptidoglycan glycan consists of a glycosaminoglycan formed by alternating residues of D-glucosamine and muramic acid

----- and ----- tend to form a-helices, while polyaspartic acid and poly glutamic acids do not.

Polyleucine or polyalanine

Polynucleotide strands are -------. Each Deoxyribose segment has --- degrees of freedom that come from the ---- single bonds along its structure. The C1-N bond also can rotate so that adds a --th.

Polynucleotide strands are flexible. Each Deoxyribose segment has 6 degrees of freedom that come from the 6 single bonds along its structure. The C1-N bond also can rotate so that adds a 7th.

----- and ----- are unusual as their peptide N atom is also part of the side chain, severely limiting rotation about the N-Ca bond

Proline and hydroxyproline There are limits on how the backbone can rotate. - The steric factors are what are going to control this. There are some other things that add to the steric strain, especially like proline and hydroxyproline that do not allow for much rotation at all because of the cyclic nature of those side chains.

What are the factors that can disrupt an alpha-helix and explain some?

Proline creates a bend because of, - The restricted rotation due to its cyclic structure - Its a-amino group has no N-H for hydrogen bonding - because of its unique cyclic structure, it really puts strain on ability to create a-helical structures. Creates a bend which breaks up the a-helix Strong electrostatic repulsion caused by the proximity of several side chains of like charge - Large, somewhat charged side chains which cause kinking (or bending) in a-helix which causes distruption in the perfect helical circle tube (ex. Lys and Arg or Glu and Asp). Creates a bend to avoid repulsion Steric crowding caused by the proximity of bulky side chains e.g Val, Ile, The

Proteins need protection from

Proteases - would disintegrate or chop up proteins - Big changes in pH Watch oxidation to make sure you don't have too much oxygen in the system - Metals in the system doing damage because they can bind and change the overall conformation Bacteria - using sterile methodologies to make sure we do not contaminate protein sample

What categories can proteins be separated into? and describe what they mean How can "identical" proteins be further broken down?

Protein subunits are separated into categories as either identical or non-identical The identical subunits are then further described as - isologous - meaning the surface of the identical interacting subunits are identical as well and create a dimeric structure - or heterologous - meaning the surface of the identical subunits is complementary but not identical and therefore does not have symmetry

What makes the interaction with water have a great influence on the folded structure of proteins?

Proteins often demonstrate amphipathic (both hydrophilic and phobic) properties

proteoglycan functions

Proteoglycans - functions Basically space out structure around structure around these connective tissues and are kind of hydrodynamic in their activities. There is a solution in between them, but keeping the rigid structure does not allow things to be compressed or compacted. Gives cushion around the cells of things like cartilage and connective tissues

· Know the basics of proteoglycans.

Proteoglycans are glycoproteins whose carbohydrate moieties are principally glycosaminoglycans. repeating disaccharide unit The purpose of these proteins involves the recognition and specific binding of other molecules either through binding to the glycosaminoglycan units, or through specific receptor domains in the polypeptide.

o What is the keto-enol tautomeric shift?

Purines and pyrimidines can undergo a keto-enol tautomeric shift. In the Enol form, the ring nitrogens can serve as H-bond donors, and the keto oxygens serve as H-bond acceptors, when interacting with other molecules.

o What is the difference between a furanose and a pyranose?

Pyranose: 6 members Furanose: 5 members

Ramachandran angles

Ramachandrans angles (phi, psi) (-180 to 180o) - designate the rotation about the C-C=o and C-NH bonds. The bonds tend to be in a transformation to avoid the steric strain. The backbone can be described by specifying the 2 angles for each residue

2 Collagens and middle sugar area Basically provides a shock absorber portion of the muscular structure/the structure in between cartilage. These are the ----

Red circle - GAG attached to the protein (glycosaminoglycan) CUSION

What are restriction endonucleases? What different types exist?

Restriction Endonucleases are those that cleave DNA based on specific sequence sites. This allows researchers to cleave DNA for processes like fingerprinting, cloning etc.

What restrictions does RNA present?

Restrictions: RNA can't form a duplex like B- DNA. This is because of steric hindrance of the 2'-OH RNA can form a duplex more like A-form DNA, with 11 bp/turn and the base aromatic rings tilted away from a perpendicular angle to the axis of the duplex One of the fundamental types of secondary structure for RNA is the "stem-loop" structure. (Eg. tRNA) More complex tertiary structures are built up from the interactions between two or more stem-loop structures tRNA molecules exhibit a characteristic "cruciform" secondary structure that includes several stem-loop structures:

ribosomal RNA, Ribosomes are the molecular ------------- that ---------- ------- transcripts into protein. They consist of approximately 65% ---------. Ribosomes are composed of ----subunits of ---------- sizes. Eukaryotic are ------- than prokaryotic ribosomes: Prokaryotic ribosomes are "----" in size (value of the sedimentation cooefficient), composed of "---" and "-----" subunits Eukaryotic ribosomes are "-----" in size (i.e. larger than prokaryotes) and composed of "40S" and "60S" subunits Ribosomal RNA's contain a variety of modified nucleotide ---------including pseudouridine, inosine, and others

Ribosomes are the molecular machines that translate mRNA transcripts into protein. They consist of approximately 65% rRNA. Ribosomes are composed of two subunits of different sizes. Eukaryotic are larger than prokaryotic ribosomes: Prokaryotic ribosomes are "70S" in size (value of the sedimentation cooefficient), composed of "30S" and "50S" subunits Eukaryotic ribosomes are "80S" in size (i.e. larger than prokaryotes) and composed of "40S" and "60S" subunits Ribosomal RNA's contain a variety of modified nucleotide bases including ------, -------, and others

Mucin what are some basic features

SOME features of Musin Protein found in the secretions of the gastrointestinal, respiratory, and reproductive tracts and also in membranes of various cells. Form protective physical barrier on epithelial surfaces, Acting like a fence to keep the antigens from getting to the surface of the cell. Anti microbial because of oligosaccharides. Exhibit high content of O-glycan chains, usually containing NeuAc. Contain repeating amino acid sequences rich in serine, threonine, and proline, , are involved in cell cell interactions, and may contain or mask certain surface antigens. Has all these polysaccharide chains attached to it and O-glyccans and NeuAc (o-linked).

How does this distinction affect the packing structure and flexibility of the molecule?

Saturated Fatty acids are very flexible with free rotation of their single bond. They are generally found in a trans (zig-zag)conformation. This formation allows for closed packing between the molecules. When double bonds are added this adds cis "kinks" to the chains that prevent this close packing and the fatty acids become more fluid.

Secondary and tertiary structure of RNA RNA molecules are generally -------- ---------nucleic acid molecules. However, they can form ---------- ------- and -------- structures due to -------- -------------

Secondary and tertiary structure of RNA RNA molecules are generally single stranded nucleic acid molecules. However, they can form stable secondary and tertiary structures due to base complementarity.

What are the simple lipids and compound lipids? How are these defined?

Separating lipids into classifications based on if hydrolyzable then They are either simple or a bit more compound due to addition of things like phosphate groups and amino groups added to the structures NONHydrolyzable are basically steroid cholesterol derivatives and or terpenes simple - fatty acids, fats and oils (triacylglycerides), waxes

What lipids fall into the hydrolysable group? What lipids fall into the non-hydrolysable group?

Separation of two groups 1. Open chain compounds (saponifiable) Fatty acids Triglycerides Phospholipids Sphingolipids Waxes 2. Closed chain (non-saponifiable) - Cholesterol, steroids (normally derivatives of cholesterol, derived

Understand the process in sequencing a protein. How do you isolate proteins? What is used to determine the N-terminus? What is used to determine the C-terminus? What type of molecules cleave disulfide bonds?

Sequencing a protein was first determined by Frederick Sange (1953). The steps used are as follows Step 1: Isolate protein strands if multimeric by means of pH, Urea, High salt conc. Etc. Step 2: Cleave disulfide bridges using 2-mercaptoethanol or DTT. Step 3 : Determine the N-terminal amino acid by Edman degradation Step 4: Identify the C-terminal amino acid by Carboxypeptidase Y cleavage Step 5: Cleave apart the main portion of the protein using hydrolytic enzymes: Trypsin, chymotrypsin, or endopeptidases: Clostripain, pepsin etc. Or using chemical methods like Cyanogen Bromide or hydroxylamine The amino acid sequence can then be determined by mass spectrometry. Electrospray Ionization MS or Matrix-Assisted Laser Desorption Ionization TOF-MS.

Simple vs allosteric

Simple - there is an active site on the protein, the ligand comes into the active site and they form the protein ligand complex, called a NON-ALLOSTERIC INTERACTION ALLOSTERIC INTERACTION, more complex - this is where there are more than one ligand. May be a ligand that activates the protein, it binds first, and that changes a conformation of a protein which opens an active site for a second ligand to bind. Basically looking at a double ligand, both having to be bound at the same time for the protein to do it's function properly

Know the general information between prokaryotic and eukaryotic.

Since bacterial cells are prokaryotic cells, they do not membrane-bound organelles. All the cellular contents are openly accessible within the cytoplasm in prokaryotes. Animal cells consist of membrane- bound organelles such as nucleus and mitochondria. This is the main difference between bacterial cell and animal cell.

Understand the importance of amino acids absorbing UV light. Which amino acids absorb UV light? What is the typical absorbance measurement? What can you determine with absorbance values? A = ebc

Spectroscopic properties of amino acids None of the amino acids have absorbances in the visible region of light. Some (aromatics) absorb UV light: Phenylalanine, Tyrosine and Tryptophan. All AA's absorb in the infrared spectroscopy region and can be looked at in terms of protein structures and interactions in this region A quick method of determining protein concentrations is measurement of absorbance at 280 nm is based on the fluorescence of the aromatic amino acids . Amino acids can be labeled with heavy isotopes like 13C or 2H and using NMR (Nuclear Magnetic Resonance) reactions studied or protein structures determined.

example calculation

Spontaneous redox reaction - Positive E , whether it is standard or non-standard, and negative DeltaG NONSpontaneous redox reaction -Negative E , whether it is standard or non-standard, and Positive DeltaG

starch

Starch, Glycogen, Chitin, Cellulose, and Dextran Energy Storage Starch is a glycan that has two polysaccharide forms: one is a linear molecule with \alphaα-1-4 linkages called amylose. The other is a branched form of amylose, where the branches have \alphaα-1-6 linkages, called amylopectin. starch can be branched (amylopectin) or linear (amylose) and is the major storage for plants. Starch is made completely of glucose units with alpha-1,4 glycosidic bonds and alpha-1,6 glycosidic bond branches. Starch has one reducing end and many non-reducing ends.

How do you tell what the pH will be after an amount of acid or base is added to a buffer solution?

Step 1: Determine the initial concentrations of the A- and HA of the solution This is done by the same process we just completed to determine the amounts of acid and base to put into our buffer Adding 1 mL The acid or base H+ in ice table goes to 0 A very minimal change in acid or base. Change in base is slightly greater because there is less acid to start with so closer to the limit of buffering capacidty. HOWEVER THERE ISNT MUCH CHANGE DUE TO BUFFER.

o Know the steroid hormones - what are the five main types and what are examples of each?

Steroid Hormones derived from cholesterol in animals. They are all involved in regulation of cellular functions. There are five main types: Androgens - Mediate development of sexual characteristics and function (e.g. testosterone, estradiol) Progestins - These regulate the menstrual cycle (Ex. progesterone) Glucocorticoids - These regulate carbohydrate, protein and lipid metabolism (Ex. cortisol. Mineralocorticoids - These regulate salt balance in tissues (ex. aldosterone) Bile acids - Act as detergents secreted by the gallbladder that help solubilize lipids in diet (Ex. chloric and deoxycholic acid)

What direction do DNA strands run?

Strands run in opposite 5' to 3' directions.

kinds of protein and characteristics in terms of secondary structure

Structural proteins - These regular structures tend to be aligned or arrayed in such a manner to give them a fiber look, often called fibrous proteins because of this Globular proteins - also contain these secondary structures but tend to be regions or domains of secondary structure followed by loops or chains that are not in the structures and then another of those more structured regions

Recall the most common disaccharides: o Sucrose What two monosaccharides compose the disaccharide? What kind of bond is created between the monosaccharides (i.e. alpha-1,2 - be more specific than "glycosidic")? Are they reducing sugars? What does it mean to be a reducing sugar?

Sucrose is comprised of glucose-\alphaα-1,2-fructose. Also known as "Table sugar", it has no free anomeric carbon so it is not a reducing sugar

Sugar Acids

Sugar Acids- Sugars with free anomeric carbons act as reducing agents and as they are oxidized become sugar acids. These sugars are called reducing sugars and are the basis of testing for diabetes. Addition of alkaline copper sulfate will result in a red precipitate of copper(I)oxide if reducing sugars (sugars with free aldehydes are present). glucose to gluconic acid

sulfur containing amino acids,

Sulfur containing amino acids Methionine - "start" amino acid, very hydrophobic, sulfur present in thioester linkage Cysteine - sulfur in form of sulfhydroyl, important in disulfide linkages (Stabilizing linkages, plays big roles), weak acid, can form hydrogen bonds so not so hydrophobic

Supercoiling (tertiary structure of dna) When does supercoiling occur? Supercoiling occurs only if the two ---------------strands of the DNA ------- ------are ------- to rotate about each other freely. relieves strain from helical structure. When the strain of ------- rotating or ------ rotating cannot be compensated by the turning of the ----- of the double helix, which is the case if the DNA is ----------- that is, there are --- free ends. Some viral chromosomes are in the form of simple circles and readily undergo ----------

Supercoiling occurs only if the two polynucleotide strands of the DNA double helix are unable to rotate about each other freely. When the strain of over rotating or under rotating cannot be compensated by the turning of the ends of the double helix, which is the case if the DNA is circular- that is, there are no free ends. Some viral chromosomes are in the form of simple circles and readily undergo supercoiling.

Purpose of supercoiling

Supercoiling of DNA reduces the space and allows for much more DNA to be packaged.

Describe the different levels of nucleic acid structure - tertiary.

Supercoiling: addition to the a-helix of dna there is an additional level of twisting

o Lipid Numbers

Take the form C:D, where C is the number of carbon atoms and D is the number of double bonds When ambiguity exits, the notation is usually paired with a ∆X notation ------------------- - Lipid numbers - have the form of C being number of carbons in fatty acid and D being the double bonds C:D , the X is going to tell us the number at which the double bond occurs

· Recognize the structure of a terpene. o What is the "base unit" of a terpene? What does this molecule look like?

Terpenes Terpenes are a type of lipids that are created from isoprene (2-methyl-1,3-butadiene) that has 5 carbons. -------------

Understand the tertiary structure of proteins. What determines the tertiary structure?

Tertiary structure - the folding a single strand of protein into a 3D structure Determined by the primary sequence Some proteins have "chaperones" that help with folding, but in dilute solutions these proteins can be folded without chaperones

The ATPase has an ------------ side chain that can be -------------(reversibly) during ATP hydrolysis. The --- conformation of the ATPase has a high affinity for ----- and -------. It is phosphorylated by coupling to the --------- --- ---- to form a conformation known as ---- which contains ----- bound Na+ ions taken from ------ the membrane . The ATPase then undergoes a ------------ ---------- due to ------------ by ATP to produce the E2-P conformation. This conformation has a low affinity for Na+, but a high affinity for ------ ions. The E2-P state releases the 3Na+ ions outside the membrane and ------- ------- K+ from the outside of the cell. . the binding of ------ and subsequent ------------- releases the K+ ions on the inside of the cell and returns the enzyme to the E1 state.

The ATPase has an aspartic acid side chain that can be reversibly phosphorylated during ATP hydrolysis. The E1 conformation of the ATPase has a high affinity for Na+and ATP. It is phosphorylated by coupling to the hydrolysis of ATP to form a conformation known as E1-P which contains three bound Na+ ions taken from in the membrane . The ATPase then undergoes a conformational change due to phosphorylation by ATP to produce the E2-P conformation. This conformation has a low affinity for Na+, but a high affinity for K+ ions. The E2-P state releases the 3Na+ ions outside the membrane and binds two K+ from the outside of the cell. Eg. the binding of ATP and subsequent dephosphorylation releases the K+ ions on the inside of the cell and returns the enzyme to the E1 state.

In biochemistry we often use the weak acid - conjugate base systems as buffers for chemical systems we are working on in lab. This equation: provides an efficient manner in which to determine the pH of a weak acid/base system.

The Henderson-Hasselbalch equation:

How do alpha-helices and beta-sheets stabilize the polar backbone?

The Internalized polar groups of the protein backbone are stabilized by hydrogen bonding with secondary structure which, reduces strain As hydrophobic forces create compaction, the helices and sheets stabilize the polar backbone through h-bonding interactions

hemiketal?

The Ketoses form five membered hemiketals, rings referred to as furanoses.

how is the linking number related to twist and writhe? what are they

The Linking number can also be equated to parameters called the Twist (T) and the Writhe (W). The twist is the number of helical turns and the writhe is the number of supercoils. L = T + W Note that as long as the DNA is in a normal unbroken relaxed form the value of L is constant.

1b Understand and describe the phase transition and the characteristics associated with it

The Phase Transition Characteristics: 1. Transitions are endothermic 2. Phospholipids have distinctive TM. The longer the chain the higher the TM. It decreases with unsaturation. 3. Pure bilayers transition over a narrow temperature range and are all or nothing in structure (gel or crystal.) 4. Biological membranes also have this phase transition, but due to their complexity and heterogeneity (lateral phase separation), the transition occurs over a much broader temperature range. 5. The volume of the cell or vesicle increases with the phase change. 6. The presence of ions or other solutes affects the phase change.

steps to reach to cell

The above Precursors and functional groups become more and more complex leading to the the cell , basic unit of life. Precursors→ metabolites (building blocks of macromolecules), whether protein or nucleotide metabolites, etc.) → macromolecules (proteins, DNA or RNA, polysaccharides) → supramolecular complexes (ribosomes and enzyme complexes) → organelles (eukaryotic cells)

What is the basic structural unit of collagen?

The basic structural unit of collagen is tropocollagen It is made up of 3 intertwined polypeptide chains

Ion exchange chromatography -

The choice of buffer pH then determines the net charge of the protein of interest In a buffer with a pH greater than the pI of the protein of interest, the protein will carry a net negative charge, therefore a positively charged anion exchange resin is chosen to capture this protein In a buffer with a pH lower than the pI of the protein of interest, the protein will carry a positive net charge, thus a negatively-charged cation exchange resin is chosen.

The Gastric H+, K+ -ATPase There is therefore a -- --------across the mucosal cell membrane of the stomach with a huge 6.6 difference. the --------- will not be maintained without effort (energy output) by the body.

The digestion of food is initiated by the very acidic interior of the stomach; pH 0.8 to 1.0. The cells that form the lining of the stomach have a preferential pH of 7.4. There is therefore a pH gradient across the mucosal cell membrane of the stomach with a huge 6.6 difference. This difference is essential but because of passive diffusion forces, the gradient will not be maintained without effort (energy output) by the body. Enter the H+, K+ -ATPase. This is a membrane protein that couples ATP hydrolysis to the pumping of H+ out of the cell and K+ into the cell. Because the charge is +1 both directions the process is electrically neutral . The K+ ion is pumped out along with a Cl- ion in another electrically neutral process using an associated membrane transport system. The net result is the maintenance of the high HCl concentrations in the stomach. It should be noted that the gastric H+, K+ -ATPase is structurally very similar to the Na+, K+ -ATPase. They share several amino acid sequences.

What is known if you know all the psi and phi angles?

The entire backbone of the protein is known if you know the psi and phi angles

Lipidomics

The global analysis of Lipid interactions with proteins and other molecules is called lipidomics. The goal is to create a database (LMSD - Lipid Maps Structural Database) that contains all biologically relevant lipids. As of 4/20/ 2020 43,811 unique lipids have been catalogued. Analysis has already shown some information on diseases like Alzheimer's. Brain white matter analysis shows that in the early stages there is a dramatic decrease in a plasmalogen with a 3-fold increase in ceramide levels.

The information that DNA carries is within the ------ ------- ---------of the DNA.

The information that DNA carries is within the unique base sequence of the DNA.

Sanger sequencing

The nucleotide sequence of DNA is determined therefore by the electrophoretic migration of a defined set of polynucleotide segments. DNA sequencing is most often accomplished using a procedure referred to by one of the following names: Sanger sequencing Di-deoxy sequencing Chain termination sequencing Each of these refers to the same method developed by Fred Sanger. It uses an enzyme, known as DNA polymerase, to replicate a polynucleotide. The occasional incorporation of a di-deoxy base in the newly produced DNA strand results in termination of that individual DNA strand. This sequencing process today has been fully automated. The newest sequencing method and the only one that does not use strand replication uses nanopores and measures the change in potential of the pores as single strands of DNA are pulled through them. The conductance changes based on the identity of the nucleotide. This method leads to direct determination of the DNA sequence.

Lecture 7 protein Know the basic principles underlying overall structure and function of proteins.

The overall structure and function of proteins follow some basic principles - Function follows structure - Structure depends on the amino acid sequence and non-covalent interactions - Protein folding patterns are multiple but can be determined - Globular protein structures are relatively stable - Stability facilitates motion - Motion enables function

What are flippases, floppases, and scramblases? Know the general difference between these - properties and function.

The proteins that can flip and flop phospholipids from one side of a bilayer to the other are called flippases, floppases and Scramblases. Flippases and Floppases are ATP-dependent - moving phospholipids to the inner and outer side of the membrane, respectively. Scramblases use Calcium ions and are bidirectional. - Their purpose appears to be to degrade transverse asymmetry.

nitrogenous bases o Which are found in DNA? Which are found in RNA?

The pyrimidines Cytosine and Thymine are found in DNA , while Cytosine and Uracil are found in RNA (note that RNA can contain small amounts of other modified bases as well). The purines Adenine and Guanine are found in both nucleic acids.

Why do we need s and r

The reason we need r and s nomenclature is that a lot of molecules have more than one stereocenter. We can name it d or L based on one of the chiral centers. All amino acids like L-threonine and D-threonine, based on alpha carbon Hydrogen. But if R group is rotated around, then they add allo

Is the same volume of base used to deprotonate the polyprotic acid - what is the driving force of this

The same volume of added base is required to remove each mole of H+ - - overall driving reaction is the formation of water, the neutralization of acid using base of some sort to create water. Because water is a covalent compound it is a one way reaction.

How many amino acids is a full turn for alpha helices?

The secondary protein structure is a formed coil held together by hydrogen bonds. One full turn of the helix takes 3.6 amino acid residues

The stands of DNA contained in our cells contains all of the information necessary to make all ========== in the cell. The --------- and -------- of the bases defines the nucleic acid as DNA. No Uracil being present. The fundamental structure of DNA is the double helix:

The stands of DNA contained in our cells contains all of the information necessary to make all biomolecules in the cell. The order and composition of the bases defines the nucleic acid as DNA. No Uracil being present. The fundamental structure of DNA is the double helix:

Proteins are held together by ? what does this mean

The structure of these proteins held together and or driven into their structure by non-covalent forces Meaning they can easily unravel Proteins are limited in the environmental conditions they can withstand The entire structure of a protein can be determined from its primary structure. However, because of the many variations that each amino acid can make based on rotation at each atom, the ability to accurately predict a final configuration is complicated

The vast majority of biological nucleotides involve the sugar hydroxyl at the ---- position or sometimes the ------- position. No -OH group is available at the --- position in DNA. Because phosphoric acid has a pKa1 of ~1.0 and a pKa2 of ~6.0, at physiological pH the nucleotide will have a net charge between -1 and -2, and be acidic.

The vast majority of biological nucleotides involve the sugar hydroxyl at the 5' position or sometimes the 3' position. No -OH group is available at the 2' position in DNA. Because phosphoric acid has a pKa1 of ~1.0 and a pKa2 of ~6.0, at physiological pH the nucleotide will have a net charge between -1 and -2, and be acidic.

Understand the quaternary structure of proteins. How do subunits fold - independently or dependently?

The way in which separate folded monomeric protein (tertiary structures) subunits associate to form an oligomeric protein is called a quaternary structure - These subunits fold independently and THEN interact. - The interaction is controlled by complementary surface structures, polar and hydrophobic interactions bound together by these non-covalent forces (seperate). Result from aggregation of two or more polypeptide subunits Become a complex that gives the functional protein Tertiary can also be tertiary, however many vital metabolism proteins are quaternary

There are three loops in tRNA secondary structure: ---------- generally contains dihydrouridine so named D ------------- - This is involved in recognition of the specific triplet of bases in an mRNA that codes for each amino acid in the protein to be translated ------------. This loop is involved in the binding to ribosomes during translation. Contains a characteristic pseudo-uridine base. tRNA's have a characteristic tertiary structure:

There are three loops in tRNA secondary structure: D loop- generally contains dihydrouridine so named D Anti-codon loop - This is involved in recognition of the specific triplet of bases in an mRNA that codes for each amino acid in the protein to be translated TYC loop. This loop is involved in the binding to ribosomes during translation. Contains a characteristic pseudo-uridine base. tRNA's have a characteristic tertiary structure:

more on terpenes common examples od terpenes

There are various orientations that the isoprene units can adopt when forming such bonds > Monoterpenes (2 isoprene units) occur in all higher plants, and are the building blocks of cholesterol and other steroids, and carotenoids (photosynthetic pigments). Long-chain polymers of isoprene units with a terminal alcohol are called polyprenols. These have functionalities ranging from carbohydrate transfer molecules to hydrophobic anchor moieties in conjugated lipoproteins. Aldehydes and alcohols of monoterpenes are aromatic compounds in plants (e.g. menthol and citronella). Rubber is a terpene polymer.

Thermodynamics importance for protein-ligand complexes

Thermodynamics helps us find out more about binding reactions by providing insights into - Affinity and specificity - Contribution of enthalpy and entropy - Dependence on temperature - If allosteric, what are the other groups - Why? If you are designing a drug, knowing binding efficiency, affinity and specificity is really important

Lipid signaling

These are all cascades that create activity in the cell by an initial lipid signal that creates a secondary messenger within the cell, that then triggers something else to occur.

What are the simplest aldose sugar and simplest ketose sugar?

These sugars are 3 carbons and thus trioses. Hexoses (6 carbons) are the most abundant monosaccharides in nature.

how are proteoglycans different from glycoproteins

They are slightly different from glycoproteins because they are much more branched and much longer branches Glycosylation - reaction in which a carbohydrate ie. a glycosyl donor, is attached to a hydroxyl or other functional group of another molecule. Proteoglycans are heavily glycosylated The basic proteoglycan unit consists of a core protein with one or more covalently attached glycosaminoglycan chains

fatty acids can be ------ or -------- with more than one double bond being ----------. The carboxyl group is normally --------- at physiological pH.

They can be saturated or unsaturated with more than one double bond being polyunsaturated. The carboxyl group is normally ionized at physiological pH.

Topoisomerases are enzymes that----- and ------- the topology of DNA. Type I topoisomerases only cut ----- strand DNA and Type 2 cut ----- strands. DNA Gyrase is a topoisomerase that creates ------------ supercoiling in DNA.

Topoisomerases are enzymes that cut and change the topology of DNA. Type I topoisomerases only cut single strand DNA and Type 2 cut both strands. DNA Gyrase is a topoisomerase that creates negative supercoiling in DNA.

Toroidal Supercoils

Toroidal supercoiling (see figure 5) can occur in negatively supercoiled DNA. This form of DNA supercoiling can be stabilized by wrapping around proteins as seen in chromosomes.

Chemical instability by what are some types

Treating a protein with different kinds of chemical treatments that break down (screw up) some kind of bonding in the protein ( usually covalent, peptide bonds or disulfide bonds, deamination of asparagine or glutamine, hydrolysis of peptide bond of aspartate residues at low pH, Oxidation of Methionine at high temp Elimination of disulfide bonds (1 of the key factors that tear protein apart, by disulfide interchange at a neutral pH) Disulfide interchange at neutral pH Other processes - thiol catalyzed disulfide interchange and oxidation of cysteine residues. (breaking disulfide bonds)

Triglycerides purpose and structure ---------- and ------------ (----------- around organs and skin and for impact) Fat soluble compounds like vitamins carrier Flavor and texture -sensory qualities

Triglycerides are one of the most common forms of fatty acids in the body. They are a storage form of energy in the body. Triglycerides are stored in body fat in animals. The structure consists of glycerol esterified with 3 fatty acids. ----------------- Esters of the trihydric alcohols (glycerol) and fatty acids Mono- and Diacylglycerol, wherein one or two fatty acids are esterified with glycerol also found in the tissues, does not have to be 3 fatty acid changes functions Naturally occuring in body lots Major in body and diet, it is how we store fat and 60% of resting energy Insulation and protection (cushioning around organs and skin and for impact) Fat soluble compounds like vitamins carrier Flavor and texture -sensory qualities

triglycerides reactions

Triglycerides reactions in the body - Act like reactions of carboxylic acids - When you have triglycerides and you add H20, H+ - (hydrolysis) you have the basically are reversing the formation of triglycerides and result in glycerol and fatty acids - If you add NaoH you saponify and results in glycerol and fatty acid salts - Nickel with hydrogen H2 - hydrogenation - forms more saturated triglyceride

What are the three types of collagen?

Type 1 is the most common and is found in bones, tendons, and skin. It has two identical and one different polypeptide chain Type 2 collagen is found in cartilage Type 3 in blood vessels Type 2 and 3 have 3 identical polypeptide chains each These proteins are high in glycine, proline and hydroxyproline aa which prevents normal secondary structure They form a unique right handed triple helix instead

What is type I and type II?

Type 1 turns - internalize the carbonyl oxygen, and are the most common Type 2 turns - internalize the hydrogen in the amine group.

What are commonly found amino acids in turns?

Type 1 turns - internalize the carbonyl oxygen, and are the most common Type 2 turns - internalize the hydrogen in the amine group.

What type is used most frequently in a lab setting? It typically ----- at a -------- sequence in --------- DNA. Upon cutting it can leave the ends of the DNA duplex as either -----, or ------. ----- ends are depicted as -----ends of the DNA with either a 5' or a 3' unduplexed overhang. The Sticky ends of different DNA fragments produced by the same enzyme are -------------- What are sticky and blunt ends?

Type II This is the type we use in the lab. It typically cuts at a palindromic (same whether forward or backward) sequence in duplex DNA. Upon cutting it can leave the ends of the DNA duplex as either "blunt", or "sticky". Sticky ends are depicted as uneven ends of the DNA with either a 5' or a 3' unduplexed overhang. The Sticky ends of different DNA fragments produced by the same enzyme are complementary.

DAG, or diaglycerol pathway

Understand that their is a membrane bound protein that is activated by a ligand that causes the release and/or activation of several secondary messengers is the key concept of lipid signaling a lipid ligand is going to attach to a what is called a G protein (big membrane bound proteins) with GTP that converts to GDP (release of phosphate group) (which is why it is called a g protein) causes a conformational change which then sends a second messenger (PIP), which activates your phospholipase C and then you have your diacyl glycerol that is activated, that then as a second messenger (these two, diacyl glycerol and IP3), go off to either basically activates Protein Kinase C (DAG). IP3 has an activity that is interactive with these membrane bound proteins that are part of a channel in the ER and this releases calcium into the cell which also activates calcium binging protein and this all leads to the cellular response that is required all of this is all put into action by this one lipid signal that creates a number of secondary messengers that activate several different enzymes and proteins in the cell

· Understand the basics of lipid signaling. o What are the four key lipid signalers? What generally occurs in each cascade? What does the lipid signal look like (structure)?

Understand that their is a membrane bound protein that is activated by a ligand that causes the release and/or activation of several secondary messengers is the key concept of lipid signaling key lipid signalers - diaglycerol (DAG) - ceramides - platelet activating factor (PAF) - arachidonic acid

What is a melting temperature and how does this relate to the proportion of bases?

Upon addition of heat, a phase transition will occur at a characteristic "melting" temperature (TM). At this temperature, the duplex will "melt" yielding separated and denatured single strands of DNA. The TM is related to the proportion of the different bases in the DNA. The G-C base pairing with three hydrogen bonds and is stronger than A-T with just two. Therefore DNA that is rich in G/C base pairs is more stable and will have a higher TM. Different species of bacteria have characteristically different percentages of the four bases. For example, E. coli is about 50% G/C and 50% A/T. However, Corynebacteria (live in soil and on skin) is about 70% G/C content (and its DNA melts at a higher temperature).

Define high energy molecules. What is the energy threshold? What are common examples?

Upon reaction with commonly found molecules (like water or oxygen etc. ) , it produced more than -25kJ/mol of Free energy. Ex. some phosphate compounds, NADH, NADPH, FADH2, and ATP, ADP, Each hydrolysis reaction generates a free inorganic phosphorus atom as a product - High energy bonds that are hydrolyzed and release energy to the system. Various reactions will use that energy to make products. High energy molecules - Equal or greater than ATP in energy (ATP actually releases less energy than other high energy biomolecules. That hydrolysis is an exergonic reaction and it yields energy. The bonds holding the phosphate onto ATP are weak. They are known as high energy bonds but not because they are strong (if they were strong it would require alot of energy to break them.

What is the hydronium concentration and pH of a 0.010 M solution of hypoclorous acid, Ka = 3.5e10-8? main steps when given buffer or usually any gen chemmer

Use ice table Do not include water, it is a liquid. Water is a pure substance and a solvent. The concentration won't change and it'll cancel out on both sides so there's no point in including it If more than a 10^3 difference you can approximate C is small

triglyceride hydrogenation

Uses nickel catalyst and add H2, Get rid of double bonds and resaturate, takes from a weak solid fat. Oil to fat

HPLC

Utilizes a non-polar stationary phase with a polar mobile phase. - Proteins are retained through nonspecific hydrophobic interactions with the stationary phase - With this separation mode, the more polar the protein, the lower the retention. Increasing the polarity of the mobile phase causes increased retention.

Various proteins are stuck to ------------ that are actually stuck to internal membrane bound proteins.

Various proteins are stuck to carbohydrates that are actually stuck to internal membrane bound proteins.

Ka Association constant or Keq Tells us about the free energy deltaG = -RTlnKd, BUT

WE really have a greater interest in the dissociation constant is the exact opposite. Kd = 1/Keq so it becomes positive deltaG = +RTlnKd

SOLID characteristics of water (not)

Water uniquely has a very polar structure. High imf, 4 H-bonds, h-bonded water increase the bonding in other mol - coop. Hydrogen attached to oxygen with two lone pairs Ice is bonded by four hydrogen bonds for each hydrogen bonded to oxygen , freezing increases volume and density decreases (so as water freezes it becomes less dense - key feature). Why ? If not, icebergs would sink to the bottom of the ocean and the ocean would remain very cold if not frozen. Structure of ice is more open This makes water very special due to its properties Solid is less dense than liquid for water which is unique among liquids. However , density does increase like a normal liquid but stops to its maximum at 4C as the rigid bonding takes place , the density decreases and floats. Ex. salts , sugars, alcohols, amines, carbonyl groups

Waxes say what u know

Waxes are a combination of a fatty acid and a long chain alcohol that are bound together by an ester linkage created in a dehydration synthesis fatty acids (14-36 carbons) long chain alcohols (16-30) generally solids at room temperature

what can we find when fractional occupancy = 1/2

What we find is that when you have the Kd = [L], we see that it is = the magnitude when half of the [M] in the protein is bond/occupied. This gives us a way to compare the binding of different proteins because we know that the concentration of the ligand when binded to half of receptor its equal. TELLS US THE AFFINITY OF THE PROTEIN FOR ITS LIGAND

what tendency of lipids is invaluable in membrane structure

When placed in water - makes either films with hydrophilic heads touching water and tails above the water If submerged in water form micelles (cell membranes)

anomer When the sugars become cyclic, the carbonyl carbon becomes ---------. Isomers that vary only in the orientation of this new carbon stereocenter are called -------. The carbon is called the -------------- carbon and if the hydroxyl group on the carbon is below the ring it is called an \-------- ring (Eg. ------D-glucopyranose). If the hydroxyl group is above the ring the sugar is referred to as a \--------D-hexopyranose (Figure 4 above). Switching between the two forms occurs and is called --------.

When the sugars become cyclic, the carbonyl carbon becomes chiral. Isomers that vary only in the orientation of this new carbon stereocenter are called anomers. The carbon is called the anomeric carbon and if the hydroxyl group on the carbon is below the ring it is called an \alphaα ring (Eg. a-D-glucopyranose). If the hydroxyl group is above the ring the sugar is referred to as a \betaβ-D-hexopyranose (Figure 4 above). Switching between the two forms occurs and is called mutarotation.

Formation of clathrate structure Negative entropy of water drives non-polar molecules together

When we have hydrophobic interactions, we form things like membranes, which are made up of hydrophilic heads which interact with solutions and tails are internalized. - Hydrophilic protein residues are also externalized in proteins while hydrophobic residues are internalized. - Water actually assists in the folding of proteins. - Molecule that has both hydrophilic and hydrophobic tendencies is called amphipathic Also called amphipathic (amphiphilic) Contain both polar and nonpolar groups Clusters form micelles While amphoteric means can act as an acid or base

why do alpha and beta helices form

When we see a repetitive structure inside of a protein, these repetitive structures tend to be develop because they provide stability so there is a free energy gain with the stabilization of the structure - 2 of the main types of secondary structures are called a-helices and B-pleated sheets - The regular conformation allows the structure to be stabilized by forming many relatively strong hydrogen bonds.

o Understand that they are used for "waterproofing" (lecture open-ended question) - protective coating.

With only a small polar ester group providing any polarity to the structure, these molecules are not very soluble and because of this they are used in the "waterproofing" of biological structures (e.g. plant leaves, feathers etc.). -------------- found on plant leaves and other microorganism , gives them protective coating that keeps water out from degrading inner systems and continually taking away the fats from the organism

If you know all of the psi and phi angles for the peptide bonds then you know the backbone structure of a protein. Allow you to determine a protein's structure. how

X-ray crystallography - these angles are determined and placed on a 3-D grid called a Ramachandran plot that allows us to determine the actual structure of the protein - deals with dihedral angles

Type 1 Requires ATP? Y or N Methylate DNA? Y or N Cut specifically? Y or N

Yes, Requires ATP for hydrolysis Yes, Is able to methylate DNA at specific locations No, Cuts at random sites

Type 3 Requires ATP? Y or N Methylate DNA? Y or N Cut specifically? Y or N

Yes, Requires ATP for hydrolysis Yes, Is able to methylate DNA at specific locations Yes, Cuts at specific nucleotide sequences YYN NNY YYY

Graphical representation of ligand binding free energy

You have a free energy of a protein and free energy of a ligand As they come together, if they are going to bind then the free energy of the complex has to be lower, meaning it has to be an exergonic reaction for the binding of the protein

This equation shows that when v is 0.5 (when half of the protein is bound to the ligand) then the ---------.

[L]=K_D the smaller the value of KD, the better the protein is at binding ligand

[M] is [L] is [ML] is

[M] is protein [L] is ligand [ML] is ligand protein complex

Strong acids and bases fully dissociate in water: BUffer preparation Best way is to calc the amount of components you need like strong acid then tweak to desired pH 2 equations will be used

[buffer] = [HA] + [A-] ph= pka + log a-/ha Equilibrium has a Ka which you can take -log to find pka, we want a pka that is +/- 1 pH unit

· Describe supercoiling. o What is the purpose? What are the two main enzymes involved? What do each do, respectively? When does supercoiling occur?

\

how they look (forms) dna --- and ---- versions are ---- handed helical structures looking at them from the side and from the top you can see the difference between a and b version where b is the -----version and a is the ----version z is a ------ handed helical structure, more spaced in the same way as b

a and b versions are right handed helical structures looking at them from the side and from the top you can see the difference between a and b version where b is the skinny version and a is the fatter version z is a left handed helical structure, more spaced in the same way as b

topological comparisons specs dna forms -- is most common, and is -----handed anti or syn

a form is fatter not as many rotations per residue, wider doesn't get as much done, Z, -30 is more strung out for a and b, the sugar they are anti z form is anti for pyridines, but syn for purines b is most common, and is right handed

agarose

a polysaccharide made by marine red algae. It is used for an edible gel and as a gel for electrophoresis.

Decorin -

a protein that is a proteoglycan. Something that would have the glycoproteins attached to it. Structurally displayed

- End up with -------- native state (lowest energy point) of protein. Idea is ANALOGY: LIKE YOU get into a relaxation into a big overstuffed chair and you wiggle around until you find the most comfortable spot (ONLY ----- MOST comfortable conformation where you expend lowest energy and entropy is reduced)

a single, one

transverse asymmetry

a transverse asymmetry of such phospholipids must be established and maintained to create this potential. Transverse Asymmetry arises when one side of the bilayer has a different lipid or protein content than the other side. This asymmetry makes sense especially for receptor molecules that are designed to bind signalling molecules in the extracellular environment. These of course will be oriented in the bilayer so they have binding regions on the side facing the extracellular environment. As we have discussed previously, glycolipids are important in cell-cell recognition, and must be located on the outer surface of the bilayer to perform this function. Since some phospholipids are charged and others polar, their distribution can affect the charge potential across a lipid bilayer. Such a potential may be critical for cell function, and so a transverse asymmetry of such phospholipids must be established and maintained to create this potential.

Arachidonic acid

acts as a second messenger that essentially gives you synthesis of things like prostaglandins, leukotrienes, and things of this nature and so large structures , second messengers, open up and create production of needed cellular responses to stress

cholesterol

acts as a stabilizing agent in the membrane because when you have low temps, the fats tend to solidify but the cholesterol (large molecule) is breaking up in the middle of them and keeps them from solidifying at low temp but because it has a higher heat capacity as temp rises keeps it from being too fluid not as susceptible to temp fluctuations as it might be otherwise

Where are triacylglycerides (triglycerides) found? Where are triglycerides the storage form of energy?

adipose tissue

aldosterone

adrenal hormones main mineralcorticoid controls blood pressure by increasing or decreasing the amount of sodium or pottasium in our systems if we increase our sodium in cells, this causes water to accumulate in the cells and as you increase water in blood stream or in cells this increases blood pressure (more fluid)

What are examples of super-secondary structures and describe them a little bit?

alpha/beta barrel Betaalphabeta - beta sheet connected to an alpha helix and then another beta sheet. Two parallel strands of beta sheet connected by a stretch of a-helix. Alphaalpha unit 2 alpha-helical units connected by a loop. 2 antiparallel alpha helices Beta-meander Just have a lot of beta sheets connected by turns and loops all together and compressed. An antiparallel sheet formed by a series of tight reverse turns connecting stretches of a polypeptide chain. Greek key: a repetitive supersecondary structure formed when an antiparallel sheet doubles back on itself Opposite direction, antiparallel sheets doubling back upon themselves

Proteins with a single transmembrane section are often anchored by a single -------- An example of this is ----------- --- aa span the entire bilayer. Thus, the helix must be somewhat stretched or the bilayer somewhat thinner than the usual 5nm.

alphaα-helix. An example of this is Glycophorin. 19 aa span the entire bilayer. Thus, the helix must be somewhat stretched or the bilayer somewhat thinner than the usual 5nm.

Ether Glycerophospholipid

an ether linkage exists off the phosphate group Phosphatidylethanolamine is part of this class of phospholipids which has an ether linkage to the hydrophobic tail at the C1 position of the glycerol, instead of an acyl linkage:

Collagen

another type of structural proten Triple helical cable - because of triple helical structure , tends to be flexible alpha helices tend to be flexible and stretchy for tendons ligaments, blood vessel, skin Bones teeth and cartilage are going to have more rigid STRUCTURE PROVIDES FUNCTION IS THE BASIS OF ALL THIS In general alpha helices, as you have different angles of alpha helices and the type that are involved it can vary in stretchiness and flexibility

Sphingomyelins

are a subclass of sphingolipids that contain a phosphate group. They are an important element in the insulating myelin sheath surrounding nerve cells. These are variations on this sphingosine backbone and depending on what the substitutions are, this defines what kind of sphingolipid it is, and more importantly where it is found and what it is going to do. Types of sphingolipids Cerebrocytes in myelin , Globosides , Gangliosides (sialic acid)

Oligosaccharides

are created by glycosidic bonds. The simplest oligosaccharide has two monomers: 3-10

Thioether-linked prenyl anchors.

arnesyl or geranylgeranyl ether to cysteine SH (Cys carboxy is methylated)

examples of simple monoterpenes

aromatic in that they have strong smells practical purposes sometimes you cant find the isoprene structure but they are still considered monoterpenes and lipids

secondary structures

arrangement of peptide backbone in space repetitive structures held together by attractions between weak links that the entire chain is held together by

When not in the standard state, determining standard state requires the adjustment from those values by following the relationship -

at eq. deltaG=0 so result is iin the picture -2.3 allows for the conversion to log

How can PH at the eq point can be determined from the pKa values

average of the pka at the above half-eq and below half-eq

prokaryotic cells/bacteria have a cell wall, how can things go though

bacteria have cell wall adds protection but makes it more difficult to get thing in and out (not as permeable) they have porins in the outer membrane which allows things to go through (open aqueous channels)

Understand the R and S system. How does the prioritization work? Is R clockwise or counter-clockwise? Is S clockwise or counter-clockwise?

based on first atom bonded to carbon, if same go to next. by atomic number, the higher, the higher priority R and s, try to rotate lowest priority to the back. - R is clockswise - S is CCW

functions of nucleotides bases serve as -------- units nucleotides make up nucleic acids also extremely important as carriers of -------. -------- bonds that they have provide energy for just about everything -------- in the body --------- nucleotides are signal ------------ and --------- of cellular metabolism and reproduction

bases serve as recognition units nucleotides make up nucleic acids also extremely important as carriers of energy. Phosphate bonds that they have provide energy for just about everything metabolic in the body cyclic nucleotides are signal molecules and regulators of cellular metabolism and reproduction

Cap and tail on mRNA (structural characteristics)

basically keeps the mRNA from being attacked by the exonuclease activity that goes on continuously in the cell also has leader and trailer sequences of nucleotides that are not part of the translated code

rna tertiary motifs

because of the ability of the nucleotides to still hydrogen bond, rna has these short segments (vs dna with long alpha helical structure) of double strandedness which creates these different secondary and tertiary structures

Long hydrophobic followed by hydrophilic

beta sheet

sodium-potassium pump

binding sodium, as it is binding which will stimulate phosphorylation by atp, which will cause a conformational change, releasing sodium into the cell simultaneously sometimes, the same protein can then bind the potassium going in the other direction and this pottassium essentially creates a restores to the original protein conformation. protein that basically has an antiport type of process where it is moving two different ions back and forth no necessarily at the same time, transporting the ions into and out of the cell

syndecan

binds intracellularly to the cytoskeleton protein actin, and extracellularly through the glycosaminoglycan units to fibronectin (another component of the extracellular matrix). In this way, syndecan is a molecular "glue" that can form a bond between the extracellular matrix and cell growth factors and other soluble molecules.

euchromatin vs heterochromatin schematic blue balls are -------- proteins that the dna is wound around ----------- is sort of an open winding while ---------- is more compact and it gets more compacted even further as it goes into chromosome structure but 92% of our dna is actually this --------- which is a less compact structure , this makes sense because we need to use them (if too compact like heterochromatin its like packing into boxes and putting it away cant be used)

blue balls are histone proteins that the dna is wound around euchromatin is sort of an open winding while heterochromatin is more compact and it gets more compacted even further as it goes into chromosome structure but 92% of our dna is actually this euchromatin which is a less compact structure , this makes sense because we need to use them (if too compact like heterochromatin its like packing into boxes and putting it away cant be used)

amylopectin

branching causes distance to reduce glumping (open) (waxy) a-1,4 and a-1,6

How is structural stability studied

by denaturing proteins and seeing what falls apart, so we look at the various structures and conformations of proteins under different conditions to determine what stabilizes them and what destabilizes them.

Name the four types of biomolecules (macromolecules) in biochemistry. What is the monomer form(s) of each biomolecule? What is the polymer form(s) of each biomolecule? What is the major role of each biomolecule? What are some examples of each biomolecule?

carbohydrates, proteins, lipids, nucleic acids

acidic amino acids,

carboxyl and amino groups Acidic amino acids - Aspartic acid, Aspartate and Glutamic acid, Glutamate Ate - when in zwitterion form due to deprotonation Contain carboxyl groups (weaker acids than a-carboxyl group, so not going to lose hydrogen as easily higher pka) Negatively charged at physiological pH, present as conjugate bases (becomes -ate, not -ic) Carboxyl groups function as nucleophiles in some enzymatic reactions Carboxyl forms tend to be negatively charged at the 7 pH because they will have pKa lower than 7 (around 2-3). So they would be present as bases as opposed to acidic conjugates.

These O-linked glycoproteins serve as

cellular signals (similar to phosphorylation) They serve as nutrient sensors and work both in concert and independently to regulate cell metabolism. They have been found to be altered in major diseases of aging (diabetes, cancer, Alzheimer's and cardiovascular disease). O-linked as cellular signals, nutrient sensors, help regulate cell metabolism, protection, help push protein to interact with substrate

What is a beta-pleated sheet?

chains are going up and then coming back and creating hydrogen bonding surface areas in between two of the strands - Because of the planarity of that peptide bond, you end up with accordion looking pleated sheets. - Can be more than one strand and can be stacked which allows for compacting of protein.

A lot of times in a cell if there is a need to export the protein from the cell these -----------

chaperones will bind to the protein to aid it in getting out of the cell prior to getting to complete structure

characterisitics of nitrogenous basis - --- ------------, moving hydrogen depending on reactions taking place because they are nitrogenous bases, they are capable of ------ --------- ------------- strong ----------- of UV light

characterisitics of nitrogenous basis - enol tautomerization, moving hydrogen depending on reactions taking place because they are nitrogenous bases, they are capable of acid base dissociations and rxns strong absorbance of UV light

studying Chemical stability (usually talking about ---- ----) involves -------------------------

chemical instability) involves loss of integrity due to bond cleavage Treating a protein with different kinds of chemical treatments that break down (screw up) some kind of bonding in the protein ( usually covalent, peptide bonds or disulfide bonds,

amino acid gets bound to transfer rna

circled is the acceptor arm circled is the trna that binds to the amino acid

o How are they classified (not based on structural commonality)? What roles do steroids play?

classification is based on hydrophobicity, not structural commonality steroids are not really classified as lipids based on it's structure, because it's structure doesn't look like any of the other lipids that we have looked at so far.

Classification of terpenes

classified based on the number of five carbon units (isoprene) that they actually contain if they have 10- carbon terpenes (they have 2 C5 units), called monoterprenes 15 carbon terpenes (three C5 units) sesquiterpenes 20- Carbon terpenes (four C5 units) are diterpenes Larger because lipids tend to have lots of carbons like triterpenes (30C), tetraterpenes (40 carbons), and poly terpenoids ((C5)n n>8

siRNA

cleaved portion of double stranded rna that then complexes and creates this cleavage (exonuclease activity) of the mRNA

trypsin

cleaves at the carboxyl end of arginine and lysine typ-KA

receptor mediated endocytosis

coated pit cytoskeletal coatings that aids in pulling membrane and vesicle formation

Beeswax

combination of myricyl alcohol and palmitic acid nice long hydrocarbon chains no double bonds which is why you end up with a solid at room temperature although we do know it at a lower temperature than usual tricontanyl palmitate wax ester major component in beeswax

The thickness of the lipid bilayer averages about 5nm thick (50Å) but the overall thickness depends on its --------. The hydrocarbon tails of the lipids in the bilayer are not always ------- but may bend and kink especially towards the middle of the bilayer.

components linear but may bend and kink especially towards the middle of the bilayer.

Ultracentrifugation

concentrates particles based on enhanced sedimentation under centrifugal force. DOES NOT depend on the charge or its residues

o What kind of reaction adds a phosphate group to a nucleotide? starting at the ----- phosphate bonded to the sugar, the P are labeled -----, -------, --------

condensation reaction adds phosphate because produces water and adds a phosphate by a phosphoric anhydride bond starting at the first phosphate bonded to the sugar, the P are labeled alpha, beta, gamma

Tautomerization

contains a phosphate ester bond and undergoes hydrolysis like atp . Once it has been through the hydrolysis reaction, it is in an enol form that immediately tautomerizes into a keto form , so it becomes much more stable and it has all the entropic effects and it has stabilization. It is the big dog on the block in terms of energy production.

Steroids

core structure consisting of (3) six-membered rings + (1) five-membered ring Steroids - doesn't look like the others Derivative of cholesterol, based on it Vary by what is linked to C17

All active transport processes are

coupled reactions.

Van der waals

created when two biomolecules come in close contact with each other - Induced dipole-induced dipole - proximity causes temporary dipoles (flinch from each other) - Other molecules (flinch in opposite manner) attractive dipole - these short interactions accumulated to have a structural influence. STRENGTH IN NUMBERS

Subunits in quaternary structures have symmetry. The most common symmetries are

cyclic (see below) dihedral (a two-fold plane of symmetry between subunits)

Sometimes chaperones just stabilize the unfolded protein to avoid any kind of ------------

degradation

Enemy of assay

denaturation - Denaturation: process by which a protein loses its "native" or active shape or conformation. Proteins are held together by weak interactions: H-bonds, ionic bonds (to some extent so ions in the solution, ionic charge interactions between side chains), Vander-waals interactions (bulk of protein being in close distance from other portions of the proteins), hydrophobic interactions These can be disrupted from wrong pH, ionic content (too high salt or too less salt), or wrong temperature. This will cause denaturation.

small interfering RNA

derived from nucleolytic cleaving of double stranded RNA'S too form these small products and they are part of formation of duplexes which regulates the mRNA so its not translated and signal for degradation (signal exonuclease activity to remove mRNA)

Because there is more than one stereocenter in most of the sugars there are more than just the two enantiomeric versions. Those isomers that are not mirror images are called --------- If they only vary at one stereocenter then they are referred to as -------, Eg. D-Ribulose and D-Xylulose are epimers since they only differ at the C-3 carbon. All of the sugars shown above are in their D-conformation. This is because in nature the D-forms are the predominant forms produced and used.

diastereomers. epimers

As say sulfur molecules come into contact with each other they will form ---------- ------- that stabilize that structure

disulfide bridges

what are the final concentrations of acid and base after adding acid or base

divide the final mmol of acid/base by the total volume in mL (volume of buffer + volume of added acid/base)

types of nucleic acids DNA - deoxyribonucleic acids, a self --------- material which is present in nearly all living organisms as the main constituent of ----------. It is the ------- of ------ information RNA - nucleic acid present in all living cells. Its principal role is to act as a -------- carrying ----------- from DNA for controlling the -------- of ---------, although in some viruses RNA rather thanDNA carries the genetic info

dna basically the genetic material that makes up the template for all of the different proteins and structures produced in bodies rna- messenger for carrying all of the information from dna to the mechanisms that create the different components like proteins

overview of dna to rna to protein

dna creates rna then rna has all of these different purposes in the cell. majority is creating proteins or a form of regulation of protein production

nucleotides found in rna vs dna dna is generally found in ------- ------- C and G bound by bonds A and T by H bonds rna is generally a s---------- stranded structure doesn't have --------that allows for H bonds

dna is thymine rna is uracil instead dna is generally found in double helix D and G bound by bonds A and T by H bonds rna is generally a single stranded structure doesn't have hydroxyl that allows for H bonds

Large globular proteins are often composed of multiple --------- These ----- are part of the tertiary structure of a protein.

domains or modules - These domains act as separate proteins with individual functions that add up to a cumulative overall functioning protein that retains the abilities of its individual domains. - These domains are part of the tertiary structure of a protein. - These domains were likely at one time individual proteins that have been duplicated. There are many domains that are replicated in the same as well as different proteins.

DNA forms double helix has several different forms depending on sequence content and ionic conditions of crystal preparation B-form DNA prevails under ----------- conditions of ----- ionic strength and a ------ degree of hydration regions of the helix that are rich in ---- ---- dinucleotides can exist in a novel ----------- helical conformation termed ----DNA This conformation results from a ------- deg change in the orientation of the bases relative to that of the more common -- and --- DNA

double helix has several different forms depending on sequence content and ionic conditions of crystal preparation B-form DNA prevails under physiological conditions of low ionic strength and a high degree of hydration regions of the helix that are rich in pC pG dinucleotides can exist in a novel left-handed helical conformation termed Z-DNA This conformation results from a 180 deg change in the orientation of the bases relative to that of the more common A- and B-DNA

Nucleases can cleave on the --------- side -- -- --------------- ---- Nucleases can be very specific. They can be ----- ------ or double -------- ---------.

either side of the phosphodiester bond. Nucleases can be very specific. They can be single strand or double strand specific.

For many exothermic reactions, Sometimes energy is released as heat energy, but does not make it to the surroundings and

energy is translated to an increase in entropy in the surroundings so it isn't able to do work. Also sometimes we lose heat to be used for heating up the surroundings

Lipid make good ------------ as they provide a large amount of -------- when -------- their structure allows

energy molecules - as they provide a large amount of energy when oxidized and - their structures allow them to be packed efficiently for storage.

Phospholipases hydrolyze -------------- that creates a -------- ---- that -------------------

ester linkages. Each action shown in figure 4 by a different phospholipase enzyme creates a different signal molecule. These molecules each signal a different cascade of cellular response. One such cascade leads to production of the eicosanoids.

cyclic nucleotides ex. -------- --- as ----------- molecules are -------- ------ and regulators of cellular ----- and ------ used throughout the body, bound to phosphate as usual but also bonded at the -- end to the same phosphate as well

ex. CyclicAmp (cAmp) nucleotide acts as signal molecules are signal molecules and regulators of cellular metabolism and reproduction used throughout the body, bound to phosphate as usual but also bonded at the 3 end to the same phosphate as well

Describe the difference between exocytosis and endocytosis.

exo - taking from inside cell to outside of cell (ex. bloodstream) endo - bring things into the cell exoxytosis: inside cytoplasmic vesicle merges with the PM and releases its contents to the exterior ex. - golgi body vesicles merge with the PM and release their contents - how nerve cells release neurotransmitters vesicle, membrane bound proteins structures where you have proteins you want to get across the membrane vesicles form around proteins, become embedded in plasma membrane and once they do, this breaks and it releases proteins to the exterior of the cell, example of how nerve cells release neurotransmitters endocytosis opposite

Enzymatic hydrolysis is carried out by two general types of nucleases:

exonucleases and endonucleases.

Proteoglycans appear to be either

extracellular matrix proteins (serglycin or Versican) or integral membrane proteins (syndecan) The purpose of these proteins involves the recognition and specific binding of other molecules either through binding to the glycosaminoglycan units, or through specific receptor domains in the polypeptide.

o Facilitated Diffusion. What is it? Down or against the concentration gradient? Examples of molecules that enact this? What is the difference between a carrier and channel protein (consider structure + active/passive transport)?

facilitated diffusion is when you actually have proteins facilitating these molecules moving across the membrane, ex. glucose is being bound to the exterior of the cell on a transport protein, that changes conformation, and never really allow glucose to come in contact with the hydrophobic core of the membrane, which is what these channel proteins and carrier proteins do channel proteins just allow specific molecules or ions to cross the membrane carrier proteins - translocate (glucose) binds and releases it on the other side carrier active is against concentration gradient specific (only allow a few types of mol to pass through)

Corticosteroids

for adrenaline and adrenal hormones glucocorticoids - (carbohydrate regulating) and mineralocorticoids (electrolyte regulating ), reflecting their preferential activities. In humans, cortisol (hydrocortisone, a cortisol hormone)is the main glucocorticoid and aldosterone is the main mineralocorticoid

monophosphates for ----- reasons bound to the nucleoside through a ------------ bond always attached to --- carbon, where the phosphate group is attached nitrogenous base is attached to carbon ------- carbon --- determines whether deoxyribose or ribose

for size reasons (one phosphate group) bound to the nucleoside through a phosphoester bond always attached to 5' carbon, where the phosphate group is attached nitrogenous base is attached to carbon 1 carbon 2 determines whether deoxyribose or ribose

Proteins fold to

form the most stable conformation

microRNA

forms complexes with the mRNA and by making these duplexes in the RNA it blocks any form of translation from taking place another post transcriptional modification that can regulate the actual production of a protein

biological importance of terpenes

found in a lot of biological type reactions antibacterial, found in sedatives, insectosidal (keep bugs from eating trees), trees use as sap, antiinflammatory menthol, which is important

G=H-TS - tells us the

free energy of system this is the total usable energy of system

Why is understanding Protein stability important (not that imp)

gives an idea - thermodynamic dynamic process (folding) high to low Es - trying to relax into a low energy conformation - Increased protein stability (over what period of time and what can stabilize it ) - may be a value in food and drug processing and in biotech and protein drugs - Treatment and drugs can specifically induce and sustain a strong chaperone (stabilized by chaperones and understand that) and protease (tear apart protein to find activity in cells

Triacylglyceride

glycerol + 3 fatty acid chains bound by an ester linkage Major in body and diet, it is how we store fat and 60% of resting energy Insulation and protection (cushioning around organs and skin and for impact) Fat soluble compounds like vitamins carrier Flavor and texture -sensory qualities

Glycerophospholipids

glycerol-3-phosphate backbone + 2 fatty acids on C1 and C2 + a polar head linked through phosphate group --------------------- Phosphoglycerides are one of the largest class of lipids in the body and are a part of all cell membranes. Glycerophospholipids are the most common subset of the general class of phospholipids. The C2 carbon of the glycerol moiety is chiral. Thus, there can be chiral forms of a phosphoglyceride.

Sialic acid caps a lot of ---- sialic acid has a lot of ------ that allow for

glycoproteins at the end of the glyco segment of the glycoprotein you see sialic acid as sort of an end cap. Has a lot of hydroxyls and a lot of sites for reaction making it really good for signals or binding different types of moleculse coming towards the cellular membranes

Proteoglycans share in common the ------------------

glycosaminoglycan units being O-linked to serine residues in the sequence Ser-Gly.

Glycosyl Phosphatidylinositol Anchors

glycosyl linkage between inositol and oligosaccharides, which is connected through ethanolamine to carboxyl terminal group of protein

transfer RNA, and

go out , find the correct amino acid and connect it to the growing chain of a protein there is at leas one transfer RNA for each of the 20 amino acids

Complete acid/base calculations. pH, titrations, weak acid/base equilibrium, Henderson-Hasselbalch, buffers, etc.

go over calcs

hnRNA

going to have transcript that is the huge 7700 bp and all of these intron after transcribed put caps on both ends (5' cap and poly A tail) added introns (noncoding regions will get removed) once they do that you will have mature mRNA that is exported into the cytoplasms to be taken to the ribosomes 7,700 to 1,872 bp all this has to take place

Understand the different protein assays discussed - what is each kind used for? What do they separate molecules based upon? Be able to choose which method you'd use to separate given molecules.

google doc Protein Assays Separation of proteins from cells is based on 2 key properties Size Electrical charge Also can be separated by using their specific affinity to another molecule. Typical protein purifications use a combination of different separation techniques

------- act as intermediates between the very high energy PEP like molecules and the lower end molecules

group transfer potentials, can be compared to reduction potential or ionization potential Just like the calculations of delta G, the same equation can be used to determine the free energy of the ATP-ADP potential

--------- are able to act as intermediates between the very high energy PEP like molecules and the lower end molecules These reactions have energy measurements called ---. explain what they are

group transfer potentials, can be compared to reduction potential or ionization potential Just like the calculations of delta G, the same equation can be used to determine the free energy of the ATP-ADP potential

structural characteristics of mRNA has a ---- cap (7-methyl guanosine triphosphate) that --------- it from -------------- activity cap is involved in the ----------- of mrna by the --------- machinery stabilizes mrna by protecting it from 5' exonuclease ------------------ if the cap is still on mrna it hasn't been translated into protein yet so you don't want the mechanisms in cell to tear apart

has a 5' cap (7-methyl guanosine triphosphate) that protects it from exonuclease activity cap is involved in the recognition of mrna by the translation machinery stabilizes mrna by protecting it from 5' exonuclease ------------------ if the cap is still on mrna it hasn't been translated into protein yet so you don't want the mechanisms in cell to tear apart SPLICING:Removes INTRONS (non-coding_EXONS (coding) are spliced to produce alternative forms of proteins

Sebum waxes

have some unsaturation which makes them a little less solid - good thing because these sebum waxes are secreted from sebaceous glands on skin and keeps skin, hair, and feathers pliable (easily bent, flexible) and water proof sebaceous glands double bonds are good because much rather it be slightly oily than solid so it can be spread uniformly over the hair, or feather to aid it and if it was clumpy you would end up with clogged pores, it being slightly less of a solid allows for better distribution

siRNA, miRNA, ncRNA

have to do with increasing and decreasing protein production

Something to remind you, if you are trying to determine the heat of an energy system and you have a hypothetical reaction, you can determine the

heat of that reaction by looking at other reaction pathways that contain the same products and reactants, by using HESS's LAW. Count up energies by looking at other known reaction pathways, bean counting.

Enthalpy =

heat of the system H=qp Heat at constant pressure because we are almost always 1 atm - In biological system the difference between deltaU /E (energy) and deltaH (enthalpy) are negligible (no much) so they are basically equal.

What interactions are present at the quaternary level?

held together by weak forces as well: - Van der Waals, - hydrogen bonds, - ionic bonds and - hydrophobic interactions As the association will be anti-entropic, the weak interactions must be sufficient to overcome this energy (approx 130 to 220 kJ/mol). Hydrophobic interactions dominate the process Disulfide bridges are also stabilizing forces in some subunits Also, open quaternary structures can polymerize to form functionally important proteins Eg. Tubulin

Fibroblast growth factor binds tightly to

heparin and other glycosaminoglycans. In binding, heparin protects the growth factors from degradation and increases their activity. This binding also provides a reserve of growth factors for later use by the cell. Another purpose of proteoglycans in their addition makes the cartilage in your body flexible. Cartilage matrix proteoglycan (see figure 2) is highly hydrated, it can release water during compression, and this may help in both lubrication and absorbing compressive blows to the joints.

Syndecan also contains the polysulfonated polysaccharide moiety called

heparin, which binds tightly to antithrombin III which accounts for its well known anticoagulant properties. This may represent a storage of growth factors that can be released upon degradation of the proteoglycan (through the action of cellular damage, developmentally-related tissue remodeling, or cancer).

Lipids

hydrocarbon chains with polar head group with examples including , - fats, sterols, waxes, oils, phospholipids - Saturated and unsaturated (double bonds) - Used for long term energy storage and structure Lipids - polymers called diglycerides, triglycerides; monomers are glycerol and fatty acids membranes - sandwich with balls on top and strings going down

Hsp70 (to remember - it likes ----)

hydrophobic - Essentially binds to unfolded polypeptides that are rich in hydrophobic residues, preventing inappropriate aggregation Keep the protein from misfolding or conglomerating the hydrophobic residues too soon Protect protein from denaturation - unfolded protein, residues are left open too solution makes them susceptible to proteases, but chaperones attach and keep protein from being denatured.

The problem with bilayers is that the --------- groups (fatty acids) are exposed to solvent at the "ends" of the bilayer (figure 1). This is still not energetically favorable. The solution is that the bilayer can ----- a continuous surface. This new structure is called a ---------. This creates both a polar interior surface to the membrane as well as a polar exterior. Such unilamellar vesicles are also called ---------.

hydrophobic wrap around upon itself to form unilamellar vesicle Liposomes. A Multilamellar Vesicle is composed of several unilamellar structures inside of each other. Each compartment can contain a different type of environment.

hydrophobic are what categories hydrophilic are what categories

hydrophobic - aliphatic, aromatic, met hydrophilic - sulfur containing, polar/uncharged, basic/acidic

which interactions dominate the process of forming quaternary structures

hydrophobic interactions

Hydrogen bonds are capable of forming with both hydrogen and nitrogen, even in nonpolar biomolecules. What role does water play in nonpolar molecules - in lipids and proteins? -

hydrophobic interactions. Water assists in the folding of proteins as the hydrophobic residues become internal and hydrophilic residues remain on the surface.

in prokaryotes rRNA vs in eukaryotes rRNA

in prokaryotes, you have a 23s and a 5s and a 16s rrna that combines with a ribosomal proteins to form the 50s and 30s subunits that ends up being a 70s in eukaryotes, you have a 28s, a 5s, and an 18s rRNA units that combine with the 2 protein subunits which is 60s and 40 s combine to form 80s ribosome

What does the addition of solutes, both covalent and ionic cause?

increase boiling points lower freezing points affect both vapor pressure and osmotic pressure in aqueous solutions.

Glycosaminoglycans

is a polysaccharide of combined amino sugars and sulfate containing groups. The polysaccharide thereby contains negatively charged polymers. It acts as a natural anticoagulant (inhibits blood clotting). Chondroitins and keratin sulfates are examples that are components of skin and tendons.

The parent compound for the glycerol-based phospholipids

is phosphatidic acid which is composed of sn-glycerol-3-phosphate (phosphate at pro-R position, which will be called C3) and C18 saturated fatty acids esterified at the C1 and C2 positions.

3 properties that can be used to separate proteins -

isoelectric point Proteins isoelectric point. Still a sequence of amino acids which always have charges and at some pH there will be an isoelectric point. You can use these to do some kind of gel separation or ion exchange column to get proteins separated from others with different isoelectric points. size exclusion chromotography, Proteins can also be separated based on size or molecular weight by SIZE EXCLUSION CHROMATOGRAPHY or by using something called SDS-PAGE (sodium dodecyl sulfate) sodium dodecyl sulfate is basically a detergent that attaches to the polypeptide chain in such a manner that stretches it out and now is no it is no longer a folded protein and becomes linearized which means the protein will pass through the gel based strictly on it's molecular weight and that allows you to separate proteins based on MW. Using polarity or hyrophobicity Normally means HPLC (high performance liquid chromatography) or FPLC (reversed-phase chromatography) in order to separate them. The reality is that it is probably you would have to run 2 or 3 or more of these processes to finally get the protein completely separated from all others.

How do helices have handedness?

it has a screw sense - The way it rotates with respect to its axis it is left handed if the helix is made of D Amino acid or rotating CCW. It is it is right handed if the helix is made of L Amino acid or rotating CW

· Further explain how a membrane is fluid through the concept of movement. o What does lateral and transverse movement mean? What is the speed of each?

lateral - phospholipids move in the lateral direction transverse - phospholipid moving along the vertical direction Lateral movements are rapid because no energy barrier transverse movements take longer cuz polar head has to travel through nonpolar region, unfavorable

Polysaccharides can differ by their components, their ------- and --------. They serve as molecules of -------- -----, ------ and --------. Starch and Glycogen are Chitin and cellulose act as Hyaluronic acid acts as a ----------- ----------- for animal cells.

length and their branching energy storage, structural and protection energy stores. structural supports. Hyaluronic acid acts as a protective coating for animal cells.

------ Energy is used by certain proteins (Bacteriorhodopsin and Halorhodopsin for example) to drive ------- processes. The ------ energy sets up a proton gradient across the protein that drives ----------- changes in the protein that facilitates proton export from the cell:

light Light Energy is used by certain proteins (Bacteriorhodopsin and Halorhodopsin for example) to drive transport processes. The light energy sets up a proton gradient across the protein that drives conformational changes in the protein that facilitates proton export from the cell:

Conclusion is that although there is a large number of domains in nature, the number is

limited. This means that it is expected that future classifications of Domains will resemble those already known

lipids used as signals

lipids can create signaling events by essentially binding to receptors in cell membranes. When this happens they produce other signaling molecules called second messengers that signal other activities in the cells

amphipathic molecules in the membrane(phospholipids, intrinsic proteins, and glycoproteins) create a ------------------- glycolipids are present on the ----------

liquid crystalline structure designation, not a solid, not a gel, not liquid, somewhere in between - liquid crystalline aggregates in which the polar groups are directed towards the outer phase and the non-polar groups are inside bilayer outer half glycolipids - talked about being signaling groups that tend to be on. the outer part of the plasma membrane, the outer layer is lesithin and sphingomyelin, inner layer is phosphatidylethanolamine and phosphotidylserine so even though it is a lipid bilayer of phospholipids, the type of phospholipids is not uniformly distributed, so it is an asymmetrical bilayer and the types of phospholipids that are involved are preferably the glycolipids that can recognize the signals and the inside something that can promote second messengers and things like that

waxes (simple lipids)

long chain monohydric (one OH) alcohol + fatty acid bound by an ester linkage Simple lipids 3: waxes Attachment to fatty acids that occurs - waxes that are esters basically Look for the ester in the middle

Fatty acids are

long hydrocarbon chains (12-24 carbons) with a carboxyl head group: energy sources and membrane constituents.

Recognize the structures of each major lipid Fatty acid

long hydrocarbons + carboxyl head

Glycosphingolipids are present in --- concentrations in cell membranes, but as mentioned previously appear to play a key role -------------- Glycosphingolipid accumulation is associated with several genetic diseases.

low in cell-cell recognition.

others terpenes with conjugated double bonds

lycopene - antioxidants b-carotene - color in fruits and veggies

mRNA has -------- and -------- areas ---------- areas of the mRNA are read as ------- (made of 3 nucleotides)

mRNA has uncoded and coded areas coded areas of the mRNA are read as codons made of 3 nucleotides

What chains are proteins made of ? what types of links

made from a single polypeptide chain or several linked together. The links can be covalent bonds, using disulfide bridges (- S - S -), or non covalent IMF's. (ex. H-bonds) Up to complete proteins forming Conglomerates that are in a quaternary stucture

Lecture 13: Structure and Function of Membranes You should be able to: · Describe different functions performed by the plasma membrane.

main function of the plasma membrane is to - separate the cytoplasm in the cell from the outside. Other functions performed by the plasma membrane or its contents include: Exclusion or removal of toxic molecules and ions Import of cell nutrients Energy transduction (typically from surroundings to system) Cell locomotion Reproduction Signal transduction Cell-cell communication The cellular membrane is vital to life functions and its structure and content are directly related to the functions it performs.

Cortisol

main glucocoricoid the main stress hormone in the body manages the accumulation or release of carbohydrate, fats, and proteins manages inflammation blood pressure and blood sugar regulator even controls sleep best known that it is part of fight-or-flight, it triggers adrenal glands to release adrenal glands and you have flight or flight hormone release

What is the difference between hypertonic, hypotonic, and isotonic solutions?

mechanisms that keep solution inside and outside of the cell , moving through the cell membrane the same - isotonic hypertonic - more ion concentration outside the cell then in, water is going to leave the cell and leads to deflated, shriveled up cells hypotonic - a lot more ions inside than outside of cell ,can cause lysis (burst) because the cell membrane cant contain the overall cell structure

Gibbs free energy can be calculated with the total

molesxenergy of each of the products - reactants deltaGo' G = H-TS Gibbs free energy (G) is a state variable, measured in KJ/mol tabulated

Globular hydrophobic Collapsed state is often referred to as a

molten globule

Fructose

monosaccharide

The carbohydrate in glycoproteins may be in the form of a ----------- One, a few, or many carb units may be present. Can have-------- oligosaccharides attached

monosaccharide, disaccharide(s), Oligosaccharides Or their derivatives (e.g. sulfo- or phospho-substituted) more than one

1 double bond is these are ------- at room temp have a ------ config and end up with a ------

monounsaturated softer Unsaturated (Oleic acid) Tend to have cis double bonds, end up with a kink (the guy doesnt cooperate) Space created between the chains Softer fat at room temperature

If you dont have a lot of buffer (ex 10 mL), change in the pH upon addition of acid/base will me a little ------- than if u had more STILL MINIMAL THOUGH

more

Globular proteins - example main roles

most abundant that we talk about, all kinds Hemoglobin, Most of these which move around (ex. albumen, casein in milk) Proteins with binding sites: enzymes, hemoglobin, immunoglobulins, membrane site receptors (globular , billions different structures, not as conserved structurally as fibrous or structural protein) Classified by function

types of ncRNAs

most of the time purpose is regulation of protein translation or gene regulation

typical protein functions

motion and locomotion catalysis structure of cells transport receptors

Proteins ------ Atoms -------- Groups of atoms make collective ---------------------- examples

move vibrate movements,eg. Tyrosine ring flips (fast but infrequent) or antigen-antibody recognition (slow hinge bending) Conformational changes can take place involving small to large segments of the protein (fast or slow).

What are the factors that affect diffusion - why?

moving passively through the cell membrane because conc on outside is greater than inside and the steeper the gradient (the larger the difference in concentration, the faster it is going to diffuse to overcome this. if molecule is small they will diffuse fast higher temps faster diffusion

heterogenous nuclear RNA (hnRNA)

mrna does not come out from transcription as a completed structure, the structure that is iterm-501mmediately created through transcription is hnRNA it is a huge structure, it will be transcribed and things like introns are going to be removed and 75% of this is going to be degraded before it even leaves as mRNA (25%)

a-helix h-bonds how many carbons away

n+4

nucleosides are simply the ------ and ------- portion of a nucleic acid add a --------- group becomes nucleotides when you start to bond -----------together thats when you have fully formed nucleic acids

nucleosides are simply the sugar and base portion of a nucleic acid add a phosphate group becomes nucleotides when you start to bond nucleotides together thats when you have fully formed nucleic acids

nucleosides is a combination of a --------- ---- and a ------- ----. Called nitrogenous bases because of all the ------------. Form either purines or pyrimidines. Know the structures

nucleosides is a combination of a nitrogenous base and a pentose sugar. Called nitrogenous bases because of all the nitrogens. Form either purines or pyrimidines. Know the structures

video on nucleosomes and replication, chromatin nucleosomes are packaged into a thread, called -------------- this fiber is then looped and coiled again a lot to form ------------ which can be seen in the nucleus of dividing cells, -------------- are not always present, they form around the time cells divide when the two copies of dna need to be separated ------------- unwinds the double helix into two strands ------------ strand is copied continuously not as easy for the other strand is cuz has to be copied backwards , drawn out ---------- and ------------ and copied one section at a time. End result is 2 new DNA molecules

nucleosomes are packaged into a thread, called chromatin this fiber is then looped and coiled again a lot to form chromosomes which can be seen in the nucleus of dividing cells, chromosomes are not always present, they form around the time cells divide when the two copies of dna need to be separated helicase unwinds the double helix into two strands one strand is copied continuously not as easy for the other strand is cuz has to be copied backwards , drawn out repeatedly and looped and copied one section at a time. End result is 2 new DNA molecules

Describe the different levels of nucleic acid structure - primary,

nucleotide sequence nucleot/sides are linked together by phosphodiester linkages to form a single strand as shown in figure 1 the phosphate ester links the 3' and 5' oxygens of two sugars -------------------

other nucleic acids

nucleotide triphosphate, high energy bonds

nucleotides most nucleotides are --------- nucelotides are -------- acids

nucleotides most nucleotides are ribonucleotides nucelotides are polyprotic acids because of the phosphate groups that can have reactions

= Describe and explain why different factor affect fluidity of a membrane. When is the membrane more fluid for each of these factors? o Length and saturation of hydrocarbons, temperature, presence of cholesterol. THIS STUFF IS ALL MOVING

o Length and saturation of hydrocarbons, type of fatty acids - more unsaturated, more fluid, shorter chain - changes ability of phospholipid to pack against one another temperature, high temps presence of cholesterol. at low temps, the presence of cholesterol increases fluidity to stabilize the membrane from becoming too rigid

Recall the most common disaccharides: o maltose What two monosaccharides compose the disaccharide? What kind of bond is created between the monosaccharides (i.e. alpha-1,2 - be more specific than "glycosidic")? Are they reducing sugars? What does it mean to be a reducing sugar?

o Maltose, Sucrose, and Lactose. Maltose is glucose-α-1,4 glucose. This is also known of as"Grain sugar". Maltose does have a free anomeric carbon and is therefore a reducing sugar.

define: Proteoglycans

o subclass of glycoproteins in which the carbohydrate units are polysaccharides that contain amino sugars, principally glycosaminoglycans

2 pathways drawn out

one of them is called the mevalonate pathway where you go from the 3(Acetyl CoA's) all the way to mevalonic acid then to the isopentanyldiphosphate and then straight chain down to polyterpenoids methylerythritol phosphate pathway if you are coming from the glyceraldehyde and pyruvate coming out of glycolysis and such, then you are going to come from the sugar pathways into the lipid pathways and it makes a different set of substrates and then you get the isoprene from this (dmap) then it continues in the same cycle to get the level of terpenes as needed

Basically, as you move into the more compact folded states, the number of -------- in terms of mobility of the different bonds is reduced, like a relaxation into a more stable conformation

options

more on terpenes1

originates from turpentine (resin in pine trees), viscous, pleasant smelling (to some), insoluble in water turpentine contains resin acids and some hydrocarbons that were originally referred to as isoprenoids (terpenes)

o Simple Diffusion. What is it? Down or against the concentration gradient? Examples of molecules that enact this?

osmotic process, where water moves through osmotic forces flows down a concentration gradient (high to low) does no use transport proteins examples include o2, co2, CO, NO, steroids other than lipophilic substances, water (exception through osmotic pressures) (mostly nonpolar, if polar very small) easily polar hydrophilic substances cannot pass directly through the lipid bilayer examples: ions, carbs

transmembrane proteins which pass throughout the the lipid bilayer like (----------- and -------------), possess their active side towards ---- phase and hydrophobic part towards ----- and fit in bilayer

outer interior transmembrane proteins which pass throughout the the lipid bilayer like (enzymes and glycoproteins), possess their active side towards ---- phase and hydrophobic part towards ----- and fit in bilayer all of the ferns on the outer portion are all of those glycolipids and glycoproteins where you have all of these fibers and ECM, and glycocalix Inside you have microfilaments of cytoskeleton, also cholesterol, integral (transmembrane proteins), and peripheral proteins

What factors affect the stability of proteins structure? Why?

pH Proteins are most stable near their pI (isoelectric point) Electrostatic interaction Generally Contribute small amount to the stability of the native state; however, there may be exceptions (repulsion of same charged species , causes destabilization) . Assist in stability attracting charged species create stabilization Ligand binding Anytime you bind the ligand to the actual functional side of the protein this is going to cause h-bonding interactions, possibly ion-dipole, vdw interactions. This is going to stabilize the structure of the protein. ANALOGY : if you have your hand lose and sort of flopping around vs putting a ball in your hand and it has to hold it, you have somewhat made the hand structure more rigid and more stable because it is having to hold on to something Binding ligands , (e.g inhibitors to enzymes , increases the stability, also applying to ion binding as many proteins bind anions in their functional sites Disulfide bonds When trying to unfold a protein, the first thing we do is treat is such that it will break the disulfide bonds If you break them (reduce them) then have a carboxymethylation with iodoacetate, this will denature the protein (ie. unfolded, or mostly unfolded). That's how important disulfide bonds are to the stabilization of the protein's tertiary structure.

videntify the factors that make equilibria more complex.

pH dependence The phosphate groups on ATP all contain ionizable hydrogens. Meaning there are multiple (4) pKa values for the dissociation of these hydrogens. The changes in pH can determine which of these hydrogens are present at any point in time. In order to calculate the exact free energy, you must take these 4 separate equilibria into account However, we will say that at physiological pH, the effect on the free energy is small enough that we don't really need to worry about it, except in certain situations. The actual value is fairly constant from pH 4-6 and increases in spontaneity by 5.7 kJ/mol for every pH unit increase over approx. 7.

Parallel vs antiparallel beta sheets

parallel- mainly hydrophobic and hydrophilic on same side antiparallel - mainly hydrophobic and hydrophilic on separated on different sides

membrane transport

passive diffusion - osmotic (ex. O2) diffusion through aqueous channel (also passive process) - some proteins are essentially a hole through the membrane and provide a tunnel through which diff. types of ions can flow . They flow because there is a charge difference between the outside and inside of cell. if the charge inside of the cell is negative Na+ of course the sodium is going to be attracted to that charge and its going to flow through any pore or channel available to it facilitated diffusion with carrier protein - carrier proteins provide a mechanism by which a molecule, (like glucose) would bind to the outside of the protein that is embedded (integral protein process) that would then transfer glucose from one side of the membrane to the other. This is considered facilitated diffusion and would require a carrier protein. Generally there is a conformational change that allows the glucose to transfer Active transport - against the concentration gradient (if you were trying to bring in to the cell something like a chloride ion) or you were doing something against the gradient where there is already a whole bunch of sodium Na+ dont need anymore, but we are facilitating it by bringing in more sodium or positively charged ion (K+). If you need to do this, then you need to pair it up with an energy source, normally it is going to be hydrolysis of a phosphate group from ATP

transport of substances across the plasma membrane

passive transport - use of osmosis to allow things to transport in and out of the cell, form of simple diffusion facilitated diffusion - may or may no be something like active transport things like endocytosis and exocytosis under bulk flow

recognize helical in sequence by identifying what?

patterns , can be both hydrophobic and hydrophilic

components of cell membrane what is glycocalyx

peripheral - not embedded just associated glycocalyx - proteins and lipids that are part of the membrane that have sugars attached to them , related to signaling and actually forms a protective barrier against disruption can provide "barbed wire fence" surrounding the plasma membrane where different molecules can't get past those sugars (protective barriers)

This two part hydrolysis leads to the generation of a

phosphate that is used to regenerate ATP in the Pyruvate Kinase reaction and generate -62.2 kJ/mol of Free energy

What kind of reaction removes a phosphate group from a nucleotide?

phosphoryl group transfers alcohol reacting with the phosphate, you are going to transfer the phosphate group to whatever the r group is and goes from nucleotide triphosphate to nucleotide diphosphate, being a single transfer pyrophosphoryl group transfer works the same except you transfer 2 phosphate groups at once the only other reaction is the once is the hydrolysis of the bond between the that cleaves the bond (between alpha and beta) that generates a lot of energy 2. Phosphoryl group transfer**Single transfer of a phosphate group R-OH + NTP ⇌ NDP + R-O-phosphate group 3. Pyrophosphoryl group transfer**Transfer of more than 1 phosphate group NTP + R-OH → NMP + R-phosphate group-phosphate group 4. Hydrolysis of Phosphoric anhydride bond Produces a lot of energy***Removes phosphate group

the protoplasm of the all cells is surrounded by the ----- -----

plasma membrane the difference is that in the eukaryotic cells, the plasma membrane goes throughout the cell and provides compartmentalization that allows for the cell to have organelles, like the ER and Mitochondria that are separated and have there own plasma membranes that act as a sort of a barrier to allow different molecules in and out of those organelles prokaryotes have little plasma membrane in extending into interior of cell as mesosomes but not extensive like animal cells

membrane transport systems

plasma membrane has hydrophobic interior that only allows selective, nonpolar, or very small molecules charged or larger need some form of transport system to help them go into and out of the cell membrane have receptor sites which interact with things like lipids or carbs like (hormones, nt, and immune proteins), that will react with something in the membrane that allows it to create a second messenger inside the cell to basically start a cellular process for cell life or metabolism

How can endocytosis be broken down further?

plasma membrane sinks inward, pinches off and forms a vesicle different particles phagocytosis - large solid particle basically pushes into cell membrane that closes up (consuming)and results in vesicle, phagosome example : bacteria, cell debris, or food Pinocytosis - smaller particle ,cell drinking - cell brings in liquid receptor mediated endocytosis you have receptor molecules like (glycoprotein or glycolipid) that recognizes something that the cell needs. receptors are lined along the coated pit, and as soon they have bound a molecule that the cell needs, it then creates a vesicle by closing around and pinching off a segment of the cell membrane the vesicle is coated has the red signaling molecules so that the vesicle is directed to the right organelle

Peptidoglycan

polysaccharide found in bacterial cell walls. Gram positive bacteria have thick walls of this polysaccharide, while gram negative have thin, single layer walls. Gram positive walls are composed of N-acetylglucosamine and N-acetylmramic acid with pentaglycine linkages and tetrapeptide (L-Ala, D-Glu,L- Lys, D-Ala) moieties. Gram negative walls are comprised of the same except the pentaglycine linkages are replaced with a direct amide bond between the L-Lys and D-Ala.

Most of the carbohydrate in nature is in the form of

polysaccharides.

2 or more double bonds is explain what happens

polyunsaturated If you continue to unsaturate with more than double bond, both are cis, start to get wavy kinky tails You get a lot of separation depending on number off kinks, turning them into liquids because not as packed together

Sex hormones (androgens)

progesterone testosterone - makes men men estrogen - makes women women hormones that promote hair growth, sexual activity development of sexual organs

Protein structure in conjunction with When talking about structure you are talking about its ----------

protein function function (structure dictates function) These structures are not static but they breath, move, have dynamic movement Add together and separate

the combination of what makes membranes unique and what are characteristics

proteins (anchored proteins strengthen membrane) can be fluid or anchored integral (fully penetrated) that have hydrophobic regions that span the bilayer because of nonpolar AA arranged as alpha helices or peripheral (surface) both proteins and lipids are free to move laterally in the plain of the bilayer only

Fluid Mosaic model (singer and nicholson, 1972) essentially lipid bilayer with proteins embedded proteins that are trans membrane( the portion extended through bilayer) typically have ---------- ------------ (----------)structures (read the picture)

proteins that are trans (integral) membrane typically have alpha-helical structures, (hydrophobic residues) sometimes single but sometimes a cluster

Lecture 10: Glycoproteins define Glycoproteins

proteins that contain oligosaccharide chains (glycans) covalently attached to their polypeptide backbone.

Because of the bond angles of both the carbon and C-O-C bonds both forms take on a ------- structure that is not planar as depicted in either projection. The chair or boat conformational drawings are more accurate with ----- substituents more stable in the equatorial bonds. Only ----- manages to have all of its bulkier substituents in equatorial positions and is thus the most stable of the sugars - probably why it is the most prevalent of all the sugars.

puckered bulky glucose

The fatty acid tail of triglycerides is rich in --------- carbon. These can be --------- with the liberation of ----- amounts of energy (about twice as much per weight in comparison to carbohydrates or proteins 38 kJ/g as opposed to 17 kJ/g).

reduced oxidized large Which is why it is so hard to lose weight. Triglycerides are also good insulators. Arctic animals rely on body fat for both energy and insulation.

reducing end

reducing end - hemiacetal nonreducing - acetal

Platelet Activating Factor (PAF)

released by different portions of skin cells and so forth which has to do with clotting, inflammation, and anaphylaxis membrane bound protein that has signaling that creates the phospholipid activation, where you see arachidonic acid and this creates things like prostaglandins which signal for other responses from cells

Parent hydrocarbons of terpenes (isoprenoids)

repetition of 5 carbon (isoprene)

D-arm of tRNA U arm

responsible for helping (providing recognition site) for the enzyme (amino acyl tRNA synthetase) that catalyzes the binding the amino acid to the acceptor arm ---------------- contains pseudo uridine, responsible for binding the transfer rna to the ribosome

ribose sugars, are the other component of --------- there are 2 different ones , -------- or -------- the difference is that at C--, you either have a hydrogen for ------- or hydroxyl for --------- when we connect these to make the actual nucleosides, they are going to connect at the C--hydroxyl and you are going to end up with an -------- carbon , the carbon is attached to two oxygens

ribose sugars, are the other component of nucleosides there are 2 different ones , Dexyribose or ribose the difference is that at C-2, you either have a hydrogen for deoxyribose or hydroxyl for ribose when we connect these to make the actual nucleosides, they are going to connect at the C-1 hydroxyl and you are going to end up with an anomeric carbon , the carbon is attached to two oxygens

all the differences between RNA and DNA.

rna is single stranded mainly vs dna is double stranded different sugars (ribose vs deoxyribose) different bases (uracil vs thymine) rna chain is made single stranded chargraff RNA does not follow base pairing rules but dna does ,cg at rna is easily destroyed by alkali's that comes from having the hydroxyl group making it easier to react with don't want rna to accumulate in the cell, you want to be able to remove it from cell where dna doesn't have dna (with double stranded structure) is more stable than rna (can be taken apart by exonucleases fairly easily) rna found in cytoplasm dna is found in nucleus rna (100-5000base pairs) is much much smaller than dna (millions) various types of rna vs dna is one type no variable physiological forms of rna but dna forms are variable (A to e and z) rna is synthesized from dna it can not form dna dna can form dna by replication, it can also form rna by transcription many copies of rna are present per cell single copy of dna per cell

So The resulting state of hydrophobic collapse may have a high content of But many amino acid side chains are not entirely ------

secondary structure fixed

The structure of a protein starts begins with a primary sequence The order of the amino acids in the primary structure allows

secondary structures to arise.

Thioester-linked fatty acid acyl anchors.

several fatty acids (myristate, palmitate, stearate, oleate) linked to cysteine SH

Ribosomal RNA (rRNA)

several kinds- variable in size combines with proteins to form ribosomes, the site of protein synthesis

rna is made --------- stranded ------------- stranded rna can be a control mechanism for --------- protein synthesis and signal ------ ---------- -------------- stranded DNA can can signal dna ------- and promote cell --------

single double stranded rna can be a control mechanism for blocking protein synthesis and signal viral infections single stranded DNA can can signal dna damage and promote cell death

Proteins with a single transmembrane section are often anchored by a ------ \alphaα-helix. (glycophorin) These types of proteins are often involved in ------- recognition. Viral proteins that give the ability of the virus to invade the cell will often have a transmembrane alphaα-helix. More embedded integral membrane proteins are often globular, as opposed to simply having single \alphaα-helix for an --------. They will have --------- alphaα-helices, each with a length that essentially spans the bilayer. betaβ-sheets are also found in integral membrane proteins for the same reasons as α-helices. The sheets will have hydrophobic residues -------- on one side and hydrophilic residues on the other. Amino acids have ---------------with respect to their location inside membranes. ------ is a good example of a \betaβ-barrel style of Integral Membrane Protein:

single, immune system anchor, multiple (~4-7) excruding, preferences, porin

micro RNA (miRNA)

small affects gene expression; important in growth and development

small interfering RNA (siRNA)

small affects gene expression; used by scientists to knock out a gene being studied

small nuclear RNA (snRNA)

small processes initial mRNA to its mature form in eukaryotes

transfer RNA

small, transports amino acids to site of protein synthesis

Many times the group bonded to the C2 is a small acetate (2-carbon) unit. This results in an increase in the aqueous --------- of the phospholipid. The group bonded to the C1 may also contain a cis-double bond in the aliphatic chain (between C1 and C2). These molecules are a class known as

solubility plasmalogens

Many transmembrane proteins are Lipid Anchored Meaning they are insol/sol --------proteins that have a ------ ------ group ------------ --------- that is ---------- into the lipid --------- and -------- the protein to the bilayer. This attachment may be -------- and therefore ------.

soluble globular lipid prosthetic Meaning they are soluble globular proteins that have a lipid prosthetic group covalently attached that is integrated into the lipid bilayer and anchors the protein to the bilayer. This attachment may be reversible and therefore regulatable.

Ceramides

spingosine and fatty acid structures sphingolipids are a part of the structure of cell membranes and when they are hydrolyzed by sphingomyelinase and when that happens it releases the ceramides which are secondary messengers

different codons start codon is AUG - always methionine

start codon starts reading frame for the protein all of these codons, have been identified as being the codon for each of the amino acids you can tell that the first 2 of the three in the codon that really is the determining factor for which of the amino acids you put on next as part of the translation

squalene

starting component of cholesterol and other steroid hormones and vitamin D. all of these are isoprene based units

Adrenocorticoid hormones

steroid molecules produced and released by the adrenal cortex the adrenal cortex synthesizes two types of steroids: the corticosteroids, for adrenaline and adrenal hormones and the androgens: sex hormones

What roles do steroids play?

steroids like cholesterol play roles in reproduction, absorption of minerals and metabolic precursors , metabolism regulation, and brain activity

rRNA

still not necessarily understood in terms of role but they seem to be part of the binding of the mRNA to the ribosome.

ribosomal RNA,

structural rna in that it is part of the ribosome which is a lot of protein but there is the 60s and 40s are part of the the protein portion of the ribosome, but each of these also contains several rna's as part of the structure

glycosphingolipids (cerebrosides and gangliosides) type of linkage

subclass of sphingolipids contain one or more carbohydrate groups in a \betaβ-glycosidic linkage to the hydroxyl group of the C3 carbon in the glycerol backbone If the carbohydrate is a single glucose or galactose then the molecule is a Cerebroside. More complex carbohydrate head groups on a glycosphingolipid produces a Ganglioside.

small nuclear RNA

subset of small rna's and they are a part of process of splicing or intron removal of primary transcript to form mature mRNA and gene regulation sRNA form complexes with proteins to form Ribonucleoprotein particles called snRNPs ------------------- part of spliceosome processiong heteronuclear rna that is the transcript from dna has an intron that has to be removed to create the processed mRNA structure snRNA attach to the segment of the intron creating a spliced intron that gets removed from mRNA, mRNA are recyled t

After that tertiary structure forms, sometimes you get multiple ------ of a single complex. Very short timespan, but a very involved process

subunits

glycocalyx

sugar groups that are part of the glycolipids and glycoproteins that are normally on the cell surface they act as mechanical barriers so that they are not going to allow certain molecules to get close enough to the cell surface to do damage they are very hydrophilic because of the sugars that can hydrogen bond with the large amounts of water around them basically has the ability to soluble the cell to interact with its environment

Topoisomerase enzyme help dna ------------- enzymes that ---- or -------- rotations from the DNA helix by temporarily -------- ---------- strands, ------ the ends --------------- -------- , and then ---------the -------- ------ the two classes are type 1: , which breaks ----- ----- of the nucleotide strands and reduces supercoiling by removing rotations type 2 : which adds or removes rotations by breaking both nucleotide strands

supercoiling enzymes that add or remove rotations from the DNA helix by temporarily breaking nucleotide strands, rotating the ends around each other , and then rejoining the broken ends the two classes are type 1: , which breaks only one of the nucleotide strands and reduces supercoiling by removing rotations type 2 : which adds or removes rotations by breaking both nucleotide strands cleave these nucleotide strands to cleave tension created by supercoiling type 1 breaks one and alleviate stress of coil type 2 breaks both and allows one side to turn and alleviate tension

syn or anti has to do with the placement of the purine or pyrimidine as being over the top of the sugar, it is ----- if not on top, on the other side, it is ------

syn or anti has to do with the placement of the purine or pyrimidine as being over the top of the sugar, it is syn if not on top, on the other side, it is anti

Sphingolipids

synthesized starting with an 18-carbon amino alcohol molecule (sphingosine) are another class of lipids commonly found in cell membranes. These lipids are synthesized starting with an 18-carbon amino alcohol molecule called sphingosine. Sphingomyelins are a subclass of sphingolipids Glycosphingolipids

tRNA molecules exhibit a characteristic ------- ------------- ------------- that includes several stem-loop structures:

tRNA molecules exhibit a characteristic "cruciform" secondary structure that includes several stem-loop structures:

transfer RNA tRNA's are ---------- molecules for ------ ------- during protein synthesis. They adopt a characteristic structure due to ------- ------ ---------- ------------ between ------ In translation, each of the ---------amino acids has -- ------ ---------------- tRNA whose job is to ------ to the ----- ------ and ------- it at the correct spot in the synthesis of a protein from --------- in the ribosome. The 3' end has the sequence ---. The 3'-OH of the --- base forms an ------ -------- bond to the amino acid it carries (the entire complex being known as an amino-acyl-tRNA)

tRNA's are carrier molecules for amino acids during protein synthesis. They adopt a characteristic structure due to intra-strand hydrogen bonding between bases. See Figure 7. In translation, each of the 20 amino acids has at least one unique tRNA whose job is to bind to the amino acid and insert it at the correct spot in the synthesis of a protein from mRNA in the ribosome. The 3' end has the sequence CCA. The 3'-OH of the A base forms an acyl ester bond to the amino acid it carries (the entire complex being known as an amino-acyl-tRNA)

tRNA's --------- amino acids to ------------- during translation of ---- into protein. The tRNA's function to bring in the appropriate amino acid for a given nucleotide sequence in the mRNA. This amino acid is then incorporated into the growing polypeptide chain. The amino acid is covalently bound to the tRNA through an ---------- --------linkage to the ---- ---- ----------- ---

tRNA's transfer amino acids to ribosomes during translation of mRNA into protein. The tRNA's function to bring in the appropriate amino acid for a given nucleotide sequence in the mRNA. This amino acid is then incorporated into the growing polypeptide chain. The amino acid is covalently bound to the tRNA through an amino-acyl ester linkage to the 3' end "acceptor arm".

terpenes o What are the two major pathways (terpene biosynthesis) ? Know the very basics.

terpenes are naturally synthesized and can come from a couple of directions one direction - literally start with acetyl CoA and they basically go through a stepwise formation to get mevalonic acid this is pyrophosphorylated, decarboxylated, and dehydrated to yield isopentyldiphosphate (IPP) IPP is the activated 5 carbon structure that is the building block of most of the terpenes

what does it mean when the pH=pKa at the half equivalence point

the concentration of the conjugate base and of the conjugate acid are equal, meaning that there is a 50% proportion of conjugate base, and a 50% proportion of conjugate acid.

equivalence point

the equivalence point is when there is no longer any of the reactants, because it has all reacted with the added base/acid. Whereas the buffering/halfway titration point is when, as they say, there are equal amounts of H- as HA, making the solution a buffer.

Semipermeability of membranes when you get into ------- or ------- molecules, they are going to need a mechanism

the inside of membrane is hydrophobic generally when looking at permeability, hydrophobic molecules can go in and out pretty readily small uncharged polar molecules (like water) can go in and out of the membrane when you get into larger or charged molecules, they are going to need a mechanism (something like an integral protein that provides a channel) to get them in and out of the membrane because no going to get let through

the linkage between ribose sugars and nitrogenous bases is called a (anomeric) -------- ------- and your going to name these nucleosides by adding idine to if its --------- or osine if it is a ------- the conformations can be ---- or ---- sugars make nucleosides more -------- --------- than free bases

the linkage between ribose sugars and nitrogenous bases is called a (anomeric)glycosidic bond and your going to name these nucleosides by adding idine to if its pyrimidine or osine if it is a purine the conformations can be syn or anti sugars make nucleosides more water soluble than free bases

For an equilibrium system, deltaG = 0 indicates

the reaction is at equilibrium and there is no net movement of products or reactants in either direction. Reaction in equilibrium - rates of the forward and reverse reactions are the same. Meaning that the amounts of products and reactants are unchanging.

the structure starts by taking the ------ ------- strand of dna and --------- it around something called a -------- (protein which are complexed) once these are wound around after that it literally creates ----------, into supercoil then as it supercoils amongst itself, you have a superhelical structure and as it coils again and again it forms into a chromosome (circled in red) small enough to fit into nucleus of cells if open chromatin, it is basically --------- (doesn't stain as darkly as heterochromatin on a slide), indicates its not as tightly wound together as the ------------ is. main difference is euchromatin is the chromatin part of the gene that contains the most ------- genes that are transcribed all the time ---------- is the less transcribed and more condensed version of chromatin (combination of dna wound around histone proteins)

the structure starts by taking the double helical strand of dna and coiling it around something called a histone (proteins which are complexed) once these are wound around after that it literally creates coils, into supercoil then as it supercoils amongst itself, you have a superhelical structure and as it coils again and again it forms into a chrmomosome (circled in red) small enough to fit into nucleus of cells if open chromatin, it is basically euchromatin (doesn't stain as darkly as heterochromatin on a slide), indicates its not as tightly wound together as the hetrochromatin is. main difference is euchromatin is the chromatin part of the gene that contains the most active genes that are transcribed all the time heterochromatin is the less transcribed and more condensed version of chromatin (combination of dna wound around histone proteins)

Free energy can be calculated by using reduction potential

the tendency of a substance to gain electrons or lose electrons to an electrode and thereby be reduced or oxidized respectively ' Biological standard reduction potentials, Eo', can be used to determine the free energy of a reaction as deltaGo' = nFEo', where the coupled reaction is used to determine the potential.

Protein stability refers to the net balance of ----------- that determine or not the protein will be native and folded into its native state or in a denatured state

thermodynamic There are many different parameters in the cell that determine the state of the protein

Anabolic steroids these are synthetic versions of ---------,

these are synthetic versions of testosterone, all different variations of testosterone but synthetic

nucleic acid = polynucleotides

through a condensation reaction form a phosphodiester bond, 3' to 5' (above ribose) fully capable because of hydroxyl to react with phosphate group to create long sequences always read 5' to 3' condensation rxn

different bases in dna and rna

thymine in dna but uracil in rna

different proteins will affect the transfers through the semipermeable membrane

transmembrane proteins tend to be alpha helical structures proteins can be attached to the structures, attached to phosphate heads of phospholipids, or literally through noncovalent interactions, like charge interactions or imfs

features of different proteins

transmembrane proteins tend to be alpha helical structures proteins can be attached to the structures, attached to phosphate heads of phospholipids, or literally through noncovalent interactions, like charge interactions or imfs

proteins very important functions

transport - charged ions large molecules enzymatic (g-proteins, signal transduction) intracellular joining where the membrane s of adjacent have to be hooked together (junction) cell to cell recognition - glycoproteins attachment of cytoskeleton and ecm - part of the protein structure

What is a uniport? A symport? An antiport? Refer to the lecture open-ended question from 6/15.

types of transport systems (proteins) uniport - movement of single molecule at a time symport - simultaneous transport of two different molecules in same direction Antiport - simultaneous transport of two different molecules in opposite direction

you can use both of these equations to to calculate the initial components of a buffer

u solve for one of the unknowns and get the other from it u can double check ur answer by plugging the [base] and [acid] back into HH eq if pH is less than pka than you will have more [acid] than [base] in your buffer and vv when finding the pH change after adding acid or base, use the mL of buffer given and multiply that by the M of acid and base needed for any buffer to get the initial mmol of acid and base then add or subtract the mmol of whatever it is to get the ratio

Lipid signal pathways in general

understand how different lipid signals can bind to integral membrane proteins (nerve growth factor), proteins are signaled with the initial messenger being a lipid hormone of some sort that interacts with the protein and creates a secondary messenger system. the sphingomyelinase creates an activation of the ceramides and then the ceramides activate a number of other molecules that are second messengers that produce some activity in the cell. Reaction in terms of nerve cells Calcium release or calcium absorption with diacylglyceride , ip3, and phosphokinase C that are part of cellular metabolisms that has to do with Calcium Calcium can activate certain proteins that then activate proteins like protein kinase C (meaning its phosphorylating things) these are all cascades that create some kind of activity in the cell by an initial lipid signal that creates a secondary messenger within the cell that then triggers a response to happen of course there is the whole inflammation sequence that takes place using arachidonic acids and some other ceramides as well so these are the main key lipid signalers you find in immune responses, inflammation, blood clotting (platelet)

Messenger RNA (mRNA)

variable directs amino acid sequence of proteins

The carbohydrate content of a glycoprotein -------

varies considerably depending on it's purpose from 1% to 85% by weight

watson and crick discovered the structure of dna a helix of two --------------- antiparallel strands wound around each other in a --------- direction and stabilized hy h bonding between bases in adjacent strands. bases are in the interior and a nearly 90 deg angle purines form H bonds with pyrimidines

watson and crick discovered the structure of dna a helix of two complementary antiparallel strands wound around each other in a rightward direction and stabilized hy h bonding between bases in adjacent strands. bases are in the interior and a nearly 90 deg angle purines form H bonds with pyrimidines

high mannose form

which basically puts these mannosidases and glucosidases process this and add mannose sugars to it, it's called a high mannose forms if it stop, if doesnt stop it will continue to form complex glycans

THREE MAJOR CLASSES OF GLYCOPROTEINS

worry about first 2

Carbon metabolism (dont worry too much)

you have carbon metabolism primary carbon metabolism - goes off to one side for the carbohydrates and the other for lipids, but they all feed back into each other so this is a kind of routing to build these terpenes

fructose forms either

●a 6-member pyranose ring, by reaction of the C2 keto group with the OH on C6, or ● a 5-member furanose ring, by reaction of the C2 keto group with the OH on C5.

The antiparallel nature of the helix stems from the ---------- of the individual strands. From any fixed position in the helix, one strand is oriented in the 5'-->3' --------- and the other in the 3'-> 5' ---------. On its ------- surface, the double helix of DNA contains two deep -------- between the ribose- ---------chains. These two grooves are of ------ size and termed the ----- and ------- grooves. The difference in their size is due to the --------- of the deoxyribose ------- and the structurally distinct dishes nature of the upper surface of a base-pair relative to the bottom surface.

The antiparallel nature of the helix stems from the orientation of the individual strands. From any fixed position in the helix, one strand is oriented in the 5'--> 3' direction and the other in the 3' -> 5' direction. On its exterior surface, the double helix of DNA contains two deep grooves between the ribose- phosphate chains. These two grooves are of unequal size and termed the major and minor grooves. The difference in their size is due to the asymmetry of the deoxyribose rings and the structurally distinct dishes nature of the upper surface of a base-pair relative to the bottom surface.

Recall the properties of living systems - what must living-systems be able to carry out?

- Complexity and internal organization (highly structured) - Biological molecules with a functional purpose -Energy transformation - ex. Think food to energy - self replication/reproduction - growth and development - homeostasis - response to their environment - ability to adapt - Manufacture materials from env. - Extract energy —-> work from env. - Metabolize, encode - simple -> complex. This means it has to be able to catalyze metabolic reaction - simply put - (do reactions to taking things that are simple from the environment and convert it them into something complex that is needed for the cell and life). - metabolic and biosynthetic process need to be encoded because they are involved in repro - Respond to environment and changes, selectively insulating - This metabolism has to regulate the organisms structure in response to changes in the environment (respond to environment), so it has to - selectively insulate itself from the environment for exchanges. propagate / reproduce - meaning it lives on So it has to evolve and - eventually die, or not part of cycle of life

Define a state function. What are examples of state functions? How are they calculated? dX = nX(products) - nX(reactants), where n is the moles of substance

- Each of the parameters is shown as a change following their status as state functions. - ATP hydrolysis is exergonic - The value of a state function is independent of path, meaning that the value is calculated as:

Affinity Chromatography

- Ligand is attached to a solid support to form a specific adsorbent to which protein is exposed - Only the molecular species that shows appreciable affinity for the ligand will be bound and the other materials will pass through the column

Sugar Alcohols what ending is added to sugars name

- Mild reduction of the carbonyl group of sugars creates sugar alcohols.An - itol ending is added to the sugar to indicate it is an alcohol. Examples are sorbitol, mannitol, xylitol

Metabolism (not in concept sheet)

- Pathway (ordered) of complex molecules working together. - Almost always catalyzed by enzymes - so they take place in a timed manner that allows for functionality. - Highly specific pathways that do 1 or 2 simple process - produce specific needed energy or needed molecules for the cell - There is a system of enzymatic control that decides whether a molecule will be produced ex. If energy is needed, reaction will create energy, if not it will store it.

Size exclusion chromatography

- Separates molecules based on their size by filtration through a gel. - Small molecules diffuse into the gel pores and their flow through the column is retarded (more difficult) according to their size - Large molecules do not enter the pores and are eluted (removed by washing with a solvent) first - Consequently, molecules are separated based on their size as they pass through the column and are eluted in order of decreasing molecular weight (MW)

Hydrophobic interactions -

- water club is exclusive - non-polar molecules dislike water - lipids are very handy for isolating from water - promotes phase separation - entropically driven effect

The red line shows the -OH group whose orientation tells D or L

Glucose and fructose have same OH's just differ in aldose and ketose In nature

The partial pressure of CO2 (pCO2) in the lungs can be varied rapidly by the rate and depth of breathing. For example, a common remedy to alleviate hiccups is to increase the concentration of CO2 in the lungs. This can be achieved by holding one's breath, by very slow and shallow breathing, or by breathing in and out of a paper bag. Under such conditions, pCO2 in the air space of the lungs rises above normal. a. How would increasing pCO2 in the air space of the lungs affect blood pH? b. It is common practice among competitive short‑distance runners to breath rapidly and deeply (hyperventilate) for about half a minute to remove CO2 from their lungs just before a race begins. Under these conditions, blood pH may rise to 7.6. Explain how hyperventilation elicits an increase in blood pH. c. During a short‑distance run, the muscles produce a large amount of lactic acid from their glucose stores. Why might hyperventilation before a short‑distance run be useful?

Blood pH is controlled by the carbon dioxide-bicarbonate buffer system represented by the equation CO2+H2O↽−−⇀H+ + HCO3 -During hypoventilation, when breathing is slowed, [CO2] increases in the lungs and arterial blood, driving the equilibrium to the right, raising [H+] and lowering pH. Blood pH would not increase because formation of carbonic acid (H2CO3) from the hydration of CO2 does not decrease H+. It would not be unchanged because H+ increases when H2CO3 releases a proton. During hyperventilation, when the breathing rate is increased, [CO2] decreases in the lungs and arterial blood, reducing [H+] and increasing pH above the normal 7.4 value. Hyperventilation removes CO2 from the lungs and bloodstream, so the availability of bicarbonate in the blood decreases rather than increasing. Hyperventilation does not increase the uptake of protons by muscle cells because it decreases the availability of H+ to the transporters rather than increasing it. Hyperventilation does not increase the production of OH− by red blood cells; this is not a function of red blood cells. Lactate is a moderately strong acid, completely dissociating under physiological conditions and thus lowering the pH of blood and muscle tissue. Hyperventilation removes H+, raising the pH of blood and tissues in anticipation of the acid buildup. Hyperventilation does not increase the ability of the liver to take up lactate from blood, as lactate and proton transport are coupled, and hyperventilation decreases the availability of H+. For this reason, hyperventilation makes lactate release from muscle more rather than less favorable. Lactate is synthesized from glucose in muscle in a process that does not depend on the respiratory rate.

2 identify the factors that make equilibria more complex.

Concentration effects As with calculation of any free energy value from equilibrium concentrations, ATP is also subject to the change in free energy with changes in equilibrium (non-standard state) concentration. The equation for calculation of the free energy will now be a In the calculations, the summations take into account all of the concentrations of the various ionic forms of the molecules. As the concentration of ATP decreases, the free energy increases (becomes more negative) . below shows a representation of this Concentration changes have even more effect on free energy than cations or pH

aliphatic hydrocarbon

Containing carbon atoms joined together in straight or branched chains

Understand the benefits of coupling reactions - what does it accomplish?

Coupled reaction - The reactions of high energy molecules have such high free energy values, meaning the reverse process (ie. putting phosphate back on AFP to form ATP) is very ENDERGONIC AND NOT SPONTANEOUS. So how does the reaction happen so we don't run out of energy? - Coupling Coupled reaction Areplentiful/rampant in metabolic systems. When you pair a high energy spontaneous reaction (-deltaG) with a non-spontaneous reaction (+deltaG), you can easily determine if the reaction will proceed by adding up the free energy values. Phosphoenol pyruvate (recharge molecule for ATP) is nearly double which is why they are coupled to it can recharge

o ∆X

Each double bond is indicated by a ∆x, where the double bond is located on the xth carbon-carbon bond, counting from the carboxylic end Eachterm-169 double bond is preceded by a cis-or trans-prefix ---------------------- Delta x is about basically Counting from the carboxyl end and counting away to find the location of double bonds and indicate whether cis or trans at that double bond This is more information

NMR use

Each nmr spectra has a unique signature for the amino acids, nmr often used to illustrate the 3-dimensional structure of proteins as well

Extended parallel beta sheets

Have interdigitating groups between them cause different physical properties in the protein and in the fibers that it produces

rearrangement

Gives off a large negative Essentially a structural rearrangement, there is a resonance stabilization that takes place upon ionization of the product. So 3-phosphoglyceric acid and it becomes after ionization 3-phosphoglycerate. Large amounts of energy given off, more than atp and can be used to add inorganic phosphate to other molecules.

What role do globular, fibrous, and structural proteins play?

Globular proteins - balled up, spherical proteins. Tend to be enzymes, catalyst, signaling proteins Fibrous - structural or connective role functional proteins Structure of the protein dictates its function

How do globular proteins fold?

Globular proteins all contain a substantial amount of secondary structure. The final tertiary structure of a globular protein is compact with hydrophobic residues tightly packed in the interior. Polar and charged aa face the outside Helices and sheets represent the starting point of folding As hydrophobic forces create compaction, the helices and sheets stabilize the polar backbone through h-bonding interactions The surface of a protein generally consists of the loops and turns that are in between these secondary structures These surface motifs (design) create the areas of complementary structures that provide the basis for enzyme interactions. These loops are held in place by side chain interactions

Why is there no third eq point

H3po4 (important in the body)titration curve - 2 eq points, not 3 because 3rd pka is so high you need a very strong base to help it reach it.

o What is a homopolysaccharide? What is a heteropolysaccharide?

Homopolysaccharides are made up of the same monomer sugars. Heteropolysaccharides are made up of two or more different monomer sugars.

method for absolute configutation

How to give absolute configuration to these amino acids. For most of them we are talking about the D and L system Carboxyl group is oriented upward and to the back and the side chain R points downward and to the back Which amino acids found in nature and proteins in the body - related to molecule called glyceraldehyde. All amino acids are designated d or l Carboxy group up R group bottom Hydrogen will be on either left (D) or right (L) Mostly concerned with L-aa's because made naturally, not D

hydrophobic collapse

Hydrophobic collapse - Folding is initiated by spontaneous collapse of polypeptide into a compact state which is mediated by hydrophobic interactions among non-polar residues. - The nonpolar, hydrophobic residues flee the surroundings because it is mostly aqueous so they collapse into these hydrophobic areas - The secondary structures (alpha helices and beta sheets) have already formed and collapse into a more compact structure based on hydrophobic forces

What is the hydrophobic effect and how does this aid in protein folding?

Hydrophobic effect - internalizing hydrophobic amino acids from the aqueous solution entropically favored Induces compact folding The Internalized polar groups of the protein backbone are stabilized by hydrogen bonding which, reduces strain

Supercoiling · Describe supercoiling. o What is the purpose? What are the two main enzymes involved? What do each do, respectively? When does supercoiling occur? In addition to the a-helix of DNA there is an additional level of twisting = --------------. • Circular DNA with no ------- turns = -------- (cuz takes ------- to supertwist) Superhelical turns serve two purposes: • 1. ------- - ---- ------ ------- 2. ----- - ---------- --- ----------- ----------- ---------- What are the two main enzymes involved? What do each do, respectively? Two enzymes work to maintain supercoiling in DNA. -------------- , ----- ------------- DNA, and DNA -------- ------ --------------

In addition to the a-helix of DNA there is an additional level of twisting = Supercoiling. Discovered by Jerome Vinograd (1963) at Caltech; noticed multiple bands of DNA in preparations of circular DNA (plasmids). • Circular DNA with no superhelical turns = relaxed (takes energy to supertwist) Superhelical turns serve two piurposes: • 1. yield a more compact shape 2. can result in unwinding of DNA helix (aids in replication) Two enzymes work to maintain supercoiling in DNA. Topoisomerases relax supercoiled DNA (sort of cut the dna and open up the double helix) , and DNA gyrase introduces supercoiling.

small RNAS

In eukaryotes, there are a small host of RNA's that have complexes with protein and are distributed in the cytoplasm and nucleus

small nuclear RNA (snRNA) In eukaryotic nuclei there are ------ (100-300 bp) RNAs that ------ with --------- proteins, forming ----------------------(snRNP's) These RNAs are involved in the --------------- of eukaryotic ------ ------------- into complete ------ molecules for --------- from the nucleus to the cytoplasm.

In eukaryotic nuclei there are small (100-300 bp) RNAs that complex with specific proteins, forming small nuclear ribonucleoprotein particles (snRNP's) These RNAs are involved in the processing of eukaryotic gene transcripts into complete mRNA molecules for export from the nucleus to the cytoplasm.

DNA in cells In more --------- organisms, the DNA is distributed among a -------- number of large molecules of DNA (multiple chromosomes) and is typically linear. Eukaryotes typically have ---- copies of each chromosome (--ploidal).

In more complex organisms, the DNA is distributed among a small number of large molecules of DNA (multiple chromosomes) and is typically linear. Eukaryotes typically have two copies of each chromosome (Diploidal).

· Explain why micelles form. o How do they encapsulate dirt and grease (nonpolar compounds)? Why? Fatty acids added to water can form a ------- on the surface, with the polar head group hydrogen bonding to solvent, and the hydrocarbon tail pointing outwards, away from solvent. Monolayers form with dilute solutions of fatty acids. What is the structure of a micelle? Refer to the lecture open-ended question from 6/15.

Lipids are key. They spontaneously form ordered structures in aqueous environments. These are formed because of the hydrophobic effect (i.e. entropy considerations of solvent) that promotes the formation of structures that remove the hydrophobic tail of the fatty acid from the aqueous extracellular environment. At higher concentrations called the critical micelle concentration, or CMC, fatty acids will form micelle structures. The CMC is typically 0.1 - 10mM. Because of the long hydrocarbon tails, micelles can be problematic with respect to packing so the formation of a lipid bilayer is more energetically favored. Fatty acids added to water can form a monolayer on the surface, with the polar head group hydrogen bonding to solvent, and the hydrocarbon tail pointing outwards, away from solvent. Monolayers form with dilute solutions of fatty acids.

· How are lipids separated?

Lipids are separated into 2 groups Hydrolyzable (saponifiable, hydrolyzable) - tend to be straight chain Not hydrolyzable (non saponifiable) - derivatives of cholesterol

What does it mean to be hydrolysable (saponifiable)? What lipids fall into the hydrolysable group? What lipids fall into the non-hydrolysable group?

Lipids are separated into 2 groups Hydrolyzable (saponifiable- can be hydrolyzed by OH- , hydrolyzable) - tend to be straight chain Not hydrolyzable (non saponifiable) - derivatives of cholesterol

Local secondary structures form ----

Local secondary structures form first

ATPase is a --- subunit -------- that pumps 3 Na+ ions out of the cell for every 2 K+ ions that comes into the cell and this process also ---------- ----ATP for each transaction

The ATPase is a two subunit protein that pumps 3 Na+ ions out of the cell for every 2 K+ ions that comes into the cell and this process also hydrolyzes 1 ATP for each transaction

· Understand how DNA can be denatured and renatured. o What holds a DNA duplex together? How can these interactions be interrupted? Denaturation and Renaturation of DNA

The DNA duplex is held together by a combination of hydrogen bonds between base pairs and the van der Waals forces associated with base stacking interactions along the helix. These interactions can be disrupted using pH, temperature or ionic strength.

What grooves does DNA possess?

The DNA helix has a major groove and a minor groove.

o Named by the number of carbons in the carbohydrate.

The name carbohydrate comes from their basic formula: (CH2O)n where n is 3 or more. Notice that this formula is basically a carbon with a water I.e. Carbo-hydrate.

phi is 0 when

carbonyls are overlappin

pump inhibitors

cardiac glycosides

o What are some common waxes?

carnauba wax , major ingedients of car wax and floor polish, comes from the leaves of a south american palm tree Beeswax - candles and things of that nature Sebum waxes - sebaceous glands

The stem-loop regions of the tRNA fold into a characteristic tertiary structure. Hydrogen bonds form between bases in the D loop with bases in the variable loop and the TYC loop. These hydrogen bonds involve a variety of non-typical base pairing interactions. Each amino acid has at least one unique tRNA molecule, although they all share similar structures. The sequence in the anti-codon loop region is -------- --------- --- -----------

unique to each amino acid.

Messenger RNA (mRNA) Carries the --------- encoded in --------- to locations within the cell where -------- -------- takes place mRNA is synthesized during the process of ------------- A enzyme (--- ---------) copies the information from a DNA template into a -------------- RNA molecule The information in the mRNA is then ----------- into a corresponding -------- ------ by the protein synthesizing machinery within a ----------- The complexity and organization of mRNA in eukaryotes and prokaryotes is ---------. In prokaryotes a single mRNA often contains information for -------- proteins. This is known as a ------------ mRNA. In eukaryotes each protein is coded by an ---------- mRNA molecule. However, this mRNA molecule usually undergoes ----- ----------- ----------- --------- is done to remove ---- -coding regions called ------- Additionally, alternative coding regions (------) can be spliced to produce -------- forms of a given protein. Eukaryotes also have stretches of 100 to 200 adenylate bases added to the 3' end of the nucleotide known as a -----------. This is believed to help stabilize the mRNA.

Carries the message encoded in DNA to locations within the cell where protein synthesis takes place mRNA is synthesized during the process of transcription A enzyme (RNA polymerase) copies the information from a DNA template into a complementary RNA molecule The information in the mRNA is then translated into a corresponding protein sequence by the protein synthesizing machinery within a ribosome The complexity and organization of mRNA in eukaryotes and prokaryotes is different. In prokaryotes a single mRNA often contains information for several proteins. This is known as a polycistronic mRNA. In eukaryotes each protein is coded by an individual mRNA molecule. However, this mRNA molecule usually undergoes post-transcriptional modifications. Splicing is done to remove non-coding regions called introns. Additionally, alternative coding regions (exons) can be spliced to produce alternate forms of a given protein. Eukaryotes also have stretches of 100 to 200 adenylate bases added to the 3' end of the nucleotide known as a poly A tail. This is believed to help stabilize the mRNA.

Catabolic vs anabolic

Catabolic - breakdown (lysis) exergonic Suppose 100 kJ are required to break the bonds in the reactants of the catabolic process, and 120 kJ are released in the formation of the bonds of the products. Then there is a net release of 20 kJ, and the reaction is exothermic. Anabolic - ener builds/creates (genesis) endergoic reactions

1 angstrom to aa

3.5 amino acids

The Shorthand for writing sequences:

5' gattcatgcgatagc 3'. This notation give the sequence of the bases in the oligonucleotide 5' p-gattcatgcgatagc 3'. Same thing but with a 5' phosphate (assumed to have 3' OH group) GATTCATGCGATAG. Same thing as the first sequence, its just that the author decided to use uppercase. The orientation is assumed to be 5' on the left.

What does it mean to be chiral?

All amino acids except glycine have different functional groups and therefore have 4 unique groups bonded to the alpha carbon. The resulting a-carbon is chiral, asymmetric.

How is reduction potential measured?

All of these cell potentials are normally reported as reduction potentials and are measured against the standard hydrogen electrode. We set the standard hydrogen electrode (ie. platinum and hydrogen gas) and the measurement of that reduction as being equal to zero (dividing line), and all of the other potentials measurements are measured against the measurement that is done for this particular potential

Recall the basics of each polysaccharide mentioned in the lecture. o Dextran - major ones. What is the polysaccharide made from? What is the function? What bonds are present? Does it have a reducing end? § Be able to recognize the structures.

Dextran, found in yeast and bacteria, is composed of a-1-6 linkages of D-glucose, with branched chains (1-2, 1-3 or 1-4 linkages between glucose units). It forms a component of dental plaque (from bacteria). Dextran is a branched D-glucose polymer by α-1,6 linkages and α-1,3 linkages at branch points with a single reducing end and multiple non-reducing ends

o Osmosis. What is it? Down or against the concentration gradient? Examples of molecules that enact this? What is the difference between hypertonic, hypotonic, and isotonic solutions?

Diffusion of water across a differentially permeable membrane water moves from high conc to low con (down concentration gradient) happens in red blood cells if there is a low conc of water in cell, conc of ions is high, water is going to flow in and actually lyse the cell this allows cell membrane to keep integrity, keeping isotonic

· Distinguish between the different types of DNA secondary structure: A-DNA, B-DNA, and Z- DNA. o What are they? How do they differ? A form -- bp per turn Pitch is ------- angstroms ------- and -------- helix than B form --------- DNA may adopt A form Probably not adopted by DNA in ---------- Most likely structure adopted by double stranded ------ DNA structure is flexible and various motif regions on the helix are capable of interacting with proteins and other molecules.

Double stranded DNA can assume one of three types of secondary structure, type A, B or Z A form 11 bp per turn Pitch is 24.6 angstroms Shorter and fatter helix than B form Dehydrated DNA may adopt A form Probably not adopted by DNA in vivo Most likely structure adopted by double stranded RNA DNA structure is flexible and various motif regions on the helix are capable of interacting with proteins and other molecules.

Utilize the following equations:

Electrons move from a less positive to a more positive potential. Reduction occurs at the cathode and oxidation occurs at the anode in a voltaic cell Ecello is calculated as Ecathode - Eanode A positive Ecello value indicates a spontaneous reaction The potential of a cell and therefore thee free energy is concentration dependent Nernst equation = using a standard state and using a correction factor -2.303 R(8.314 J/molk)T/n(number of electrons transferred) x F (Faraday's constant)(96500 coulombs/mol of electrons) If at 298 k , it simplifies to a different value 0.0592 This will allow you to take non-standard state equilibria information and still be able to get the cell potential for any cell that you are working with It is very likely biochemical systems will not be at 1 M, so if you are going to have to do potential calculations for a biochemical cell, you are probably going to have to work with this equation

More triglycerides

Example of triglycerides Palmitic, oleic and stearic are the most abundant fatty acids

Having metal ions coordinate with portions of the protein (example iron with hemoglobin)

Example where three histidine residues are attracted and coordinate with a Zinc metal ion in this protein. How the coordination would stabilize the different areas of the protein, bringing it together.

What is the "free energy funnel"?

Free energy funnel - unfolded states are characterized by a high degree of conformational entropy and relatively high free energy - Process has often been discussed in terms of a energy funnel - Basically, as you move into the more compact folded states, the number of options in terms of mobility of the different bonds is reduced, like a relaxation into a more stable conformation - End up with a single native state (lowest energy point) of protein. Idea is ANALOGY: LIKE YOU get into a relaxation into a big overstuffed chair and you wiggle around until you find the most comfortable spot (ONLY 1 MOST comfortable conformation where you expend lowest energy and entropy is reduced)

Glycerophospholipids and sphingolipids act as ---------------------------- via their ------------------ ----------- Because they are membrane bound for the most part their signaling is local. The signals they produce are --------- --------- ---------

Glycerophospholipids and sphingolipids act as chemical signals via their modification and breakdown. Because they are membrane bound for the most part their signaling is local. The signals they produce are short-lived and highly regulated.

which direction does heat travel

Heat travels from a Hot temperature to a cool so the travel of the heat will be to the cooler until they equal.

Acetals, Ketals and Glycosides - what do hemiacetals and hemiketals react with to form acetals and ketals through dehydration

Hemiacetals and hemiketals react with alcohols in acidic solution to form acetals and ketals through dehydration. The pyranose and furanose forms react with alcohols in acidic solution to form glycosides. Methyl a-D-glucopyranoside

DNA gyrase

Introduce supercoiling /// Creates negative supercoiling 2 Manners: 1. Negative Supercoiling Strands are unwound Most common 2. Positive supercoiling Strands are overwound

Z- DNA. ---------handed ------- helix ---- and ---------- forms can interchange First observed in --------- repeating DNA ---------- of ----- bases can cause B to Z conformational change. Z DNA may be --------------- -relevant in regulation of DNA expression.

Left-handed duplex helix B and Z forms can interchange First observed in CGCGCG repeating DNA Methylation of C bases can cause B to Z conformational change. Z DNA may be physiologically relevant in regulation of DNA expression.

Membrane Active Transport Systems This is diffusion (up or down) against a concentration or potential gradient spontaneous or not result in higher or lower PE

Membrane channel proteins carry out active diffusion. uphill Such processes represent transport resulting in a higher potential energy state (i.e. energetically it goes uphill; this represents a form of stored potential energy) E.g. NOT spontaneous.

Membrane characteristics

Membrane characteristics - groups of various macromolecules held together by noncovalent forces including - HYDROPHOBIC interactions between aqueous environment inside and outside the cell with lipid in the membrane. - Macromolecules are embedded in membranes to provide functionality to the inside and outsides of cells. - Complexes of predominantly proteins and lipids but also have other. Maintained by hydrophobic interactions and ncovalent interactions. - Occur naturally because of hydrophobic interaction with the environment. Membranes allow formation of compartments.

Lecture 14: Nucleosides & Nucleotides You should be able to: · Recall all (5) nitrogenous bases. Nucleotide polymers are the basis of our ------- ------- Deoxyribonucleic acid (DNA) is the ----- -------- in cells. Ribonucleic acid (RNA) ---------and --------- this information into -------------. Basic Structural Units The nitrogenous bases found in nucleic acids are derivatives of either --------- or ---------:

Nucleotide polymers are the basis of our genetic code. Deoxyribonucleic acid (DNA) is the genetic material in cells. Ribonucleic acid (RNA) transcribes and translates this information into proteins. Basic Structural Units The nitrogenous bases found in nucleic acids are derivatives of either pyrimidines or purines:

Nucleotides are -------- Phosphates A nucleotide is formed when phosphoric acid is ------ to a sugar hydroxyl of a nucleoside.

Nucleotides are Nucleoside Phosphates A nucleotide is formed when phosphoric acid is esterified to a sugar hydroxyl of a nucleoside.

O-linked, what do they involve?

O-Links are formed through - serine, - threonine, - hydroxylysine hydroxyl groups to N-acetylgalactosamine.

· Recall the two major classes of glycoproteins.

O-linked, N-linked

fast and simple assays

One way (UV range) - If you are doing an assay and want to know how much protein is present in solution, just to get a relative number to start with. - The simplest and most direct way is to get the concentration of the protein at 280 nm. Phe, Tyr, Trp all have absorbances in this range and if protein has some of these, you can get a relative concentration of your protein based on that knowledge. - You can measure this either as percent transmittance or absorbance. - You are basically going to look at the conc of the protein Other way (spectroscopic analysis) Look at activity Place some of the substrate in with your protein and you monitor the change of either the substrate conc or the appearance of the product conc to determine if you still have activity in your protein simple way to determine protein activity and or protein concentration

There are three basic types of membrane transport processes:

Passive diffusion Facilitated diffusion Active transport

· Determine major differences between peripheral and integral membrane proteins. o What are they? do they penetrate the hydrophobic region What is the distribution of polarity? Where are they found? Can they be separated/detached from the membrane - is it easy or difficult? Why?

Peripheral Membrane Proteins - These are polar proteins that associate with the polar head groups of the bilayer surface via hydrogen bonds and ionic interactions. They do not penetrate the hydrophobic region of the bilayer, and can be dissociated from the surface under buffer conditions that disrupt ionic interactions (e.g. pH, and high salt)

· Recall the pentose sugars. What sugar is found in DNA and what is its structure? What is the sugar found in RNA and what is its structure?

RNA and DNA contain ribose sugars in addition to a purine or pyrimidine nitrogenous base as part of their structure:. RNA contains a ribose molecule and DNA contains a deoxy-ribose molecule (2'-deoxy-ribose).

Review oxidation and reduction. Which gains electrons? Which loses electrons? How does oxidation number change? Where does oxidation occur? Where does reduction occur? What indicates a spontaneous reaction?

Reduction is when electrons are gained, - oxidation number decreases Oxidation is when the electrons are lost, oxidation number increases Electrons move from a less positive to a more positive potential Reduction occurs at the cathode and oxidation occurs at the anode in a voltaic cell A positive Ecell value indicates a spontaneous reaction The potential of a cell and therefore the free energy is concentration dependent

roles of different types of proteins

S and m support or maintenance - more stretched, linear fibrous, not so globular E and h - regulatory, hormones (signal upregulation/downregulation), enzymes (catalysts) Fluid balance - proteins ensure body fluids are equally dispersed in and out of cells. Utilize pumping actions that use things like ions in and out of cells so they can maintain (isotonic , inflating /deflating)

SDS-PAGE - Sodium Dodecyl Sulfate PolyAcrylamide Gel Electrophoresis.

SDS - anionic detergent - Application of SDS to a protein produces an even charge across the length of protein, making it linear. - Placing the linearized proteins into a polyacrylamide gel, the electric field acts as the driving force, pulling the SDS coated proteins towards the anode with larger proteins moving more slowly than small proteins In order to identify proteins by size, standards of a known size run under the same conditions

polypeptide syntesis

Solid phase peptide synthesis has been used to create proteins like insulin, ribonuclease A and an HIV protease. These proteins contain up to 134 residues Resin (yellow) - made of polymers, like polystyrene , SWELLS in solvent Functional group with protecting group, then deprotection Resin loading (first coupling) Deprotection Coupling Deprotection before global cleavage (where resin (with its associated functional group) and protection of R-group are cleaved)

How are the subclasses sphingomyelins and glycosphingolipids (cerebrosides and gangliosides) defined?

Sphingomyelins are a subclass of sphingolipids that contain a phosphate group. They are an important element in the insulating myelin sheath surrounding nerve cells. picture is titled sphingolipid classes

The Density of a supercoiled helix is ------- than its relaxed form. This density can be calculated by determination of the change in the linking number upon supercoiling.

The Density of a supercoiled helix is greater than its relaxed form. This density can be calculated by determination of the change in the linking number upon supercoiling.

The Eicosanoids

The Eicosanoids are local hormones that are produced in response to injury and inflammation.

· Understand the difference between a nucleoside and a nucleotide. o Nucleoside = ---- + ------ Is the glycosidic bond always alpha or beta? How do you name nucleosides?

The complete structure of a nitrogenous base + a ribose sugar (glycosidic bond) is called a Nucleoside. The Glycosidic bonds in nucleosides are always betaβ-type (see above). Nucleosides are named by adding the suffix "-idine" to the pyrimidine or "-osine" to the purine name.

what is a reducing end

The end of the molecule containing the free anomeric carbon is called the reducing end, and the other end is called the nonreducing end. So non-reducing sugars that cannot reduce oxidizing agents.

Cholesterol is the

The principle component of animal cell plasma membranes is a steroid called Cholesterol. It is also a component of lipoprotein complexes in blood, and of plaques that form on arterial walls in atherosclerosis. The numbering system shown above applies to cholesterol and all other steroids.

There are always ----- stereoisomers possible, where N is the --- of chiral centers.

There are always 2N stereoisomers possible, where N is the number of chiral centers.

o What are the major differences between RNA and DNA? There are two main differences between DNA and RNA: 1. ............ 2. --------------- Consequences of RNA's --- group is that it allows RNA to be ---------- more readily than DNA. This makes DNA the more ----- of the two polymers. Consequences of the Uracil inclusion in RNA. Cytosine base pairs with ------- in DNA. Uracil base pairs with ------- in RNA. But --------- can ---------- to form Uracil at a slow but steady rate in living systems. This means there can be ------ in DNA if left --------. There is a system in DNA replication that removes the ------- and replaces it with ---------. If ------- were a regular nucleotide in DNA there would be no way to know if the U was really a U or a ------ ---- ----.

There are two main differences between DNA and RNA: RNA has OH group at 2' position, whereas, DNA has only a hydrogen DNA contains Thymine, RNA has Uracil instead Consequences of RNA's OH group is that it allows RNA to be hydrolyzed more readily than DNA. This makes DNA the more stable of the two polymers. Consequences of the Uracil inclusion in RNA. Cytosine base pairs with guanine in DNA. Uracil base pairs with Adenine in RNA. But Cytosine can deaminate to form Uracil at a slow but steady rate in living systems. This means there can be Uracil in DNA if left unchecked. There is a system in DNA replication that removes the Uracil and replaces it with Cytosine. If Uracil were a regular nucleotide in DNA there would be no way to know if the U was really a U or a C gone bad.

· Recognize the structure of a wax.

These are esters of long-chain alcohols with long chain fatty acids. ----------------

Importance of association constant

They have some molecule that they are responsible for binding to and changing in some fashion and then releasing They act almost like catalysts, they bind to something in order for their activity to take place. (ex. Muscle contraction, binding to ions and releasing) Binding and release of ligand are important How this takes place and how can you measure their specificity and affinity for their binding

With exception of some of the structural proteins, majority of proteins work off of what is called a ligand

They have some molecule that they are responsible for binding to and changing in some fashion and then releasing They act almost like catalysts, they bind to something in order for their activity to take place. (ex. Muscle contraction, binding to ions and releasing) Binding and release of ligand are important How this takes place and how can you measure their specificity and affinity for their binding

THIOL ESTERS (thioesters)

Thiol and a sulfur with acetyl COA being an example Not a phosphate but a sulfide group that causes the high energy breaking of the bond

Chromatography

Very Common process in separation of proteins. At least one or two types of chromatography are normally run. It is a flow of solution through a column. The column is usually packed with different materials. Some are ion exchange where they bind to the column based on ionic differences Sometimes hydrophobic columns or size exclusion columns - column is basically packed with porous beads and if you are trying to get a large protein separated from smaller molecules. Smaller molecules will get trapped into the pores of the beads whereas the larger molecules will exude (get through) first because they dont get trapped in molecules COUNTERINTUITIVE you would think larger would have difficulty passing through but because smaller proteins/molecules get trapped it takes them longer to get through. Elutes based on size

what can change the pH of water

Weak electrolytes and Acids and Bases are the predominant compounds that change the pH of water. - Strong electrolytes do not hydrolyze (react with) water so they do not have an effect on the pH of the solution. Strong electrolytes like highly soluble salts also fully dissociate in water. Slightly soluble salts and weak acids and bases only partially dissociate in water causing changes in the pH. These are equilibrium events and the concentration of H+ or OH- must be calculated using equilibrium methods (eg. ice tables).

What are the cons (drawbacks) of weak forces?

Weak forces are easily torn apart, life is fragile Can be easily denatured Weak bonds are vulnerable to changes (increase or decrease) in temp, energy, pH Narrow range of liveable conditions - Without enzymes in cells (proteins which run metabolism), because they will become denatured, the cell dies.

Extraction processes Methods

any one or several will be used to break up the cell and extract protein from the cell Repeated freezing and thawing - if you freeze cells, a lot of the times they will lyse and this will allow their internal portions to pour out to get proteins - Sonication - using sound to break or lyse the cell and free the proteins - Homogenization at high pressure and/or filtration - Permeabilization by organic solvent - adding organic solvent that literally breaks down the cell membrane

if there are no temp changes, pka are ---- for a weak acid because it comes from ka

constant

o Active Transport. What is it? Down or against the concentration gradient? Examples of molecules that enact this? What are the different types of energy that can drive this process?

different types - movement of particles across the plasma membrane against the concentration gradient, that is from low to high concentration (or other depending on what is transporting) energy is always given by ATP generally requires a specific carrier protein to carry molecules in or out of the cell examples of active transport: absorption of glucose and amino acids by cell in the small intestine Na+ K+ ATPase

As long as you havent used up the buffer completely, the pH will still have ---------- change

minimal

Cell surface carbohydrates are basically ---------

molecular recognition molecules and there are many types.

Equation to get the total energy of system If there is no change in volume, it goes to zero and the internal energy of system of system is just equal to heat. This internal energy value is not very useful for thermodynamics of biological systems because ---------- so ----- is used because -------.

nearly all work done in system is at constant pressure but not constant volume, SO ENTHALPY IS USED IN BIOCHEM Enthalpy is related to the internal energy of the system + change in volume x pressure After plugging in the initial formula for the change in energy you end up with enthalpy = heat of the system.

Some fatty acids are "Essential". These fatty acids are needed for ------ growth, but only --------- can make them. So animals must consume ------ that contain these fatty acids (e.g. linoleic, and g-linoleic acid).

needed for animal growth, but only plants can make them. So animals must consume plants that contain these fatty acids (e.g. linoleic, and g-linoleic acid). Cardiovascular disease has been linked to the excess consumption of both saturated fatty acids as well as hydrogenated "trans" fats. So moderate consumption is recommended.

almost all plasma membrane have a potential difference inside usually pos/neg with respect to outside, favors entry of pos/neg charged ions, and opposes pos/neg transport by carrier proteins can be ------------- whereas transport by channel proteins is ------------

negative positive negative either active or passive always passive

What extracts carbon from atmosphere and creates carbohydrates out of those carbons? Complex sugars can be hydrolyzed into ------

photosynthesis simple sugars All three sugars are important to human diet but none are directly absorbed. They are hydrolyzed first into their component sugars by both acid and bacteria in the digestive system.

structural characteristics of tRNA

primary - nucleotide sequence secondary - forms several regions of double stranded RNA that give it a clover leaf look

chromosome packing dna into small spaces why do we need to pack the dna into chrmomosomes?

really big relative to size of cell or nucleus it is in 4.64 million base pairs in Ecoli single molecule of dna in chromosome, 1000 time size of its cell Humans have 6 billion base pairs of DNA, so much longer than nucleus so needs to be packed to fit in small spaces

Bulk Flow. Does this process require energy?

requires vesicles (used to get really big molecules in and out of cells) across the PM - requires energy types exocytosis endocytosis - phagocytosis - pinocytosis - receptor mediated

anticodon arm of tRNA

responsible for recognizing the complimentary to the codons in the mRNA part of reading of the codons

o Know some functions of glycoproteins.

tend to be receptors on proteins, you have a protein bound in the cell membrane and it acts and looks like an antenna (it acts like a carbohydrate antenna on the protein that acts as a receptor for various other proteins that come to interact at the membrane. These glycoproteins affect the chemical and physical properties of the proteins (solubility, mass and electrical charge). They function as stabilizers as well as signals. There is recent evidence to show they assist in protein folding in the ER. "Collagens - structural molecules but also glycoproteins Mucins - lubricants and protective agents, glucose molecules act as protective agents Transferrin ,ceruloplasmin - transport Immunoglobulins - immune system glycoprotein recognition Hormonal - mediated by glucoproteins Enzymes