Exam 2 BIOCHEM

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).

what are the features of a carb that allows it to function the way it does

- 1 or more asymmetric centers, ability to form ring/linear structure, form polymers through glycosidic bonds, hydrogen bonding ability

- How are the subclasses sphingomyelins and glycosphingolipids (cerebrosides and gangliosides) defined?

- Cerebrosides (glycolipid): ceramide plus monosaccharide: galactocerebroside is an important component of the brain, sulfogalactocerebroside is found in myelin - Gangliosideds (glycolipid): globoside plus one or more sialic acid residues: found mainly in ganglions.

what does it mean to be saturated vs unstatured

- Saturated means no double bond, unsaturated has.

what is the purpose of superhelical forms

- yield compact shape - result in unwinding of dna helix 2 enzymes work to maintain supercoiling in dna

what are the two types of N-glycosylation

-glcNac, L-fructose, NANA present - contain mainly mannose

Understand and describe the phase transition and the characteristics associated with it.

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.

how many stereoisomers of heptulose? how many d vs l

16, 8d 8l it has 4 chiral centers 8 names

what are the 2 motifs of o links

1: leukosialin 2: LDL receptor, decay accelerating factors

how many epimers of d glucose, a-d- glucose?

2 and 3

how many stereoisomers are available

2^n n=chiral centers

only ____ sugars form rings

5-7 C 6 atoms: pyranose, 5 atoms: furanose

1 turn of helix has ___ glucose units

6

fructose forms either

6C pyranose ring, by rxn of C2 keto group with OH on c6 or 5C furanose ring by rxn of c2 keto group with OH on C5

What is the general structure of a glycerophospholipid?

A glycerophospholipid is made of one polar head region constructed from an amino alcohol and a phosphate group, and two non-polar tails that are fatty acids.

How are nucleotides made from nucleosides?

A nucleoside consists of a nitrogen base and a ribose or deoxyribose sugar. It can be converted to a nucleotide by adding a phosphate to the 5-OH of the sugar component.

define bile acids (steriods)

Act as detergents secreted by the gallbladder that help solubilize lipids in diet (Ex. chloric and deoxycholic acid)

Calcium ions travel through the cell membrane into the cell, using an integral protein. There is a higher concentration of calcium in the cell.

Active transport is a process that uses a transport protein and energy in the form of ATP to transport molecules against their concentration gradient. Since molecules are moving against their concentration gradient in the scenario, we know it must be active transport

what are the msot abundant aa found in histones and why

All histones have a high percentage of arginine, lysine, and positively charge aa that give them a net positive charge. Positive charges attract the phosphate backbone of dna

What part of the structure of all phospholipids is considered the polar region?

All phospholipids have a polar region made of an amino alcohol attached to a phosphate group.

define androgen (steriod)

Androgens - Mediate development of sexual characteristics and function (e.g. testosterone, estradiol)

Why aren't lipids soluble in water?

Because they are predominantly hydrocarbons, hydrophobic.

What are the two sugars found in the nucleosides used to make DNA and RNA?

Both of the sugars found in nucleic acids are pentoses. Ribose is found in RNA, and 2´-deoxyribose is found in DNA.

which structures is a 20:2 (Delta4, 9) FA

CH3(CH2)9CH=CH(CH2)3CH=CH(CH2)2COOH

what is the difference between a channel and carrier protein

Channel proteins: provide corridors that allow a specific molecule or ion to cross the membrane. Carrier proteins: undergo a subtle change in shape that translocate the solute binding site across the membrane. Most passive transport proteins are solute specific. simple diffusion and passive transport by membrane transport proteins (facilitated diffusion) occur spontaneously. Active transport requires an input of metabolic energy. Only carrier proteins can carry out active transport =, both carrier proteins and channel proteins mediate facilitated diffusion. Transport by carrier proteins can be either active or passice, whereas transport by channel proteins is always passive

what is chromatin

Chromatin: chromosome material which does not stain strongly except during cell division, it represents the major genes and is involved in transcription. Comprises the most active portion of the genome.

Oxygen molecules travel through the cell membrane into the cell, passing between the phospholipids. There is a higher concentration of oxygen outside the cell.

Diffusion is a passive process that does not require energy. Molecules that diffuse are also small and hydrophobic enough to pass through the phospholipid bilayer without the assistance of channel proteins.

osmosis

Diffusion of water across a differentially permeable membrane. Water moves from a high concentration to a low one. Down the concentration gradient

lipid nomenclature, delta 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 ▪ Each double bond is preceded by a cis- or trans- prefix

what is endocytosis

Endocytosis is the opposite. Brings things into the cell. The plasma membrane sinks inward, pinches off and forms a vesicle, vesicle often merges with golgi for processing and sorting of its contents.

describe glycogen

Energy Storage, . . 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.

what is starch and its function

Energy storage, it is a glucan with 2 polysaccharide forms.

what are open chain saponifiable lipids

FA, TG, phospholipids, sphingolipids, waxes

what are the factors that affect diffusion

Factors affecting diffusion rate: steepness of concentration gradient... steeper gradient, faster diffusion, molecular size: smaller molecules, faster diffusion, temperature: higher temperature, faster diffusion

how does the distinction between saturated and unsaturated affect packing structure and flexibility

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.

describe flippases and floppases

Flippases and floppases Are ATP dependent moving phospholipids to the inner and outer side of the membrane respectively.

omega reference , lipid nomenclature

Indicates the number of carbons, the number of double bonds, and the position of the double bond closest to the omega carbon

What is the difference between integral and peripheral proteins?

Integral proteins extend through the lipid bilayer, and peripheral proteins are just on the surface of the inside or outside of the cell.

what are lipid signaling events

Involve lipid messengers which can bind to receptors and mediate certain processes lipid signalling is normally a response to some inner or outer stimulus leading to the release of lipids moieties

What is an anomeric Carbon and its relationship to "reducing sugars"?

Isomers that vary only in the orientation of this new carbon stereocenter are called anomers. Sugars with free anomeric carbons act as reducing agents and as they are oxidized become sugar acids. These sugars are called reducing sugar

Why is cholesterol known as a sterol?

It contains a hydroxyl group on carbon 3.

what is euchromatin

It contains the most active genes. Undergoes the normal process of condensation and decondensation in the cell cycle.

Describe supercoiling

It is an additional level of twisting 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 of the DNA circular that is there are no free ends some viral chromosomes are in the form of simple circles and readily undergo supercoiling

when does supercoiling occur

It occurs only if two polynucleotide strands of the DNA double helix are unable to rotate about each other freely.

describe lactose

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.

Which statement is true about lecithins and cephalins?

Lecithins always have choline as their amino alcohol group and cephalins have either an ethanolamine or a serine as their amino alcohol group.

what is heterochromatin

Less transcribed chromatin Remains in a highly condensed state throughout the cell cycle, even during interphase. Activity of genes is modified or suppressed.

what is a linking number

Linking Number (L) - This is the basic parameter used to characterize supercoiling. It is the number of times the two DNA strands are intertwined.

describe maltose

Maltose is glucose-\alphaα-1,4 glucose. This is also known of as"Grain sugar". Maltose does have an anomeric carbon and is therefore a reducing sugar.

what is a uniport

Movement of single molecule at a time

describe negative vs positive supercoiling

Negative supercoiling - left-handed - strands are underwound. Positive supercoiling - right-handed - strands are overwound

hypotonic

Net movement of water into cell, cell will burst.

hypertonic

Net movement of water out of cell cell shrinks

What type of linkage holds nucleotides together to make a nucleic acid?

Nucleotides are held together in nucleic acids by bonds between the phosphate and the ribose or deoxyribose sugar. These bonds are called phosphodiester bonds.

linkages between proteins can be

O or N

how are rings formed in a sugar

OH group on hexose will attack the C1. when rings forms a new asymmetric C is intoduced, the OH on new asymmetric c can be drwan to appear on same side of ring forming oxygen or on side away

Which molecule(s) would be expected to diffuse into a cell using passive transport?

Passive diffusion only occurs for small non-polar molecules where the concentration is lower inside the cell than outside. Carbon dioxide is the only small non-polar molecule listed.

what is phagocytosis

Phagocytosis: cell earing. Membrane sinks in and captures solid particles for transport into the cell ex: bacteria, cell debris

How do nonsteroidal anti-inflammatory drugs (NSAIDs) reduce inflammation and elevated temperatures?

Prostaglandins are a diverse set of molecules that can cause pain, inflammation, and fever. NSAIDs block their production, thus decreasing these effects.

how does chargaffs rule relate to DNA vs RNA structure

RNA doesnt follow the role while dna does

Which best describes the role of RNA in biological systems?

RNA is involved in the process in which the sequence information from DNA is translated into the sequence information specifying the sequence of amino acids in proteins.

What is the purpose of cholesterol in cell membranes?

Reduce the flexibility of the cell membrane

describe scramblases

Scramblases use calcium ions and our BI directional their purpose appears to be to degrade transverse asymmetry

what is an antiport

Simultaneous transport of two different molecules in opposite directions.

what is a symport

Simultaneous transport of two different molecules in same direction.

Which of the following statements is true about fats and oils?

Solid fats tend to contain saturated fatty acids, whereas liquid oils tend to contain saturated fatty acids. It is generally true that as the number of C=C double bonds increases, the melting point of a fatty acid decreases, thus oils tend to have lower melting points than fats.

sphingolipid

Sphingolipids = synthesized starting with an 18-carbon amino alcohol molecule (sphingosine

What is the structural difference between glycerophospholipids and sphingomyelins?

Sphingomyelins have a sphingosine group and glycerophospholipids do not. Solution:Sphingomyelins have a sphingosine replacing glycerol.

what is a ceramide

Spingosine plus fatty acyl group: core structure

describe sucrose, the bonds, is it reducing

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.

lipid nomenclature 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

Which of the following is true If a sample of DNA is shown to be 30% adenine?

The DNA contains equal amounts of adenine and thymine, so it will contain 30% thymine. That leaves 40% for guanine and cytosine which are also equal and must be 20% of each.

In the nucleus of a cell, double-stranded DNA is bound to protein molecules called _____

The DNA is a cell's nucleus is bound to protein molecules called histones. The complex forms structures called nucleosomes, which are part of the material called chromatin that form chromosomes.

What is the complementary strand for the DNA strand 5´-AAGGCAGG-3´?

The complementary strands run in opposite directions. T binds to A, C binds to G and G binds to C. U is not found in DNA. The complementary strand is 3´-TTCCGTCC-5´.

what do all proteoglycans share in common

The glycosaminoglycan units being olinked to serine residues in the sequence Ser Gly

What is the major structural difference between PGE and PGF?

The major difference between PGE and PGF is that PGE has a ketone at carbon 9, while PGF has an alcohol. This makes PGF slightly more soluble in polar solvents.

What is the name of the three nucleotide sequence found in tRNA that identifies a particular amino acid for protein synthesis?

The three nucleotide sequence in messenger RNA which specifies a particular amino acid is called a codon. The three nucleotide sequence in transfer RNA which is complementary to the codon and therefore delivers the correct amino acid to the binding site is called the anticodon.

how does the linking number related to twist and writhe

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.

Which best describes the structure of the phospholipids of the lipid bilayer?

There are two layers of phospholipids. The polar heads are on the surfaces of the membrane, and the non-polar tails are on the inside of the membrane.

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.

define glucocorticoids (steriod)

These regulate carbohydrate, protein and lipid metabolism (Ex. cortisol.

define mineralocorticoids (steriod)

These regulate salt balance in tissues

define progestin (steriod)

These regulate the menstrual cycle (Ex. progesterone)

where do proteoglycans appear

They appear to be either extracellular matrix proteins (syndecan versican) or integral membrane proteins

what does amphipathic mean

They have a hydrophilic and hydrophobic region Why

what are the two enzymes involved in superociling

Topoisomerases: relax supecoiled DNA. They are enzymes that add or remove rotations from the DNA Helix by temporarily breaking the nucleotide strands rotating the ends around each other and then rejoining the broken ends DNA gyrase: introduces supercoiling

Which of the following abbreviations for a nucleotide is not commonly possible?

Uracil is not found in DNA so it is not commonly found in a nucleotide containing deoxyribose. Therefore dUMP is not a common abbreviation for a nucleotide.

what is bulk flow

Vesicles are used to transport large particles across the PM, requires energy. Types: endocytosis (phagocytosis, pinocytosis, receptor-mediated) and exocytosis

what is the purpose of supercoiling

Yield a more compact shape, can result in unwinding of DNA helix (aids in replicationg)

Which of the following base pairings is correct for RNA?

a and u

which of the following molecules is a typically FA

a molecule that has one cis double bond in a linear carbon chain

Glycolipids contain what additional chemical unit that other lipids are lacking?

a saccharide

the structure of a DNA in a chromosome is considered

a tertiary structure

what is a glucosyl group

a univalent free radical or substituent structure obtained by removing the hemiacetal hydroxyl group form the cyclic form of a monosaccharide and by extension, of a lower oligosaccharide.

Which of the following is not a component of a nucleic acid?

aa

O-glycosylation

addition can happen on the OH o on the side chain of hydroxy lysine, hydroxyproline, serine, or theronine

N-glycosylation

addition of sugar chains can happen at amide nitrogen on asparagine side chain

what bases are found in dna

adenine, guanine, cytosine, thymine

what bases are found in rna

adenine, guanine, cytosine, uracil

What four bases are found only in DNA? rna?

agct, agcu

What amino acid is coded by the codon GCC?

alanine

how are monosaccharides named

aldehyde group present: aldose sugar ketone group present: ketose sugar the aldo has carbonyl on C1, keto is on C2

describe the antifreeze glycoprotein

allow fish to live in freexing water [ala-ala-Thr]n-ala-ala n=4-6,12,17,28,45,50

what is the purpose of branching

allows several sites for simultaneous synthesis and degradation. Speeds up degradation. glycogen phosphorylase cleaves 1 glucose at a time from non-reduced end of glycogen makes glycogen an efficient way to sstore glucose

OH below the rings

alpha

what are N link glycoprotein

amide group on asparagine to N-acetul galactosamine, but also have mannose branched triad

what are the two forms of starch

amylose (linear) alpha 1-4 links and amylopectin (branched) alpha 1-6 links it is insoluble and the major storage of carbs in plants starch has one reducing end and many non reducing ends

define an ether glycerophospholipid

an ether linkage exists off the phosphate group o

what are the five main types of steriods

androgen, progestin, glucocorticoid, mineralocorticoid, and bile acids

A-D- glucose is the ____ of B-D- glucose

anomer

what adds to the diversity of the sugar code

anomeric status, linkage positions, addition of branches, site specific intro of substitutions

What is the best description of how the two strands are aligned with each other in the double helix of DNA?

anti parallel

. Homopolysaccharides

are made up of the same monomer sugars.

Heteropolysaccharides

are made up of two or more different monomer sugars.

what is the best term to describe the distribution of different types of phospholipid molecules in a plasma membrane

asymmetrical

each aldose with > or equal to 3c and ketose with > or equal to 4cs has

at least 1 chiral carbon

Which of the following is a commonly used mechanism for anchoring a protein to a membrane?

attaching a farnesyl group to a cysteine residue to form a thioether

what is a nucleoside

base + sugar via glycosidic bond=anomeric conformation is either syn or anti

D vs L sugars based on

based on configration about the single assymmetric C in glyceraldehyde they are greater than 1 chiral center, refers to the asymmetric C farthest from aldehyde or ketone

what are the functions of nucleotides

bases serve as recognition units cyclic ones are signal molecules and regulators of cell metab and reproduction

Oh above the rings

bea

which is a characteristic of both waxes and terpenes

both can contain oxygen

what is a characterisitc of both tg's and glycerophospholipids

both contain FAs and are saponifiable

Which carbon atom do steroids differ at?

c17

hemiacetals

carbons surrounded by O that are attached to 1 c group and 1 H allows to be reducing sugar

what are some common waxes

carnuba, beeswax, sebum waxes- sabaceous glands

what is pinocytosis

cell drinking, ccell brings in liquid.

Sphingolipids serve what function in biological systems?

cell membrane components Sphingolipids are found in membranes along with phospholipids and cholesterol.

what are the functions of O link glycoprotein

cell signals, nutrient sensors, regulate cell metab. Found to be altered in diseases of aging. found in 2 structural motifs: highly extended above membrane surface, support to push the active protion above membrane

active transport

cells also require transport proteins that can actively pump certain solutes across the membrane against their electrochemical gradients (uphill). This is known as active transport and is always mediated by carrier proteins. In active transport, the pumping activity of the carrier protein is directional because it is tightly couple to a source of metabolic energy such as ATP hydrolysis or an ion gradient. It is the movement of particles across the plasma membrane against the concentration gradient. That is from a region of low concentration to a region of high concentration. Energy is provided by atp molecules. This transport required a specific carrier protein to carry molecule in and out of the cell. Ex: ansorpotion of glucose and aa by cell in the small intestine (NA, K ATPASE

what is a glucoside (glycolipid)

ceramide plus 2 or more hexoses: lactosylceramide is present in erythocte membranes

what is a sphingomyelin

ceramide plus phosphocholine head group: component of erythrocyte and neuronal membranes

amylopectin

characterized by increase in viscocity, clarity, stability, and resistance to gellling.

when sugars become cyclic, the carbonyl carbon becomes

chiral

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

cholesterol

what are clsed chain non-saponifiable lipids

cholesterol, steriod, derived.

glycopeptide

consists of carb linked to an oligopeptide. composed of L and or D aa's

glycosyl aa

consists of saccharide linked through a glycosyl linkage (o- or n- or s-) to an aa

what are glycoproteins

contain oligosaccharide chains (glycans) and are covalentaly attached to polypeptide

Which steroid hormone is produced in the adrenal glands?

cortisone, aldosterone, cortisol

All active transport reactions are

coupled reaction

glycosidic bond

covalent bond between anomeric OH of cyclic sugar and hydroxyl of 2nd sugar. the resultant molecule is glycoside. linkage of two monosaccharides to form disaccharide involves glycosidic bond.

describe oligosaccharides

created by glycosidic bonds, limited to hexoses: glu, mannose, galactose (all aldoses) and fructose pentoses: ribose, xylose

what is exocytosis

cytoplasmic vesicle merges with the PM and release their contents, ex: golgi body vesicles merge with the PM and release their contents, how nerve cells release neurotransmitters.

what are the four key lipid signalers

diacylglycerol (DAG), ceramides, platelet activating factor (PAF), arachidonic acid

what is an anomer

differ in stereochemistry around ring forming C. since alpha and beta differ in only 1 chiral center anomers=epimers

describe ribose sugars

difference shown at 2' carbon, nitrogenous base attach at 1' carbon

secondary structure of nucleotides (base pair)

double helix formed by 2 anti-parallel dna strands bind together by h bonding

what are carbs

either aldehydes or ketones with many OH groups or substances that form these when hydrolyzed. (simple sugars: glucose, complex: starch and cellulose

D vs L sugars are mirror images or

enantiomer

what process is directly linked to bulk flow

endocytosis

what are the functions of these nucleotides atp gtp ctp utp

energy metab protein synthesis lipid synthesis carb metab

exergonic

energy of products < energy reactants endergonic is opposite

what are the functions of carbs

energy production, cell structure, and recognition process

what is the activation energy

energy required for rxn to go from reactants to products through transition state

what are the functions of polysaccharides

energy storage and structural support. starch/glycogen: energy stores chitin/cellulose: structural

glycosylation vs glycation

enzymatic attachment of sugars to proteins non-enzymatic

what are the features of O-glycosylation

enzymes involved are located in various subcompartments of golgi apparatuse. Each reaction involves appropriate nucleotide sugar. occurs post-translationally at cetain ser and thr residues

what are coenzyme/cofactors

enzymes that require additional non-protein to be active some vitamins are cofactors

correct name for the relationship between D-fructose and D-picose

epimers

glucose and galactose are

epimers and diasteromers

isotonic

equal movement of water into and out of cell.

waxes

esters of fa with long chain monohydric alcohol

versican

extracellular matric proteoglycan

Water molecules travel through the cell membrane into the cell, passing through aquaporin, a channel protein. There is a higher concentration of water outside the cell.

facilitated diffusion

a plasma membrane with a high unsaturated FA content will be less fluid due to the higher amount of spacing created between the phospholipid tails in the interior of the bilayer true or false

falase

a glycosidic bond is formed via a hydrolysis reaction true or flase

false

Proteins that can flip and flop phospholipids from one side of a bilayer to the other are called

flippases, floppases, and scramblases

what are O links glycoproteins

formed through serine, threonine, hydroxlysine, hydroxyl groups to N-acetyl galactosamine

describe nucleotide

formed when phosphoric acid is esterified to a sugar hydroxyl of nucleoside -polyprotic -most are ribonucleotides -nucleoside phosphate=nucleotide phosphoric acid esters of nucleoside

What are the functions of n-linked glycoproteins

found in immunoglobuins g and m, ribonuclease B and ovalbumin. They affect chemical and physical properties and function as stabilizers/signals6

feats of mucin

found in secretions of gi, respiratory, and reproductive tracts, membranes of cells have high contents of o-glycan chains usually containing NeuAc have repeating aa sequences rich in serine, threonine, proline form protective physical barrier on epithelial surfaces, invovled in cell to cell interations and contain surface anetigens

how are carbs formed

from dehydration synthesis and hydrolysis

describe dna and rna

genetic materical in cells. main constituent of chromosomes transcribes/translate info into protein. acts a a messenger, carrying instructions from dna for controlling pro synthesis

what are the features of N-glycosylation

glc2Man9(giNAC)2 is transferred from dolichol-P-P- in rxn catalyzed by oligosaccharide: protein transferase. occurs in the er. protein bound oligosaccharide is then partially processed by glucosides and mannosides

what is the function of glycogen

glucose reserve, atp from glycolysis.

sugar esters

glucose, fructose, and others with added phosphate groups

what are the two simplest sugars

glyceraldehyde (Aldose) dihydroxyacetone (ketose)

fats and oils

glycerol + 3 FA by dehydration synthesis =tg

Which of the following chemical components is not found in sphingomyelins?

glycerol backbone

define a glycerophospholipid

glycerol-3-phosphate backbone + 2 fatty acids on C1 and C2 + a polar head linked through phosphate group

which lipids would be in the phospholipid categoru

glycerophospholipids and sphingomyelins

peptidoglycan

glycoaminoglycan formed by alternative residues of D-glucosamine and muramic acid

proteoglycan

glycoprotein whose carb moieties are glycosaminoglycans have repeating units of ser-gly aa's are either extracellular matrix proteins (serglycin/versican) or integral membranes (syndecan)

what are the major types of histones

h1, h2a, h2b, h3, h4

amino sugars

have amino groups instead of hydroxyl at c2

how do you make acetals/ketals

hemiacetals/hemiketals + OH in an acidic solution, through dehydration

what are the two lipid type

hydrolyzable (saponifiable) those that arent

defined disaccharide

hydrolyzed to form 2 monosaccharides

define oligosaccharide

hydrolyzed to form 3-12 monosaccharides

define polysaccharide

hydrolyzed to form many monosaccharides

superhelical forms occur only

if 2 poly nucleotide strands are unable to rotate freely

functions glycoproteins immunoglobin histocompatibility HCG,TSH

immunological antigens hrmone

How do intercalating agents affect structure of DNA? What are examples of 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.

describe 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.

anomers

isomersthat vary only in orientiation of carbon stereocenters

What is the Arrhenius equation?

k = Ae^(-Ea/RT)

What amino acid is coded by the codon CUA?

leucine

selections role in inflammation

leukocytes: roles in inflammatory phenom. they are single chain ca binding transmembrane proteins that control domains. amino terminal ends have lectin domain which is involved in binding to carb ligands

lipids

long chain hydrocarbon, non-polar, polar motif FA that allow to be amphipathic, also has glycerol

FA

long hydrocarbon chain (12-24) with carboxyl head. found esterified to glycerol and can be saturated/unsaturated/polyunsat

glycogen

major storage form in animals. branched with alpha 1-6 branches. hydrlyzed by alpha and beta amylases to yield glucose and maltose. stored in muscle and liver.

functions of oligosaccharides

modulate physicochemical properties: solubilty, viscocity

what are the three groups of carbs

monosaccharides, disaccharides, polysaccharides, oligosaccharides

what are simple sugars

monosaccharides: defined by inability to be hydrolyzed. (CH2O)n N=3 or more.

describe polysaccharides

most common carb in nature aka glycans. They are synthesized from monosaccharides

cellulose

msot abundant natural polymer, polymer of b-d glucose. resistant to hydrolysis. cellulse is needed to hydrolyze glycosidic bonds . 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.

The porin proteins (e.g., maltoporin) utilize the ____ structural motif.

multiple β-sheet

what are the basic structural units of dna

nitrogenous bases found in nucleic acid are derivatives of pyrimidines/purines

simple diffusion

nonpolar, hydrophobic molecules diffuse directly through the lipid bilayer. Does not require the use of transport proteins. Ex: o2, co2, co, no, steroids other lipophilic substances, ethanol, h2o. Polar, hydrophilic substances cannot pass directly through the lipid bilayer. Ex: ions, carbs Down the concentration gradient

What component of a nucleotide consists of a sugar bound to a nitrogen-containing base?

nucleoside

describe the primary structure of nucleotides

nucleosides linked by phosphodiester links to form single strand. phosphate ester links 3' and 5' O's of 2 sugars 5' a-t-g-c-a 3'

What is the repeating monomer of a nucleic acid?

nucleotid. The repeating monomer of a nucleic acid is a nucleotide, which consists of a nitrogen base, a ribose or deoxyribose sugar, and a phosphate. A nucleoside consists only of a nitrogen base and a ribose or deoxyribose sugar.

which of the following is not a main component of a plasma membrane

nucleotides

what are the three major classes of glycoproteins

o link, n link, and those linked to the carboxyl terminal aa of a protein via a phosphoryl-ethanolamine moeity joined to an oligosaccharide (glycan) which in turn is linked via glucosamine to phosphatidylinositol (PI

what specific molecule is shown to represent passive diffusion

o2

acetals

oxygens are both attached to C's

what can endocytosis be broken down into

phagocytosis, pinocytosis, receptor-mediated

Flippases are enzymes that flip:

phospholipids across to the other side of a membrane.

what is the key difference between phospholipids and tgs

phospholipids have 2 fas, tgs have 3

where do carbs come from

photosynthesis

what are peptidoglycan

polysaccharides found in bacterial cell walls. gram positive bacteria have thick walls of this.. composed of N-acetyl glucosamine and N-acetylmramic acid with pentaglycine links and tetrapeptide (L-ala, D-glu, L-lys-d-ala) moieties

what are glycosaminoglycans

polysaccharides of combined amino sugars and sulfate containing groups, acts as a natural anticoagulant

describe B form dna

prevails under physiological conditions of low ionic strength and increase degree of hydration

chain of glycoproteins

protect proteolysis, affect proteolytic processing of precursor proteins to smaller productss. are involved in biological activity = ex: hcg affect insertion into membrans, intracellular migration, sorting /secretion affect embryonic development of differentiation

what are histones

proteins in chromatin

decorin

proteoglycan secreted by fibroblasts

purine bases form H bonds wiht

pyrimidines (base pairing)

what is receptor mediated endocytosis

receptor proteins on RM bind specific substances, membrane sinks in and forms a pit, called a coated pit. Pit pinches closed to form a vesicle around the bound substances. Cytoskeleton aids in pulling in the membrane and vesicle formation.

what are sugar acids

reducing sugars, as oxidized they become acids

sugar alchols

reduction of carbonyl group of sugars, -itol

describe z form dna

regions of helix rich in pC pG dinucleotide can exist in left handed helical form results from 180 degree change in orientation of base relative to that of a and b dna

whst are topoisomerases

relax supercoiled dna gyrase: introduces supercoiling

Normal dna is the ___ handed ___form

right, B

enol form of dna

ring nitrogrns serves a h bond donors, keto oxygens as h bond acceptros

what are the pentose sugars in dna and rna

rna: ribose + purine/pyr dna: deoxyribose

glycoamino acid

saccharide attached to a single aa by any covalent bond

Nearly all of the calcium ions in muscle are sequestered inside vesicles called:

sarcoplasmic reticulum.

Which of the following is true regarding membrane function?

scaffolding proteins, particularly those containing BAR domains, result in curvature of the cell membrane membrane fusion with vesicles is often accomplished with the aid of a snare protein

What term(s) best describe cell membranes?

semi-permeable, fluid mosaic model, phospholipid bilayer, liquid like

What amino acid is coded by the codon AGC?

serine

importance of lipids

serve as structural components of biological membranes provide energy reserves in form of triacylglycerol serve as vitamins/hormones lipophilic bile acids aid in lipid solubilization

facilitated diffusion

small polar molecules and ions diffuse through passive transport proteins (Carriers and channels) ex: glucose enters/leaves cells through facilitated diffusion. Down the concentration gradient

d-glucose vs d-fructose

structural isomers, they have different functional groups

functions glycoproteins collagen mucins transferrin immunoglobins

structural molecule lubricant/protective agent transport molecule

what are the three common disaccharides

sucrose (glu +fruc), lactose (galact +glu), maltose (glu x2)

the o linked glycoproteins of eukaryotes usually have their sugar chains attached to

the OH of Ser or Thr residues

what are proteoglycans

the carb units are polysaccharides that contain amino sugars, such polysaccharide are known as glycosaminoglycans

Active transport is uniquely characterized by:

the tight coupling of an input of energy to drive a thermodynamically unfavorable reaction.

Z dna occurs when

there are g-c rich regions in the dna strands in the helix

In passive diffusion, the transported species moves across the membrane in the ____ favored direction ____.

thermodynamically; without a specific transport system/molecule

in cell membranes, carbs in glycoproteins are oriented?

towards the outside the cell

In the Na+, K+-ATPase mechanism, ATP is involved in all EXCEPT:

transferring a phosphate group to make sodium phosphate.

Syndecan

transmembrane proteoglycan. Syndecan binds intracellularly to the cytoskeleton protein actin, and extracellularly through the glycosaminoglycan units to fibronectino

define trna rrna mrna

transports aa to site of pro synthesis combines with protein to form ribosome, site of pro synthesis directs aa sequence of protein

name of carbs based on number of C;s 3-6

trioses, tetroses, pentoses, hexoses,

what is the smallest type of Rna

trna

The Variable Arm in a tRNA (according to the lecture) will be classified as __ if it is composed of only a few nucleotides.

type 1

what are the two topoisomerase classes

type 1: breaks 1 of nucleotide strands and reduces supercoiling by removing rotation type 2: adds/removes rotations by breaking both nucleotide strands

which of the following has a double bond their hydrocarbon chains

unsaturated fats

amylose

unstable due to intermolecular attaction and association of neighboring amylose molecule. leads to increase in viscocity and retrodegradation

what is an epimer

used when comparing sugars with many chiral centers. only 1 center is differnt