Biochemistry Test 2 (7-8, 10)

Secondary structure of nucleic acid

folding patterns of segments of chain (generally double helix)

Deamination

mutation -about 100 C to U per cell per day -removed enzymatically with base excision -important to have T, not U, in DNA

UV radiation

mutation of pyrimidine dimers -esp. thymine dimers -creates radicals, puts a kink in the DNA, blocks DNA polymerase Ionizing radiation also breaks strands, opens rings, fragments bases.

Mutagens and Carcinogens

mutation that acts through similar radical methods as UV radiation (esp. oxygen radicals) -many mechanisms for repairing DNA

Depurination

mutation where purine removed from nucleic acid, forming an apurinic residue -about 10,000/cell/day -depyrimidation is much slower -accelerated in acidic conditions -again enzymatic repair through base excision

Nucleoside

no phosphate group

Nucleotide linkage

phosphodiester linkage 5' to 3'

Nucleotide binding fold

-specific binding site for adenosine -common motif in enzymes -both ATP binding and those with adenosine cofactors

Fat soluble vitamins

A, D, E, and K -A/D: hormone precursors -E/K: redox cofactors

Other functions of nucleotides

Energy: mainly ATP (a little GTP, UTP, and CTP as well)

How do we control the opening up of DNA to make copies and/or RNA segments?

Enzymes give excellent specificity and control to perform a variety of necessary functions with DNA.

Water soluble vitamins

B and C -taking these supplements is basically a waste of money because they mostly wash right through and pass out in your urine

Polysaccharide functions

Fuel/energy storage -starch, glycogen, dextran Structural strength/support -Cellulose, chitin

Which of the fatty acids we named are Omega-3 and Omega-6 fatty acids?

Linoleic is omega-6. Alpha-linoleic is omega-3.

Waxes

Long-chain fatty acid esterified with long-chain alcohol -long length and ability to aggregate gives higher melting point -soft at solid room temperature Energy storage (plankton), water repellant (waterfowl), prevents water evaporation (plants)

Working with carbohydrates

More difficult than proteins to study -Branching makes sequencing difficult -Not consistent linkages Modern technology helping tremendously -Finely tuned MS and NMR methods

alpha

OH down

What types of polysaccharides take a helical 3D shape, and what types take a sheet-like shape?

Storage polysaccharides generally take a helical 3D shape to fill as little space as possible. Structural polysaccharides generally take a sheet-like shape to be as strong as possible over an extended length.

Which bonds in alpha-D-glucose must be broken to change its configuration to beta-D-glucose? Which bonds convert D-glucose to D-mannose> Which bonds to convert one chair form of D-glucose to the other?

The α/β switch for glucose requires going from ring to straight chain and then back to ring in the opposite configuration. That requires breaking and re-forming the bond between C1 and the O on C5. Glucose and mannose differ only at C2, so switching from one to the other would require the C-H and C-O bonds on C2 to be broken and then re-formed with the H and OH switched. Switching between two chair conformations does not require the breaking or forming of any bonds.

Purines (2 rings)

adenine and guanine

Tertiary structure of nucleic acid

complex folding of entire chain (how it folds into chromosomes or large tRNA and rRNA molecules)

Pyrimidines (1 ring)

cytosine, thymine, uracil

Circle the fatty acid in each pair that has the higher melting temperature. (a) 18:1Δ9 18:2Δ9,12 (b) 18:0 18:1Δ9 (c) 18:0 16:0

(a) left (b) left (c) left

Naming fatty acids

-# C: # double bonds (∆location double bonds) -18: 1(∆^9) 18 carbons; 1 double bonds; double bond on the 9 carbon

Ether lipids

-1 ester linkage replaced with ether-resistant to enzymatic cleavage -common in heart cell membranes

Starch and Glycogen

-All glucose polymers with (α14) linkages -Differ in branch points [(α16) linkages] 2 starch arrangements: -Amylose: no branches -Amylopectin: some branches Glycogen more branched than amylopectin

Determining Lectin binding

-Attach various oligosaccharides on fixed surface -Add lectin (+ fluorescent probe) Rinse -Determine what oligosaccharide(s) lectin binds

Why do fats store so much energy?

-Because they're completely anhydrous and reduced. Thus oxidizing them can release large amounts of energy. 1g of triacylglycerol releases about 9 kcal of energy. 1g of carbohydrates (sugars) releases about 4 kcal of energy. (think about electron transport chain) -Nonpolar, so it sticks around a long time for storage; however since it is non polar it isn't in the cell and readily available

Lectins

-Carbohydrate-binding proteins -High affinity and specificity -Used in cell-cell recognition, signaling, and adhesion -Often see Lectins attached to a cell membrane. They bind a specific sugar/group of sugars, which then sends a signal to the interior of the cell.

The Sugar Code

-Cells use specific oligosaccharides to encode information -"Sugar code" not nearly as well understood as genetic code More structural variety than DNA or proteins 20 monomers, different linkages, branch points, several modifications available

Lipid function

-Energy storage -Structure -Signaling/cofactors -Insulation -Water repellant -Buoyancy control -Pigments -Antioxidiants

DNA methylation

-Enzymes regulate modification of DNA. -Most common form: methylating individual bases (usually A/C) -methylation sticks out from the major groove, exposed to enzymes interacting with the DNA, easy for enzymes of immune system to recognize, blocks enzymes that move along the major groove -Reasons not fully known: ID your DNA vs. invaders, silence genes when want them inactive

Fatty acid structure

-Even # of C -mostly unbranched -Saturated: all single bonds -Monounsaturated: 1 double bond -Polyunsaturated: 2+ double bonds

Phosphoglycerides

-From glycerol-3-phosphate instead of glycerol-amphipathic -2 fatty acids instead of 3 -Typically, 1st = 16 or 18 saturated 2nd = 18 or 20 unsaturated -Saturated on end, unsaturated in the middle. And the middle tends to be a bit longer. Evens things out overall, ensures proper spacing. -2 OH where we can get esterification with fatty acids now -Polar head, two nonpolar tails. Works well for even space for straight line from a bunch of these together. It's a phospholipid bilayer.

Nonenzymatic Transformations

-Get transformations we want using enzymes -Bad transformations happen out of control >> mutations -4 primary types: 1) deamination, 2) depurination, 3) UV radiation, 4) dangerous chemicals (carcinogens, mutagens)

Peptidoglycan

-Gives bacterial cell walls strength -Envelopes entire cell and makes it able to stand up to osmotic pressure so the cells don't lyse. -Heteropolymer polysaccharide chains: Cross-linked by polypeptide chains -Lysozyme destroys (β14) linkage -Penicillin prevents formation of AA cross-links

Polysaccharide Folding

-Governed by similar forces as protein folding H-bonding vital with all those OH groups. Much more so than in proteins, because much more prevalent. Most monomers can make 4-5 H-bonds, as opposed to 1-2 for AA. H-bonds are the strongest noncovalent forces, so that's why we can get tremendous strength in polysaccharides. -All the information for folding present in "primary structure"

Main forces determining secondary structure of DNA

-H-bonding: responsible for complementarity (A with T, G with C) -Pi stacking: main stabilizing force of double helix

Fischer Projections

-Horizontal bonds coming towards you, vertical going away

Hybrid Duplexes

-If two species have close enough sequences, DNA from each species can bind, creating a cross-species double strand (hybrid) -Why important? very helpful for testing for the presence of a single gene in another species (you know a gene is in one species, you can find out if it's present in another species)

Omega-6 and omega-3 Fatty Acids

-Last C is ω, number backwards from there -Our body needs ω-3, cannot synthesize -Can get all we need from α-linoleic acid -ω-6/ω-3 ratio very important

This is a summary of some of the interactions mediated by the sugar code.

-Lectin binding, which is used for b-f -Viruses use to identify host cells -So do bacterial toxins -And bacteria -Many cell-cell interactions, including helping the immune system leukocytes (white blood cells) get to the right spot -Identify lysosomal enzymes that get transferred into the lysosome (degrades biomolecules

Chitin

-Like cellulose, but C2 OH replaced with acetylated amine -This gives even more H-bonding. Replaced just one OH with an NH and C=O. Can stack in staggered ways (since it alternates up and down) to really be strong.

Melting point trends for fatty acids

-Longer= higher melting point -More unsaturated= lower melting point The double bonds make kinks, thereby lowering the melting point

Epimers

-Multiple chiral centers, differ at only 1

Glycoproteins

-Oligosaccharides attached to proteins -Important in signaling and recognition -Protein with a sugar attached and sticking out

Why can't we use cellulose for energy?

-Our digestive enzymes only break down alpha linkages, not beta, so we can't use cellulose for energy. Neither can most vertebrates. -grass eating vertebrates have bacteria that live in their digestive systems and break cellulose down for them.

Polysaccharides

-Polymers of high MW (>20k) -Most carbs in this form -aka glycans -No fixed MW -Homo/hetero -Branched/unbranched

Triacylglycerols (triglycerides)

-Small amount of fatty acids circulate in blood bound (noncovalently) to serum albumin -Most fatty acids exist as triacylglycerols -Most are mixed (different fatty acids attached to 1 glycerol)

Lectin/carbohydrate specificity

-Sterics and noncovalent interactions lead to high specificity -Greater specificity due to multiple lectin/oligosaccharide interactions -Hydrophobic interactions can also be important for specificity

Omega-6 and omega-3 Fatty Acids: Diet

-There are other omega-3 fatty acids we need, but we can convert alpha-linoleic to them. We cannot, however, make any of the omega-3 FA from scratch. So we need them in our diet. The ratio of omega-6 to omega-3 is vital. Needs to be between 1:1 and 4:1 for optimal health.

Enantiomers

-They are all chiral (in at least one place), and just like with amino acids, the D/L form is hugely important for 3D shape, and thus interactions with other molecules. -What were most amino acids? (L) Most carbohydrates are D.

Cellulose

-Unbranched glucose polymer with (β14) linkages -2 H-bonds between each glucose monomer make it very rigid and strong, even over long polymers (up to 15,000 monomers long). -It also has abilities on the ends to cross-link with a monomer in another chain, which provides additional strength and support.

Mutarotation

-Will eventually reach equilibrium -Important in glucose blood monitors (diabetes) -Could start with one sample of all alpha and one of all beta, and eventually they'll reach the same point, which is about 2/3 beta and 1/3 alpha, with trace amounts of straight chain.

Why does spoiled food become rancid?

-air oxidizes the double bonds in unsaturated fats -this forms short, volatile aldehydes and carboxylic acids-smell bad -cooking oils hydrogenated to improve shelf life

Stability of DNA

-antiparallel alignment -pi stacking between bases in individual strands, minimizes polar-nonpolar interactions with water -H-bonding stabilizes double helix -H-bonds between bases of two strands

Palindromic DNA sequences

-can base pair within a strand -role: unsure yet but believed to be important for determining protein sequence and structure

Phospholipases

-continually degrading and replacing membrane lipids to maintain structural integrity -specific enzyme for specific cleavages

Vitamin A

-derived from beta-carotene -oxidized from retinol to retinal-different in dark and light -present in carrots and other yellow/orange vegetables -lack leads to problems with eyesight and dry skin/mucus membranes

Agarose

-double-stranded helix that traps water in the middle -They are formed from these galactose units, but every other galactose has that ether bridge, and a few are sulfonated.

Structural lipid use

-energy -cell membrane structure

Nucleotide Functions

-energy for metabolism (ATP) -enzyme cofactors (NAD+) -signal transduction (cAMP)

Lipid roles

-energy storage -structure -signaling/cofactors -insulation -water repellant -buoyancey control -pigments -antioxidants

Storage lipids

-fatty acids and their derivatives -COO (polar) head -CH (non polar) tail -Tails can be anywhere from 4-36 C long. Most commonly are found between 16-24 C. -They're at very low oxidation states (just C and H)

Vitamin D

-formed in skin cells using UV radiation (sunlight) -converted to calcitriol >> regulates calcium uptake in bone tissue -deficiency leads to insufficient calcium in bones and incorrect bone formation -lack leads to Rickets

Lactose

-galactose and glucose

Sucrose

-glucose and fructose

Secondary structure of DNA

-major and minor grooves -3.4 angstroms = one base pair -one complete twist = 36 angstroms, 10.5 base pairs -20 angstroms in width -pi stacking to keep water out -antiparallel strands - 5' to 3' top to bottom and 3' to 5' bottom to top

Storage polysaccharides conformation

-most stable conformation is the formation of a helix --60° angle for each relative to the last monomer, so then how many per turn? (6) -How many AA per turn in an alpha helix? (3.6) more stretched out, but this allows for maximum H-bonding, and is big enough to get a 2nd one interwoven for the double helix to save space.

What makes a lipid and lipid?

-no characteristic function -no characteristic structure -unifying trait: insoluble in water (mostly nonpolar)

Sphingolipids

-sphingosine instead of glycerol/glycerol derivative -already has one long CH chain -adds one fatty acid too by amide linkage -ether linkage to head group (R) -important for signaling, often found in nerve membranes

Sterols

-steroid nucleus (4 fused rings) with polar head group (OH) -most common/important is cholesterol -polar head, nonplar tail (can also be embedded in membranes)

Nuclei Acid Functions

-storage of genetic info (DNA) -transmission of genetic info (mRNA) -processing of genetic information (ribozymes) -protein synthesis (tRNA and rRNA)

Melting point of DNA

-temperature at which it is half denatured -varies from species to species because depends on G/C content (these form 3 H-bonds, so more energy stored, takes more energy to overcome that, thus higher melting point) -measure by absorbance (absorbs strongly ds than ss due to pi stacking) -interestingly, RNA typically has a higher mp (about 20 degrees) than DNA

Vitamin E

-tocopherols: biological antioxidants -very nonpolar so associate with cell membranes, lipid deposits, and blood lipoproteins -protect lipids from oxidation by destroying radicals that would oxidize them (aromatic ring does this) -thus, the only way to oxidize lipids is enzymatically which allows for exquisite control which lets us use lipids both for energy storage and signaling without any problems -found in eggs, wheat, vegetable oils

Fatty acid structure unsaturation trends:

-usually cis -no conjugation -1st C=C between 9 and 10, the 12-13 or 15-16

Adenosine Cofactors

-wide variety - typically involved in binding (often, adenosine makes initial contact with the substrate and guides it into the active site) or can be used to help stabilize binding in the active site -often involved in guiding substrate to binding site -Why adenosine? convenience. There is way more adenosine in the cell than other nucleotides so the cell finds as many uses for it as possible

Steps to synthesizing DNA

1) 1st nucleotide protected by DMT (dimethoxythrityl). Attach 3' end to solid Si 2) Acid wash removed the DMT 3) Add the next nucleotide, activating group makes P-O bond possible 4) Oxidize the phosphate with I to for triester (as opposed to usual diester) Repeat steps 2-4 with each nucleotide. Wash away excess nucleotide before repeating 5) Removing protecting groups from bases 6) Remove cyanoethyl from phosphates 7) Cleave chain from silica support

Why use polysaccharides? Why not just glucose monomers?

1) Control. Enzymes break down to glucose only when you need it. That way you easily control glycolysis through the enzymes that break down glycogen and starch. 2) Osmotic pressure. All the glucose in the cell is about 0.4M, but in glycogen that's only 0.01M. Thus the cell doesn't have water rush in and burst. 3) We've already talked about limiting the reducing ends for further control of the cell.

How to separate oligosaccharides

1) Methylation. In a strong base and CH3I, all free OH groups become methyl esters. Then acid cleaves glycosidic linkage, and now all exposed OH (which you can try to identify through a variety of methods, including NMR and MS) were location of a linkage. 2) Use specific enzymes that cleave at known points, then piece fragments together. 3) You can just break them all up in strong acid to ID monosaccharide units. IDs type of sugars present and their relative abundance. Useful information.

3 Most important structural lipids

1) Phosphoglycerides 2) Sphingolipids 3) Sterols

2 ether lipids

1) Plasmalogen: makes up 50% of heart membrane lipids 2) platelet activating factor: is actually an important signal molecule. It stimulates platelet aggregation so blood can clot.

Ring formation

1) it's the OH on the 5th C, not 6th, that forms the ring. So methylhydroxy group sticking up off C left of the O. Always sticking up. 2) Groups that were on the left go up. If they were on the right, they go down.

Nucleic acid

1+ phosphate/monomer

Samples of DNA are isolated from two unidentified species of bacteria. Species X has 32% A, species Y 17% A. ID the proportions of C, G, and T in each species. One of the species was isolated from a hot spring (64°C). Which one?

1. % T = %A. So X has 32% T, Y has 17% T. The rest is split evenly between C and G. X has 64% A/T, so 36% C/G (18% each). Y has 34% A/T, so 66% C/G (33% each) 2. Species Y. It has higher G/C content, which is more stable due to H-bonds. Its DNA would not unwind in a hot spring.

Cellulose conformation

180° (fully extended) most favored -Similar to beta sheets Strong h-bonding between chains They form strong fully extended strands that are stabilized by H-bonding between monomers.

alpha, beta, gamma phosphates

1st phosphate from sugar = alpha 2nd phosphate from sugar = beta 3rd phosphate from sugar = gamma

Thymine

2 H-bonds with adenine

Adenine

2 H-bonds with thymine

Disaccharides

2 monosaccharides joined together by glycosidic bond -Easily broken by acid, stable to base

several sugars interact with a receptor protein

2 receptors that come together to bind sugar. This conformational change triggers an activation of GTP-binding protein, which then triggers an electrical signal being sent to the brain that is interpreted as sweet.

Guanine

3 H-bonds with cytosine

Cytosine

3 H-bonds with guanine

Show the basic structure of all glycerophospholipids.

3C with ester linkages, 1 to phosphate and 2 to fatty acids. Typically middle fatty acid is longer (18C) and unsaturated, while end one is shorter (16C) and saturated. In 3D, phosphate points away from rest. Often a polar head group attached to phosphate opposite from phosphoester bond.

Which of the following best describes the cholesterol molecule? a) Amphipathic b) Nonpolar, charged c) Nonpolar, uncharged d) Polar, charged e) Polar, uncharged

A

Compare the dimensions of a molecule of cellulose and a molecule of amylose, each with an Mr of 200,000.

Amylose forms helices, kind of like alpha helices, so it will be shorter and fatter. Cellulose forms fully extended straight sheets, kind of like beta sheets, so it will be longer and skinnier.

You isolated two new species of bacteria. Bacterium brrrrius grows best at 10°C, while Bacterium hottius grows best at 40°C. Which species would you expect to have a higher amount of saturated fatty acids in its membrane phospholipids? Why?

Bacterium hotius needs to have a higher melting point so its lipids will hold up at warmer temperatures, so it likely has more saturated (and longer) fatty acids.

Why do some strands of DNA have higher melting points than others?

Because C-G pairings have 3 H-bonds while A-T have only 2. Thus DNA strands with more C-G take more heat to denature.

Why do we have a sugar code instead of just using amino acids?

Because sugars can be connected in a variety of ways, there are more unique options for small chains of sugars than there are for small chains of amino acids.

Why do we used carbohydrates for energy, when fat is the preferred source?

Because they're more readily available. Water-soluble and in cell, plus much faster to break down. Breaking down fat is a slower process, plus it's stored in a separate cell, which makes it ideal for long-term energy storage.

Describe the common structural features and the differences for each pair: D-glucose and D-fructose

Both glucose and fructose are hexoses, sugars with 6 C. Glucose is an aldose, which means the C=O is on C1, while fructose is a ketose, where the C=O is on C2.

Describe the common structural features and the differences for each pair: Maltose and sucrose

Both maltose and sucrose are disaccharides containing at least one glucose. They differ in the 2nd sugar (glucose for maltose and fructose for sucrose) and in the linkage (α14 for maltose and α1β2 for sucrose).

Which of the following statements about starch and glycogen is false? a) Amylose is unbranched; amylopectin and glycogen contain many (α16) branches. b) Both are homopolymers of glucose. c) Both serve primarily as structural elements in cell walls. d) Both starch and glycogen are stored intracellularly as insoluble granules. e) Glycogen is more extensively branched than starch.

C) Both serve primarily as structural elements in cell walls

Describe the common structural features and the differences for each pair: Cellulose and glycogen

Cellulose and glycogen are both polymers of glucose connected by 14 linkage. Cellulose is connected by β linkage, while glycogen is connected by α linkage.

Glycogen and cellulose are both glucose polymers, yet cellulose is much stronger. Why?

Cellulose is connected by β linkage, while glycogen is connected by α linkage. The β linkage of cellulose allows for a straight chain with 2 H-bonds between each monomer, and strong H-bonding between sheets. This adds more strength than the α linkage, which spirals and has less H-bonding between monomers.

Structural Polysaccharides

Cellulose>>> plants Chitin>>> arthropods and insects

Which of the following statements about membrane lipids is true? a) Glycerophospholipids are found only in the membranes of plant cells. b) Glycerophospholipids contain fatty acids linked to glycerol through amide bonds. c) Lecithin (phosphatidylcholine), which is used as an emulsifier in margarine and chocolate, is a sphingolipid. d) Some sphingolipids include oligosaccharides in their structure. e) Triacylglycerols are the principal components of erythrocyte membranes

D. and what are those oligosaccharides used for? signaling

Why do our cells focus more resources on repairing DNA than RNA or proteins?

DNA is the original source of everything, the blueprint. DNA need to keep that correct. It lasts much longer in our bodies, and gets passed to our offspring. As long as the source stays fine, the RNA and proteins made based on the information it carries will work out. The cell can simply destroy a mutated protein or RNA.

Sphingolipids and blood types

Different oligosaccharides in blood cell membranes determine blood type

Glycosaminogycans

Gel-like heteropolysaccharides -Repeating disaccharide units Fill ECM to hold cells together Easy to diffuse nutrients and O2 between cells High degree of negative charge determines the structure. They form a long rod-like helix with the negative groups pointing out in alternating directions. Desire to avoid the negative/negative interactions gives that helix great strength and rigidity over long distances. Also keeps neighboring helices away so there's empty space in the middle.

When is glucose, glycogen, and fat used for energy?

Glucose = immediate glycogen = intermediate fat = long-term

Naming monosaccharides

Group name has 3 parts 1)C=O location (aldo/keto) 2) # of C (tri/pent/hex) 3) ose ending

Annealing

Happens spontaneously -much faster if part of strand stays together -"zipping back up" -optimal at middle temps

Denaturation

Happens spontaneously in harsh conditions (temperature, pH, solvents) Why? -H-bonds messed with so DNA falls apart

Reducing Sugars

Have exposed aldehyde/ketone, easily oxidized to COOH -Ketones less so, but can still reduce. Why? :Ketones can undergo tautomerization to become aldehydes, and then reduce. So they're still reducing sugars, but less reducing. Will reduce even mild oxidizing agents like Cu2+

Sphingolipid signaling

Head group is often sugar Why? sugar code... lots of variability Head group acts as recognition sites for external signals and are embedded in the membrane. They serve the same polar/nonpolar membrane formation, but give you built-in signaling pathways.

Why do most fatty acids exist as triaglycerols?

It greatly reduces the solubility. Polar head gone now, they're completely nonpolar and insoluble in water. Thus it's a stronger force driving them to avoid water, aggregate together, and store energy.

DNA sequencing (Sanger method)

Main idea: build up one nucleotide at a time based on complementary strand -put in enzyme needed to synthesize complementary strand, put in all 4 nucleotides so it has the parts it needs, add it to an analog of one nucleotide that has no OH on it, so it can't connect and ends the sequence

Base Pair Specificity

Must pair A/T and G/C -otherwise, H-bonding doesn't line up properly Must pair a purine with a pyrimidine -two purines are too far apart, two pyrimidines would be too crowded -remember: pyrimidines have one bend on the N that connects to the backbone. This gives just enough flexibility to get ideal H-bonding alignment Straight H-bonds are stronger than bent H-bonds -in DNA, all straight for maximum strength

Is D-2-deoxygalactose the same chemical as D-2-deoxyglucose? Explain.

No, these are not the same molecules, because glucose at galactose differ at C4, not C2. If you had d-4-deoxyglucose and d-4-deoxygalactose, those would be the same molecule.

Nucleophile and electrophile?

O of OH nucleophile, C of C=O electrophile

beta

OH up

Which can produce a greater variety of structures for signaling: oligopeptides with 5 different amino acid residues or oligosaccharides with 5 different peptide residues? Why?

Oligosaccharides. Same # monomers, but they can be linked in different ways and branch. Peptides only form straight chains and all have the same linkage.

Why is too much cholesterol bad?

Our cells only need so much to put into membranes. Need a few for other functions - precursors for steroid hormones - but when you have too much, they have nothing to do with all of it. Lot of it is nonpolar, so it aggregates in blood vessels and starts to block blood flow.

Why is it important that the bases in nucleotides are (mostly) planar?

Planar bases allow for strong pi stacking that stabilizes the helix and helps it pack tightly so that there's no room for water. The little bit of flexibility from the non-planar N that connects to the ribose (and the one additional non-planar N in U, T, and G) ensures that each base pair can reach an orientation that is optimal for H-bonding between the bases.

Correct artificial synthesis of carbohydrates difficult, why?

Polysaccharides are difficult to artificially synthesize because the reactions can happen at any OH, and there's an OH at almost every C. Have to somehow block all but the correct OH with a protecting group, then link, then remove protecting groups.

Carbohydrates

Primary energy source for living organisms -Energy storage -Oxidized to release energy -Structural support in cell walls & exoskeletons -Cell signaling pathways -Cn(H2O)n Monosaccharides, disaccharides, oligosaccharides, polysaccharides

General Process of synthesizing DNA

Put it on a solid support to control which way the strand grows. Protect everything, remove protecting groups in specific areas to control the reaction. Very similar to proteins

What are sphingolipids and why are they important?

Sphingolipids consist of a sphingosine molecule with one fatty acid attached. They then get a substituent placed on the head and embed in the membrane. Full structure shown below. They are important because they serve as signaling that is part of the phospholipid bilayer that makes the membrane. The head group is usually a small group of sugars that serves to bind cells or organelles that have an appropriate lectin.

Energy storage

Starch>>>plants Glycogen>>>animals Dextrin>>>bacteria and yeast All are glucose polymers

What is different between a steroid and sterol? Why is this important for sterol function?

Sterols have an alcohol on the bottom left of a steroid ring, while steroids have a ketone. Most steroids also have oxygenated groups elsewhere on the steroid, while most sterols are only C and H elsewhere. This keeps sterols amphipathic; the polar OH and nonpolar rest of the molecule helps them fit well in the membrane. Steroids have higher solubility due to the additional oxygens, this helps them be soluble in the bloodstream so they can carry signals throughout the body.

Why do we need a sugar code to carry information?

Structural diversity in short oligosaccharides. Roughly 20 monomers, like 20 AA, but they can connect in different ways. Can also be sulfonated in different areas. Huge amount of diversity

Waxes melting points

These are very long, which helps raise the melting point, but also can aggregate together, so they are solids at room temperature. They have a variety of uses in nature.

Why do polysaccharides not have a fixed Molecular Weight?

They have enzymes that help them join together, but there's nothing telling them when to stop. So they will go to different lengths and have different MW.

Cellulose could provide a widely available and cheap form of glucose, but humans cannot digest it. Why not?

They lack the enzyme to break down the B1->4 bonds

Why do the healthiest foods spoil the fastest?

Unfortunate side affect of hydrogenation: partial hydrogenation leads to trans double bonds in the fat, which changes structure and leads to higher rates of cardiovascular disease. Trade off between keeping food good for longer and having healthier food.

Variability in phosphoglycerides

We get a lot of variety within this same class. Mainly due to different substituents attached to the phosphate group. This leads to a variety of properties, especially relating to charge at physiological pH.

In glycoproteins, the carbohydrate moiety is always attached through the amino acid residues: a) asparagine, serine, or threonine. b) aspartate or glutamate. c) glutamine or arginine. d) glycine, alanine, or aspartate. e) tryptophan, aspartate, or cysteine

asparagine, serine, or threonine Because of OH

Vitamin K

cofactor that helps enzyme prothrombin form blood clots -prothrombin splits peptide bonds in the blood protein fibrinogen. this converts it to fibrin, which is fibrous and forms the clots -vitamin helps the mechanism by undergoing a redox cycle with its aromatic ring. that redox cycle is essential for moving electrons correctly to break the peptide bond. -lack of this vitamin leads to not clotting well which can be fatal -present in leafy greens

Eicosanoids

derivatives of arachidonic acid -paracrine hormones, act as cells near point of hormone synthesis -wide variety of functions; mainly health -act locally (not transported through blood)

Which of the following molecules or substances contain, or are derived from, fatty acids? a) Beeswax b) Prostaglandins c) Sphingolipids d) Triacylglycerols e) All of the above contain or are derived from fatty acids.

e

Which of the following pairs is interconverted in the process of mutarotation? a) d-glucose and d-fructose b) d-glucose and d-galactose c) d-glucose and d-glucosamine d) d-glucose and l-glucose e) α-d-glucose and β-d-glucose

e) α-d-glucose and β-d-glucose

Leukotrienes

eicosanoid -3 conjugated double bonds -named because 1st found in leukocytes (white blood cells) -stimulate contraction of smooth muscle lining airways to the lungs -producing too many leukotrienes leads to asthma attacks -anti-asthma medicines stop the enzymes that produces them from arachidonate

Thrombaxanes

eicosanoid -6-carbon ring with an ether -produced by blood platelets (thrombocytes) -involved in blood clotting/reducing flow to blood clot region -inhibited by non-steroidal anti-inflammatory drugs such as aspirin and ibuprofen (inhibit enzyme that produces them from arachidonate)

Prostglandins

eicosanoid -all have 5-carbon ring -names because 1st found in prostrate gland -some ether soluble (nonpolar) -others phosphate buffer soluble (polar) -variety of functions: stimulate smooth muscle contraction during menstruation/labor, cause fever, inflammation, and pain as immune response, impact wake/sleep cycle, control blood flow to specific organs -inhibited by non-steroidal anti-inflammatory drugs such as aspirin and ibuprofen (inhibit the enzyme that produces them from arachidonate)

Vitamins

essential to health, cannot be synthesized -must be obtained in diet -fat soluble or water soluble

Secondary messengers

nucleotides can carry signal from outside cell within cell (mostly A) -signal comes from outside cell, binds to something on external membrane (often a lectin), activates enzyme inside cell that creates a second messenger to carry the signal within the cell -most common example: cAMP

Steroids

oxidized sterol derivatives (nonplar alkyl chain of sterols changed to polar oxy group makes steroids soluble enough to be carried through the body in the blood thus can carry signals over long distances) -bind to nuclear receptor proteins to modify gene expression -slow but long-lasting -wide variety of uses -unique structures, protein receptors they bind to are highly specific (makes steroids extremely powerful in very low doses)

Primary structure of nucleic acid

sequence of nucleotides

Synthesizing DNA

similar strategy to protein method -attach 3' end to solid support -build on 5' end -protect groups/remove protection as needed -only good for short sequences (50-100 nucleotides)... helpful for primers

Storage polysaccharides

starch-amylose and amylopectin-and glycogen