Biochemistry

Front 1

What are the acidic amino acids?

Back 1

Front 2

What are the basic amino acids?

Back 2

Front 3

What are the aliphatic amino acids?

Back 3

Front 4

What are the aromatic amino acids?

Back 4

Front 5

What is the cyclic amino acid?

Back 5

Front 6

What are the hydroxyl or sulfur-side chain amino acids?

Back 6

Front 7

What are the hydrophobic nonpolar amino acids?

Back 7

Front 8

What are the polar uncharged amino acids?

Back 8

Front 9

What are the three letter and 1 letter names for the amino acids?

Back 9

Front 10

What are approximate pka values for the amino acids?

Back 10

Tyrosine and Lysine is about 10. Alpha carboxyl groups and alpha amino groups have different pka values in free amino acids from those in peptides (2 or more amino acids bonded together).

Front 11

What are the functions of lipids?

Back 11

Front 12

What is the structural nature of lipids?

Back 12

Front 13

What are the non-polar residues of lipids?

Back 13

Front 14

What is the difference between saturated and unsaturated fatty acids?

Back 14

Front 15

What is the nomenclature for saturated fats?

Back 15

Front 16

What is the nomenclature for unsaturated fats?

Back 16

Front 17

What is the structure of palmitic acid?

Back 17

Front 18

What is stearic acid?

Back 18

Front 19

What is the structure of oleic acid?

Back 19

Front 20

What is the structure of linoleic acid?

Back 20

Front 21

What are the properties of fatty acids?

Back 21

Front 22

What are triacylglycerols?

Back 22

An acid (fatty acid) and an alcohol (glycerol) always form an ester bond.

Front 23

What is the function of triacylglycerols?

Back 23

Front 24

What is the structure of tristearin?

Back 24

Front 25

What does prochiral mean and what numbering system is used for glycerols?

Back 25

Front 26

What are glycerophospholipids?

Back 26

Fatty acids are linked to glycerols via ester linkages. Phosphates are linked to glycerols via phosphate esters. Each of the glycerolipids are amphipathic. These glycerophopholipids have a cylindrical shape (no kinks).

Front 27

What is the structure of
Phosphatidylethanolamine?

Back 27

Front 28

What is the structure of Phosphatidylserine?

Back 28

Front 29

What is the structure of phosphatidylglycerol?

Back 29

Front 30

What are lysophospholipids, ether phospholipids, and plasmalogens?

Back 30

The PAF is water soluble because it only has 1 hydrophobic carbon chain. Phosphatidylcholine is a bulkier head group.

Front 31

What is the structure of phosphatidylcholine?

Back 31

Front 32

What are sphingolipids?

Back 32

The chemical bond made when forming ceramide is the amide bond (peptide bond). There is a vinyl group at the C1 carbon.

Front 33

What is the structure of ceramide?

Back 33

Front 34

What is an example of a phosphosphingolipid and 2 examples of a glycosphingolipid?

Back 34

With glycosphingolipids, the charged polar phosphate head group is replaced with a polar uncharged sugar head group.

Front 35

What is the structure of sphingomyelin?

Back 35

Front 36

What are the similarities and differences between sphingomyelin and phosphatidylcholine?

Back 36

They both have the same phosphate/amino head group. For phosphatidylcholine, the Carbon 2 of the 3 carbon backbone has an ester linkage with a hydrophobic carbon tail (fatty acid). Sphingomyeline has an amide linkage at the carbon 2 of the 3 carbon backbone with a hydrophobic carbon tail (fatty acid). For sphingomyelin, at the Carbon 1 of the 3 carbon backbone, there is an OH group and a vinyl group, with a hydrophobic 13 carbon tail. For phosphatidylcholine, there is only an H group with an ester linkage to a hydrophobic carbon tail (fatty acid).

Front 37

What do gangliosides always contain and where are they found in the body?

Back 37

Gangliosides have a polar, charged head group. The COO- is the charge.

Front 38

What are waxes?

Back 38

Front 39

What are terpenes?

Back 39

Tetraterpenes are C40.

Front 40

What are polyisoprenoids?

Back 40

Here, there is usually a terminal OH group, but it got phosphorylated.

Front 41

What are cholesterol, steroid hormones, and bile acids?

Back 41

Sterols form an important group among the steroids. Sterols are an important class of organic molecules. The most familiar type of animal sterol is cholesterol. Sterols are derived from terpenes.

Front 42

What is the structure of cholesterol?

Back 42

Front 43

What is an overall summary of lipids?

Back 43

Front 44

What is the nomenclature for carbohydrates?

Back 44

Where n = 3 or more, so there are 3 or more carbons in a sugar unit.

Front 45

What are monosaccharides?

Back 45

Front 46

What configuration do aldoses relate to and what configuration do ketoses relate to?

Back 46

Configuration means that you can't interpose or transpose the molecule without breaking the bond.

Front 47

How do you calculate the number of isomers of aldoses and ketoses? Which kind of sugar has more isomers?

Back 47

Aldoses have more isomers than ketoses because they have 1 more chiral center. This is why there are more aldoses than ketoses - simply because aldoses have 1 more chiral carbon than ketoses so there are more isomers as a result.

Front 48

How do you decide if a sugar is D or L?

Back 48

Front 49

What do aldotrioses, aldotetroses, aldopentoses, and aldohexoses look like?

Back 49

Front 50

What do ketotrioses, ketotetroses, ketopentoses, and ketohexoses look like?

Back 50

Front 51

What is the structure of D-glyceraldehyde?

Back 51

Front 52

What is the structure of dihydroxyacetone?

Back 52

Front 53

What is the structure of D-ribose?

Back 53

Front 54

What is the structure of D-ribulose?

Back 54

Front 55

What monosaccharides should I know?

Back 55

Remember that disaccharides are 2 sugar unit residues. Trisaccharides are 3 sugar unit residues. Oligosaccharides are 2 to 10 sugar unit residues. Polysaccharides are polymers of sugar residues.

Front 56

What are enantiomers and diastereomers?

Back 56

Front 57

How are hemiacetals, hemiketals, acetals, and ketals formed?

Back 57

Front 58

What are furanose and pyranose structures?

Back 58

Note that furanose means 5 ATOMS and pyranose means 6 ATOMS.

Front 59

What are alpha and beta anomers?

Back 59

Front 60

How can you tell whether a structure is an alpha or beta anomer from the Fischer projection?

Back 60

Front 61

What is mutarotation?

Back 61

For any monosaccharide, 1 anomer is favored over the other. In any solution, you will find a mix of the 2 anomers. Equilibrium constants can deal with 2 anomers. In cyclic structures, one axial and one equitorial position is favored.

Front 62

How is the formation of furanoses different from the formation of pyranoses?

Back 62

Forms a 5 membered ring even though there are 6 carbons.

Front 63

What is the boat and chair conformation?

Back 63

Neither pyranose nor furanose rings can adopt true planar structures, instead, they take on puckered conformations. For pyranose rings, the 2 favored structures are the chair conformation and the boat conformation. The ring substituents in these structures can be equatorial or axial.

Hint 63

2 general rules dictate the conformation: 1) Bulky substituent groups on such rings are more stable when they occupy equitorial positions rather than axial positions and 2) chair conformations are SLIGHTLY more stable than boat conformations. B-D-glucose is the only D-aldohexose that can adopt a conformation with all its bulky groups in an equitorial position. With this advantage of stability, B-D-glucose is the most widely occurring group in nature and the central hexose in carbohydrate metabolism.

Front 64

What are the conformational isomers of ribose?

Back 64

Deoxyribose - remember "De" means without. With deoxyribose, the #2 position of the carbon is missing an OH group. C2' endo means that the C2' is above the plane because endo means up. C2' is referring to the 2nd carbon. C1' is the first carbon. If something is labeled C3'-endo, that means that the 3rd carbon is sticking up.

Hint 64

Remember, these are CONFORMATIONS, not configurations. There is steric hindrance with RNA and the OH group at the C2 carbon. Therefore, RNA is not found with C2'-endo, because the OH group would be sticking up. Instead, it is always in the C3'-endo conformation. The C2'-endo is typically found in DNA, because there is no OH group there.

Front 65

What are sugar acids, sugar alcohols, and deoxy sugars?

Back 65

Myo-inositol and glycerol are components of lipids.

Front 66

What is the structure of glycerol?

Back 66

Front 67

What is the conformation of sugar acids?

Back 67

Front 68

What sugar alcohol builds up in the eyes of diabetics? What 2 sugar alcohols are composed of lipids? What sugar alcohol is a component of flavin coenzymes?

Back 68

Front 69

What 2 deoxy sugars are found in glycolipids and glycoproteins? What sugar is Rhamnose derived from? What sugar is Fucose derived from?

Back 69

Front 70

What are sugar esters, amino sugars, and glycosides?

Back 70

Front 71

What is the structure of Glucose-1-phosphate?

Back 71

Front 72

What is the structure of ATP?

Back 72

Front 73

What is the structure of D-erythrose?

Back 73

Front 74

What is the structure of D-threose?

Back 74

Front 75

What is the structure of D-erythrulose?

Back 75

Front 76

What is the structure of D-Glucose?

Back 76

The symbol for glucose is (Glc). Remember that substituents drawn to the LEFT in a Fischer projection are drawn ABOVE the ring in the corresponding Haworth projection. Substituents drawn to the RIGHT in a Fischer projection are BELOW the ring in a Haworth projection.

Front 77

What is the structure of D-Mannose?

Back 77

Front 78

What is the structure of D-galactose?

Back 78

Front 79

What is the structure of D-fructose?

Back 79

Front 80

What is the structure of 2-deoxyribose?

Back 80

Front 81

What are the different projections of sialic acid?

Back 81

Front 82

What are glycosidic bonds?

Back 82

Front 83

What are N-glycosidic bonds?

Back 83

Front 84

What are disaccharides?

Back 84

Front 85

What is the structure of lactose?

Back 85

Front 86

What is the structure of sucrose?

Back 86

Front 87

What are the 2 basic reactions that link carbohydrates together?

Back 87

Front 88

Is lactose a reducing sugar?

Back 88

Front 89

What is the most abundant carbohydrate and is it a reducing sugar?

Back 89

Front 90

What are oligosaccharides?

Back 90

Front 91

What are the mechanisms of sugar polymerization?

Back 91

Front 92

What are polysaccharides?

Back 92

Front 93

What are homopolysaccharides?

Back 93

Front 94

What is the structure of amylose?

Back 94

Amylose, composed exclusively of the relatively bent alpha (1 to 4) linkages, prefers to adopt a helical conformation

Front 95

What is the structure of amylopectin?

Back 95

Front 96

What is structure of glycogen?

Back 96

Glycogen is similar in structure to amylopectin, but branches more frequently.

Front 97

What are cellulose, chitin, and alginates?

Back 97

Cellulose can adopt a fully extended conformation with alternating 180° flips of the glucose units. Because it's not branched, it can stack on top of each other. Hydrogen bonding inherent in such extended structures is responsible for the great strengths of tree-trunks and other cellulose-based materials.

Front 98

What is the structure of cellulose?

Back 98

Front 99

What are inter- and intra-chain H bonds of cellulose?

Back 99

Front 100

What are the difference between cellulose and chitin?

Back 100

Chitin has N-acetyl-D-glucosamines as repeating units at the C2 position. Parallel chains are where all the reducing ends are together at one end of a packed bundle and all of the nonreducing ends are together at the other end. Antiparallel is where each sheet of chains have the chains arranged oppositely from the sheets above and below.

Hint 100

Natural cellulose seems to occur only in parallel arrangements. Chitin, can occur in 3 forms. Alpha chitin is an all parallel arrangement of the chains. Beta chitin is an all anti-parallel arrangement of the chains. δ-chitin (delta chitin) the structure is mixed between parallel and antiparallel.

Front 101

What are agarose and glycosaminoglycans?

Back 101

Front 102

What are glycoproteins?

Back 102

Carbohydrate groups may be linked to polypeptide chains via O-linked saccharides or N-linked saccharides.

Front 103

What are the 2 ways that glycoproteins are linked?

Back 103

Front 104

What are ABO blood group antigens?

Back 104

Type A blood has A antigens. Type B blood has B antigens. Type O blood has no antigens. Type AB blood has both A and B antigens.

Front 105

What is a summary of carbohydrates?

Back 105

Front 106

What are the features of membranes?

Back 106

Front 107

What are the functions of membranes?

Back 107

Front 108

What are lipid aggregate structures?

Back 108

For bilayers, the nonpolar lipid tails are in contact with each other on the inside and the polar heads are on the outside. Micelles form best with conically shaped lipids. Cylindrically-shaped lipids do not form micelles as well.

Front 109

What is the critical micelle concentration?

Back 109

The CMC value for any micelle molecule tells you the potency. The lower the CMC value, the more potent the micelle will be, meaning, the more readily detergent will form micelle - it forms micelles much more easily. The potency is it's ability to disrupt membrane and protein structures, so low CMC values means it will more easily disrupt membranes after it forms the micelles.

Hint 109

Note the very different CMC values for the picture. The CMC value of 0.24mM means the molecule has a high effective micelle formation. The value of 0.071mM means it is really effective at forming micelles. The value of 25mM means that it's not as effective at forming micelles.

Front 110

What are liposomes?

Back 110

Liquid can be trapped inside the unilamellar vesicle.

Front 111

What were some of the early membrane models?

Back 111

Front 112

What is the fluid mosaic model?

Back 112

Front 113

What is the evidence for membrane fluidity?

Back 113

Front 114

What is membrane "phase transition"?

Back 114

In the gel form, the membrane is thicker and the polar head groups are tightly packed. In the liquid-crystal form, the polar head groups are a little more separated because there is more movement. The membrane will be thinner and this facilitates transport across the membrane. The liquid crystal form is more disordered than the gel form.

Front 115

What are the conformations of the nonpolar tails as it transitions from gel to liquid crystal?

Back 115

As the membrane gets warmer, it absorbs more heat to make the conformational change. The gauche conformation is more disorderd than anti, and that is why the membrane is thinner with the gauche conformation.

Hint 115

Cholesterol's property is significant in that it is kind of a buffer in the membranes. It is mixed in the membrane and at lower temperatures, helps to keep the membrane more fluid and at higher temperatures, helps to keep the membrane more solid. Cholesterol spreads out the anti and gauche conformations. That's what graph b is showing. Without cholesterol, the transition is much more abrupt and that is what the pure phospholipid bilayer is. The pure phospholipid bilayer isn't a true membrane with stuff mixed in, it is purely made of lipids with phosphate heads.

Front 116

What is lateral asymmetry?

Back 116

Lateral asymmetry arises when lipids or proteins of particular types cluster in the plane of the membrane.

Front 117

What is transverse asymmetry?

Back 117

Proteins are inserted in an oriented manner. With flippases, lipid moves laterally closer to the flippase protein, then the flippase flips the lipid, then the lipid diffuses away laterally on the other side. Transmembrane proteins do not flip in and out of the membrane and do not flip across the lipid bilayer, inverting their orientation.

Front 118

What is an example of lipid asymmetry in the red blood cell membrane?

Back 118

Lipid asymmetry means that the outer part of membrane does not have the same composition of lipids as the inner part of membrane. For instance, there is more phosphatidylcholine (a phospholipid), on the outer part of the membrane than on the inner part of the membrane.

Front 119

What are the 3 classes of membrane proteins?

Back 119

Peripheral proteins adhere non-covalently to the membrane by electrostatic forces like H-bonds. These are not tight interactions. Integral proteins are partially or totally extended through the membrane. Peripheral proteins are predominantly polar on the surface. There are nonpolar interactions between membrane lipids and integral proteins.

Front 120

What are Beta strands and Beta barrels?

Back 120

Hint 120

The alpha helix is not the only structural motif by which a protein can cross a membrane. Some integral transmembrane proteins use structures built from Beta strands and Beta sheets to diminish the polar character of the peptide backbone as it crosses the nonpolar membrane core. The Beta barrel structure's interior is large enough to accomodate water molecules. In all transmembrane Beta barrels, the polar and nonpolar residues alternate along the Beta strands, with polar residues facing the center of the barrel and nonpolar residues facing outward, where they can interact with the hydrophobic lipid milieu of the membrane.

Front 121

What are the 4 types of lipid-anchored proteins?

Back 121

These are proteins that are covalently linked to lipid molecules. The lipid moieties can insert into the membrane bilayer, effectively anchoring their linked proteins to the membrane.

Front 122

What are thioether-linked prenyl anchors?

Back 122

A thioether is a functional group with the connectivity R-S-R', where R is any hydrocarbon group. A thioether is similar to an ether except that it contains a sulfur atom in place of the oxygen. Because oxygen and sulfur belong to the same group in the periodic table, the chemical properties of ethers and thioethers are somewhat similar.

Front 123

What are glucosyl phosphatidylinositol anchors?

Back 123

The net charge is -1 because of the phosphate. The sugar in glucosyl phosphatidylinositol is different from a hexose because there no oxygen in the ring.

Hint 123

The glycosyl phosphatidylinositols have 2 fatty chains, compared to other groups with 1 fatty chain. The galactose carbohydrates makes the vesicular stomatitis head group big and bulky.

Front 124

What is passive diffusion and facilitated diffusion?

Back 124

Rate of transport is saturable, similar to that observed with substrate binding by enzymes. The dependence of transport rate on solute concentration takes the form of a rectangular hyperbola, so the transport rate approaches a limiting factor, Vmax at very high solute concentration (becomes saturated to the point where it doesn't transport any more, it's filled). Because passive diffusion doesn't involve formation of a specific solute-protein complex, the plot of rate versus concentration is linear, not hyperbolic.

Hint 124

The particles that can easily dissolve in a hydrocarbon layer of membrane are small nonpolar molecules. These can be diatomic molecules like O2, H2, CO2, any symmetrical gases can diffuse across a membrane. Carrier proteins of facilitated diffusion are intervening to help move species across. Proteins in facilitated diffusion display an affinity and specificity for the transported solute.

Front 125

How do glucose transporters and anion transporters work?

Back 125

The inside of the membranes are different from the outsides. Transporters can specify between galactose and glucose and mannose, even for the position of individual hydroxyl groups. The anion transporter is an antiport and it does an electrically neutral exchange (no change in charges between bicarbonate and chloride ion).

Front 126

What are the thermodynamics of transport?

Back 126

ΔG is the overall energetics of the PROCESS. This is NOT a chemical reaction, there is no ΔG'° and the RTln is NOT negative. The destination is in the eyes of the solute. The destination is C2 and C1 is where the solute is coming from. If the destination [C2} is smaller than [C1], then ΔG is negative. If the destination [C2] is larger than [C1], then ΔG is positive.

Front 127

What are the thermodynamics of a charged species?

Back 127

For this equation, we have the concentration term and the electrical term. Memorize Faraday's constant (96,500 J/(volt*mol))

Front 128

What are the 3 types of ATPases?

Back 128

ATP hydrolysis occurs on the cytoplasmic side of the membrane and the net movement of 1 positive charge outward per cycle makes the sodium pump electrogenic in nature.

Front 129

What is the Na+/K+ ATPase?

Back 129

Memorize the overall reaction of Na+ and K+. Getting out [Na+] is from [low] to [high] and pumping of K+ from [low] to [high] is unfavorable, so need to couple it with hydrolysis of ATP. The alternation between high and low affinities for Na+, K+,and ATP serves to tightly couple the hydrolysis of ATP and ion binding and transport.

Front 130

What are Ca2+-ATPases?

Back 130

Ca2+-ATPases are bone-destroying proteins. The hydrolysis of ATP shoots out protons and more protons help dissolve the bone.

Front 131

What are H+-ATPases?

Back 131

Front 132

What is ion gradient driven active transport?

Back 132

Front 133

What is light driven transport?

Back 133

Note the peptide backbone of lysine and the amino group of lysine. Light driven transport is another form of transport to get energy.

Hint 133

There are numerous alpha helices spanning the membrane of the bacterium. Retinal is an isoprenoid and acts as a channel when in trans isomerization. Proton gradients can be generated to drive ATP synthesis. The purple patches of the bacterium are formed in low oxygen conditions. The cis to trans isomerization is a configurational change - it requires breaking and forming of the bond.

Front 134

What are 2 examples of specialized membrane pores?

Back 134

Gap junctions undergo a conformational change upon binding of Ca2+ - it closes the junction.

Front 135

What are ionophores?

Back 135

Channel forming peptides forms a pore through the whole membrane. These small molecules are non-energy requiring.

Hint 135

Ionophores are used as antibiotics for certain feed animals. Carrier molecules are integral proteins that binds on 1 side of the membrane and releases on the other side and facilitates diffusion. The direction is based on the concentration gradient and is entropically driven. Entropically driven means that same charge ions like to avoid each other. Ions like to go from a more crowded place to a less crowded place. Things are more disordered when there is more room. This is also why solutes move from [high] to [low].

Front 136

What are 2 examples of ionophores?

Back 136

Gramidicin is a left handed helix, NOT an alpha helix. Actually, the 6.3 residues per turn of gramidicin is FAR wider than an alpha helix. Gramidicin is found in nature as a natural antibiotic. Gramidicin is a channel former and can deplete Na+. For gramidicin as well as valinomycin, transfer is based mostly on concentration gradient and is entropically driven.

Front 137

What is a summary of membranes and transport?

Back 137

Front 138

What is the effect of sequence on structure?

Back 138

Front 139

Where is rotation possible about a peptide?

Back 139

Front 140

What are the steric constraints of phi and psi angles?

Back 140

For each of these bond angles, a value of 0° corresponds to an orientation with the amide plane bisecting the H-Alpha carbon-R (side chain) angle and a cis conformation of the main chain around the rotating bond in question.

Hint 140

The entire path of the peptide backbone is known if the phi and psi rotation angles are all specified. Some values of phi and psi are not allowed due to steric interference between nonbonded atoms. Values of phi = 180° and psi = 0° are not allowed because of the forbidden overlap of the N-H hydrogens. Similarly, phi = 0° and psi = 180° are forbidden because of unfavorable overlap between the carbonyl oxygens.

Front 141

For an alpha helix:
1) What are the number of residues per turn?
2) What is the rise per residue?
3) What is the rise per turn?
4) What are the phi and psi angles?
5) How are the R groups faced?
6) What direction are the H bonds?

Back 141

Certain amino acids tend to occur in alpha helices, whereas others are less likely to be found in them. Polyleucine and polyalanine, for example, readily form alpha helices. In contrast, polyaspartic acid and polyglutamic acid, which are highly negatively charged at pH=7, form only random structures because of strong repulsion between the R groups along the peptide chain. At pH = 1.5 to 2.5, however, where the side chains are protonated, and thus uncharged, these latter species spontaneously form alpha helical structures.

Hint 141

Similarly, polylysine is a random coil at pH values below 11, where the repulsion of positive charges prevents helix formation. At pH = 12, where polylysine is a neutral peptide, it readily forms an alpha helix. Proline and glycine do not work well in alpha helices. Proline contrains rotation because of it's bulky side chain and glycine is too small and leaves gaps.

Front 142

What do alpha helices look like?

Back 142

The hydrogen bonds are dotted lines. The pink balls are oxygens, the blue balls are nitrogens. The side groups are yellow balls.

Hint 142

Helices can be formed from either D or L amino acids, but a given helix must be composed entirely of amino acids of one configuration. Alpha helices cannot be formed from a mixed copolymer of D and L amino acids. An alpha helix composed of D-amino acids is left handed. L amino acids, and therefore right handed alpha helices, are more commonly found in nature, just as D sugars are more commonly found in nature.

Front 143

What are the characteristics of Beta pleated sheets?

Back 143

For parallel beta sheets, on the same side of the sheet, there are both hydrophilic and hydrophobic side chains, meaning both sides have both hydrophobic and hydrophilic side chains. For antiparellel beta sheets, on the same side of the the sheet, there is either only hydrophobic or hydrophilic side chains, meaning one side has hydrophobic side chains and one side has hydrophilic side chains.

Hint 143

Interstrand bonding is bonding between 2 strands, while intrastrand bonding is bonding between 1 strand. Parallel sheets characteristically distribute HYDROPHOBIC side chains on BOTH SIDES of the SHEET, whereas, antiparallel sheets are usually arranged with all their HYDROPHOBIC residues on ONE side of the sheet. For the primary sequence of antiparallel beta sheets, there is an alternation of hydrophilic and hydrophobic residues because every other side chain projects to the same side of the sheet. Antiparallel helices are more stable than the parallel helices.

Front 144

What are some examples of amino acids that have a higher propensity for alpha helices or beta sheets?

Back 144

Alanine has a higher probability to be in an alpha helix than proline. Phenylalanine is fairly more frequent in Beta sheets than proline. Acidic residues (aspartic acid and glutamic acid) are not likely to be in Beta sheets, but are highly likely in alpha helices. Know which residues are more or less probable in an alpha helix.

Hint 144

Tyrosine is highly unlikely to be in a alpha helix, but highly likely to be in a beta sheet. Cysteine is unlikely to be in an alpha helix, but likely to be in a beta sheet. Alpha helices all follow 1 pattern, while beta sheets follow 2 patterns.

Front 145

What are Beta and Alpha turns?

Back 145

Because it lacks a side chain, glycine is sterically the most adaptable of the amino acids, and it accommodates conveniently to other steric constraints in the Beta turn. Proline, however, has a cyclic structure and a fixed phi angle, so to some extent, it forces the formation of a Beta turn (induces a kink). Such bends promote the formation of antiparallel Beta-pleated sheets. 2 large bulky, acidic, or basic amino acids facing the same way can have steric or electronic hindrance.

Hint 145

Beta turns (also known as tight turn or Beta bends), are where the peptide chain forms a tight loop with the carbonyl oxygen of one residue is hydrogen bonded with the amide proton of the residue THREE positions down the chain. This H-bond makes the Beta turn a relatively stable structure. The Beta turn allows the protein to reverse the direction of the peptide chain. Type I is more common than Type II. Proline best fits in the 3 position of the type I turn. In type II turn, proline is preferred in the 2 position, whereas the 3 position is prefers glycine or small polar residues.

Front 146

What is a Ramanchandran map?

Back 146

A Ramanchandran map is a probability map. If we make D amino acids, we could create left handed alpha helices. The numbers, like -2, means a left handed helix with 2 residues per turn. There may be some unusual angles with glycine, since it is such a small amino acid. There is clashing at 180° and 0° and 0° and 0° is the worst clash.

Front 147

What are motifs of tertiary structures? What are domains? What is an example of a fibrous protein, a globular protein, and membrane protein?

Back 147

Front 148

What are fibrous proteins?

Back 148

Keratin is highly represented by Ser, glu + gln, and cys. Fibroin by Gly, ala, and ser. Collagen: gly, ala, and pro. These fibrous proteins favor certain amino acids.

Front 149

What is alpha keratin?

Back 149

The helices clearly sacrifice some stability in assuming this twisted conformation, but they gain stabilization energy from the packing of side chains between the helices. In other forms of keratin, covalent disulfide bonds form between cysteine residues of adjacent molecules, making the overall structure even more rigid, inextensible, and insoluble, impt properties for structures like claws, fingernails, hair, and horns.

Hint 149

There are van der Waals and hydrophobic interactions between the hydrophobic residues. Glycines interact via Van der Waals and serines interact with hydrogen bonding.

Front 150

What are the characteristics of Beta Keratin?

Back 150

Front 151

What are the characteristics of collagen?

Back 151

The triple helix is a structure that forms to accomodate the unique composition and sequence of collagen. Since collagen has a lower % of hydrophobic amino acids, it is more soluble than other structures. We are assuming glycine is polar.

Hint 151

In the triple helix, every 3rd residue faces or contacts the crowded center of the structure. This area is so crowded that only Gly can fit, and thus every 3rd residue must be a Gly. The triple helix is a staggered structure, so that Gly residues from the 3 strands stack along the center of the triple helix and the Gly from 1 strand lies adjacent to an x residue from the 2nd strand and to a y from the 3rd. This allows the N-H of each Gly residue to hydrogen bond with the C=O of the adjacent x residue. The triple helix is further stabilized and strengthened by the formation of the interchain H bonds involving hydroxyproline because we have 3 chains in the triple helix. These hydrogen bonds also make the collagen more soluble. Scurvy is caused by a complete lack of Vitamin C (ascorbic acid) - it is the weakening of connective tissue.

Front 152

What are the characteristics of globular proteins?

Back 152

Globular proteins are named for their spherical shape and are far more numerous.

Front 153

Should globular proteins be viewed as static or dynamic structures?

Back 153

Front 154

What are protein domains?

Back 154

Larger, globular proteins are usually made up of two or more recognizable and distinct structures, termed domains or modules - compact, folded protein structures that are usually stable by themselves in aqueous solution. Typical domain structures consist of hydrophobic cores with hydrophilic surfaces.

Hint 154

Individual domains often possess unique functional behaviors, for example, the ability to bind a particular ligand with high affinity and specificity, and an individual domain from a larger protein often expresses its unique function within the larger protein in which it is found. Multidomain proteins typically possess the sum total of functional properties and behaviors of their constituent domains.

Front 155

What are the 3 classes of globular proteins?

Back 155

Front 156

What are antiparallel alpha helices?

Back 156

Antiparallel a-helix proteins are structures heavily dominated by a-helices. Many of these are regular, uniform structures, but in a few cases (uteroglobin, for example) one of the helices is tilted away from the bundle. Tobacco mosaic virus protein has small, highly twisted antiparallel b-sheets on one end of the helix bundle with two additional helices on the other side of the sheet. Notice in Figure 6.29 that most of the antiparallel a-helix proteins are made up of four-helix bundles.

Hint 156

The globin structure can be viewed as two layers of helices, with one of these layers perpendicular to the other and the polypeptide chain moving back and forth between the layers.

Front 157

What are parallel or mixed beta sheets?

Back 157

Parallel b-sheets are thus typically found as core structures in proteins, with little access to solvent. Another important parallel b-array is the eight-stranded parallel b-barrel. Each b-strand in the barrel is flanked by an antiparallel a-helix. The a-helices thus form a larger cylinder of parallel helices concentric with the b-barrel. Both cylinders thus formed have a right-handed twist.

Hint 157

Another parallel b-structure consists of an internal twisted wall of parallel or mixed b-sheet protected on both sides by helices or other substructures. This structure is called the doubly wound parallel b-sheet because the structure can be imagined to have been wound by strands beginning in the middle and going outward in opposite directions. Whereas the barrel structures have four layers of backbone structure, the doubly wound sheet proteins have three major layers and thus two hydrophobic core regions.

Front 158

What are antiparallel beta sheets?

Back 158

The minimal structure for an antiparallel b-sheet protein is thus a two-layered structure, with hydrophobic faces of the two sheets juxtaposed and the opposite faces exposed to solvent. Such domains consist of b-sheets arranged in a cylinder or barrel shape. These structures are usually less symmetric than the singly wound parallel barrels and are not as efficiently hydrogen bonded, but they occur much more frequently in nature.

Hint 158

Barrel structures tend to be either all parallel or all antiparallel and usually consist of even numbers of b-strands. Good examples of antiparallel structures include soybean trypsin inhibitor, rubredoxin, and domain 2 of papain. Topology diagrams of antiparallel b-sheet barrels reveal that many of them arrange the polypeptide sequence in an interlocking pattern reminiscent of patterns found on ancient Greek vases (Figure 6.33) and are thus referred to as a Greek key topology. Several of these, including concanavalin A and g-crystallin, contain an extra swirl in the Greek key pattern (see Figure 6.33). Antiparallel arrangements of b-strands can also form sheets as well as barrels. Glyceraldehyde-3-phosphate dehydrogenase, Streptomyces subtilisin inhibitor, and glutathione reductase are examples of single-sheet, double-layered topology. Rubredoxin is a small iron-sulfur protein found in various sulfur-metabolizing bacteria. Note how compact rubredoxin is.

Front 159

What are the thermodynamics of folding?

Back 159

It is always entropically unfavorable to go from a random coil to a folded structure. So going form unfolded to folded will be a net LOSS of entropy. The greater the number of nonpolar residues, the higher the hydrophobic effect, so that makes it more favorable when folded because in a polar solution, the clathrate forms. Takeaway: 1) The largest contribution to the stability of a folded protein is the entropy change for the water molecules associated with the nonpolar residues and 2) the overall free energy change for the folding process is not large, like -20 to -60 kJ/mole.

Hint 159

The ΔH for myoglobin is zero, meaning it makes no difference of whether the protein is folded or not folded on the ΔH. The favorable side of the diagram is on the left and the unfavorable side is on the right. Per the diagram, if a protein is folded, there is a net -ΔG. When ΔG, -TΔS, and ΔH are measured for the polar and nonpolar side chains, you will find that the enthalpy and the entropy changes for the polar residues cancel each other out and the ΔG of folding of the polar residues is about 0. Both ΔH and -TΔS for the nonpolar residues are positive and thus make unfavorable contributions to the folding free energy. However, large #s of water molecules restricted and immobilized around nonpolar residues in the nonpolar protein are liberated in the FOLDING process. The burying of nonpolar residues in the FOLDED protein's core produces a dramatic entropy INCREASE for these liberated WATER molecules (not for the folded protein). This is just enough to make the overall ΔG for folding negative and thus favorable.

Front 160

What is a hydropathy plot?

Back 160

Front 161

What is the significance of the protein folding pathways?

Back 161

Folding is a dynamic process - it is not straightforward. There are many alternative conformations. Since proteins don't fold quickly, something is driving the folding. The energy landscapes tell you that there is an uneven energy levels. With the energy landscape, the top of the rim represents the many possible unfolded states for a polypeptide chain, each characterized by high free energy and significant conformational entropy.

Hint 161

Predictive algorithms consider the composition of short segments of a polypeptide. If these segments are rich in residues that are found frequently in helices or sheets, then that segment is judged likely to adopt the corresponding secondary structure. The a-helix-forming and b-sheet-forming propensities, Pa and Pb are found for the 20 amino acids. These residues are classified as strong helix formers (Ha), helix formers (ha), weak helix formers (Ia), indifferent helix formers (ia), helix breakers (ba), and strong helix breakers (Ba). Such algorithms are only modestly successful in predicting the occurrence of helices and sheets in proteins. Polypeptides fall down the wall of the funnel as contacts made between residues establish different folding possibilities. The narrowing of the funnel reflects the smaller # of available states as the protein approaches its final state, and bumps or pockets on the funnel walls represent partially stable intermediates in the folding pathway. The most stable (native) folded state of the protein lies at the bottom of the funnel.

Front 162

What is the molten globule and what are molecular chaperones?

Back 162

Front 163

What are protein dynamics and time scales of motion?

Back 163

Even once folded, proteins are dynamic structures. Atoms in small functional groups may move quickly in short distances. Larger groups move more over a wider range and a slower time scale.

Front 164

What are modules or domains and how is this related to the term "mosaic proteins"?

Back 164

Front 165

What is quaternary structure? What are the advantages of quaternary structure?

Back 165

Weak forces stabilize quaternary structures. The energy of Van der Waals interactions at protein surfaces contributes little to the stability of the dimer. Hydrophobic interactions at the subunit-subunit interface are generally very favorable and the subunit association process buries a lot of the surface area previously exposed to solvent.

Hint 165

Many proteins exist as oligomers, complexes composed of noncovalent assemblies of 2 or more monomer subunits. Homomultimers are proteins composed of a single type of monomer subunit and heteromultimers are proteins composed of several different kinds of subunits. The way in which separate folded monomeric protein subunits associate to form the oligomeric protein constitutes the quaternary structure of that protein. Proteins with 2 to 4 subunits predominate in nature, but many cases of higher numbers exist. The terms polypeptide and protein are used interchangeably in discussing polypeptide chains. Proteins with 1 polypeptide chain are monomeric proteins. Proteins with more than 1 polypeptide chain are multimeric proteins. Multimeric proteins can only have 1 kind of polypeptide chain, and are called homomultimeric, or they may have more than 1 kind of polypeptide chain and are called heteromultimeric.

Front 166

What are isologous and heterologous associations between protein subunits?

Back 166

Oligomeric associations of protein subunits can be divided into those between identical subunits and those between nonidentical subunits. Interactions among identical subunits can be further distinguished as either isologous or heterologous.

Hint 166

In isologous interactions, the interacting surfaces are identical and the resulting structure is necessarily dimeric and closed, with a twofold axis of symmetry. If any additional interactions occur to form a trimer or tetramer, these must use different interfaces on the protein's surface. In contrast, heterologous associations among subunits involve nonidentical interfaces. These surfaces must be complementary, but they are not generally symmetric.

Front 167

What is a summary of protein folding?

Back 167

Front 168

What are simple proteins, prosthetic groups, apoproteins, and holoproteins?

Back 168

Front 169

What are the 7 classes of conjugated proteins?

Back 169

Note that phosphate groups have a negative charge.

Front 170

What is solid-phase synthesis of proteins?

Back 170

Front 171

What 5 properties of proteins that are used to purify them?

Back 171

Front 172

What 3 properties of proteins are used to separate them based on solubility?

Back 172

Front 173

How are proteins separated according to their electrical charges?

Back 173

Front 174

What is ion exchange chromatography?

Back 174

Front 175

What is hydrophobic interaction chromatography?

Back 175

Front 176

What is affinity chromatography?

Back 176

Front 177

What is the dialysis technique for separating proteins?

Back 177

Front 178

What is size exclusion chromatography?

Back 178

The large particles elute first because they don't fit. The medium-sized particles are someone retarded in the column. The small particles are the last to elute.

Front 179

What is a summary of protein purification techniques?

Back 179

Front 180

What are the consequences of acid hydrolysis of proteins?

Back 180

Front 181

What are the steps in protein sequencing?

Back 181

Front 182

What is the step of the cleavage of disulfide bridges for protein sequencing?

Back 182

Front 183

What is the alkylation step of the cleavage of disulfide bonds?

Back 183

Front 184

What are the 3 carboxypeptidases and where do they cleave?

Back 184

This technique is used to identify the amino acid at the C-terminal end of the protein.

Front 185

What is the Edman reagent and how is it used?

Back 185

This technique is used to identify the amino acid residing at the N-terminal end of a protein.

Front 186

Where do trypsin, chymotrypsin, clostripain, and staphylcoccal protease cleave?

Back 186

Remember, all cleave the PEPTIDE bond on the C-side of the amino acid.

Front 187

What does Cyanogen Bromide do to proteins?

Back 187

Front 188

What is protein homology?

Back 188

Cytochrome c is found in the mitochondria of all eukaryotic organisms. A phylogenetic tree is a diagram illustrating the evolutionary relationships among a group of organisms.

Front 189

Can protein homology occur between proteins that are functionally different?

Back 189

Front 190

What is a summary of primary, tertiary, and secondary structure of proteins?

Back 190

Front 191

What are the properties of living systems?

Back 191

Front 192

What is the hierarchical nature of biomolecules?

Back 192

Front 193

What are the inorganic precursors, the building blocks, and the metabolites?

Back 193

Front 194

What is the hierarchy of biological systems?

Back 194

Front 195

What are macromolecules, supramolecular complexes, and organelles?

Back 195

Front 196

What is the organizational structure of cells?

Back 196

Front 197

What are ionic interactions and Van der Waals interactions?

Back 197

Front 198

What are hydrogen bonds?

Back 198

Front 199

What are the unique properties of water?

Back 199

Water has a very strong dipole moment. The covalent bond is shorter, meaning its stronger. The Van der waals bond is longer, meaning it's weaker. Water is bent because of the lone pairs.

Hint 199

The angle is 104.3° and not 109° because of the lone pairs. The long pairs push the H+ bonds closer together, instead of the H2O taking on the ideal tetrahedral shape.

Front 200

What is the tetrahedral ice structure? What is a dielectric constant?

Back 200

Front 201

What is the hydration shell and what is the hydrophobic effect?

Back 201

The attraction between nonpolar solutes is an entropy-driven process due to a net decrease in order among the water molecules. Hydrophobic interactions between nonpolar molecules are maintained not so much by direct interactions between inert solutes themselves as by the increase in entropy when water cages coalesce and reorganize.

Hint 201

The apparent affinity of nonpolar structures for one another is called hydrophobic interactions.

Front 202

What are amphilic molecules and whate are chaotropic agents?

Back 202

With micelles, the nonpolar heads face inwards and the polar heads face outwards. An example is detergent.

Hint 202

Fatty acids will create globular structures, but are still nonpolar because of the long nonpolar tail. Fatty acids can't form micelles because they are more cylindrical in shape, while micelles have a wedge shape. Micelles have a bulky head group on the outside and narrower tails face in toward each other.

Front 203

What are the 2 definitions of an acid and base?

Back 203

Front 204

What is the auto-ionization of water? What is the [H+] and [OH-] in pure water?

Back 204

Front 205

which antibiotics used to treat meningitis can achieve therapeutic levels in CSF with high IV doses?

Back 205

beta lactams (penicillin, 3rd gen cephalosporins, carbapenems), vancomycin

Front 206

What are nucleic acids?

Back 206

Front 207

What is the numbering system for purines and purimidines?

Back 207

Front 208

What is the structure of cytosine? What is the pKa of cytosine? What is the name of cytosine attached to a sugar?

Back 208

Front 209

What is the structure of thymine and uracil? What is the pKa of thymine? What is the name of thymine and uracil attached to sugars?

Back 209

Front 210

What is the structure of guanine? What is the pKa of guanine? What is the name of guanine attached to sugar?

Back 210

Front 211

What is the structure of adenine? What is the pKa? What is the name of the adenine attached to sugar?

Back 211

Front 212

How are RNA bases chemically modified?

Back 212

Front 213

What is the predominant tautomer of guanine, thymine, and uracil at pH = 7?

Back 213

Uracil isn't in the powerpoint, but it also a tautomer. In contrast, the enol form of cytosine predominates at pH 7. The pKa values specify whether protons are associated with the various ring nitrogens at neutral pH. As such, they are important in determining whether these nitrogens serve as H-bond donors or acceptors.

Hint 213

The aromaticity of the pyrimidine and purine ring systems and the electron-rich nature of their carbonyl and ring nitrogen substituents endow them with the capacity to undergo keto-enol tautomeric shifts.

Front 214

Do you need to draw the structure of each base in the form that predominates at pH 7 and in its unprotonated form above/below it's pKa? Does the phosphate group ionize?

Back 214

Front 215

What is the absorbance of pyrimidines and purines? What is the hyperchromic effect?

Back 215

Hypochromism is when chromophores are stacked, they decrease the transition dipoles and inhibit absorbance by neighbors. This means that there is lesser total absorbance. Aromatics are most absorbant, with tryptophan at the top. Also, Tm is dependent on the ionic strength of the solution: the lower the ionic strength, the lower the Tm. Because cations suppress the electrostatic repulsion between the negatively charged phosphate groups in the double helix, the double-stranded form of DNA is more stable in dilute salt solutions. DNA in pure water melts even at room temperature.

Hint 215

Hyperchromic effect: As the temperature increases and the DNA starts to melt, you see a higher absorbance because the nonstacked bases will absorb more. When they are fully melted, they are at maximum absorbance. The sigmoidal curve of the absorbance vs. temp tells us that it's a cooperative process, once the change happens, it facilitates the neighboring strands and is cooperatively reversible in a cooperative way. Tm is melting temperature. The absorbance increase, or hyperchromic shift, is due to the fact that the aromatic bases in DNA interact via their pi-electron clouds when stacked together in the double helix. Because UV absorbance of the bases is a consequence of pi-electron transitions, and because the potential for these transitions is diminished when the bases stack, the bases in duplex DNA absorb less 260nm radiation than expected for their numbers. Unstacking alleviates this suppression of UV absorbance. The rise in absorbance coincides with strand separation and the midpoint of the absorbance increase is called the melting temperature (Tm). DNAs differ in their Tm values because they differ in relative G+C content. The higher G+C content of DNA, the higher its Tm because G:C pairs have higher base stacking energies than A:T pairs.

Front 216

What is the pentose found in RNA and the pentose in DNA?

Back 216

Front 217

What is 2'-endo and 3'-endo?

Back 217

RNA is always in 3'-endo conformation because the OH group in 2' position creates a steric clash. 2'-endo means the group at the 2' position is tilted, 3'-endo means the group at the 3' position is tilted.

Front 218

What is a nucleoside? Where is the glycosidic linkage of the pyrimidine and purine? What is anti and syn conformation?

Back 218

Front 219

what is the function of astrocytes?

Back 219

nourishment of neurones, synapse cleaner, relationship with blood vessels - plug leaks

Front 220

What is the structure of cytidine, uridine, adenosine, thymidine and guanosine?

Back 220

Front 221

what do oligodendrocytes do?

Back 221

make myelin, anti-regeneration

Front 222

What are nucleotide functions? What are some examples of coenzymes (cofactors)?

Back 222

Remember, memorize the structure of ATP. Notice there are slight differences in some of the cofactors - those differences are for recognition purposes.

Front 223

What are the features of RNA primary structure?

Back 223

Front 224

What are the features of DNA primary structure?

Back 224

Front 225

How many degrees of freedom are in the DNA molecules? How do you count the bonds per nucleotide?

Back 225

All the oxygen to phosphate to carbon linkages are single bonds. This differs from the partial double bonds of proteins which restricts rotation of the protein. There is much more free rotation of the nucleotides (DNA and RNA). The only limitation of nucleotides is steric hindrance.

Front 226

What is the biosynthesis reaction of DNA and RNA polymers?

Back 226

NDP means nucleoside 5'-diphosphates, and NTP means nucleoside 5' triphosphates. dNTP means deoxynucleotide triphosphate. DNA+1 means 1 nucleotide longer. PPi is pyrophosphate. New nucleotides always add to the 3' end.

Front 227

What are the biological roles of DNA and RNA?

Back 227

Front 228

What is the complementary relationship of DNA?

Back 228

Pitch length is the rise per turn. DNA always has a deoxyribose in a 2'-endo conformation. DNA is antiparallel double helix. There are about 10 base pairs per turn or 3.4nm bp per rise. RNA is transcribed as a single strand, but can fold. Structure is related to function with DNA and proteins.

Front 229

What are the base pairs and what hydrogen bonds?

Back 229

For G:C, the hydrogen bonds are between 1)the C6 of guanine and C4 of cytosine, 2) the N1 of guanine and N3 of cytosine, and 3) the C2 of guanine and C2 of cytosine.

Hint 229

For A:T, the hydrogen bonds are between 1) the C6 of adenine and C4 of thymine, and 2) the N1 of adenine and N3 of cytosine. Once I know the numbering, I should be able to place where the hydrogen bonds are.

Front 230

How are the major and minor grooves formed with the DNA?

Back 230

Major groove edge is at the top, minor groove edge is at the bottom. The 1.11nm is the distance of the glycosidic bond and the angles are about 50 degrees. Major grooves have more opportunity for specific recognition than do minor groups.

Front 231

What are helical twists?

Back 231

Helical twist is the rotation (around the axis of the double helix) of one base pair relative to the next.

Front 232

What are the differences between the A-form RNA and the B-form DNA and their major and minor grooves?

Back 232

The B-form of the DNA's major groove is large and proteins can bind their there. DNA is an excellent place for proteins to bind and DNA has the information. The minor groove of DNA is much more narrow - proteins can't bind there. The major groove for RNA is quite deep and very narrow - it is impossible for proteins to fit and bind. The minor groove for RNA is wide but flat - it's not ideal for binding either. RNA holds information like DNA, but proteins can't bind to RNA.

Front 233

What would form if there was an extended DNA or RNA strand?

Back 233

A hydrophobic hole would form. Bases prefer to be stacked due to the hydrophobic effect. A water molecule or a vacuole could fit in between the 2 strands. If the strands slide across each other, it still allows an optimal distance between the bases and the 6 angstroms between the phosphates is still maintained.

Hint 233

This ladderlike structure converts to a double helix when given a simple right-handed twist. Helical twisting brings the base-pair rungs of the ladder closer together, stacking them 0.34nm apart, without affecting the sugar-sugar distance of 0.6nm. Because this helix repeats itself approximately every 10bp, its pitch is 3.4nm. This is the major conformation of DNA in solution, and it is called B-DNA.

Front 234

Why do helixes form?

Back 234

Double-stranded DNA is a regular 2-chain structure with hydrogen bonds formed between opposing bases on the 2 chains. Such H-bonding is possible only when the 2 chains are antiparallel. The polar sugar-phosphate backbones of the 2 chains are on the outside. The bases are stacked on the inside of the structure; these heterocyclic bases, as a consequence of their pi-electron clouds, are hydrophobic on their flat sides.

Hint 234

One purely hypothetical hypothetical conformational possibility for a 2-stranded arrangement would be a ladderlike structure in which the base pairs are fixed at 0.6nm apart because this is the distance between adjacent sugars along a polynucleotide strand. Because water molecules could fit into the spaces between the hydrophobic surfaces of the bases, this conformation is energetically unfavorable.

Front 235

What are the rotations in which a helix is formed?

Back 235

Front 236

What is tilt of DNA helices?

Back 236

In the picture, propeller twist is wrong - should be tilt.

Front 237

What is propeller twist?

Back 237

Front 238

What is the effect of changing roll on helical geometry?

Back 238

Notice that the axis goes straight through each of the base pairs for the first diagram. R = roll, T=twist, S=slide. The first diagram only has twist, the second has twist and roll.

Hint 238

The second diagram requires a very flexible axis.

Front 239

What is the effect of changing slide on helical geometry?

Back 239

There is no change in roll in the second diagram. Still requires a very flexible axis.

Front 240

What are A-form and B-forms of DNA?

Back 240

Front 241

What are the characteristics of Z-dna?

Back 241

In contrast with the B-DNA, which has all of its bases in the anti conformation, the Z-DNA helix alternates between the anti and unusual syn conformation.This dinucleotide repeat causes the backbone to follow a zigzag path - giving rise to it's name Z-dna.

Hint 241

In Z-dna, there is only a single narrow groove that corresponds to the minor groove of B-DNA. There is no major groove. Remember: RNA or DNA can take on the A-form, though there are differences in major and minor grooves. Only DNA can take on the B-form, and Z-DNA can only be for DNA - it has very little grooves.
The methylation of C is believed to favor a B to Z switch because in B-DNA, these hydrophobic methyl groups would protrude into the aqueous environment of the major groove and destabilize its structure. In Z-DNA, the same methyl groups can form a stabilizing hydrophobic patch.

Front 242

What are the differences between A-form, B-form, and Z-DNA?

Back 242

Front 243

Why can't RNA assume the B-form?

Back 243

Front 244

What are the chemical differences between DNA and RNA?

Back 244

RNA is relatively resistant to the effects of dilute acid, but DNA is not. The glycosidic bonds between pyrimidine bases and 2'-deoxyribose are not affected, and in this case, DNA's sugar-phosphate backbone remains effect.

Front 245

What does RNA get hydrolyzed by bases so easily and DNA does not?

Back 245

Front 246

What are exonucleass? What are endonucleases? What is an a type nuclease? What is a b type nuclease? What is an example of an a type and b type nuclease?

Back 246

Front 247

What are restriction endonucleases?

Back 247

Front 248

How do proteins interact with DNA?

Back 248

There are complementary partners among the R groups with proteins and the DNA. The bases have some hydrophobic character because of the number of carbons. The polar groups of the bases are exposed in the grooves. The stacked part of bases are hydrophobic. There are H-bond interactions with R groups and the polar parts of bases.

Front 249

What is a description of restriction sites?

Back 249

Front 250

What is restriction mapping?

Back 250

Front 251

What are the principles of DNA cloning?

Back 251

Front 252

How does DNA sequencing use chemicals or enzymes?

Back 252

Front 253

What is the Sanger method of DNA sequencing?

Back 253

Front 254

How do automated sequencers work with DNA sequencing?

Back 254

Front 255

What are some of the causes of DNA denaturation?

Back 255

A chromophore is a particle that absorbs light. Riboses and phosphates don't absorb light, only bases. Tryptophan of proteins absorb light at 280nm. The higher the G:C content, the higher the Tm because the G:C pairs have higher base stacking energies than A:T pairs due to 3 H-bonds.

Hint 255

The melting point is a linear increase with increase in G:C content and ionic strength. G:C is more stable than A:T because it has 3 H-bonds. The negative charges of the phosphates repel each other in the water, so it is not stable in water alone. As you add salt (with the positive cations), there will be less repulsion between the negative charges of the phosphates and will make a more stable helix - the lower the ionic strength, the lower the melting point. The melting point with absorbance graph is a sigmoidal curve - very cooperative process. The higher the G:C content, the more stable the helix, the higher the Tm,

Front 256

What is the process of reannealing of DNA?

Back 256

Front 257

What is a Van't Hoff plot?

Back 257

Van't hoff plot is RTlnKeq vs. 1/T. Measure by finding Keq and T.

Front 258

Are G:C base pairs more stable only because of H bonds?

Back 258

No! G:C base pairs are not only stable because of H-bonds! An experiment showed that G:C base pairs without H-bonds were more stable than A:T base pairs without H-bonds - it's not that simple.

Hint 258

Stability of a helix depends on the order of base stacking. Helix stability depends on the optimal stacking of 1 base over another and the functional groups. Even though the amount of G:C base pairs matter, it has a lot more to do with the optimization of stacking than it does for the number of H-bonds. So don't say it just depends on H-bonds!

Front 259

What is negative and positive supercoiling?

Back 259

Twist and writhe always add up to the L, the linking number. Writhe relieves some of the strain (energy) from the twist. Writhe is the left handed cross over, which is still positive (+). Twist is right-handed (+). The linking number is the number of times the 2 strands are intertwined, and provided both strands remain covalently intact, L cannot change.

Front 260

What are the enzymes that introduce positive and negative supercoiling in DNA?

Back 260

Front 261

What are 3 issues of DNA packaging?

Back 261

Front 262

What are nucleosomes and chromatin?

Back 262

Front 263

What are chromatomes and nucleosome cores?

Back 263

Note the amount of alpha helices in the proteins.

Front 264

What is a proposed packaging pathway for DNA?

Back 264

Front 265

What are 3 alternative structures of DNA?

Back 265

Telomeres form quadruplexes. Telomeres are structures that define the ends of chromosomes and buffer against DNA replication in which the lagging strand of DNA loses some information after each round. Telomeres have no genetic information.

Front 266

What are the features of RNA secondary and tertiary structure?

Back 266

Front 267

Can mismatched base pairs form with RNA and DNA?

Back 267

Yes! Chemically modified bases can be used for recognition purposes and binding.

Front 268

What are some examples of RNA secondary structural motifs?

Back 268

Paired regions of RNA cannot form B-DNA type double helices because the RNA 2'-OH groups are a steric hindrance to this conformation. Instead these paired regions adopt a conformation similar to the A-form of DNA having about 11 bp per turn (instead of 10).

Hint 268

A-form double helices are the most prominent secondary structural elements of RNA. Stems, loops, bulges, and junctions are the 4 basic secondary structural elements in RNA.

Front 269

What are 2 turn motifs commonly found in RNA?

Back 269

Front 270

What are the 2 types of metal ions and what kinds of ligands do they prefer?

Back 270

Front 271

What are the features of transfer RNA?

Back 271

Front 272

What are the features of messenger RNA?

Back 272

Front 273

What are spliceosomes?

Back 273

Front 274

What are snRNAs?

Back 274

RNA itself can do the splicing reaction (they are ribozymes).

Front 275

What are some examples of small nucleolytic ribozymes?

Back 275

Front 276

What are the features of rRNA?

Back 276

Front 277

What does the peptidyl transferase do and how do we know the catalytic activity of ribosomes is with the rRNA?

Back 277

Front 278

What are tetraloops, tetraloop receptors, pseudoknots, U-turns, "A-minor" motif, "A-platform" motif, and four-way junctions?

Back 278