Biochemistry Unit 1

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80 Terms

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Glycine (Gly/G)

Nonpolar, aliphatic R Groups

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Alanine (Ala/A)

Nonpolar, aliphatic R Groups

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Proline (Pro/P)

Nonpolar, aliphatic R Groups

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Valine (Val/V)

Nonpolar, aliphatic R Groups

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Leucine (Leu/L)

Nonpolar, aliphatic R Groups

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Isoleucine (Ile/I)

Nonpolar, aliphatic R Groups

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Methionine (Met/M)

Nonpolar, aliphatic R Groups

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Phenylalanine (Phe/F)

Aromatic R groups

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Tyrosine (Tyr/Y)

Aromatic R groups

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Tryptophan (Trp/W)

Aromatic R groups

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Serine (Ser/S)

Polar, uncharged R groups

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Threonine (Thr/T)

Polar, uncharged R groups

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Cysteine (Cys/C)

Polar, uncharged R groups

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Asparagine (Asn/N)

Polar, uncharged R groups

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Glutamine (Gln/Q)

Polar, uncharged R groups

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Lysine (Lys/K)

Positively charged R groups

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Arginine (Arg/R)

Positively charged R groups

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Histidine (His/H)

Positively charged R groups

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Aspartate (Asp/D)

Negatively charged R groups

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Glutamate (Glu/E)

Negatively charged R groups

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What is the maximum number of hydrogen bonds that water can form?

4

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The strongest hydrogen bonds have angles of .

180 degrees

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The spontaneous clustering of lipids is driven by an energetically favorable increase in the _ of water.

Entropy

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Phosphoric acid has a pKa of 2.1. At what pH will 75% of phosphoric acid be in the conjugate base form?

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math hints: log 3 = 0.5 and log 0.33 = -0.5

2.6

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All of the amino acids are chiral except:

Glycine

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Which amino acids are negatively charged at a neutral pH?

Glutamate, aspartate

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The pKa values of most carboxylic acid groups is about . At pH 7, the majority of these groups will have a ___ charge.

about 2

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negative

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The pKa values of most amino groups is about . Above pH 9, the majority of these groups will have a ___ charge.

about 9

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neutral

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What amino acids have positive ionizable groups?

Lysine, Arginine, Histidine

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What amino acids have negative ionizable groups?

Aspartate, Glutamate

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What amino acids are nonpolar?

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

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What amino acids are aromatic?

Phenylalanine, Tyrosine, Tryptophan

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What amino acids are polar, uncharged?

Serine, Threonine, Cysteine, asparagine, glutamine

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What technique separates proteins based on size?

Gel filtration chromatography

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Which technique is generally used for protein analysis but not protein purification?

SDS-PAGE

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How do you elute a peptide from an ion exchange chromatography column?

Change salt conditions

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In a size exclusion chromatography column, which proteins come out first?

Largest

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In a size exclusion chromatography column, is the protein denatured first?

No, SDS-PAGE does

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In an SDS-PAGE gel, which proteins travel farthest?

Smallest

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In an SDS-PAGE gel, is the protein denatured first?

Yes, by an anionic detergent. So for example, if a protein has 4 subunits, you have to divide the mass by 4 in order to determine order.

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Which amino acids absorb UV light?

Tryptophan and tyrosine

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Which technique is used to sequence a protein?

Edman degradation

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Which of the following bonds in a protein does not rotate? Psi, Phi, or peptide?

Peptide

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How many hydrogen bonds will be found in an alpha helix that is n amino acids long?

n-4

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T/F: Beta sheets are flat.

False, they are pleated

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What kind of bonds for between beta sheets?

Hydrogen bonds

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What interaction contributes to the most protein stability?

Hydrophobic effect

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T/F: Myoglobin does not have a quaternary structure.

True

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What hemoglobin state is stabilized by oxygen binding?

R state

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Where does oxygen bind to hemoglobin?

Heme group in the center

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Where does CO2 bind to hemoglobin?

N terminal of each tertiary structure

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Where do hydrogen ions in a low pH environment bond to hemoglobin?

Amino acid side chains that can accept H's

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What hemoglobin state is stabilized by CO2 binding?

T state

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What amino acids in hemoglobin are carbamylated at low pH?

The first amino acids of each subunit

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What shape is the oxygen-binding curve for hemoglobin in the absence of BPG?

Hyperbolic

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What is Km?

Concentration of the substrate required to achieve 1/2 Vmax

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What does BPG do?

decreases the binding affinity of hemoglobin for oxygen. Without BPG the binding curve is hyperbolic, there is no cooperativity.

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BPG stabilizes state.

T

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Enzymes may increase the rate of a reaction by _ fold.

10^5 - 10^17

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Enzymes (raise/lower) the activation energy of a reaction.

Lower

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Enzymes have evolved to bind most tightly to the _ state.

Transition

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What is a cofactor?

a substance (other than the substrate) whose presence is essential for the activity of an enzyme.

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Some enzymes are comprised of _ instead of protein.

RNA

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What is the best measure of catalytic efficiency?

kcat/Km

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What is located in the active site of the enzyme chymotrypsin and participates in covalent catalysis?

The side chain of serine

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What is located in the active site of the enzyme chymotrypsin and acts as both a general base and general acid?

Histidine

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What stabilizes the transition star oxyanion that forms during chymotrypsin catalysis?

Hydrogen bonds from N-H groups

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A series of enzymes perform a multiple-step reaction pathway to produce the nucleotide cytidine triphosphate (CTP). CTP allosterically inhibits the first enzyme in the pathway. This is an example of:

Feedback inhibition

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List the following lipids in order of decreasing melting point: 13:0, 15:0, 17:1, 17:2

15:0, 13:0, 17:1, 17:2

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Long, saturated lipids have the highest melting point. They are able to pack more tightly due to the hydrophobic effect.

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Triacylglycerides have fatty acids and a backbone.

3, glycerol

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Glycerophospholipids have fatty acids and a backbone.

2, glycerol

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Sphingolipis have fatty acids and a backbone.

1, Sphingosine

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What did Anfinsen's RNase and protein folding experiment demonstrate?

That the primary sequence of a polypeptide is sufficient for proper protein folding and

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activity.

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What does the Bohr Effect state?

An increase in hemoglobin's affinity for oxygen with increasing pH