Amino Acids in Proteins

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1

What is the name of the carbon adjacent to the carbonyl carbon?

the alpha-carbon

2

What are the two groups of an amino acid involved in peptide bond formation?

the carboxyl group and the amino group

3

What is the approximate pKa of the carboxyl group?

pKa ~ 2

4

What is the approximate pKa of the amino group?

pKa ~ 9-10

5

All amino acids except glycine are L-amino acids or R-amino acids?

L-amino acids

6

In order to form a peptide bond, does water need to be removed or added?

removed; dehydration synthesis

7

What are the amino acids found in the nonpolar, aliphatic group?

Glycine, alanine, leucine, isoleucine, valine, and proline

8

True or False? Because of proline's cyclic conformation, it is known as a helix disruptor?

True

9

Which amino acids are considered aromatic?

Phenylalanine, tyrosine, and tryptophan

10

What amino acids are considered polar but uncharged?

asparagine, glutamine, serine and threonine

11

What are the sulfur-containing amino acids?

Methionine and cysteine

12

Methionine is often involved in what type of modification?

Methylation

13

Cysteine is involved in what kind of bonds?

disulfide bonds

14

Serine and threonine are often involved in what kind of linkages and additions?

glycosidic linkages and phosphorylation

15

What types of environments see the use of disulfide bonds?

highly oxygenated environments

16

In the endoplasmic reticulum, which amino acid is recognized most frequently for protein modification?

Asparagine

17

Which amino acids are considered positive (basic)?

Arginine, lysine, histidine

18

Which amino acids are considered negative (acidic)?

Aspartate and glutamate

19

What is pKa?

the point at which their is an equal number of protonated and unprotonated species

20

What is the Henderson-Hasselbalch Equation?

pH = pKa + log([A-]/[HA])

21

What is the isoelectric point?

the point at which an amino acid has a net neutral charge

22

What kind of interactions occur between amino acid R-groups?

1. hydrophobic
2. hydrogen bonding
3. disulfide bond formation
4. Salt bridges

23

What three things can affect salt bridges?

1.pH
2. heat
3. ion concentration

24

What is the primary structure?

the sequence of amino acids

25

What is the pKa of Asp?

3.9

26

What is the pKa of Glu?

4.1

27

What is the pKa of His?

6.0

28

What is the pKa of Cys?

8.4

29

What is the pKa of Tyr?

10.5

30

What is the pKa of Lys?

10.5

31

What is the pKa of Arg?

12.5

32

What determines the sequence of amino acids?

The codon sequence of a mRNA

33

True/False? Why? Hemoglobin is a gene ortholog of myoglobin?

False; Hemoglobin is a paralog because they are descended from the same gene. Generically they are know as orthologs.

34

What is conservative substitution?

Replacing one amino acid for one that is similar i.e. leucine for valine or aspartate for glutamate

35

What is meant by "hidden variations"?

amino acid sequences can be altered but this does not critically change the structure or function

36

In general, a non-conservative substitution can lead to what with regards to structure and function?

1. increased activity
2. decreased activity
3. altering of structural integrity

37

What is a polymorphism?

sequence variations in an allele within a population

38

What is an isoform?

A protein isoform is one of several different forms of the same protein. Isoforms often occur because of tissue specificity.

39

What is an isozyme?

Enzymes with same function but different structure.

40

Why is species-specific insulin use the most optimal choice for treating diabetes in humans?

Species variations can lead to an immune response by the immune system

41

What happens to insulin when it complexes with zinc?

When insulin complexes with zinc, it precipitates out.

42

According to lecture, what are two kinds of carbohydrate addition?

O-glycosylation and N-glycosylation

43

What amino acid(s) and functional group are involved in O-glycosylation?

Ser, thr, and tyr; -OH

44

What amino acid(s) and functional group are involved in N-glycosylation?

Asn; -NH2

45

What is palmitoylation?

The addition of palmitic acid (C16) to the -SH of cys

46

What is myristoylation?

The addition of myristic acid (C14) to the NH of N-terminal glycine

47

What is phenylation?

fatty acid addition to the SH of cys

48

Which amino acid(s) and functional group are involved in phosphorylation?

OH of ser, thr, and tyr

49

Which amino acid(s) and functional group are involved in acetylation?

NH2 of lysine, terminus

50

ADP-ribosylation involves which amino acid(s) and functional group(s)?

N of arg and gln, S of cys

51

Which amino acid(s) are involved in oxidation?

pro and lys

52

Which amino acid(s) are involved in carboxylation?

glu