Amino Acids and Protein Structure Flashcards Preview

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Flashcards in Amino Acids and Protein Structure Deck (69):
1

L-alpha-AA is a ___ acid with an amino group on carbon ___

carboxylic; 2 (the alpha carbon)

2

What is the role of the Hydrogen on an AA

prevents bulkiness and allows side chains to fit

3

Almost all AAs are ___ AAs

L-alpha

4

How many AAs are coded for by DNA?

20

5

What are the non polar AAs?

glycine, alanine, proline, valine, leucine, isoleucine

6

What are the aromatic AAs?

phenylalanine, tyrosine, tryptophan

7

What are the polar, uncharged AAs?

asparagine, glutamine, serine, threonine

8

What are the sulfur-containing AAs?

Methionine, Cysteine

9

What are the negatively charged AAs?

aspartate, glutamate

10

What are the positively charged AAs?

arginine, lysine, histidine

11

Aspartate has a pKa of 3.9. Give the ratio of COOH to COO- at a pKa of 2.9, 1.9, and 4.9

pKa 2.9: 10 times more COOH
pKa 1.9: 100 times more COOH
pKa 4.9: 10 times more COO- or 10 times less COOH

12

What is the isoelectric point?

at a certain pH, there will be an equal number of postive and negative charges

13

In regards to protein structure, what is unique about the isoelectric point

proteins are least stable at pI

14

This AA forms disulfides

cysteine, between 2 cysteine molecules

15

disulfide bridges have what affect on protein structure?

stability

16

This is found in only a few enzymes and is incorporated via a specialized tRNA which is then incorporated into a protein

Selenocysteine

17

At any given pH, a peptide will have a characteristic charge. Changes in a pH will do what?

change the charge on the peptide

18

Which AAs are involved in carbohydrate addition, specifically O-glycosylation?

serine, tyrosine, and threonine

19

Which AAs are involved in carbohydrate addition, specifically N-glycosylation?

asparagine

20

Which AAs are involved in lipid addition, specifically palmitoylation?

cysteine

21

Which AAs are involved in lipid addition, specifically prenylation?

cysteine

22

Which AAs are involved in lipid addition, specifically myristoylation?

glycine

23

Which AAs are involved in regulation, specifically phosphorylation?

Serine, Threonine, and Tyrosine

24

Which AAs are involved in regulation, specifically ADP-ribosylation?

arginine, glutamine, cysteine

25

Which AAs are involved in regulation, specifically Acetylation?

lysine

26

Which AAs are involved in modification, specifically oxidation?

proline, lysine

27

Which AAs are involved in modification, specifically carboxylation?

glutamate

28

This is the bond between the alpha-carboxyl group of one amino acid and the alpha-amino group of another amino acid

peptide bond

29

The peptide bond is ___, with the alpha-carbon, the carbonyl carbon, the carbonyl oxygen, the nitrogen, the nitrogen-hydrogen and the second alpha-carbon all in the same plane

planar

30

Adjacent R groups of two amino acyl residues are almost always in the ___ configuration

trans

31

What is primary structure of a protein

sequence of AAs

32

Residue #1 is the amino terminal or ___-terminal; The last residue is the carboxyl terminal or ___-terminal

N-terminal; C-terminal

33

Different protein isoforms or isozymes may be expressed at different developmental stages. true or false?

true, ex: HbF, HbA

34

Give an example of different protein isoforms or isozymes expressed simultaneously but restricted to different tissue

creatine kinase isoenzymes and lactate dehydrogenase isozymes

35

In regards to primary structure, give an example of species variation

insulin

36

What is secondary protein structure

recurring, localized structures found within regions of a polypeptide chain - primarily alpha helix and beta sheets

37

The alpha helix is stabilized by ___ bonds between the amide hydrogen of an amino acyl residue and the carbonyl oxygen atom of a second amino acyl residue located four amino acyl residues down the chain

hydrogen

38

Which AA can't be part of an alpha helix

proline

39

True or false? beta sheets form a planar surface

true

40

The surfaces formed by B-pleated sheets are often ___

twisted

41

What are some other secondary structures that are less repetitive and uniform than alpha helices and beta sheets?

bends, loops, and turns

42

patterns of secondary structures are frequently found in several different proteins. These repeating patterns often function similarly to each other and represent what?

motifs and domains

ex: nucleotide binding domains are found in many proteins which bind and hydrolyze ATP

43

What is tertiary protein structure?

the folding pattern of the secondary structural elements into a 3D conformation

44

What five forces are involved in tertiary protein structure?

1. hydrogen bonds
2. salt bridges
3. hydrophobic interactions
4. van der waals forces
5. disulfide bridges

45

Globular proteins soluble in aqueous environment are part of tertiary structure. The "core" of a soluble globular protein usually contains a high proportion of ____ amino acyl residues and ____ ____ amino acyl residues are usually concentrated on the surface of soluble globular proteins

hydrophobic; charged polar

46

Globular proteins in tertiary structure interact with a polar aqueous environment to form ___ ___ to stabilize structure

salt bridges

47

In regards to tertiary structure, transmembrane proteins are membrane spanning domains made up of what?

alpha helices and hydrophobic residues that are exposed to the lipid environment

48

In transmembrane proteins, extracellular and intracellular domains may be more characteristic of ___ interactions

hydrophillic

49

What is quaternary protein structure?

association of individual polypeptide chain subunits into one functional protein

50

In regards to quaternary structure, what are the four forces involved in globular proteins

1. hydrogen bonding
2. hydrophobic interactions
3. salt bridges
4. rarely disulfide bonds

51

In regards to quaternary structure, in fibrous (connective tissue) and other structural proteins, there may be extensive ___ linkages to other proteins

covalent

52

What is an example of cooperativity between subunits?

hemoglobin-O2 binding

53

The ___ structure of a protein specifies the folding of the mature protein

primary

54

What do heat shock proteins do?

prevent improper folding of proteins

55

Other heat shock proteins that require energy do what?

promote proper folding

56

The following describes a technique used in protein purification and analysis:
separations of compounds based on the relative affinity of the compounds for a given stationary phase and for the mobile phase

chromatography

57

This chromatography medium is porous beads. The protein mixture flows through a column. Smaller proteins can enter the pores of the beads, and therefore take longer to flow through the column. Larger proteins elute first.

size exclusion chromatography

58

In ion exchange chromatography, the medium is resin beads with covalently bound chemicals which bear a charged group. Explain the difference between cation exchange and anion exchange

cation exchange
1. the bound chemicals have a negative charge
2. positively charged compounds (cations) will adhere to the column

anion exchange
1. chemicals have a positive charge
2. negatively charged compounds (anions) will adhere to the column

59

Describe hydrophobic interaction chromatography

medium contains hydrophobic groups; proteins with exposed hydrophobic surfaces will adhere to column; adhering proteins are eluted by decreasing polarity of the eleuent

60

The following describes what type of chromatography?
medium contains a bound ligand; proteins which bind ligand will adhere to column; adhering proteins may be eluted by adding excess ligand

affinity

61

In this type of chromatography, eluent is pumped under high pressure - separation is faster and at a higher resolution and usually uses hydrophobic interaction.

high-pressure liquid chromatography

62

Separation based on migration of charged molecules in an applied electrical field is called what?

electrophoresis
ex: hemoglobin isoforms

63

Describe what happens in an SDS-PAGE

large number of SDS (detergent) molecules interact with each protein molecule, producing proteins of approximately equal charge-to-mass ratios, also disrupting quaternary structure and separation into monomers - then migration through the PA gel is based on sized, smaller proteins migrating faster

64

Special, proprietary buffers are used to generate a pH gradient within a PA gel. proteins will migrate to the pH which is equal to the protein's pI. Once at the pH which equals the pI, the protein will no longer migrate. What technique is this?

Iso-electric focusing

65

Give the first and second dimension of two-dimensional electrophoresis

1. IEF
2. SDS-PAGE

66

Describe a western blot

1. proteins separated by electrophoresis (usually SDS-PAGE) are transferred to synthetic membrane
2. membrane is incubated with antibody (primary antibody) to a specific protein
3. a second antibody (to the primary antibody) conjugated with a reporter molecule is added to visualize the specific protein

67

The following description is of what technique:
1. penylisothiocyanate reacts with N-terminal
2. derivative can be removed, analyzed, and AA identified
3. a new N-terminal is produced which is subjected to a 2nd round of the reaction
4. process may be repeated multiple times to determine the AA sequence of a peptide

edman sequencing

68

Mass spec separates molecules based on what?

their mass

69

When would you use mass spec?

to identify protein through determination of masses of peptides produce from tryptic digestion of protein; to detect covalent modifications of a protein