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DDS Q1 Quizzes and Exams > Biochem-Exam 1 > Flashcards

Biochem-Exam 1 Flashcards

1
Q

Name the non-polar amino acids:

A

Glycine Alanine Tryptophan Valine Leucine Cysteine Tyrosine Phenylalanine Isoleucine Methionine Proline —-Grab At That Very Large Crusty The PIMP

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2
Q

Name the uncharged polar amino acids:

A

Threonine Asparagine Glutamine Serine —-Remember “Uncharged T.A.G.S.”

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3
Q

Name the charged polar amino acids:

A

Glutamate Aspartate Lysine Arginine Histidine —-Remember “Charged G.A.L.A.H.”

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4
Q

What is the acronym for the non-polar amino acids

A

Grab At That Very Large Crusty The PIMP

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5
Q

Quick way to tell the buffering zone of most amino acids?

A

+/- 1 from neutral pH (aka, zwitterion pH)

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6
Q

What is the MOST charged form of an amino acid?

A

Zwitterion

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7
Q

At what pH is an amino acid likely in its zwitterion form?

A

pH=6 to pH=8

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8
Q

What is a tell-tale sign of a polar-covalent bond?

A

Anything bonded to Oxygen or Nitrogen

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9
Q

What is the main reason that proteins assume a 3-d shape?

A

Hydrophobic effect

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10
Q

What are the four main components of an amino acid?

A

Carboxyl group, Amino group, H, and R group

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11
Q

Which bond is called the “Phi” bond in an amino acid?

A

The N-C(alpha) bond

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12
Q

What do INTRA-polymer bonds form in a polypeptide?

A

Alpha helices

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13
Q

What do INTER-polymer bonds form in a polypeptide?

A

Beta-pleated sheets

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14
Q

What three things can denture a protein?

A

pH Thermal energy Detergent

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15
Q

In what direction is DNA read?

A

3’ to 5’

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16
Q

In what direction is DNA synthesized?

A

5’ to 3’

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17
Q

In what direction does the DNA template strand run

A

3’ to 5’

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18
Q

What DNA base pairs are Purines?

A

Adanine and Guanine “Pure As Gold”

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19
Q

What DNA base pairs are Pyrimidines?

A

Cytosine and Thymine “Cut The Pie”

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20
Q

What two types of Tertiary structures are there?

A
  1. Fibrous 2. Globular
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21
Q

What is the difference between a nucleoside and a nucleotide?

A

There is a phosphate group on a nucleotide

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22
Q

What makes rRNA?

A

RNA Pol 1

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23
Q

What makes mRNA?

A

RNA Pol 2

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24
Q

What makes tRNA?

A

RNA Pol 3

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25
Q

What is the acronym used to remember which RNA is made by which RNA polymerase?

A

“Run Mr. T” o rRNA via RNA Pol 1 o mRNA via RNA Pol 2 o tRNA via RNA Pol 3

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26
Q

How many H-bonds aqueous Cl- have around it?

A

6

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27
Q

What is the relationship that can be used to express pH, pKa, base, and acid

A

If pH > pKa, then b > a If pH

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28
Q

What are the pKa’s of the charged polar amino acid Glutamate and Aspartate?

A

pKa=4-5

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29
Q

What are the pKa’s of the charged polar amino acid Histidine?

A

pKa=6-7

30
Q

What are the pKa’s of the charged polar amino acid Lysine?

A

pKa=9-10

31
Q

What are the pKa’s of the charged polar amino acid Arginine?

A

pKa=12

32
Q

Which non-polar amino acids are amphiphilic?

A

Tyrosine and Tryptophan

33
Q

What is the pKa of the carboxylic acid part of glycine?

A

2.34

34
Q

What is the pKa of the ammonium part of glycine?

A

9.6

35
Q

What is the isoelectric point of glycine?

A

5.97

36
Q

What is the REACTIVE part of the Glutamate and Aspartate side chains?

A

—COO-

37
Q

What is the reactive part of Glycine?

A

H

38
Q

What is the REACTIVE part of Serine?

A

—OH

39
Q

What is the REACTIVE part of Arginine and Lysine?

A

It can have positively charged ammonium groups

40
Q

What is the structure of Histidine?

A
41
Q

What is the structure of Proline?

A
42
Q
A
43
Q

Which bond is called the “Psi” bond in an amino acid?

A

The C(alpha)-C=O bond. I.e, the one further from N.

44
Q

What is a Ramachandran diagram and how is it read?

A

It shows

45
Q

What is the general orientation of the amnio acid backbone and associated side chains of an alpha helix?

A

The backbone spiral in the the clockwise direction. The side chains come out of the spiral 3-4 residues apart.

46
Q

How is an alpha helix formed (what bonds to what and where)?

A

C=O is H-bonded to an amide 4 residues down the chain.

47
Q

What percentage of actual proteins have alpha helices?

A

0-90%

48
Q

How are beta-pleated sheets formed?

A

Formed when polypeptides line up in a parallel or anti-parallel arrangment, and there is H-bonding between the donor of one strand and the acceptor of another.

49
Q

How are the R-groups arranged in a beta-pleated sheet along a given strand?

A

Each is oriented opposite to the adjacent R-group (above and below the sheet)

50
Q

How are beta-turns (aka, hairpin loops, hairpin turns/bends) formed?

A

When R-groups that are 3 residues from each other H-bond. For example, when #1 NH h-bonds to #4 C=O

51
Q

What are Loops in a polypeptide chain?

A

When segments longer than beta turns ( > 4 residues apart) reverse the direction of the chain

52
Q

Where are loops frequenty found in a protein?

A
53
Q

What is one protein mentioned in lecture that shows examples of alpha helices, beta sheets (parallel and antiparallel), beta turns, and loops?

A

Thioredoxin

54
Q

Which side chain destabilizes alpha helices and beta sheets?

A

Proline

55
Q

Why does Proline destabilize alpha helices and beta sheets?

A

The proline side chain is basically jammed into the space that should be occupied by the backbone of the alpha helix

56
Q

What is the usual structure and function of fibrous proteins (tertiary structure)? Give an example of a fibrous protein

A

Long, thin chains. Interchain H-bonds cause side chains to point away from fiber axis (no INTRAchain sidechain interactions). Mechanical support

Collagen (triple helix fibrous protein)

57
Q

What are the two main regions of globular proteins and how do they form?

A

Surface–Forms when there is H-bonding with surrounding environment

Interior (core): forms when there is little to no interaction with surrounding environment (ex. no h-bonding with water)

58
Q

What are proteopathies?

A

A classification of the many disorders resulting from misfolded proteins

59
Q

What is the general term for what binds to a proteins active site?

A

Ligand

60
Q

What complimentary interactions (non-covalent interactions) cause tertiary structure to form?

A

Complementary shape, size, and polarity

61
Q

Where are polar UN-charged side chains found in a globular protein (surface or interior)?

A

BOTH

(ha ha trick question)

62
Q

Which amino acid can form di-sulfide bonds (covalent)?

A

Cysteine

63
Q

What is the beta-alpha-beta motif and how does it form?

A

Its a supersecondary structure formed by:

2 parallel beta strands

4 or more can form an alpha-beta barrel

64
Q

What types of supersecondary structures are considered DNA binding motif?

A

helix-turn-helix

zinc finger

65
Q

What causes quaternary structure to form?

A

Complimentarity of shape, size, and polarity

66
Q

What are structural domains?

A

Independently folded sections within
one polypeptide chain of larger proteins

67
Q
A
68
Q

What is most generally true about the location of a reverse (beta) turn in a globular protein?

A

It is partially exposed to the surface, and partial interior exposure. Remember, beta sheets and alpha helices have amphipathic traits.

69
Q

How many H-bonds can the backbone of each amino acid form with an opposing strand in a beta-pleated sheet conformation (same for parallel and anti-parallel)?

A

2 h-bonds per amino acid backbone residue

70
Q

What CANNOT form if a protein has mostly, if not all, polar side chains?

A

Tertiary structure

71
Q
A

DDS Q1 Quizzes and Exams (3 decks)

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