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Biochemistry > Exam 1 Lectures 4-5 > Flashcards

Exam 1 Lectures 4-5 Flashcards

1
Q

What is the ‘backbone’ structure of an aa?

A

Always:

Amine (-NH2), a carboxyl (-COOH), and (R) side chain attached to an alpha carbon

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2
Q

What is the pKa for carboxyl to loose H+?

A

Around 2

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3
Q

What is the pKa for amine to lose H+?

A

Around 9

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4
Q

At physiological pH, the aa is a __ and have a net __ charge

A

A zwitterion (pI) and have net neutral charge at physiological pH.

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5
Q

Chirality = chiral centers have __

A

2 enantiomers are possible

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6
Q

What is an enantiomer

A

Mirror images.

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7
Q

What configuration do we want?

A

L configuration (S absolute configuration)

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8
Q

What are the 4 aa categories Dr Ford wants us to learn?

A
  1. Polarity
  2. Size/shape
  3. Synthesis
  4. Proteinogenic and nonproeinogenic
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9
Q

What aa s sometimes polar bc of ring?

A

Tyrosine

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10
Q

What is the aa that can perform redox rxns and what is this important for?

A

Cysteine and for disulfide linkages

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11
Q

The suffix -ate eludes to

A

Deprotonated

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12
Q

Side chains pKa tells us when ___

A

Acidic

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13
Q

Cannot make ourselves or we make it but don’t make enough is an __ aa

A

Essential aa

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14
Q

We can make aa means its a __ aa

A

Non-essential

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15
Q

Tyrosine and its synthesis role as being non-essential:

A

Tyrosine: we can make it but making it from an essential aa phenylalanine

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16
Q

What does proteinogenic aa mean

A

Making proteins from genetic code

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17
Q

What does non-proteinogenic mean

A

Not directly decoded from genome

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18
Q

What is an example of non-proteinogenic aas

A

Aas made via translational modifications

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19
Q

How can we ‘expand’ the universal genetic code

A

By reassigning a stop codon: UAA, UAG, UGA

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20
Q

What is the 21 aa?

A

Seleocysteine (Sec, U)

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21
Q

What is Sec’s pka?

A

5.2

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22
Q

Sec is protonated or deprotonated at physio pH

A

Deprotonated

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23
Q

Sec is synthesized from which aa?

A

Serine

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24
Q

Sec can be process to __ in plants, algae, and yeast

A

Selenomethionine

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25
Q

Sec can be processed to __ in animals

A

Alanine

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26
Q

What stop codon Sec uses?

A

UGA (opal)

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27
Q

In mito, Sec uses UGA which is a __ codon

A

W

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28
Q

In some ciliates, Sec uses UGA which is a __ codon

A

C

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29
Q

Sec was recognized as an opal __ in 1981

A

Repressor

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30
Q

Sec is found in:

A

All 3 domains of life: bacteria, euks, and archea

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31
Q

Sec uses its own __ and __ sequence

A

Uses own tRNA and SECIS

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32
Q

Proteins that incorporate Sec are called:

A

Selenoproteins

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33
Q

Selenoproteins are important and good for health via:

A

Reduce oxidative stresses, for growth and coordination in cerebellum neurons, moderate inflammatory responses (ex IBD)

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34
Q

What happens to a selenoprotein when Sec cis not available?

A

Proteins end up truncated (stop codon) ie non functional selenoproteins

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35
Q

Selenium deficiency results in:

A

Myopathies: keshan disease, statin intolereance, and immune-incompetence

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36
Q

What is Keshan disease and how can it be treated

A

A cardiomyopathy and with SE suppluments

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37
Q

What is stain intolerance and how treated

A

Rhabodmyolysis (muscle death) and treated by discontinuing statin

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38
Q

Statins inhibit __ which causes statin intolerance

A

Sec-tRNA

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39
Q

Statins are drugs that do what

A

Block the formation of cholesterol in the liver

40
Q

Too much selenium results in:

A

Hair and nail brittleness, “garlic breath”
Gastrointestinal/neurological lesions
Myopathies, renal failure, and death

41
Q

What is the 22 aa

A

Pyrrolysine (Pyl, O)

42
Q

Pyl uses what stop codon? And that codon can be an or codon in some organisms

A

Uses UAG (amber) can also be an L or Q codon

43
Q

Pyl are found only in some proks and all are __

A

Methanogens

44
Q

T/F: Pyl uses own tRNA

A

True

45
Q

T/F: Several members of the human intestinal microbiome make/use Pyl including archaea and ebuacteria

A

True

46
Q

How can nonproteinogenic aas come to exist?

A

Post-translational additions to proteinogenic aas (ie addition of a phosphate group, D-enantiomers, metabolism intermediates, and pre-biotic or extraterrestrial origin

47
Q

Antibiotic use this to make nonproteinogenic aas:

A

Non-ribosomal protein synthesis (NRPS)

48
Q

Statins are made by __ synthesis (nonproteinogenic)

A

Polyketide synthesis (PKS)

49
Q

1’ structure =

A

Chain of aas

50
Q

2’ structure =

A

Local folding of polypeptide chain, connected by H bonds

51
Q

3’ structure=

A

Folding of the 2’ structure, connected by disulfide linkages

52
Q

4’ structure =

A

Interaction of multiple peptides

53
Q

Single bonds means rotation is possible, but not always preferred. This results in:

A

A planar chain with side chains alternating up and down (important for 2’ structure and keeps big side chains away from each other)

54
Q

What are the 2 interactions that govern protein folding stability

A

Non-covalent interactions: easy to form easy to break
Hydrophobic interactions: escaping from H20 increases chances of hydrolyzing (breaking apart) is high thus aggregation adds stability

55
Q

What are examples of non-covalent interactions

A

Vand der waals
Short range repulsion
Hydrogen bonds
Electrostatic forces (ion pairs and salt bridges)

56
Q

How does a hydrophobic molecule in the presence and absence of H20

A

Non-polar groups act non favorably with H20 and favorably when they excluding themselves from H20

57
Q

What is a major factor in protein folding and stability?

A

Hydrophobic interactions

58
Q

Via Van der Waals, molecules interact and nullify by

A

Their charge and how far they are away from one another

59
Q

Short range repulsions can be explained by molecules that are too far have __ attraction, too close __, and therefore require __distance

A

Too far have no attraction
Too close molecules diffuse together and repulse. Not viable and high energy
Require optimal distance that is LOW ENERGY and just the right amount of distance away from one another

60
Q

what are possible H bonds

A

N-H
O-H
F-H

Ie halogens in H bonds

61
Q

T/F: H bonds are much stronger that covalent bonds

A

False. WEAKER

62
Q

T/F: H bonds are longer than covalent bonds

A

True

63
Q

What is the energy range for H bonds

A

1-5 kcal/mol

64
Q

T/F: H bonds are flexible and easily formed

A

True

65
Q

What is the pro of a electrostatic forces

A

Electrostatic (+ and -) easy to from and easy to break down

66
Q

Effect of high levels of salt

A

Break up proteins, technique used for isolating proteins

67
Q

What is the hydrophobic effect

A

Non-polar molecules escaping from H20 and fuse together

68
Q

What are the determinant of folding

A

Secondary structure equals efficient packing
Hierarchical folding = certain groups fold
Hydrophobic effect, in primary sequence, aggregate in the central of the structure (core of protein) escaping from aqueous environment
Context dependent =folding differently and functioning differently

69
Q

Characteristics of 2’ structure

A

Flexible
Rich in H bonds (what gives the flexible structure)
Contains:
Alpha-helical structure is space saving
Beta-sheet less flexible but provides stability (a parallel structure)

70
Q

How are alpha-helices stabilized

A

By intrachain H bonds (disulfide bonds in same sequence) btwn N-H and C=O groups

71
Q

Intrachain H bond in alpha-helix is a H bond that forms __ ahead in sequence

A

4 aas

72
Q

In alpha-helix, each aa residue is related to the next one by:

A

A rise of 1.5 A along the helix axis
A 100 degree rotation
3.6 aa residue per turn of helix

73
Q

T/F: alpha-helix can be either left or right handed screw sense? Which one is more energetically favorable?

A

True. Almost always right bc energetically more favorable

74
Q

How are beta-sheets stabilized?

A

H bonding btwn polypeptide strands

75
Q

beta-sheet formed?

A

Composed of 2 or more polypeptide chains called beta-strands via H bonds

76
Q

Beta-sheets are fully extended?

A

Yes

77
Q

Distance btwn adjacent aas along a beta-strand

A

3.5 A

78
Q

B-sheet can run:

A

In parallel or anti-parallel direction

79
Q

Reversal directions provide __ for polypeptide chain

A

Compact and globular shapes

80
Q

What are the types of turns and what do they all provide?

A

Reverse turn, beta-turn, and hairpin turn. All provide flexibility

81
Q

In many reverse turns, _ and _ groups form H bonds for __ which is useful because proteins are social structures

A

C=O and N-H groups; for stability

82
Q

Type of loop?

A

Omega loop

83
Q

Loops do not have regular periodic structure but instead:

A

Are well defined and rigid, positioned on the surface of the protein, and participates in protein-protein interactions and interactions with other molecules

84
Q

Super helix, alpha-helical coiled coil folding provides:

A

Proteins long fibers that are useful in structural role (alpha-keratin, collagen, cell cytoskeleton, muscle proteins) and involved in biological functions (regulate gene expression, oncoproteins)

85
Q

Super helix, alpha-helical coiled coil 2 helices like in a-keratin associate via:

A

Weak interactions like van der waals and ionic interactions

86
Q

Super helix, alpha-helical coiled coil characterized by a __ region of 300 aas that contain __ repeats which provide?

A

Central region that contain heptad repeats. Provides 2 alpha-helices to interact with one another and observed in intermediate filament proteins

87
Q

adding B-mercaptoethanol allows what to happen?

A

breaks incorrect sulfate bridges to allow to form properly

88
Q

Why are repeating motifs important?

A

proteins have regions that have an affinity for X but will not bind without motif

89
Q

what is the repeating motif in cadmodulin?

A

ca2+ binding site

90
Q

why is context dependent important?

A

a sequence can adopt an alternative conformation in different proteins. ex VDLLKN has alpha helix in one protein and a beta strand in another

91
Q

what is the molten globule state?

A

intermediate transient state btwn native and fully unfolded globular protein

92
Q

why is the radius of the molten globule larger than the native state?

A

so the hydrophobic region can be exposed and aqueous environment interacts with center to form new H bonds’; provides flexibility for peptide bonds to properly fold

93
Q

why does the unfolded state have high energy?

A

number of possible conformations are numerous

94
Q

why does the folded state have low entrophy?

A

bc only 1 conformation

95
Q

the native structure is the _

A

lowest free energy structure

96
Q

the denatured structure is _

A

a high conformational entropy unstructured state

97
Q

percentage of native contacts increase in protein folding because

A

they are stabilizing

Biochemistry (32 decks)

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