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Biol 200 > Lecture 20 - Protein structure > Flashcards

Lecture 20 - Protein structure Flashcards

1
Q

To what level is protein synthesis necessary to life

A

Necessary for protein turnover but not necessary for second to second survival

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2
Q

Peptides/oligopeptides def

A

20-30 a.a

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3
Q

Polypeptides def

A

> Peptides

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4
Q

Protein def

A

Natural polypeptides or complexes of polypeptides with WELL-DEFINED STRUCTURE

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5
Q

Unit of measurement for protein mass

A

daltons (1 Da = 1 g/mol)

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6
Q

Average weight of an amino acid

A

110 Da

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7
Q

Average length of a protein/which length it is usually higher than

A

> 1000 a.a.

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8
Q

largest known polypeptide, length, where it’s found, MW and what to say about his gene

A

Muscle protein titin, 30 000 a.a, MW = 3 MDa, but not the biggest gene

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9
Q

2 things that determine protein function

A

1) Overall shape

2) Distribution of amino acids throughout it and their distinctive chemical properties

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10
Q

2 major classes of amino acid side chains

A

1) Hydrophilic (polar charge distribution) - Can be charged or not
2) Hydrophobic (non polar charge distribution)

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11
Q

Entropy def

A

Measure of disorder

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12
Q

What is the hydrophobic effect

A

When hydrophobic molecule is in water, water molecules around it adopt a cage-like organization. When hydrophobic molecules coalesce, less water molecules are necessary to surround them and more are free so entropy is higher.

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13
Q

Oil drop model

A

Hydrophobic side chains of a protein on its inside

Hydrophilic side chains of a protein on its outside

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14
Q

Why hydrophobic side chains go on the inside in the oil drop model

A

To not force the cage structure of the water molecules around the hydrophilic side chains on the outside. (Basically, few or no cage structures necessary -> higher entropy)

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15
Q

Possible structures that a protein could adopt based only on the oil drop model and how many it really adopts

A

Infinite number but will adopt one or a small number of similar structures called conformations

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16
Q

Why protein adopts only one shape

A

Hierarchy of structural interactions define specific protein shape

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17
Q

What are called the specific local structural interactions in a peptide and what they do

A

Secondary and Tertiary structures : They define the peptide backbone in space

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18
Q

What would be a primary structure and where does it come from

A

a.a sequence. Is what is obtained from the ribosome

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19
Q

Secondary structure def

A

Local folding

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20
Q

Tertiary structure def

A

Overall conformation of the protein

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21
Q

Quatenary structure def.

A

Multimeric structure (assembly of independent peptides)

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22
Q

Supramolecular structure def

A

large-scale assembly (ex. ribosome)

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23
Q

Name 6 functions of proteins. What is function related to

A

Regulation, Structure (ex. in cell) , Movement, Catalysis, Signaling, Transport. Function related to structure

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24
Q

What is a secondary structure

A

Interactions within the peptide BACKBONE that can be stable and form regular parts in a protein

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25
Q

2 secondary structures

A

Alpha helix and Beta sheet

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26
Q

What is a tertiary structure/what defines it

A

Defined by the way alpha helices and beta sheets interact together

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27
Q

Assembly of alpha helices and beta sheets can form __________ within the tertiary structure

A

domains

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28
Q

Structure of amino acid

A

alpha carbon (central one), hydrogen, amino group, carboxyl group

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29
Q

Peptide bond formation and 2 names for the reaction (think about other product of that reaction)

A

Link between amino group of on a.a and carboxyl group from another a.a. Dehydration/Condensation (you obtain a water molecule)

30
Q

why do we say that polarity is conserved within a peptide

A

because always free amino group and free carboxyl group at its ends

31
Q

N terminus corresponds to the ___ end of the mRNA and C terminus of a peptide corresponds to the _____ end of the mRNA

A

N - 5’ end

C - 3’ end

32
Q

2 major peptide chain backbone conformation and their proportion in a polypeptide

A

alpha-helix and beta-sheet. 60% of length of average polypeptide consists of those

33
Q

What is the absence of a secondary structure (in some part of a protein) named

A

random coil

34
Q

What bond is responsable for secondary structures within a polypeptide (same for the 2)

A

Bond between oxygen on carbonyl of peptide bond and hydrogen of an amino group

35
Q

What is peptide bond exactly

A

N-terminus —- alpha carbon (C alpha) - carbonyl group - N-H group - alpha carbon (C alpha) —— C-terminus Peptide bond between C of carbonyl and N of N-H

36
Q

alpha helix which groups on the peptide do H bonding

A

All polar groups of peptide backbone (all N-H and C=O)

37
Q

alpha helix amount of residues by turn and reason

A

3.6 residues/turn because H bonds are tilted a little

38
Q

alpha helix how it is formed and what is an important property of that

A

O on carbonyl does H-bond with H on N-H that is 4 residues (a.a) further. PERIODICITY

39
Q

Surface of alpha helix, what its properties depend on

A

depend on side chains properties

40
Q

Gross structure and how it is in reality

A

Straight rod but in fact is a little tilted because of H bonds

41
Q

Beta sheet how it is formed

A

H bond formed but between a.a that are further away.

42
Q

2 conditions for beta sheet to form

A

Folding will allow it to form and nothing in the way

43
Q

Where side chains end up on beta sheet

A

Pointing to the top and to the bottom

44
Q

Beta sheets can form between independent ________

A

peptides

45
Q

Strands within a beta sheet can be _________ or ________

A

parallel or anti-parallel

46
Q

Tertiary structure : overall conformation of the polypeptide which refers to the _____________ of its multiple _______ structures

A

spacial organization of its multiple secondary structures

47
Q

5 ways of representing a tertiary structure

A

1) alphaC backbone trace
2) Ball-and-stick model
3) Ribbon diagram
4) Water-accessible surface
5) Hybrid model

48
Q

C alpha backbone trace characteristics

A

shows secondary structures based on colour

49
Q

Ball-and-stick model characteristics

A

shows every atom so rarely used because too busy

50
Q

Ribbon diagram characteristics

A

Most popular. Secondary structures are represented as ribbons but not random coils so allows to identify random coils and secondary structures

51
Q

Water-accessible surface characteristics

A

shows surface in 2 colours for positive and negative charge. Important because it’s what is seen by the milieu

52
Q

Hybrid model characteristics

A

Enveloppe (surface) + backbone elements)

53
Q

What is Ras

A

a small GTPase

54
Q

3 motifs of protein secondary structure

A

1) Coiled-coil motif
2) EF hand/helix-loop-helix motif
3) Zinc-finger motif

55
Q

Coiled-coil motif description

A

2 alpha helices of same or different protein that coil together because have a repeat of 7 a.a in which 1st and 7th a.a are hydrophobic so these go on the inside

56
Q

other name for Coiled-coil motif + its exact shape

A

(leucine) zipper. Looks like a straight rod but is a little tilted

57
Q

What is the function of coiled-coil motif

A

Involved in protein-protein interactions

58
Q

EF hand/helix-loop-helix motif description

A

loop between 2 helices contains amino acid that binds calcium

59
Q

Function of EF hand/helix-loop-helix motif

A

Ca 2+ binding motif

60
Q

Zinc-finger motif description

A

Part is an alpha helix and other part is a sheet of antiparallel beta strands. These parts bind a zinc 2+ ion

61
Q

Zinc-finger motif function/ex of molecule it can help bind to/protein where we saw it

A

Common in transcription factors : binds to DNA/RNA

62
Q

4 major structural classes of proteins

A

Fibrous, Globular, Transmembrane and intrinsically disorder proteins

63
Q

Intrinsically disorder proteins def.

A

Random coils under physiological conditions and therefore exposed to proteolysis by proteases and phosphorylation by kinases

64
Q

Typical function of intrinsically disorder proteins (3) (very generally)

A

1) signaling molecules
2) regulators of other molecules
3) scaffolds for multiple proteins, small molecules and ions.

65
Q

2 main things intrinsically disorder proteins do

A

1) Interact with partner proteins

2) Fold into well-defined conformation after binding to partner proteins

66
Q

what could make a protein intrinsically disorder (2)

A

High net charge (rich in polar amino acids such as proline) and poor in hydrophobic residues

67
Q

What drives intrinsically disorder protein’s function

A

their flexibility

68
Q

4 exemples of function/advantages of intrinsically disorder regions within a protein

A

1) Flexibility
2) Site for post-translational protein modification
3) Site for protease digestion (autoinhibition)
4) Intracellular sorting of proteins

69
Q

2 exemples of disorder proteins seen with Zetka

A

CTD tail of Pol II (phosphorylated)

N-termini of histones (PTMs such as acetylation, methylation)

70
Q

2 exemples of tests for identifying intrinsically disorder proteins

A

1) Protease digestion sensitivity (more disordered = more vulnerable)
2) Spectroscopy

Biol 200 (30 decks)

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