Lecture 20 - Protein structure

Question 1

To what level is protein synthesis necessary to life

Answer 1

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

Question 2

Peptides/oligopeptides def

Answer 2

20-30 a.a

Question 3

Polypeptides def

Answer 3

> Peptides

Question 4

Protein def

Answer 4

Natural polypeptides or complexes of polypeptides with WELL-DEFINED STRUCTURE

Question 5

Unit of measurement for protein mass

Answer 5

daltons (1 Da = 1 g/mol)

Question 6

Average weight of an amino acid

Answer 6

110 Da

Question 7

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

Answer 7

> 1000 a.a.

Question 8

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

Answer 8

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

Question 9

2 things that determine protein function

Answer 9

1) Overall shape

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

Question 10

2 major classes of amino acid side chains

Answer 10

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

Question 11

Entropy def

Answer 11

Measure of disorder

Question 12

What is the hydrophobic effect

Answer 12

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.

Question 13

Oil drop model

Answer 13

Hydrophobic side chains of a protein on its inside

Hydrophilic side chains of a protein on its outside

Question 14

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

Answer 14

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)

Question 15

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

Answer 15

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

Question 16

Why protein adopts only one shape

Answer 16

Hierarchy of structural interactions define specific protein shape

Question 17

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

Answer 17

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

Question 18

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

Answer 18

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

Question 19

Secondary structure def

Answer 19

Local folding

Question 20

Tertiary structure def

Answer 20

Overall conformation of the protein

Question 21

Quatenary structure def.

Answer 21

Multimeric structure (assembly of independent peptides)

Question 22

Supramolecular structure def

Answer 22

large-scale assembly (ex. ribosome)

Question 23

Name 6 functions of proteins. What is function related to

Answer 23

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

Question 24

What is a secondary structure

Answer 24

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

Question 25

2 secondary structures

Answer 25

Alpha helix and Beta sheet

Question 26

What is a tertiary structure/what defines it

Answer 26

Defined by the way alpha helices and beta sheets interact together

Question 27

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

Answer 27

domains

Question 28

Structure of amino acid

Answer 28

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

Question 29

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

Answer 29

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

Question 30

why do we say that polarity is conserved within a peptide

Answer 30

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

Question 31

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

Answer 31

N - 5' end | C - 3' end

Question 32

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

Answer 32

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

Question 33

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

Answer 33

random coil

Question 34

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

Answer 34

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

Question 35

What is peptide bond exactly

Answer 35

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

Question 36

alpha helix which groups on the peptide do H bonding

Answer 36

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

Question 37

alpha helix amount of residues by turn and reason

Answer 37

3.6 residues/turn because H bonds are tilted a little

Question 38

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

Answer 38

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

Question 39

Surface of alpha helix, what its properties depend on

Answer 39

depend on side chains properties

Question 40

Gross structure and how it is in reality

Answer 40

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

Question 41

Beta sheet how it is formed

Answer 41

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

Question 42

2 conditions for beta sheet to form

Answer 42

Folding will allow it to form and nothing in the way

Question 43

Where side chains end up on beta sheet

Answer 43

Pointing to the top and to the bottom

Question 44

Beta sheets can form between independent ________

Answer 44

peptides

Question 45

Strands within a beta sheet can be _________ or ________

Answer 45

parallel or anti-parallel

Question 46

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

Answer 46

spacial organization of its multiple secondary structures

Question 47

5 ways of representing a tertiary structure

Answer 47

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

Question 48

C alpha backbone trace characteristics

Answer 48

shows secondary structures based on colour

Question 49

Ball-and-stick model characteristics

Answer 49

shows every atom so rarely used because too busy

Question 50

Ribbon diagram characteristics

Answer 50

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

Question 51

Water-accessible surface characteristics

Answer 51

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

Question 52

Hybrid model characteristics

Answer 52

Enveloppe (surface) + backbone elements)

Question 53

What is Ras

Answer 53

a small GTPase

Question 54

3 motifs of protein secondary structure

Answer 54

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

Question 55

Coiled-coil motif description

Answer 55

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

Question 56

other name for Coiled-coil motif + its exact shape

Answer 56

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

Question 57

What is the function of coiled-coil motif

Answer 57

Involved in protein-protein interactions

Question 58

EF hand/helix-loop-helix motif description

Answer 58

loop between 2 helices contains amino acid that binds calcium

Question 59

Function of EF hand/helix-loop-helix motif

Answer 59

Ca 2+ binding motif

Question 60

Zinc-finger motif description

Answer 60

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

Question 61

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

Answer 61

Common in transcription factors : binds to DNA/RNA

Question 62

4 major structural classes of proteins

Answer 62

Fibrous, Globular, Transmembrane and intrinsically disorder proteins

Question 63

Intrinsically disorder proteins def.

Answer 63

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

Question 64

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

Answer 64

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

Question 65

2 main things intrinsically disorder proteins do

Answer 65

1) Interact with partner proteins | 2) Fold into well-defined conformation after binding to partner proteins

Question 66

what could make a protein intrinsically disorder (2)

Answer 66

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

Question 67

What drives intrinsically disorder protein's function

Answer 67

their flexibility

Question 68

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

Answer 68

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

Question 69

2 exemples of disorder proteins seen with Zetka

Answer 69

CTD tail of Pol II (phosphorylated) | N-termini of histones (PTMs such as acetylation, methylation)

Question 70

2 exemples of tests for identifying intrinsically disorder proteins

Answer 70

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