Chapter 5- Primary peptide structure

Question 1

What are steric interactions?

Answer 1

How close two atoms can get together without repulsion . 2 atoms can’t occupy the same region of space simultaneously.

Question 2

What happens when 2 atoms are very close?

Answer 2

1. electron clouds overlap
2. pauli exclusion principle applies- quantum mechanic principal that states that no two identical atoms/fermions can occupy the same quantum state simultaneously

Question 3

When is repulsion highest?

Answer 3

When molecules are close together. Short-range repulsion has an exponential dependence on interatomic distance.

Question 4

Steric interaction result in what types of folding in molecules?

Answer 4

Alpha helix, beta sheets

Question 5

steric interaction tell us about conformational behaviour of amino acids- which bond spin and which don’t?

Answer 5

single bonds spin/ rotate, where as double/ triple bonds don’t.

Question 6

What happens when a peptide bond is formed?

does it require energy ?

Answer 6

water comes on then water comes off per 2 two amino acids.
yes- because although hydrolysis is thermodynamically favoured the rate constant is small meaning that the reaction rate is slow, that is why ATP/ enzymes is needed!

Question 7

The peptide bond is metastable= HYDROLYSIS is the favoured reaction at room temperature in aqueous solution. Since the uncatalyzed reaction is so slow catalysis need to happen via what?

Specific catalysis is provided by what?

Answer 7

Acids and bases.

proteolytic enzymes and proteases

Question 8

What formation is the peptide bond usually found in?

What bond character does it have?

Answer 8

trans

It has 40% double bond character, (shorter than a single but longer than a double bond). the 6 atoms are always planar. N is partially positive and O partially neg

Question 9

What are the numbers like in peptide bonds (angle and bond length)?

Answer 9

The are all different

Question 10

What is the geometry of peptide bonds like?

Answer 10

The geometry is best represented as a hybrid of 2 structures. One structure is =O and has free rotation, the other is C=N restricted rotation. (slide 12)

Question 11

What is the geometry of peptide bonds like?

Answer 11

The geometry is best represented as a hybrid of 2 structures. One structure is =O and has free rotation, the other is C=N restricted rotation. (slide 12)

Question 12

What gives the peptide bond partial double bond character ?

Answer 12

delocalisation of pi elections.

Question 13

Why is the peptide group rigid and planar?

Answer 13

resonance interactions which give the partial double bond character.

Question 14

Which peptide configuration is favoured cis/ trans?

Answer 14

trans- more stable, especially with bulky R groups. cis= RARE

Question 15

In a peptide bond where is the pi-electron delocalisation

Answer 15

over the O-C-N fragment.

Question 16

what does the resonance stabilisation result in?

Answer 16

planar structure

Question 17

Why are adjacent alpha carbons in trans configuration?

Answer 17

to prevent steric hinderance

Question 18

Is hydrolysis in peptide formation thermodynamically favoured?

Answer 18

yes

Question 19

Polypeptides are unstable so to make them want mechanism is required?

Answer 19

Coupling ATP hydrolysis

Question 20

Are free amino acids used to make polypeptides/proteins in cells, why?

Answer 20

NOOOOO, because the delta G (free energy) is positive not spontaneous

Question 21

What are aminoacyl-RNAs? and what are they used for?

Answer 21

they are the high energy intermediates used to form polypeptides

Question 22

ATP+ RNA+ Amino acid>

Answer 22

Aminoacyl RNA+ ADP + Pi

Question 23

What does the ribosome do?

Answer 23

promotes peptide bond formation

Question 24

What is the amino end of a polypeptide called?

Answer 24

N terminus

Question 25

what is the carboxyl end of a polypeptide called

Answer 25

C-teminus

Question 26

What is the polypeptide structure

Answer 26

N with 2 H attached to a C with an H and R attached to. C=O and (OH) is attached to N with one H attached to C with H and R etc.

Question 27

What is the difference between an amino acid residue and an amino acid?

Answer 27

A residue is inside a polypeptide chain and is missing an H on the N and the C terminus is missing OH and its bound to something because a water is removed

Question 28

What is peptide bond?

Answer 28

The special name given to the bond between the a-carboxyl group of one amino acid and the a-amino acid of another. an amide bond formed between 2 amid acids

Question 29

What Is an alpha carbon

Answer 29

the central carbon bound to an amino group and carboxyl group

Question 30

define oligopeptides?

Answer 30

peptide which a few amino acid residues 12-20

Question 31

define polypeptides?

Answer 31

long chain peptides with many residues 20+

Question 32

How is the linear sequence of amino acid written in a peptide?

Answer 32

N>C, in 3 or 1 letter code eg. Glu-Gly-Ala

Question 33

define peptide

Answer 33

A short polymer of amino acids joined by peptide bonds, classified by # of amino acids in chain

Question 34

define dipeptide, tripeptide, polypeptide

Answer 34

a molecules containing 2 amino acids joined together by a peptide bond, 3, many

Question 35

define protein

Answer 35

A biological macromolecule of molecular weight 5000g/ ml , consists of many polypeptide chains

Question 36

Peptide are polyampholites, what does this mean?

Answer 36

they contain different charges

Question 37

What makes a polypeptide ionizable?

Answer 37

the amino groups, the carboxyl groups and the r groups

Question 38

Solubility, structure and function are determined by what?

Answer 38

pH

Question 39

What is the isoelectric point?

Answer 39

pH which the net charge is 0

Question 40

What is the primary structure of a protein?

Answer 40

The order of amino acid resides- sequence

Question 41

how to find the combinantion of molecules amino acids can make...

Answer 41

20^(#of aa)

Question 42

What are enkephalins?

Answer 42

pentapeptide that binds to opioid receptors.

Question 43

What is the sequence for a leucine enkephalin?

Answer 43

Try-Gly-Gly-Phe-Leu | Y-G-G-F-L

Question 44

What is the sequence for a methionine enkephalin?

Answer 44

Try-Gly-Gly-Phe-Met | Y-G-G-F-M

Question 45

What encodes the amino acid sequence?

Answer 45

the nucleotide sequence of DNA

Question 46

Explain how the MALDI Mass Spectometer works?

Answer 46

ions are generated by a laser firing at the target plate, the time of firing of the laser and the arrival time of ion at detector are known , the relative masses can be calculated. Only single charged ions are generated.

Question 47

Explain solid-phase peptide synthesis.

Answer 47

the c terminus is covalently bound to a solid support/ resin then 3 chemical reaction are repeated for each added amino acid. 1. deprotection 2. activation 3. coupling

Question 48

What happens during coupling?

Answer 48

the active ester from an amide bon with the deprotected amino group at the end of the peptide chain then a new cycle begins. When synthesis is complete chemical cleavage removes side chain protecting groups from the peptide and synthetic peptide from the resin support.

Question 49

What is reaction to from a peptide bond?

Answer 49

condensation