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Biochemistry > Chapter 5- Primary peptide structure > Flashcards

Chapter 5- Primary peptide structure Flashcards

1
Q

What are steric interactions?

A

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

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2
Q

What happens when 2 atoms are very close?

A
  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
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3
Q

When is repulsion highest?

A

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

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4
Q

Steric interaction result in what types of folding in molecules?

A

Alpha helix, beta sheets

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5
Q

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

A

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

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6
Q

What happens when a peptide bond is formed?

does it require energy ?

A

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!

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7
Q

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?

A

Acids and bases.

proteolytic enzymes and proteases

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8
Q

What formation is the peptide bond usually found in?

What bond character does it have?

A

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

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9
Q

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

A

The are all different

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10
Q

What is the geometry of peptide bonds like?

A

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)

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11
Q

What is the geometry of peptide bonds like?

A

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)

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12
Q

What gives the peptide bond partial double bond character ?

A

delocalisation of pi elections.

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13
Q

Why is the peptide group rigid and planar?

A

resonance interactions which give the partial double bond character.

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14
Q

Which peptide configuration is favoured cis/ trans?

A

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

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15
Q

In a peptide bond where is the pi-electron delocalisation

A

over the O-C-N fragment.

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16
Q

what does the resonance stabilisation result in?

A

planar structure

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17
Q

Why are adjacent alpha carbons in trans configuration?

A

to prevent steric hinderance

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18
Q

Is hydrolysis in peptide formation thermodynamically favoured?

A

yes

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19
Q

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

A

Coupling ATP hydrolysis

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20
Q

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

A

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

21
Q

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

A

they are the high energy intermediates used to form polypeptides

22
Q

ATP+ RNA+ Amino acid>

A

Aminoacyl RNA+ ADP + Pi

23
Q

What does the ribosome do?

A

promotes peptide bond formation

24
Q

What is the amino end of a polypeptide called?

A

N terminus

25
Q

what is the carboxyl end of a polypeptide called

A

C-teminus

26
Q

What is the polypeptide structure

A

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.

27
Q

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

A

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

28
Q

What is peptide bond?

A

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

29
Q

What Is an alpha carbon

A

the central carbon bound to an amino group and carboxyl group

30
Q

define oligopeptides?

A

peptide which a few amino acid residues 12-20

31
Q

define polypeptides?

A

long chain peptides with many residues 20+

32
Q

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

A

N>C, in 3 or 1 letter code

eg. Glu-Gly-Ala

33
Q

define peptide

A

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

34
Q

define dipeptide, tripeptide, polypeptide

A

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

35
Q

define protein

A

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

36
Q

Peptide are polyampholites, what does this mean?

A

they contain different charges

37
Q

What makes a polypeptide ionizable?

A

the amino groups, the carboxyl groups and the r groups

38
Q

Solubility, structure and function are determined by what?

A

pH

39
Q

What is the isoelectric point?

A

pH which the net charge is 0

40
Q

What is the primary structure of a protein?

A

The order of amino acid resides- sequence

41
Q

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

A

20^(#of aa)

42
Q

What are enkephalins?

A

pentapeptide that binds to opioid receptors.

43
Q

What is the sequence for a leucine enkephalin?

A

Try-Gly-Gly-Phe-Leu

Y-G-G-F-L

44
Q

What is the sequence for a methionine enkephalin?

A

Try-Gly-Gly-Phe-Met

Y-G-G-F-M

45
Q

What encodes the amino acid sequence?

A

the nucleotide sequence of DNA

46
Q

Explain how the MALDI Mass Spectometer works?

A

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.

47
Q

Explain solid-phase peptide synthesis.

A

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
48
Q

What happens during coupling?

A

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.

49
Q

What is reaction to from a peptide bond?

A

condensation

Biochemistry (7 decks)

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