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BCMB2002 > Protein structure and function (wk 1) > Flashcards

Protein structure and function (wk 1) Flashcards

1
Q

List four main functions of proteins

A

Catalysis
Transport e.g. hemoglobin and O2
Structure
Motion e.g. actin

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2
Q

Proteins are linear ______ made of ______

A

heteropolymers made of alpha amino acids

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3
Q

List the 4 classes of protein structure

A

Primary
Secondary
Tertiary
Quaterny

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4
Q

T/F:

Only D amino acids can be incorporated into proteins

A

False

Only L

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5
Q

What is a chiral carbon?

A

Carbon attached to four different groups

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6
Q

What are the 5 groups used in amino acid classification?

A 
Non polar, aliphatic
Aromatic
Polar, uncharged
Positively charged
Negatively charged
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7
Q

What is the isoelectric point?

A

pH where the amino acid has a neutral charge (pI)

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8
Q

What is pKa?

A

pH where 50% of the protons are dissociated

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9
Q

What nm do proteins absorb light in?

A

280nm

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10
Q

Which proteins have the ability to interact with DNA and RNA?

A

The aromatic ones

Phenylalanine, tyrosine and tryptophan

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11
Q

Which types of amino acids can form H bonds?

A

Polar amino acids

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12
Q

Which amino acid can form a disulfide bond?

A

Cysteine
Polar amino acid
Sulfur bond gives some rigidity, important for the folding of the protein

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13
Q

Which group are aspartate and glutamate a part of?

A

Negatively charged

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14
Q

List three important reactions glutamic acid and aspartic acid are involved in

A

Amination of R group
Ketone formation
Remove carboxyl group from alpha carbon

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15
Q

What is tyrosine a precursor of?

A

Dopamine

Noradrenaline

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16
Q

Where is the cut off for polypeptide vs peptide vs protein

A 
Peptide= <10kDa
Polypeptide= up to 10kDa
Protein= >10 kDa
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17
Q

What type of reaction occurs to make a polypeptide?

A

Condensation reaction

Water is excluded

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18
Q

The peptide bone allows ______

A

Resonance

rotation around the bond is restricted because there is a partial double bond

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19
Q

T/F:

The next amino acid of a polypeptide is added on at the C terminus

A

True

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20
Q

A protein starts with a ____ charge and ends in a ____ charge. Therefore the overall charge is _____.

A

A protein starts with a positive charge and ends in a negative charge. Therefore the overall charge is neutral.

21
Q

List some functions of peptides

A

Hormones/pheremones e.g. insulin, oxytocin
Neuropeptides e.g. substance P
Antibiotics e.g. polymyxin B
Protection e.g. toxins like chlorotoxin in scorpions

22
Q

What is the native fold of a protein?

A

Protein molecules adopt a specific 3D conformation that is favourable
The structure is able to fulfill a specific function, it is biologically active

23
Q

What are some favourable interactions within a protein?

A

Hydrophobic effect
H-bonds
London dispersion
Electrostatic interactions

24
Q

The peptide bond has resonance

What does this result in?

A

The peptide bond is less reactive compared to esters
It is quite rigid and nearly planar
It exhibits a large dipole moment in the favoured trans configuration

25
Q

In the peptide bond, the carbonyl oxygen has a partial _____ charge and the amide nitrogen has a partial ____ charge

A 
Oxygen= partial negative
Nitrogen= partial positive
26
Q

Phi is the angle between _______

Psi is the angle between ________

A 
Phi= angle between alpha carbon and amide nitrogen
Psi= angle between alpha carbon and carbonyl
27
Q

In a fully extended protein, both phi and psi are ____ degrees

A

180

28
Q

A ____ plot shows the distribution of phi and psi dihedral angles found in a protein

A

Ramachandran

29
Q

Which two amino acids tend to ‘break the rules’ when it comes to a Ramachandran plot?

A

Glycine and Proline

30
Q

What are the two main types of secondary structures?

A

Alpha helix

Beta Sheet

31
Q

T/F:

Alpha helixes are usually left handed

A

False

usually right handed

32
Q

In an alpha helix, the backbone is held together by _____ bonds between the backbone amides of n and ____ amino acids

A

held together by hydrogen bonds between the backbone amides of n and n + 4 amino acids

33
Q

How many amino acids per turn in an alpha helix?

A

3.6

34
Q

In an alpha helix, side chains point _____

A

outwards

35
Q

T/F:

the inner diameter of an alpha helix is too small to fit many molecules inside and only DNA binds here

A

False
it is too small to fit anything inside so it is often an empty space
The outer diameter binds with the major groove of dsDNA

36
Q

What stabilizes the structure of an amino acid?

A

The carbonyl group of amino acid 1 forms a hydrogen bond with the amide nitrogen of amino acid n + 4

37
Q

Negatively charged residues in an alpha helix often occur near the ______ end of the helix dipole

A

positive end

38
Q

The sheet-like arrangement of a beta sheet is held together by _______ between the _____

A

hydrogen bonds between the backbone amides in different strands

39
Q

How are the side chains in a beta sheet arranged?

A

Protrude from the sheet alternating in an up and down manner

40
Q

Compare and contrast an anti-parallel and parallel beta sheet

  • orientation
  • length of the bonds
  • strength of the bonds
A

Anti-parallel:
Amino group is followed by the carboxyl group
H bonds run in opposite directions which results in linear H bonds = stronger

Parallel:
H bonds run in the same direction= bent H- bonds= weaker
Longer H-bonds

41
Q

What is a beta turn?

A

Occurs when the strands in a beta sheet change direction
The 180 turn is accomplished over 4 amino acids
It is stabilized by a hydrogen bond from a carbonyl oxygen to amide protein three residues down the sequence

In type 1: proline is in position 2 (breaks the structure to push it to the other side)

In type 2: glycine is in position 3 (provides some flexibility)

42
Q

What are the two major classes of protein tertiary structure?

A

Fibrous and globular

43
Q

List some forces that might be found in protein tertiary structures

A 
hydrophic interactions
polar interactions
disulfide bonds
h bonding between peptide groups
metal ion coordination
ionic linkages
44
Q

What is the quaternary structure of a protein?

A

Formed by the assembly of individual polypeptides into a larger functional cluster

45
Q

What are some interactions you may find in a quaternary structure?

A

Hydrogen bonds

Disulfide bonds

46
Q

What are some benefits for a protein to occur in a quaternary structure?

A

Stability- reduction of surface to volume ratio
Genetic economy and efficiency
Brings catalytic sites together
Cooperativity

47
Q

What is denaturation and how can it occur?

A

Loss of structural integrity with accompanying loss of activity

heat or cold
pH extremes
organic solvents
chaotropic agents

48
Q

How many strands do you need to form a beta sheet?

A

2

49
Q

Describe some diseases related to protein mis folding

A

refer to written notes cbf to write it all out here sorry future eva

BCMB2002 (9 decks)

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