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MCBG > Protein Structure > Flashcards

Protein Structure Flashcards

1
Q

Proteins are polypeptides; what are polypeptides?

A

Macromolecules made up of amino acids

Amino acids joined covalently to give the sequence of the protein

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2
Q

What determines the amino acid sequence of a protein?

A

The amino acid sequence of a protein is encoded by a gene

The nucleotide sequence of a gene determines the amino acid sequence of a protein

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3
Q

What does the folding of proteins depend on?

A

The polypeptide chain folds into a complex and highly specific three-dimensional structure, determined by the sequence of amino acids

The folding of proteins depends on the chemical and physical properties of the amino acids

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4
Q

Describe the structure of an amino acid

A 
Amino acids consist of a central carbon atom (the a-carbon) covalently bonded to: 
• an amino group (-NH2) 
• a carboxyl group (-COOH) 
• a hydrogen atom (-H) 
• a distinctive R group (side chain)
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5
Q

Which two parts of an amino acid can ionise and how?

A

NH2 + H+ NH3+
COOH COO- + H+

Both the carboxyl and animo group can ionise

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6
Q

Define zwitterion

A

Molecule (esp AA) containing both a positively charged functional group and a negatively charged functional group

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7
Q

What are amino acids classified according to?

A

Chemical properties of the R groups - acid base behaviour determined by the R groups

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8
Q

What is an amino acid residue?

A

The part of an amino acid that remains after it has been joined by a peptide bond to form a protein

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9
Q

Name chemical properties of the R groups

A 
Hydrophobic
Hydrophilic
Polar
Non-polar
Acidic
Basic
Neutral
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10
Q

Name physical properties of amino acids?

A

Aliphatic

Aromatic

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11
Q

What is Ka?

A

Acid dissociation constant

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12
Q

What is pKa?

A

-log Ka

The lower the pKa, the stronger the acid

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13
Q

When will a group of protonated/deprotonated in solution?

A

If the pH of the solution < the pK value then the group will be protonated
If the pH of the solution > the pK value then the group will be deprotonated

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14
Q

What is the primary structure?

A

The linear amino acid sequence of the polypeptide chain

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15
Q

What is the secondary structure?

A

Local spatial arrangement of polypeptide backbone - the conformation - e.g. Alpha helices/beta pleated sheets

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16
Q

What is the tertiary structure?

A

The overall 3D configuration of the protein

17
Q

What is the quaternary structure?

A

Association between different polypeptides to form a multi-subunit protein

18
Q

How is a peptide bond formed?

A

Condensation reaction: COOH of one AA forms bond with NH2 of another giving CONH and releasing H2O

19
Q

Name properties of a peptide bond

A

Planar: C alpha, C, O, N, H and C alpha all lie in the same plane
Rigid: The C-N bond has partial double bond characteristics - unable to rotate - contributes to planarity
Exhibit a trans conformation: C alpha on opposite sides of peptide bond (cis would lead to steric clashes)
Bonds on either side of the peptide bond are free to rotate

20
Q

What does the amino acid sequence o a protein determine

A

The way in which the polypeptide chain folds

The physical characteristics of the protein

21
Q

What is the Isoelectric point?

A

The isoelectric point, pI, of a protein is the pH at which there is no overall net charge
I.e the pKa of entire protein

22
Q

When are proteins protonated/deprotonated in terms of pI?

A

BASIC PROTEINS
pI > 7
Contain many positively charged (basic) amino acids

ACIDIC PROTEINS
pI < 7
Contain many negatively charged (acidic) amino acids

If pH < pI protein is protonated
If pH > pI protein is deprotonated

23
Q

How long are peptides/ogliopeptides?

A

A few amino acids in length

24
Q

How long are polypeptides/proteins?

A

Many amino acids - biologically active peptides and proteins come in a varying range of sized
Proteins are generally 100+AA

25
Q

What are conjugated proteins?

A

Have covalently linked chemical components in addition to amino acids

26
Q

What holds the primary structure together

A

Covalent bonds

Angles determine the conformation of the peptide backbone and hence the fold of the protein

27
Q

What bonds are found in the alpha helix

A

Hydrogen bonds between N-H and C=O stabilise the structure.

The backbone -C=O group of one residue is H bonded to the -NH group of the residue 4 amino acids away

28
Q

What affects the stability of the alpha helix?

A

Not all polypeptide sequences adopt a-helical
structures
• Small hydrophobic residues such as Ala and Leu are strong helix formers
• Pro acts as a helix breaker because the rotation around the N-Ca bond is impossible
• Gly acts as a helix breaker because the tiny R-group supports other conformations

29
Q

Describe the arrangement of a beta strand

A

Beta strand:
Fully extended conformation
0.35nm between adjacent amino acids
R groups alternate between opposite sides of chain

30
Q

What are the 2 types of beta pleated sheet?

A

Antiparallel b-sheet: adjacent b-strands run in opposite directions, with multiple inter-strand H-bonds stabilizing the structure - r groups on opposite side

Parallel b-sheet: strands run the same way, kinked H bonds

31
Q

Describe fibrous proteins and give an example

A

Role - support, shape, protection
Long strands or sheets
Single type of repeating secondary structure
E.g. Collagen

32
Q

Describe globular proteins and give an example

A

Role - catalysis, regulation
Compact shape
Several types of secondary structure
E.g. Carbonic anhydrase

33
Q

Give examples of various tertiary structures o globular proteins

A

Beta-alpha-beta-loop

Beta barrel

34
Q

Define motif

A

Motifs - folding patterns containing 1 or more elements of secondary structure

35
Q

Define domains

A

Part of a polypeptide chain that folds into a distinct shape - often has a specific functional role

36
Q

Describe the folding of water soluble proteins

A

Polypeptide chains old so that hydrophobic side chains are buried and the polar charged chains are on the surface

37
Q

Describe the folding of membrane proteins

A

Often show inside out distribution of amino acids

MCBG (18 decks)

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