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BIOSCI 107 > Lecture 14: Protein structure and function > Flashcards

Lecture 14: Protein structure and function Flashcards

1
Q

What is a protein?

A

A chain of amino acids linked by peptide bonds - polypeptide

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2
Q

Describe the structure of an amino acid

A

A central carbon atom bonded to an amine (NH2) group and a carboxyl (COOH) group and a hydrogen and a R group

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3
Q

What is a zwitterion?

A

The ion form of an amino acid where the H from carboxyl group is donated to the amine group

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4
Q

What is a condensation reaction?

A

Formation of peptide bond forming a H2O molecule

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5
Q

What are the properties of peptide bonds?

A
  • Cannot rotate due to resonance
  • O-C-N-H of peptide bonds co-planar
  • Rotation can occur at single bonds between carbons
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6
Q

What are the two orientation of peptide bonds?

A

Cis- R groups on same side
Trans - R groups on opposite sides

Cis orientation is less stable due to steric repulsion of the side chains and is rare

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7
Q

How many amino acids are there?

A

20

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8
Q

What is the lock and key theory?

A

Protein structure determines function - the shape of the protein (enzyme) is specific to a substrate

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9
Q

What is the induced fit theory?

A

Binding of substrate causes conformational change locking the molecule in

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10
Q

What are the 4 stages of protein structure?

A

Primary
Secondary
Tertiary
Quaternary

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11
Q

What is the primary structure of a protein?

A

The sequence of amino acids - formed from peptide bonds

Determined by DNA sequence of gene coding for protein

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12
Q

What is the secondary structure of a protein?

A

Localised folding of the polypeptide due to hydrogen bonding between amino acids

Two types include Beta pleated sheet and alpha helix

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13
Q

How do Beta pleated sheets form?

A

H bonding between amine group on one strand and a carbonyl (C=O) group on another strand

Two types: parallel and anti-parallel

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14
Q

How do alpha helix form?

A

H bonding between a backbone amine group and carbonyl group 3 or 4 residues earlier

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15
Q

Is it possible to predict the secondary structure of an amino acid?

A

Yes, certain amino acids favour one type of secondary structure due to their R group

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16
Q

What is the tertiary structure of a protein?

A

The 3D shape of a protein - due to interactions of the side chains

17
Q

What are the bond types that form tertiary structure?

A

Hydrogen bonding - between polar R groups of amino acids
Disulphide bridge- covalent bond between R groups of amino acid cysteine
Ionic bonding - between charged portions of R groups
Van der waals
Hydrophobic interactions - when non-polar hydrophobic R groups orient themselves towards the inside of the protein molecule
Hydrophilic interactions - when polar R groups orient themselves towards the outside of the protein towards water

18
Q

What are co-factors or prosthetic groups?

A

Molecules which bind to part of the protein changing structure or activating the function of protein.

19
Q

What is the quaternary structure of a protein?

A

Binding together of multiple folded protein subunits due to interactions between groups of adjacent amino acids

20
Q

What are the two types of proteins with quaternary structure?

A

Homooligomers - same proteins binded together

Heterooligomers - different proteins bound together

21
Q

What are the types of protein?

A

Globular
Fibrous
Membrane proteins

22
Q

Are globular proteins and fibrous proteins soluble?

A

Globular proteins are soluble

Fibrous proteins are insoluble

23
Q

What are the functions of globular proteins?

A

Usually transport, enzymes, immune

24
Q

What are the functions of fibrous proteins?

A

Structural

25
Q

Describe the stability of fibrous and globular proteins?

A

Fibrous proteins are highly stable and globular proteins are lower stability

26
Q

What are the function of membrane proteins?

A

Signalling, receptors, transport, adhesion

27
Q

What is the Abbe’s Diffraction limit?

A

Minimum resolution able to observed- half the wavelength of the medium of light used (0.2 micrometers)

28
Q

What are the two types of protein imaging?

A

X-ray crystallography

Cryo-electron microscopy

29
Q

What are the features of X-Ray Crystallography?

A 
Sample must be crystallised 
Any size macromolecule
Atomic resolution can be achieved
Crystallisation can only occur with some proteins and the proteins could be damaged in the process
Takes long
30
Q

What are the features of cryo-electron microscopy?

A

Frozen in its native state and observed via an electron microscope (small wavelength electron beam)
Only large proteins can be observed
Near-atomic resolution
Fast preparation

31
Q

What is resolution?

A

Distance corresponding to the smallest observable feature

32
Q

What is Levinthal’s paradox?

A

Very large number of degrees of freedom in an unfolded polypeptide chain
e.g.
100 aa protein will have 3^198 different conformations

BIOSCI 107 (29 decks)

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