Amino acids and protein structure Flashcards by Emily Harper

Describe the general structure of an alpha amino acid

C-H
N-H2: amine group
C-O2-H: carboxylic acid group
R: side chain/variable group

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What are the charges on an alpha amino acid at pH 7?

Positive charge on N of the amine group

Negative charge across the O2 of the carboxylic acid group

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What is the charge on a protonated alpha amino acid (i.e. below pH 5)?

Positive charge on N of the amine group

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What form is an alpha amino acid in between pH 3 and pH 8?

Zwitterionic form

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What is the charge on a deprotonated alpha amino acid (i.e. above pH 7)?

Negative charge across the O2 of the carboxylic acid group

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Using ‘CO-R-(H)-N’ law, a clockwise CO-R-(H)-N is known as what type of isomer?

A D isomer

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Using ‘CO-R-(H)-N’ law, an anticlockwise CO-R-(H)-N is known as what type of isomer?

An L isomer

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What type of bond forms between 2 amino acids?

A peptide bond

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How would we describe a C omega bond angle of 180 degrees?

Trans

Favoured

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How would we describe a C omega bond angle of 0 degrees?

Cis

Disfavoured

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Is the change from free rotation about the C-N bond to a planar C-N bond reversible or irreversible?

Reversible

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Describe the C-N bond when there is free rotation

Single bond, no charge

Double bond on C=O

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Describe the C-N bond when it is planar

Double bond, negative charge on the O, positive charge on the N
(Single bond on C-O)

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Name some important bonds/interactions in protein structure in order of decreasing strength

Covalent bonds
Ionic (electrostatic) interactions
Hydrogen bonds
Hydrophobic interactions
Van der Waals forces

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Define covalent bonds

Strong bond, arising from the sharing of one or more pairs of electrons between atoms

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Define ionic (electrostatic) interactions

Between 2 charged groups

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Define hydrogen bonds

Sharing of a hydrogen atom between 2 other atoms (= hydrogen donor and acceptor)

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Define hydrophobic interactions

Tendency for ‘water-hating’ molecules to cluster together to exclude water

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Define van der Waals forces

Non-specific attractive force when 2 atoms are in close proximity (0.3-0.4nm)

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Give an example of where a disulphide bond could form

Between 2 cysteines

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What type of reaction forms a disulphide bond?

Oxidation reaction

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What type of reaction breaks a disulphide bond?

Reduction reaction

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What is released when a disulphide bond forms between 2 cysteines?

2H+ ions

2e-

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Use chemical equations to demonstrate how an ionic interaction works

HA + H2O A- + H3O+

HA+ A + H3O+

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What is the equation for Ka?

Ka = ([A-][H3O+]) / ([HA]) OR Ka = ([A][H3O+]) / ([HA+])

What is the equation for pKa?

pKa = -log(Ka)

What is the equation for pH?

pH = -log(H3O+)

What is pKa?

The pH were 50% is ionised

What does a low pKa indicate?

Acidic

What can ionic interactions occur between?

Negative (acid) charged side chains - negatively charged, hydrophilic residues Positive (basic) charged side chains - positively charged, hydrophilic residues

What is significant about ionic interactions?

Between charged groups Positive attracts negative Importance of environment

What is the distance between hydrogen-bond donors and acceptors?

~2.8 An = 0.28 nm

Give examples of hydrogen-bond donor and acceptor interactions

``` (-)dipole - (+)dipole _ (-)dipole N-H_N N-H_O O-H_N O-H_O ```

What is significant about hydrogen bonds?

They are directional, weakening as the (donor-H-lone pair) becomes less linear

What do 4 sp3 hybrid orbitals form?

A tetrahedron

Give examples of amino acids with side chains that can form hydrogen bonds

``` Residues with polar groups: Asparagine Cysteine Glutamine Neutral histidine Serine Threonine Tryptophan Tyrosine ```

What can't hydrophobic groups form?

Hydrogen bonds

What do co-locating hydrophobic regions allow?

Water to maximise both hydrogen bonding and entropic potential

Give examples of amino acids with side chains that can form hydrophobic interactions

``` Nonpolar, hydrophobic residues Alanine Isoleucine Glycine Leucine Methionine Phenylalanine Proline Valine ```

In terms of van der Waals forces, what does a positive charge cause?

An induced dipole on a neighbouring atom

In terms of van der Waals forces, what does an induced dipole cause?

Mutually induced dipoles (transient) on neighbouring atoms

Define primary structure

The sequence of amino acids linked by covalent peptide bonds. Amino (N-) and carboxy (C-) termini.

Why is the peptide group rigid and planar?

Because the carbon-nitrogen bond has partial double-bond character. Also: Peptide has dipole Peptide N is a hydrogen bond donor, the carbonyl O an acceptor

Where is there freedom of rotation about bonds?

Either side of C alpha - dihedrals phi and psi

Define secondary structure

Regular structural motifs alpha-helix and beta-strand/sheet | H-bonding between -NH and -CO groups in protein backbone

Describe the properties of an alpha-helix

The peptide N is a hydrogen bond donor, the carbonyl O an acceptor Main chain carbonyl group is H-bonded to main chain amino group four residues away All polar groups of main chain are H-bonded so compatible with hydrophobic environment inside a protein, e.g. can have hydrophobic one side and hydrophilic the other side

At what ends are the positive and negative dipoles of the alpha-helix?

Positive dipole is at the N-terminal end | Negative dipole is at the C-terminal end

What binds to the heme group of myoglobin?

An iron atom

What secondary structural make up myoglobin?

Helix-turn-helix

Which side of the Ramachandran plot do beta-strands and alpha-helices lie?

Beta-strands at the top left | Alpha-helices at the bottom left

What is the Ramchandran plot a plot of?

psi vs. phi

In what orientation can beta-sheets lie?

Parallel or antiparallel

How do beta-strands combine and give and example of a molecule where this combination may occur?

In various ways with both parallel and antiparallel parts in a sheet E.g. in part of an antibody molecule

What are the various ways secondary structures combine known as?

Motifs

What can the hairpin be extended to form?

The Greek-key

What forms the beta-alpha-beta motif? And what can this motif form?

The simple combination of a beta-sheet and a helix forms the motif The motif can form larger structures, e.g. the TIM barrel

Is the barrel structure common or uncommon?

Very common, as it provides a good structural scaffold for forming an active site in an enzyme

In the right-handed beta-alpha-beta unit, where does the helix lie ?

The helix lies above the plane of the strands

Beta-alpha-beta can double up to form what?

Nucleotide binding domain with signature g-x-g-x-x-g found in e.g. dehydrogenases (Known as the Rossman fold)

Describe how a barrel might form

Trimer of left-handed beta-helices with alpha-helical region at C-terminus

Alpha-helices can also combine to form what? And give an example of one of the most important

Form motifs | One of the most important is the helix-turn-helix that has been found in many DNA-binding proteins

Where can you fins a similar helix-loop-helix motif?

The calcium-binding EF hand | Electronegative oxygens around Ca2+

Give examples of other motifs worth knowing about

The four-helix-bundle | The leucine zipper

What might proteins also have bound?

Metal ions, they may be important for the structure, and an example is the zinc finger found in DNA binding proteins

What can some large polypeptides fold into?

Domains

What is the fundamental unit of tertiary structure?

Domains

Define domain

A polypeptide chain or part of a polypeptide chain that can fold independently into a stable tertiary structure

What are domains also units of?

Also units of function, they may be recognisable from an analysis of sequence May be subunits, if the oligomeric protein consists of more than one chain

Give examples of a domain

SH2 (Src-homology-2) and SH3 (Src-homology-3) domains

Define tertiary structure

Folding of polypeptide, stabilised by side chain interactions (covalent, ionic, H-bonding, hydrophobic, van der Waals)

Describe the properties of the amino acids in myoglobin

Hydrophilic and polar amino acids on the outside, hydrophobic amino acids on the inside

Describe the distribution of amino acids in a membrane protein

'Inside out' Water-filled hydrophobic channel Largely hydrophobic exterior

Define quaternary structure

Associations between polypeptides - multisubunit molecules, e.g. Hb. Mainly side chain interactions (covalent, ionic, H-bonding, hydrophobic, van der Waals)

Where do disulphide bonds primarily occur? And give an example of a biological molecule that contains disulphide bonds

Primarily occur in extracellular proteins Can be intra- or intersubunit Can be found in insulin

Amino acids and protein structure Flashcards

(74 cards)