protein structure and function 1

Question 1

Give some examples of roles of proteins

Answer 1

Catalyst- enzymes
transporters
structural support
immune protection
ion channels
receptors

Question 2

Ionisation state of amino acids

Answer 2

zwitterion
COO-
NH3+

Question 3

Why are the amino acids important in a proteins acid-base behaviour

Answer 3

Our group to give unique properties to proteins

Question 4

Properties of side chains of amino acids are classified by chemical properties or physical properties

Answer 4

Chemical:
hydrophobic
hydrophilic
polar
nonpolar
acidic basic
neutral

Physical:
aliphatic
aromatic

Question 5

PK values of ionised will side chains

Answer 5

pH pKa pH

protonated De protonated

Question 6

Describes the properties of peptide bonds

Answer 6

Planar - peptide bond resonance partial double bond characteristics unable to rotate
trans confirmation as cis confirmation would cluster it clashes
bond left of alpha carbon phi
bond right of alpha carbon psi

Question 7

The amino acid sequence of the protein determines

Answer 7

The way in which the polypeptide chain folds

the physical characteristics of the protein

Question 8

Isoelectric point of protein

Answer 8

PH in which there is no overall charge
pi PH PI
protonated Deprotonated

Question 9

Tertiary structure

Answer 9

The overall 3D confirmation of the protein

Question 10

Types of secondary structure

Answer 10

Alpha helix
right-handed, hydrogen bonds between N-H and C=O of 4 residues away. Small hydrophobic residues, no proline as Rotate around N-C alpha bond and no glycine

Beta sheet
strands run antiparallel
into strand hydrogen bond stabiliser structure

Question 11

Types of tertiary structure

Answer 11

Fibrous: support shape protection
long strands or sheets
single type of repeating secondary structure such as collagen

Globular: catalysts regulation compact shape
several types of secondary structure

Question 12

Collagen

Answer 12

An example of a Quaternary protein as it is 3 fibrous proteins wrapping together to make a helix
GLY-X-Y repeat in sequence
hydrogen bond stabilises interaction between chains

Question 13

Globular proteins have variety of tertiary structures

Answer 13

Beta Alpha beta loops
beta barrel
motifs- voting patterns containing one or more element of secondary structure
domains- part of the polypeptide chain that fold into the distinct shape and has a specific functional role

Question 14

Bonds involved in tertiary structure

Answer 14

Covalent (disulphide)
hydrogen bonds - form between electronegative atom and a hydrogen bond to another electronegative atom
ionic (positive and negative charged amino acids)
Van der waals - dipole dipole interaction
hydrophobic - interactions between hydrophobic side chains

Question 15

Bonds involved in quaternary structure

Answer 15

Covalent (disulphide)
hydrogen bonds - form between electronegative atom and a hydrogen bond to another electronegative atom
ionic (positive and negative charged amino acids)
Van der waals - dipole dipole interaction
hydrophobic - interactions between hydrophobic side chains

Question 16

Protein denatured by

Answer 16

ph-alters ionisation state of amino acids

heat- increases vibrational energy

Question 17

Proteins fold in an ordered structure

Answer 17

Each step involves localised folding and with stable confirmations maintained
driven by the need to find the most able confirmation

Question 18

Protein disorder can cause disease give some examples and explain

Answer 18

kuru CJD BSE

Normal alpha helix secondary structure converted into beta sheets. These are now amyloid fibres which are insoluble mis-folded proteins