Protein structures

Question 1

peptide bond

Answer 1

amino acids form linear chains - polypeptides

water released, CONH bond formed

sequence written from amino or N terminus to carboxy or C terminus

Question 2

properties of peptide bonds

Answer 2

very stable
cleaved by proteolytic enzymes - proteases or peptidases
partial double bond
flexibility around C atoms that aren’t involved in bond, allows multiple conformations

Question 3

protein structure and function

Answer 3

large polypeptide, usually from 10s to 1000s amino acids

huge variety of functions arises from huge number of different 3D shapes

function depends on structure

Question 4

forces holding proteins together

Answer 4

Van de Waals forces
hydrogen bonds
hydrophobic forces
ionic bonds
disulphide bonds

Question 5

van de waals forces

Answer 5

weak attractive interactions between atoms due to fluctuating electrical charges

only important when 2 macromolecular surfaces fit closely in shape

repulsive at v short distance

Question 6

hydrogen forces

Answer 6

type of van de waals force - strongest

interaction between dipoles, involving hydrogen and oxygen/nitrogen/flourine

partial negative charges bind to partial positive charge on hydrogen

between amino acid side chains, main chain o and n and water

Question 7

hydrophobic forces

Answer 7

uncharged and non polar side chains are poorly soluble in water

form tight packed cores in the interior of proteins and exclude water

Question 8

ionic bonds

Answer 8

between fully or partially charged groups

weakened in aqueous systems by shielding by water molecules or other ions in solution

Question 9

disulphide bonds

Answer 9

covalent bonding between side chains of cysteine residues

2 sulphur atoms

Question 10

primary structure

Answer 10

linear sequence of amino acids linked by peptide bonds

primary structure determines its 3d conformation

Question 11

secondary structure - alpha helix

Answer 11

hydrogen bonds between each carbonyl group and the H attached to the N which is 4 aa along the chain

side chains look outwards

proline breaks the helix (ring + no H)

Question 12

secondary structure - beta pleated sheet

Answer 12

formed by H bonds between linear regions of polypeptide chains

chains from 2 proteins, or same protein
parallel or antiparallel chains, pleated or not
if chain is folding back, structure is usually a 4 aa turn - hairpin loop or b-turn

Question 13

supersecondary structures

Answer 13

combination of secondary structures

Question 14

examples of supersecondary structures

Answer 14

helix-turn-helix
b a b unit
leucine zipper
zink finger

Question 15

tertiary structure

Answer 15

overall 3d conformation of protein

electrostatic, hydrophobicity, h bonds and covalent forces

Question 16

conformational domains in tertiary structures

Answer 16

barrels, bundles, saddle

Question 17

factors affecting conformations in tertiary structures

Answer 17

pH, temp, etc

Question 18

quaternary structure

Answer 18

3d structure of a protein composed of multiple subunits

same non-covalent interactions as tertiary structures

Question 19

factors affecting the rate of a chemical reaction

Answer 19

temp
conc of reactants
catalysts
sa of solid reactant
pressure of gaseous reactants or products

Question 20

enzymes

Answer 20

bind reactants and convert them to products
release products and return to their original form

speed up reaction and regulate rate

Question 21

regulation of enzymes

Answer 21

conc of substrates, products, activators and inhibitors, temp, pH

modification of enzyme by phosphorylation or modulator/activator proteins

Question 22

isoenzymes

Answer 22

enzymes with different structure and sequence, but catalyse the same reaction

Question 23

coenzymes

Answer 23

complex organic structures which help maximise the repertorie of enzymes functional groups

can be metal ions, organic or both

Question 24

activation-transfer coenzymes

Answer 24

form covalent bond and are regenerated at the end of the reaction

Question 25

oxidation-reduction coenzymes

Answer 25

reactions where electrons are transferred

Question 26

porphyrin ring

Answer 26

holds an iron atom
heme
oxygen binding

Question 27

taking in of CO2 into RBCs

Answer 27

CO2 reacts with water and becomes carbonic acid (H2CO3) via carbonic anhydrase

H2CO3 releases proton, dissociates into H+ and HCO3-

protons bind to Hb, forming HHb
O2 released from Hb to tissues

reverse for converting O2 from lungs into CO2 to be exhaled

Question 28

immunoglobins function

Answer 28

antibodies

produced to bind antigens (toxins or proteins on surface of microbial agents)

labelled for destruction by immune system cells or by lysis through the complement system

Question 29

antigens

Answer 29

toxins or proteins on the surface of microbial agents

Question 30

properties of antibodies

Answer 30

diff. types: IgG, IgM, IgA etc

binding specific - one antibody matches with one antigen

Question 31

antigen-antibody binding

Answer 31

bound by variable domain - amino acids can be varied to produce a potentially infinite variety of 3D shapes, to recognise an infinite variety of foreign antigens (not self)

Question 32

antibody structure

Answer 32

disulphide bonds define loops characteristic of Ig

light chains, heavy chains

variable regions
constant regions

Question 33

multiple domain proteins

Answer 33

antigen binding sites at variable regions on light chain

binding to other antibodies and complement binding on heavy chain