Semester 1

Question 1

Hydrophobic

Answer 1

Will not interact with water e.g. Lipids (means that they can pass through lipid bilayers)

Question 2

Hydrophilic

Answer 2

Polar, interacts with water. Reduces storage ability - cannot pass through lipid bilayers unassisted.

Question 3

Roles that proteins play

Answer 3

Catalysts (enzymes)
Transporters (haemoglobin)
Structural support e.g.Collagen (in skin and bones)
Machines (muscular contraptions- actin)
Immune protection (antibodies)
Ion channels
Receptors e.g. Hormones
Ligands in cell signalling

Question 4

Cytoplasm role

Answer 4

Metabolism of carbohydrates, amino acids and proteins.

Fatty acid synthesis

Question 5

Lysosomes

Answer 5

Membrane bound structure with digestive enzymes - cellular digestion

Question 6

Golgi complex

Answer 6

Series of flattened sacs with associated vesicles. It is involved in the export of proteins (modifies them chemically, sorts and packages them) and carries out detoxification reactions

Question 7

Plasma membrane

Answer 7

Controls what goes in and out of the cell, cell morphology and transport

Question 8

Mitochondria

Answer 8

Long structures with a double membrane. The inner membrane is folded to form cristae. It is involved in ATP production,

Question 9

Endoplasmic reticulum

Answer 9

Network of membranous tubules in the cytoplasm. Involved in detoxification reactions, protein synthesis (RER), export of proteins, membrane synthesis and lipid and steroid synthesis

Question 10

Nucleus

Answer 10

Round body surrounded by nuclear envelope. Contains nucleolus with RNA and DNA. Used for DNA synthesis and repair, RNA synthesis, RNA processing and ribosome Assembly and transport of ions and small moelcules

Question 11

Ribosomes

Answer 11

Small particles in the cytoplasm or attaches to Endoplasmic reticulum made of protein and RNA. For protein synthesis

Question 12

Base

Answer 12

Accepts protons

Question 13

Acid

Answer 13

Donates protons

Question 14

Conjugated proteins

Answer 14

Proteins containing covalently linked chemical components in addition to amino acids

Question 15

Aliphatic

Answer 15

Straight chain of carbon atoms only

Question 16

Aromatic

Answer 16

Benzene rings

Question 17

Pk

Answer 17

Acid dissociation constant - The higher the pKa value the lower the tendency of the acid to dissociate so the stronger the acid

Question 18

Peptide bond characteristics

Answer 18

Carbonyl oxygen and Amide hydrogen in trans orientation
No rotation about peptide bond
All atoms involved in the bond are planar

(Planar and rigid)

Question 19

Isoelectric point pI

Answer 19

The pH at which there is no overall net charge

Question 20

Basic proteins

Answer 20

Have a pI over seven and they include positively charged basic amino acids (lysine, arginine)

Question 21

Acidic proteins

Answer 21

PI is less than seven, contains many negatively charged acidic amino acids like glutamate and asparate

Question 22

Primary structure

Answer 22

The linear amino acid sequence of the polypeptide chain

Covalent bonds

Question 23

Secondary structure

Answer 23

The local special arrangement of the polypeptide backbone

Hydrogen bonds

Question 24

Tertiary structure

Answer 24

3D arrangement of the atoms in the polypeptide chain

Covalent bonds
Ionic bonds
Disulphide bridges 
Van der Waals 
Hydrophobic interactions

Question 25

Quaternary structure

Answer 25

3D arrangements of the polypeptide sub units ``` Ionic bonds Covalent bonds Van der Waals Hydrophobic interactions Disulphide bridges ```

Question 26

Alpha helix

Answer 26

3.6 amino acids per turn 0.54nm pitch Right handed helix The hydrogen bonds occur between amino acids four residues away from each other Small hydrophobic residues are strong helix forms (ala and leu) Pro and gly are helix breakers

Question 27

Beta sheets

Answer 27

Fully extended conformation 0.35nm between adjacent amino acids R groups alternate between opposite sides of the chain They can be parallel or antiparallel. There are multiple inter strand hydrogen bonds, which are more angular when the sheets are parallel

Question 28

Fibrous proteins

Answer 28

Have a structural role, long strands or sheets, single type of repeating secondary structure with little or no tertiary structure e.g. Collagen. They are insoluble

Question 29

Globular proteins

Answer 29

Role in catalysis and regulation. Have a compact shape with several types of secondary structure and a complex tertiary structure. Soluble e.g. Enzymes

Question 30

Motifs

Answer 30

Folding patterns containing one or more elements of secondary structures

Question 31

Denaturation

Answer 31

Disruption of protein structure Disulphide bridges - reducing agents Hydrogen bonds - changes in pH Ionic interactions - changes in pH Hydrophobic interactions -detergents

Question 32

Chaperones

Answer 32

Assist with protein folding

Question 33

Protein that Fe binds to in myoglobin and haemoglobin

Answer 33

Histidine residue

Question 34

Myoglobin

Answer 34

``` Single polypeptide chain One haem group Fixed affinity for oxygen No cooperative binding Hyperbolic curve ```

Question 35

Haemoglobin

Answer 35

``` Tetramer structure Two alpha and two beta sub units Four haem groups Cooperative binding Sigmoidal curve Exists in T and R state - T state is low affinity as binding site is less exposed - conformation changes in the R state ```

Question 36

3 things that reduce affinity of haemoglobin to oxygen

Answer 36

BPG (2,3 bisphosphoglycerate) H+ CO2

Question 37

Sickle cell anaemia

Answer 37

Mutation of glutamate to valine in beta globin. Polymerisation of haemoglobin occurs as sticky hydrophobic pockets form They are rigid so may block microvasculature and also lyse (release contents)

Question 38

Thalassaemias

Answer 38

Group of genetic disorders where there is an imbalance between the number of alpha and beta globin chains. Beta is when there are decreased or absent beta chains. The alpha ones cannot form stable tetramers. The alpha one is where the alpha chains are absent and beta ones are able to form stable tetramers but they have an increased affinity for oxygen.

Question 39

Transition state

Answer 39

High energy intermediate that lies between the substrate and product

Question 40

Activation energy

Answer 40

Minimum energy that the substrate must have for the reaction to occur.

Question 41

Enzymes

Answer 41

Biological catalysts that increase the rate of reaction by finding an alternative pathway with a lower activation energy

Question 42

Features of enzymes

Answer 42

``` Highly specific Unchanged after a reaction Do not affect the reaction equilibirum Increase the rate of reactions Proteins May require assisted cofactors ```

Question 43

Km

Answer 43

The substrate concentration that gives half the maximum rate of reaction

Question 44

Vmax

Answer 44

The maximum rate of reaction which occurs when all the active sites of the enzymes are saturated with the substrate

Question 45

Enzyme inhibitors

Answer 45

Molecules that slow down or prevent an enzyme reaction Irreversible -covalent bonds Reversible - non covalent bonds that can freely dissociate

Question 46

Competitive inhibition

Answer 46

Bonds to the active site, competition between the inhibitor and the substrate. Km increases but V max stays the same as adding enough substrate overcomes the effect of the inhibitor

Question 47

Non competitive inhibition

Answer 47

Binds to a site other than the active site which changes the shape of the active site. Vmax decreases but Km stays the same.

Question 48

Basic positively charged amino acids

Answer 48

Lysine | Arginine

Question 49

Amphiphatic

Answer 49

Molecules with a polar and non polar region at either end