Proteins

Question 1

Describe the functions of proteins

Answer 1

Proteins have a huge range of functions within the body.
o	Movement
o	Protection
o	Transport
o	Enzymes
o	Receptors
o	Structural
o	Storage
o	Hormones
o	Control of gene expression

Question 2

Define the primary structure of a protein

Answer 2

The sequence of amino acids in a polypeptide chain. This is the source of versatility in protein structure and function.

Question 3

Define the secondary structure of a protein

Answer 3

The spatial arrangement of amino acid residues that are near each other in the linear sequence.
• Alpha Helices
A telephone cord shape held in place by H Bonds between the N-H group and the C=O group of the amino acid in the next turn of the helix.
• Beta Sheet
The pleated structure is held together by H bonds between the amide groups of linear polypeptide chains.

Question 4

Define the tertiary structure of a protein

Answer 4

The spatial arrangement of amino acid residues that are far apart in the linear sequence. This depends on:
•	Van der Waals
•	Ionic Interactions
•	Hydrogen Bonding
•	Disulphide bridges
•	Hydrophobic interactions

Question 5

Define the quarternary structure of a protein

Answer 5

Refers to the spatial arrangement of individual polypeptide chains in a multi-subunit protein.

Question 6

Define the 4 classes of naturally occurring amino acids.

Answer 6

Basic
Acidic
Uncharged polar
Polar

Question 7

Name some acidic amino acids

Answer 7

• Aspartic Acid

* Glutamic Acid

Question 8

Name some basic amino acids

Answer 8

• Lysine
• Arginine
• Histidine

HAL is basic af

Question 9

Name some uncharged polar amino acids

Answer 9

• Asparagine
• Glutamine
• Serine
• Threonine
• Tyrosine

STTAG (e.g. stag horns)

Question 10

Name some polar amino acids

Answer 10

• Glycine
• Alanine
• Valine
• Leucine
• Isoleucine
• Proline
• Phenylalanine
• Methionine
• Tryptophan
• Cysteine

Question 11

Name some sulphur containing amino acids

Answer 11

Cysteine

Methionine

Question 12

Name some aromatic amino acids

Answer 12

Phenylalanine
Tyrosine
Tryptophan

Question 13

Describe the basic structure of an amino acid

Answer 13

Amino acids are biologically important organic compounds containing amine (-NH2) and carboxylic acid (-COOH) functional groups, along with a side-chain (R group) specific to each amino acid

Question 14

How many codons are there in the genetic code?

Answer 14

64, some redundancy

Question 15

What occurs in protein denaturation?

Answer 15

• Denaturation of proteins involves the disruption and possible destruction of both the secondary and tertiary structures.
• Denaturation reactions are not strong enough to break the peptide bonds, so the primary structure remains the same after a denaturation process

Question 16

What can cause protein denaturation?

Answer 16

• Acids
• Heat
• Solvents - Ethanol, methanol
• Cross linking reagents - Formaldehyde
• Chaotropic agents – Urea (disrupts hydrogen bonding between water molecules, affects stability of other molecules in solution)
• Disulphide bond reducers - 2 mercaptoethanol

Question 17

What effects does denaturation have on proteins?

Answer 17

• Decreased solubility
• Altered water binding capacity
• Loss of biological activity
• Improved digestibility

Question 18

Name the enzyme involved in protein degradation and describe its different activity

Answer 18

Peptidases - cleave peptide bonds
Endopeptidases - cleavage of internal bonds
Exopeptidases - cleave off one aa at a time
Carboxypeptidases - cleave from carboxylic end
Aminopeptidase - cleave at amine end

Question 19

Describe the composition of a glycoprotein

Answer 19

Protein + carbohydrate

Formed by post translational modification reaction glycosylation, e.g. immunoglobulins

Question 20

Describe glycosylation and where it occurs in a cell

Answer 20

• Glycosylation is the reaction in which a carbohydrate, i.e. a glycosyl donor, is attached to a hydroxyl or other functional group of another molecule (a glycosyl acceptor). In biology glycosylation mainly refers in particular to the enzymatic process that attaches glycans to proteins, lipids, or other organic molecules.
• Process occurs in the ER and Golgi network.

Question 21

Describe lipoproteins and their function, including some examples

Answer 21

Protein and lipids that are either covalently or non-covalently bonded together. Their main function is for the transport of water-insoluble fats and cholesterol in the blood e.g. HDL, LDL

Question 22

Describe some metalloproteins and their functions

Answer 22

Protein molecule with a bound metal ion. Functions include:
o Enzymes
o Storage
o Signalling
o Transport
Importance can be seen in anaemia, when there is an iron deficiency that affects the functionality of haemoglobin.

Question 23

Describe haemoglobin’s structure, and the role of its structure in its function

Answer 23

Haemoglobin is the iron-containing oxygen-transport metalloprotein in the red blood cells of all vertebrates as well as the tissues of some invertebrates.
The hemoglobin molecule is an assembly of four globular protein (2 x α + 2 x β) subunits. Each subunit is composed of a protein chain tightly associated with a non-protein heme group. Each protein chain arranges into a set of alpha-helix structural segments connected together in a globin fold arrangement, so called because this arrangement is the same folding motif used in other heme/globin proteins such as myoglobin. This folding pattern contains a pocket that strongly binds the heme group.
A heme group consists of an iron (Fe) ion (charged atom) held in a heterocyclic ring, known as a porphyrin.
Haem group at the centre of each polypeptide chain binds one molecule of oxygen.
So that one haemoglobin molecule can bind four molecules of oxygen
Cooperative binding

Question 24

What is cooperative binding?

Answer 24

Seen in oxygen binding to haemoglobin.• The binding of O2 to one sub-unit alters its shape.
This in turn causes a change in the shape of the other sub-units, so that they bind O2 more easily.

Question 25

Describe sickle cell anaemia, the properties of sickle cell haemoglobin, and its clinical features

Answer 25

Single base change (single point mutation, 1 base substitute) in the DNA chain A is swapped for T at postion 6 on the B chain. Causing the hydrophilic amino acid glutamic acid to be replaced with the hydrophobic amino acid valine at the sixth position. Properties of Hb S: o Insoluble o At low O2 levels forms crystals and polymerises to form long chains, causing the RBC to change shape (sickle shape) Clinical features o Severe haemolytic anaemia o Hb S gives up oxygen in the tissues more easily than Hb A.

Question 26

Describe some illnesses arising from an error in collagen production

Answer 26

Scurvy • Vit C required to convert proline to hydroxyproline, and lysine to hydroxylysine • Hydroxyproline and hydroxylysine are essential for stabilising the crosslinks between collagen chains • Weaker collagen produced Osteogenesis imperfecta • Glycine substituted for larger amino acid • The protein no longer folds to form a tight coil • Reduced interaction between fibrils • Loss of secondary, tertiary structure • Weakened and brittle collagen produced

Question 27

What is the LDL receptor, what does it recognise, and name an illness associated with its dysfunction

Answer 27

The Low-Density Lipoprotein (LDL) Receptor is a mosaic glycoprotein that mediates the endocytosis of cholesterol-rich LDL. It is a cell-surface receptor that recognizes the apoprotein B100, which is embedded in the outer phospholipid layer of LDL particles. Familial hypercholesterolemia

Question 28

What is Levinthal's paradox?

Answer 28

Levinthal’s paradox is that finding the native folded state of a protein by a random search among all possible configurations can take an enormously long time. Yet proteins can fold in seconds or less. Therefore protein folding must be guided by local interactions and transition states.

Question 29

What class of amino acids is proline in?

Answer 29

Other - connects to backbone twice to make it the only amino acid which forms a five membered nitrogen containing ring

Question 30

What doesn't the central dogma account for?

Answer 30

Reverse flow of information from RNA to DNA

Question 31

What two functional groups are found on amino acids?

Answer 31

``` Amine (-NH3) Carboxylic acid (-COOH) ``` Also have specific R chains

Question 32

Describe briefly peptide bond formation

Answer 32

Covalent bond between amine and carboxylic acid functional groups of two amino acids with the loss of water

Question 33

Describe the formation of alpha helices

Answer 33

Hydrogen bonds between N-H and oxygen of C=O in next turn | Turns every 4 amino acid residues

Question 34

Name some proteins who show alpha helical structures

Answer 34

Myoglobin Troponin Ferritin

Question 35

Describe the formation of beta-sheets

Answer 35

H bonds between amide groups of linear polypeptide chains

Question 36

Name some proteins which show beta sheet structure

Answer 36

Fatty acid binding protein | Porin

Question 37

What is the role of glycosylation?

Answer 37

``` Protein stabilisation Solubility Protein orientation Signalling Cell recognition ```