IMED1002

Define the basic structure of amino acids (AA) (5)

Alpha carbon, hydrogen, amino group, carboxylic acid group, side chain (R)

Identify the AA chemical classifications

3 basic, 2 acidic, 5 uncharged polar, 10 non polar

What is the importance of the side chain (R) group? Make reference to the basic, acidic and uncharged polar AA

Determines the AA's unique properties and thus each side chain varies among the 20 AA.

Basic AA: N can be protonated

Acidic AA: COOH that can lose proton

Uncharged Polar AA: electronegative atoms

Discuss AA chirality with reference to the form of AA found in our proteins, as well as binding sites

• L & D forms; L AA found in our proteins

• Binding sites are specific for reactants, thus positioned so that only one enantiomer of the reactant binds correctly

What relationship is the chirality nomenclature based on?

D and L glyceraldehyde

What happens to the carboxyl and amino groups of AA in water?

Carboxyl loses H+ and Amino gains H+ = ZWITTERIONIC FORM

Amino acids are amphoteric. What does this mean?

Dual ability to act as both a base (proton acceptor) and acid (proton donor)

Base = Cation

Acid = Anion

At physiological pH, state the charges of the neutral AA, basic AA, and acidic AA

• Neutral AA = Zwitterions = 0 charge

• Basic AA = +1 charge

• Acidic AA = -1 charge

Define Isoelectric point (pl). What is the relation between pl and solubility?

• pH where > 99.9% of the AA is zwitterion, no net charge

• AA fairly soluble in water, BUT least soluble at their pl

What happens when a hydrophobic side chain is placed in water?

Highly structured cage of water molecules form around it = entropy of water solvent decreases

Draw the following molecules: Gylcine, Alanine, Phenylalanine, Tyrosine

Answer on Diagram

What is the cause and solution of PKU?

• Impaired conversion of Phenylalanine to Tyrosine, due to lack/defective phenylalanine hydroxylase

• Decrease dietary intake of Phe

What are peptide bonds? What is unique about the C-N peptide bond?

• Join AA together to form peptides; strong covalent bonds

• Has double bond character due to resonance

What process results in peptide bond formation? Identify the products of this reaction

• Condensation

• Peptide and water

Draw and label the following components of peptides: Amino Acid Residue & Peptide Bond

See diagram for answers

Identify the two termini of a protein

Amino terminal end & Carboxyl terminal end

Outline the structure of a disulphide bond

2 thiols (-SH) join together to form a disulphide bond (S-S)

Identify the rotatable and non-rotatable bonds in peptides

Non-rotatable = C-N bond

Rotatable = C(alpha)-C & N-C(alpha)

How many rotatable backbone bonds are there per RESIDUE? Does this affect number of structures for this protein

• 2

• No, for any given AA sequence, it only ever forms one structure; Interactions of R chains determines shape

Why is it beneficial that non-covalent interactions determine protein shape and stabilise protein structure?

If unwinding is required it's easier to break non-covalent interactions than covalent interactions

Outline the primary (1) level of protein structure. What bonds are involved?

• Sequence of AA covalently bonded

• Peptide Bonds

(Side chains projecting out)

Outline the secondary (2) level of protein structure. What bonds are involved?

• Folding of AA CLOSE TO each other on the chain, to form repeating patterns

• H Bonds (weak)

• B-pleated sheet vs a-helix

Distinguish between B-pleated sheet & a-helix

• B-sheets are more rigid; parallel or antiparallel; can be within the same structure

• a-helix: Carbonyl 'O' atom of a peptide bond forms H bond to amide 'H' atom of the AA; 4 residues away = close

Outline the tertiary (3) level of protein structure. What bonds are involved?

• Folding and bonding of AA that are FAR AWAY on the chain to form 3-D structure; inter folding of B-sheets & a-helices

• Protein folding driven by hydrophobic interactions & disulphide bonds

Explain the effect of hydrophobic forces on protein folding.

Hydrophobic R groups buried inside, hydrophilic groups outside = increases randomness of protein-water interaction = increases molecule stability

Outline the quaternary (4) level of protein structure. Give an example?

• Proteins that contain one or more chain (subunit) - arrangement of subunits & their contacts

• Haemoglobin: 4 subunits (2 alpha and 2 beta)

Define a protein domain

Protein domains are able to independently fold to form compact, stable structures

Why are the primary structures of a protein vital?

Primary structures of a protein determine shape, and shape determines function

What are the effects of changes in primary structure? (can tolerate some changes as long as its chemistry is similar)

no effect (genetic variation in species); little effect (interspecies variation: diabetics requiring insulin example); enormous effect (disease-causing mutation: sickle cell anaemia)

What is the effect of disulphide bonds in proteins?

Stabilise protein conformation

Define a simple protein

Proteins containing only AA and no other chemical groups (insulin)

Define a conjugated protein

Proteins containing other chemical components in addition to AA (Hb)

Define a prosthetic group

Non-amino acid part of a conjugated protein - play an important role in biological function (iron in Hb which binds oxygen)

Give 3 conjugated proteins

Lipoproteins; Metalloproteins; glycoproteins

Identify the relationship between protein domains and evolution.

Similar domains found in evolutionary distant organisms; increased organism complexity results in increased number of domains

Protein conformation is dependent on...

AA sequence

Define a native protein

Native proteins have the correct conformation & hence should function properly

Define a denatured protein

Denatured proteins do not have the correct shape & so won't be able to perform the normal function

Define the process of denaturation (does not break peptide bonds)

Altering/destroying the conformation of a protein and thus nearly always loses its biological activity as it changes secondary, tertiary, and quaternary structures (NOT PRIMARY)

Identify 7 agents causing denaturation

Heat; Chemicals; Acids, bases & salts; Detergents; Heavy metals

Is denaturation reversible?

Sometimes, if a protein is denatured and the agent is removed it may be able to reform

Name the 10 different categories of protein function

Enzyme; Structural Protein; Transport Protein; Motor (Movement) Protein; Storage Protein; Signal Protein; Receptor Protein; Gene Regulatory Protein; Special Purpose (other) Protein; Defence Protein

Outline protein families

More similar AA sequences cluster on same branches of evolutionary tree; protein functionality often reflected in clustering

Can AA sequences be quite different, yet have a very similar tertiary structure?

Yes

Can proteins be similar in structure yet very different in function?

Yes; may have descended from common ancestor but varied in function through evolution

Distinguish between Fibrous and Globular proteins (SPADES)

• Long & narrow v Spherical

• Structural role v Functional role

• Repetitive v Irregular AA sequence

• Less sensitive v More sensitive to changes in pH, temp

• Fibrin v Haemoglobin

• Insoluble v soluble in water

Proteins bind ligands (ions, small molecules, macromolecules) through weak non-covalent interactions in binding site. Give an example.

E.g 1. Enzymes bind specific ligand (substrate), alters the conformation = easily changed into product and enzyme remains unchanged

E.g 2. Antigen (ligand) binds to Immunoglobulins

True or False: Enzymes change the equilibrium of a reaction?

False - If a reaction can't take place, then an enzyme won't make it happen; they speed up the reaction

"A --(Enzyme 1)--> B --(Enzyme 2)--> C --(Enzyme 3)--> D" - With reference to enzyme function, what is this referring to?

The product of one reaction can influence the product of another reaction; several reactions linked form a metabolic pathway

Outline how enzymes can sometimes be regulated?

Phosphorylation - changes the shape and thus activity of the enzyme

Outline the action of ligase

Catalyses the formation of bonds (joining)

Outline the action of polymerase

Catalyse polymerisation reactions (DNA & RNA synthesis)

Outline the action of kinase

Catalyses addition of phosphate groups to molecules

Outline the action of phosphatase

Catalyses hydrolytic removal of a phosphate group from a molecule

Outline the action of protease

Break (hydrolyse) peptide bonds in proteins

Outline the action of oxidoreductase

Catalyses oxidation/reduction

Outline Oxidation & Reduction

OILRIG; The compound that is reduced is the oxidising agent & the compound that is oxidised is the reducing agent