BIOL10212 Biochemistry

Functional group

Functional groups are small groups of atoms/bonds that confer specific

reactivity to a molecule

Covalent bonds

Strong - 200-800 kJ/mol

Sharing elections in the valence shell

Non-covalent bonds

Weak - <30kJ/mol

Based on unequal sharing of electrons between nuclei: polarised bonds and polar molecules

Intermolecular and intramolecular interactions

Dipole

Partial separation of charge

Hydrogen bonds in biomolecules

Dipole-dipole interaction

One of the strongest of non-covalent interactions (~30kJ/mol)

x10 weaker than a covalent bond

Only strong if all three atoms are aligned

Polar bonds and partial charges on atoms

Charge-charge interactions

Electrostatic interactions between opposite charges

Stronger than a H-bond

Can extend over greater distances than other non-covalent interactions

Salt bridges/ion pairs

In solutions screening effect by counterions and water itself

Van der Waals forces

Attraction between stable/inducible dipoles - non polar molecules

Only works at a short optimal distance

Much weaker than other dipole forces however large numbers of interactions add up to significant stabilising force in biomolecules

Crucial for macromolecular structure and interactions

Electrostatic attractions (ion pairs, salt bridges)

Attraction of opposite charged groups or repulsion of like charges

Hydrophobic interactions

Association of non polar groups with most energy attributed to the exclusion of water (increased entropy)

Solvation/hydration

A molecule is considered solvated/hydrated if it is surrounded by solvent or water molecules

Polar molecules

Contain a high proportion of polar/ionic groups, making them hydrophilic

Polar groups increase H-bonding and solubility

Relationship between polarity and solubility

The higher the polarity, the more soluble it is due to hydrogen bonding between water and polar groups

Non polar groups

Few or no polar/ionic groups, making them hydrophobic as they minimise contact with water

Entropic effect

Entropic effect

Water around hydrophobic molecules have reduced mobility

Enantiomers

Stereoisomers which are mirror images of each other

Aliphatic

Side chains are non-aromatic hydrocarbons

Proline (Pro)

Contains a heterocycle (pyrrolidine)

Much less hydrophobic

Rotation around N-Cα bond restricted

Aromatic amino acids

Alternating (conjugated) double bonds → delocalised π electrons

Hydroxyl amino acids

Polar groups

Hydrogen donors + acceptors

Form phosphate esters

→ Signalling

Amino acids containing sulphur: cysteine

Some similarity with serine: weak hydrogen bonds

Ionisable (→ thiolate anion)

Forms disulphide bonds (stabilises extracellular proteins)

Amino acids containing sulphur: methionine

Fairly hydrophobic

Always the first amino acid in protein biosynthesis

Acidic amino acids

Form salt bridges & polar interactions with water; H bonding

Side chain pKa = 3.9 (Asp) and 4.1 (Glu)

Amides of acidic amino acids

Not ionisable, but highly polar; strong H donor and acceptor

Basic amino acids

N atoms with free electron pair are basic

Side chain pKa = 10 (Lys) and 12.5 (Arg)

Examples of aliphatic amino acids

Glycine (Gly, G)

Alanine (Ala, A)

Valine (Val, V)

Leucine (Leu, L)

Isoleucine (Ile, I)

Branched chain amino acids - aliphatic

Valine (Val, V)

Leucine (Leu, L)

Isoleucine (Ile, I)

Examples of aromatic amino acids

Phenylalanine (Phe, F)

Tyrosine (Tyr, Y)

Tryptophan (Trp, W)

Histidine (His, H)

(Decreasing hydrophobicity)

Examples of hydroxyl amino acids

Tyrosine (Tyr, Y)

Serine (Ser, S)

Threonine (Thr, T)

Examples of amino acids containing sulphur

Cysteine (Cys, C)

Methionine (Met, M)

Examples of acidic amino acids

Aspartate (Asp, D)

Glutamate (Glu, E)

Examples of amides of amino acids

Asparagine (Asn, N)

Glutamine (Gln, Q)

Examples of basic amino acids

Lysine (Lys, K)

Arginine (Arg, R)

Protein primary structure

Linear sequence of amino acids

Unique sequence for a protein

Primary sequences may be compared against an entire database of sequences such as the Swiss-Prot database

Swiss-Prot database

May reveal relationships e.g. similar protein fold, similar function, evolutionary relationships

Formation of a peptide bond

Condensation of the alpha-carboxyl of one amino acid with the alpha-amino of another

Peptide bond is a type of amide bond

Protein secondary structure

Regions of regularly repeating conformations of the peptide chain, such as alpha-helices and beta-strands (local folding)

Protein tertiary structure

Describes the shape of the fully folded polypeptide chain

Closely packed 3D form

Adapted for a particular biological form

Stabilised by disulphide bonds and non-covalent interactions between side chains

Protein quaternary structure

The arrangement of two or more polypeptide chains into a multi-subunit molecule

Subunits have a defined stoichiometry and arrangement

Subunits may be identical or different

Associate through many weak, non-covalent bond and covalent disulphide bond (rare)

Feature of regulated proteins (e.g. metabolic enzymes)

3D structure and function: protein conformation/fold

Three dimensional shape

3D structure and function: native conformation

A polypeptide chain (protein) folds into a single stable shape under physiological conditions

Determined by the sequence of amino acids and other important factors

Biological function of a protein depends entirely on its native conformation

Two key factors that contribute to protein structure

1. Allowable bond rotations define the possible conformations of the polypeptide chaine

2. Weak, non-covalent interactions between the backbone and side chain groups (e.g. hydrophobic, H-bonding, electrostatic)

Conformational properties of planar peptide groups

C-N peptide bond has double bond character due to resonance resulting in:

1. No bond rotation

2. 6 atoms all lying in the same plane (peptide group)

Cis/trans conformation around the peptide group

Cis conformation is less favourable than trans due to steric interference of alpha-carbon side chains

Nearly all peptide chains are in the trans conformation

Secondary protein structures

Alpha helix

beta strands/sheets

Loops and turns

Secondary protein structures are favoured by...

Allowable phi and psi bond angles

Stabilising hydrogen bonds

Secondary protein structures: alpha helix

Right handed - backbone turns clockwise, viewed from the N terminus

Each C=O forms a hydrogen bond with the amide hydrogen of residue n+4

C=O groups point towards the C-terminus

Side chains point outwards

Stabilisation of alpha helix in secondary structures

By many hydrogen bonds

Hydrogen bonds are nearly parallel to the long axis od the helix

Key properties of the alpha helix

Pitch is 0.54 nm

Rise is 0.15 nm

3.6 amino acids per turn

Alpha helix: pitch

The advance along the helix long axis per turn

Alpha helix: rise

Each residue advances by ____ along the long axis of the helix

Beta strands

Polypeptide chains that are almost fully extended

Beta sheets

Multiple beta strands arranged side by side

Stabilised by hydrogen bonds between C=O and -NH on adjacent strands

Parallel beta sheets

Strands run in the same N- to C- terminal direction

Antiparallel beta sheets

Strands run in opposite N- to C- terminal directions

Interactions of beta sheets

Beta strand sidechains project alternately above and below the plane of the beta sheet

Beta sheets are pleated

R groups (side chains) are on alternating surfaces

Sidechains on adjacent strands are usually in adjacent positions (on the same face)

Side chains can influence interactions of a beta sheet with other parts of a protein structure

Loops and turns

Connects alpha helices and beta strands and allow a peptide chain to fold back on itself to make a compact structure

Loops and turns: loops

Often contain hydrophilic residues and are found on protein surfaces

Loops and turns: turns

Loops containing 5 residues or less

Motifs/supersecondary structures

Recurring protein folding patterns, observed in many proteins

Comprises of at least two connected secondary structure elements

Supersecondary structures: helix-loop-helix

Two helices connected by a turn

Found in many proteins which binds DNA

The longer helix contains residues which bind DNA

The smaller helix mediates protein dimerisation

Supersecondary structures: coiled coil

Two amphipathic alpha helices that interact in parallel through their hydrophobic edges

Some proteins that bind DNA and some structural proteins

Supersecondary structures: helix bundle

Several alpha helices that associate in an antiparallel manner to form a bundle

3-5 helices

Supersecondary structures: beta-alpha-beta unit

Two parallel beta strands linked to an intervening alpha helix by two loops

Found in many metabolic enzymes

Supersecondary structures: hairpin

Two adjacent antiparallel beta strands connected by a beta turn

Supersecondary structures: beta meander

An antiparallel sheet composed of sequential beta strands connected by loops or turns

Supersecondary structures: Greek key

4 antiparallel strands (1 and 2 in the middle, 3 and 4 on the outer edges

Supersecondary structures: beta sandwich

Stacked beta strands or sheets

Domains

Independently folded, compact units in proteins

~25 to ~300 amino acid residues

May be connected to each other by loops

Associated together by non-covalent interactions between side chains

Standalone function

Multiple domains can be combined for a multi-functional protein

Four categories of protein structure

1. All alpha

2. All beta

3. Mixed alpha/beta

4. alpha+beta

Four categories of protein structure: all alpha

Consists of almost entirely of alpha helices and connecting loops

Four categories of protein structure: all beta

Contains only beta sheets and connecting loop structures

Four categories of protein structure: mixed alpha/beta

Contains motifs (supersecondary elements) such as the beta-alpha-beta unit, where regions of the alpha helix and beta strand alternate or are interdispersed

Four categories of protein structure: alpha + beta

Consists of local clusters of alpha helices and beta sheet in separate, clearly distinct regions

Examples of tertiary structure and classification: all alpha

Human serum albumin (helix bundles)

Examples of tertiary structure and classification: all beta

UDP NAG-acyltransferase (beta helix domain)

Concanavalin A (beta-sandwich)

Examples of tertiary structure and classification: alpha/beta

Alcohol dehydrogenase

Rossman fold domain

Examples of tertiary structure and classification: alpha + beta

Pilin

Neisseria gonorrhoea

Carbohydrates

Structures of monosaccharides and polymerisation

Polysaccharides (storage and structural)

Glycoproteins

Nucleic acids

Structure of nucleotides in DNA and RNA

Basic nomenclature of carbohydrates: monosaccharides

One monomeric unit

Basic nomenclature of carbohydrates: oligosaccharides

2-20 monosaccharides

Basic nomenclature of carbohydrates: polysaccharides

More than 20 monosaccharides

Basic nomenclature of carbohydrates: glycoconjugates

Linked to proteins or lipids

Monosaccharides

Two families based on the position of the most oxidised carbon: aldoses and ketoses

Fischer projection of monosaccharides

Useful for understanding stereochemistry

Horizontal bonds point out of the plane

Vertical bonds point into the plain

Hemiacetals/hemiketals

Formed from a reaction between an aldehyde/ketone group reacts with an alcohol group

Hemiacetal formation

Generates two different isomeric forms (anomie's) at the C1 carbon atom

This is called the anemoeric C atom

Pyranoses

6 membered ring (5C + O)

Hexoses commonly form pyranoses

Furanoses

5 membered rings

Pentoses commonly form furanoses

Glycosidic bonds

Links monosaccharides together

The anomeric carbon reacts with an -OH group on the second monosaccharide

Hemiacetal --> acetal

Polysaccharides: homoglycans

Homopolysaccharides containing only one type of monosaccharide

Polysaccharides: heteroglycans

Heteropolysaccharides containing residues of more than one type of monosaccharide

Glucose storage of polysaccharides

D-glucose is stored intracellularly in polymeric forms

Plants as starch

Animals/fungi as glycogen

Polysaccharides: starch

Mixture of amylose and amylopectin

Starch: amylose

D-glucose linked by alpha 1 --> 4 glycosidic bonds

Compact

Helix/spiral

Starch: amylopectin

Spiral chains

Branches due to alpha 1 --> 6 glycosidic bonds

Branches every 24-30 glucose units

Branches increases compactness and increase the number of chain ends (faster formation and degradation)

Polysaccharides: glycogen

Very similar to amylopectin but usually larger (more glucose units)

More branches (every 8-12 residues)

This causes a more compact structure and fast metabolism

Structural polysaccharides: cellulose

Component of plant cell wall

Most abundant biopolymer on earth

Beta 1-4 linkages - relatively straight and unbranched chains

Adjacent chains - hydrogen bonds

Forms fibrils which associate into a high strength insoluble polymer

Structure of DNA dinucleotide

Deoxynucleotide triphosphates (dNTPs) are joined by a phosphodiester linkage

Inorganic pyrophosphate is a leaving group on formation of linkage