Biochemistry: Amino Acids, Proteins, Ptm

Mostly, hydrophobic core region is inside, and hydrophilic outside as it can form polar side chains outside.

Exeption is intermembrane proteins such as aquaporin where hydrophobic is outside and hydrophilic inside.

•Covalent; disulphide bridges (not all proteins have them)

• Non covalent

--> hydrogen bonds

--> electrostatic interactions

--> Van der Waals forces

--> Hydrophobic effect

The primary structure of a protein is the amino acid sequence including any disulphide linkages

The spatial arrangement or amino acids near to each other in the linear sequence

The spatial arrangement of amino acids usually far apart from each other in the primary sequence

The spatial arrangement in a protein made up from more than one polypeptide chain

In a protein made up from multiple polypeptide chains each chain is called a subunit

Subunit can be same (homo) or different (hetero) polypeptides

Protein with a quaternary structure of four subunits

Eg haemoglobin (2 alpha subunits and 2 beta subunits)

• Hydrolyse RNA

• 124 amino acids (bovine)

• 4 disulphide links in native conformation

--> 26-84, 40-95, 58-110, 65-72

The primary structure of a protein determines its tertiary structure

• Involves solutions containing 8M urea or 6M guanidine hydrochloride

• in these solutions proteins denature into random coils

• Also used B-mercaptoethanol which is a reducing agent and breaks disulphide bonds --> He dissolved RNAse in this solution and 8M urea --> RNAse loses all activity (completely denatured)

But when he removed the urea and mercaptoethanol using dialysis--> RNAse spontaneously regains all enzyme activity...RNAse has renatured

Non random folding--> allows protein to fold very rapidly

•The 3D arrangement of protein atoms in its structure

• conformation is independent of the number of chains in a protein

• Delay folding

• Change environment ( as inside of cell is not the ideal environment for protein folding)

• Disulphide bonds in keratin chain broken by thick reduction

• Hair wrapped around curling rods with H2O2

• heat and moisture disrupts hydrogen bonds

• Neutraliser allows disulphide bonds to reform between the multiple strands

• Aggregates of misfolded proteins

• Form fibrils and plaques

• Linked to >50 human diseases

• Often neurodegenerative e.g. Huntington's, Alzheimers, Parkinson's

• The modification of selected residues in a protein after it has been made but not as a component of synthesis

•Acetylation

•Hydroxylation

•Glycosylation

•Phosphorylation

•acetyl coenzyme A (Acetyl coA) •N-acetyl transferase enzymes (NATS)

•Hydroxyproline and hydroxylysine

•Hydroxyproline is a major component of collagen (some hydroxylysine also present)

--> hydroxyproline involved in H-bonding within collagen fibre--> key for its structural stability

• prolyl hydroxylase

• requires ascorbic acid as cofactor (vitamin C)

•lack of vitamin C causes scurvy (loss of teeth, bruising, poor wound healing, eventually death)

•Lack of vitamin C means proline in collagen is not hydroxylated

•Lack of H binding prevents collagen from forming correct structure which is essential for its function

•Lack of functional collagen leads to symptoms of Scurvy (role of collagen in wound healing and in connective tissue)

• Attachment of sugar molecules to specific residues in proteins

• Occurs in eukaryotes and takes place in the lumen of the endoplasmic reticulum and in the golgi apparatus

•N-glycosylation

•O-glycosylation

•Involves attachment oligosaccharide to an asparagine residue

• Only occurs in sequence N-X-S/T except where X is a proline

• Oligosaccharide consists of 2 molecules of glucosamine, 9 molecules of mannose and 3 molecules of glucose

•Involves attachment of sugar to O group of threonine and serine

•Unlike N-glycosylation there is no characteristic sequence involved

• Phosphoryl group (dervived from ATP) is attached to the OH group in the side chains of

--> Threonine

--> Serine

--> Tyrosine

• kinases attach

• Phosphotases remove

• Ubiquitination

• Sumolation

• Nucleotide addition

• Nitrosylation

• Sulfonylation

• Carbonylation

• Biotinylation

• Process by which specific peptide bonds between amino acid residues are hydrolyzed

• this is performed by enzyme proteases

•Metalloproteases e.g. carboxypeptidase A

• Serine proteases e.g. Chymotrypsin

•Aspartyl proteases e.g. HIV protease

• Digestive enzyme

• Member of metalloproteases

• All metaloproteases have metal ion in active site of enzyme

• Carboxypeptidase A contains zinc (Zn2+)

•Cleaves off (hydrolyses) last C-terminal residues from polypeptide chain

• Functions best when residue is aliphatic l

• Digestive enzyme found in gut

• Member of large family of proteins called the Serine Protease

• All serine proteases have critical serine residue in active site

• Cleaves off peptide bond on the carboxyl side of aromatic or large hydrophobic residues

• Firstly role of HIV protease is to cleave its self out of a large polypeptide chain produced from the viral genetic material

• HIV protease then proceeds to chop up remaining hits of polypeptide into functional proteins

• Critical to viral replication

• Critical aspartic acid in active site

• Many gastric proteases synthesised in pro-form ("Zymogens")

• Need to be cleaved by other proteases into active form

--> carboxypeptidase S and chymotrypsin initially synthesized as zymogens

--> both cleaved by site-specific protease Typsin into active forms