6-7 Amino Acids and translation

Fibrous proteins

• insoluble and provide structure

• cytoskeleton

• coatings (seeds)

• ie silk

Globular

• enzymes (catalysts)

• transport protein (haemoglobin)

• hormones (insulin)

• defense (antibodies)

• toxins (snake venom)

• Receptor (rhodopsin)

Amino acid: general structure

Zwitterionic

posesses both positive and negative charges

Chiral

amino acid property- only L amino acids exist in biology (glycine is not chiral)

Amino acid properties

• Zwitterionic

• Chiral

• range of sidechain / R groups

Aliphatic

• No charge on sidechain

• increasing in hydrophobicity with sidechain size

• Glycine, Alanine, Valine, Leucine, Isoleucine

Imino acid

• only amino acid with a secondary amine group present. all others primary amines

• sidechain from 5 membered ring- looping from the c alpha to the nitrogen

• confers diff properties on the polypeptide chain

• proline

Polar

• sidechains contains hydroxyl groups

• H-bond acceptors/ donors

• hydrophbic in nature

• Serine, Threonine

Basic

Lysine, Arginine, Histidine

Which amino acid has a pKa of 10

lysine

which amino acid has a pKa of 12

Arginine

which amino acid has a pKa of 6.5

Histidine

Acidic and amide derivatives

• change o- (carboxyl group) to H2N

• Aspartate, Aspargenine, Glutamate, Glutamine

Formation of a peptide bond:

Carboxylic acid reacts with amine

how do you estimate molecular mass of a protein

take number of amino acids and multiply by 110

how do you describe an amino acid

start at N- terminus (Amide) and then end at C terminus (hydroxyl group)

Tautomers

same molecule but can exist in 2 states

properties of a peptide bond

• planar structure

• partial double bond characteristic

• exist as tautomers

Protein backbone conformation

• each Ca carbon has 2x peptide planes connected to it

• orientation of these is defined by phi and psi

what determines backbone conformation

phi and psi

what is glutamic acid used as

excitatory neurotransmitter

whats glycine used for

inhibitory neurotransmitter

amino acids not from the standard 20 amino acids

• Hydroxyproline: hydroxylation of of proline in collagen

• Gamma amino butyric acid: signaling molecule in the brain

• Natural antibiotics e.g. texiobactin a new class of antibiotics to treat drug resistant bacteria

• D- amino acid, methylated phenylalanine and alpha amino acid enduracididine

Prokaryotic

• 70S

• subunit (small and large)

  • Large (50S)

    • 34 proteins

    • 3rRNAs

  • Small (30S)

    • 21 proteins

    • 1rRNA

Eukaryotic

• 80S

• 2 Sununits:

  • large (60S)

    • 49 proteins

    • 3 rRNAs

  • small (40S)

    • 33 proteins

    • 1rRNA

Svedberg coefficient

rate at which a particle sediments in a centrifuge

Binding sites on tRNA

• A site (amino acid)

• P site (peptide)

• E site (exit)

Phe

UUC UUU

Leu

UUA, UUG, CUU, CUC, CUA, CUG

Ile

AUU, AUC, AUA

Met

AUG

Val

GUU, GUC, GUA, GUG

ser

UCU, UCC, UCA, UCG

Pro

CCU, CCC, CCA CCG

Thr

ACU, ACC, ACA, ACG

Ala

GCU, GCC, GCA, GCG

Tyr

UAU, UAC

Stop

UAA, UAG, UGA

His

CAU, CAC

Gln

CAA, CAG

Asn

AAU, AAC

Lys

AAA, AAG

Asp

GAU, GAC

Glu

GAA, GAG

Cys

UGU, UGC

Trp

UGG

Arg

CGU, CGC, CGA, CGG

Ser

AGU, AGC

Arg

AGA, AGG

Gly

GGU, GGC, GGA, GGG

where does protein synthesis occur

cytoplasm/ surface of the ER

Inhibitor and mode of action

• tetracycline: block binding of aminoacyl- tRNA to the A- site

• Streptomycin: Blocks the transition from the initiation of translation to enlongations

• Chloramphenicol: prevents the peptidyl transferases reaction

• Erythromycin: Block the tunnel where the nascent peptide emerges preventing protein synthesis