Amino Acids and Proteins 1.What is an amino acid / protein 2.Where are they found 3.Properties of the amino acids 4.How are proteins synthesized 1.Transcription

Amino Acids and Proteins

1.What is an amino acid / protein

2.Where are they found

3.Properties of the amino acids

4.How are proteins synthesized1.Transcription & translation

Amino Acids

Amine and carboxyl groups. Sidechain ‘R’ is attached to C-alpha carbon

The amino acids found in Living organisms are L-amino acids

Amino Acids - peptide bond

N-terminal C-terminal

Transcription & translation

DNA | TranscriptionmRNA

| TranslationProtein

In higher organisms thepicture is a bit more complex.DNA -> pre-mRNA -> mRNA->protein

Protein might need a chaperonein order to fold correctly.

movie

Subcellular location

An animal cell:

Proteins - where are they found

1. Proteins are found in all living organisms2. In humans there are approx 25.000 proteins3. Each protein has a specific function

1. Making up the human tissue - skin, hair, heart ...2. Degrading the food we eat3. Immune system4. Transportation of Oxygen in blood5. Triggering the growth of cells6. The brain - neural signalling

4. Typically a protein is approx 220 aa in human5. Proteins talk, i.e. Protein-protein interactions

1. To relay a signal across the cell-membrane

1 and 3-letter codes

1.There are 20 naturally occurring amino acids2.Normally the one/three codes are used

Ala - ACys - CAsp - DGlu - EPhe - FGly - GHis - HIle - ILys - KLeu - L

Met - MAsn - NPro - PGln - QArg - RSer - SThr - TVal - VTrp - WTyr - Y

Graphic stick representationDifferent aa, different

property

Ile - Hydrophobic

Phe - Hydrophobic & aromatic

The 20 amino acids

Charged amino acids(sidechain in red)

QuickTime™ and a decompressor

are needed to see this picture.Arg - R

Lys - K

Asp - D

Glu - E

His - H


are needed to see this picture.







Neutral amino acids

Ile - I

Leu - L

Met - M

Phe - F

Pro - P











Property of amino acids (I)neutral, polar or charged ?

Ala - A

Asn - N

Cys - C

Gln - Q

Gly - G











Property of amino acids (II)neutral, polar or charged ?

Ser - S

Thr - T

Trp - W

Tyr - Y

Val - V











Protein structure

Primary structure: Amino acids sequences

Secondary structure: Helix/Beta sheet

Tertiary structure: Fold, 3D cordinates

Protein structure-helix

helix 3 residues/turn - few, but not uncommon-helix 3.6 residues/turn - by far the most common helixPi-helix 4.1 residues/turn - very rare

Protein structurestrand/sheet

Protein structure

Ribbon representation - easy to see the secondary structure elements

Protein structure

Protein structureHydrophilic/hydrophobic & stacking

Protein folds

Class4’th is ‘few secondary structure

ArchitectureOverall shape of a domain

TopologyShare secondary structure connectivity

Summary

DNA -> mRNA -> Protein

transcription translation

1.20 naturally occurring amino acids

2.Each amino acid has different properties, but can be grouped into:1.Charged, neutral, polar (basic, acidic)

3.Secondary structure. -helix & -strand/-sheet

4.Protein hydrophobic inside, polar on the outside

5.Folds or classes: all , all , +, few secondar structure elements

SummaryThe amino acids

A - Ala

C - Cys

D - Asp

E - Glu

F - Phe

G - Gly H - His

I - Ile

K - Lys

M - Met N - Asn

P - Pro

Q - Gln

R - Arg

S - Ser

T - Thr

V - Val

W - Trp

Y - TyrL - Leu

Documents

Amino Acids and Proteins 1.What is an amino acid / protein 2.Where are they found 3.Properties of the amino acids 4.How are proteins synthesized 1.Transcription