Amino Acids & Proteins Flashcards
What is a peptide?
A smaller unit of a protein
What are amino acids?
The building blocks of peptides
They contain and amine and a carboxylic acid
The chemistry happens at the R group
Zwitterion (two ions)
What form do amino acids normally appear in?
L amino acids are S
However there is one exception where L amino acid is R
Name the aliphatic amino acids
Glycine (H)
Alanine (CH3)
Serine
Threonine
Name the greasy hydrophobic amino acids
Valine (CH2(CH3)2)
Isoleucine (Ch2(CH3)Ch2(ch3)
Leucine (ch2ch2(ch3)2
Name the aromatic amino acids
Phenylamine
Tyrosine- good for electron transfer
Tryptophan
Name the carboxylic acids and their amides amino acids
Aspartic acid Glutamic acid Aparagine Glutamine (COOH)- provide H+
Histidine
Arginine
Lycine
(Amine)- basic side chains
Name the sulfur containing and proline amino acids
Proline- links in peptide chains
Cystine- provides a thiol
Methionine- can be oxidised to protect against O2
How are peptide bonds formed?
Condensation reaction between amino acids
Water is leaving group
(See mechanism)
What makes the peptide bond planar?
The possible resonance forms makes the peptide bond planar
Outline Chemical vs biological peptide bond formation
Chemical- acyl chlorides- cl- is a good leaving group
DCC + activated esters
Biological- activated esters from tRNA (good leaving group)
- see mechanism
What is the primary structure?
The linear amino acid sequence
Describe the process of Sanger sequencing
F is leaving group then H3O+
This is used to sequence polypeptide chains
See mechanism
Sangers reagent is used- bonds to chain- breaks off one amino acid
What constrains the secondary structure
Planority of amide bond (resonance)
Available conformations due to free rotation around N-C and C-C bonds
NC is phi (dihedral angle)
CC is psi (dihedral angle)
How can the secondary structure be estimated?
On the basis of the
1) planar peptide bond
2) estimated rotations around psi and phi
3) emerging 3D structures
Describe the secondary structure alpha helix
Peptide coil shaped rod
Governed by H bonding- amide backbone can H bond to another amide bond
R groups are projected outwards
Describe the secondary structure beta strand
Extended confirmation (120 torsional angle)
Side chains are projected in different directions
The B strands can align together to form a beta sheet (parallel or antiparallel) (NH2 terminus are on different sides)
What is the secondary structure?
The arrangement into local folding units stabilised by hydrogen bonds
What are examples of tertiary structure?
Beta barrel
Mix of B strands and alpha helix strands
Coiled coils- alpha helix
Describe the oil drop model
This explains folding and structure
The chains fold to minimise interactions between hydrophobic regions and water (fold to protect hydrophobic chain on inside)
Hydrophilic region is on the outside
What interactions provide stability to tertiary structure
1) hydrogen bonds
2) hydrophobic interactions between side chains
3) charged amino acids- electrostatic interactions
4) metal ion binding
5) disulfide bonding
- energetically driven to fold in water
How do you form a disulfide bond?
Two SH groups react in oxidation reaction with O2 to form S-S bridge (+ 2H+ and 2e-)
See mechanism
- this requires an oxidising environment so happens extracellularly ( as there is little oxygen inside cells )
What is quaternary
This is where two different proteins come together (dimers)
Proteins can also form strings
CTB= 5 individual same proteins- pentamer
What do proteins need to be active and stable?
To be active proteins need to fold
To be stable they need interactions
How can proteins cause disease?
Protein misfolding
Why are co factors necessary?
They provide additional chemistry as many biological functions cannot be achieved with the standard 20 amino acids
Proteins recruit additional chemistry groups to aid functionalities
Give examples of co factors?
Metals- redox chemistry
Haem group- carry O2
Diverse co factors derived from vitamins
What is post translational modifications
These are chemical changes to a folded protein
They are covalent modifications of proteins to change its function
Give examples of post translation modifications
Phosphorylation- phosphate attachment Glycoslation- sugar attachment Acylation- acyl attachment Alkylation- alkyl attachment Addition of other proteins
What is protein phosphorylation?
-reversible
Attach a phosphate group using an enzyme
You can switch proteins on and off with enzymes (phosphorylation)
- some proteins may only be active when phosphorylated
