S1: Amino Acids and Protein Synthesis Flashcards
Why are amino acids optically active?
The central carbon is a chiral carbon and has 4 different groups attached
Where are D- amino acids found?
In the peptidoglycan bacterial wall
What is the structure of an amino acid?
(Pic)
What type of amino acids are found in humans/nature?
L- amino acids which are optically active
What are a- amino acids
An amino acid where the central carbon bound to the amino group is also bound to the acidic carboxyl group.
What is the ‘R’ group in amino acids?
The ‘R’ group is variable and it also known as the side chain.
It is different in each type of amino acid.
At a neutral PH (isoelectric point), what do amino acids exist as?
They exist as zwitterions. When an amino acid is a zwitterion, the carboxyl group is deprotonated and positively charged, while the amine group is protonated and positively charged.
What happens to an Amino Acid when the PH is low (3/4)?
The carboxyl group gets protonated as well as the anime group already being protonated which gives the amino acid a positive charge.
What happens to an Amino Acid when the PH is high (above 9/10)
The amino group will get deprotonated (and is no longer ionised) and the carboxyl group will remain deprotonated giving the amino acid a negative charge.
How are the 20 different side chains in amino acids grouped?
Polar/apolar
Hydrophobic/hydrophilic
Where do polar and non polar amino acids exist in the cell?
Polar amino acids tend to exist in the hydrophilic regions of the cell.
Non polar amino acids tend to exist in the hydrophobic parts of the cell
What are the subdivisions of polar amino acid side chains ?
Polar acidic
Polar neutral
Polar basic
What are the subdivisions of non polar amino acid side chains?
Aliphatic (straight/branched chains)
Aromatic (ring)
These can be further broken down into being acidic or basic
How do we get essential amino acids that our body cannot make?
We consume them in our diet
What is a polypeptide?
A polypeptide is a chain of amino acids
A protein can be constructed from one or more polypeptide chain
What type of reaction form a peptide bind between the carboxyl and anime group on two different amino acids?
A condensation reaction where water is released
Which groups in the polypeptide form hydrogen bonds?
Keto group from carboxyl group and free hydrogen group from amine group are able to hydrogen bond
What does amino acid residue?
Amino acids once they have formed peptide bonds
What type of bond is a peptide bond?
A covalent bond
What is the primary protein structure?
A sequence of a chain of amino acids
What is the secondary protein structure?
Hydrogen bonding of the peptide backbone causes the amino acid to fold into a repeating pattern
What is the tertiary protein structure?
3D folding of a protein due to side chain interactions They use bonds such as: - ionic - hydrogen - hydrophobic - disulphide
What is the quaternary protein structure?
Protein consisting of more than one polypeptide
A prosthetic group may also be added
What is beta pleated sheet?
It is a form of secondary structure where the side chains of adjacent amino acids point in opposite directions either side of sheet, out of plane of sheet.
What bond forms in beta pleated sheet?
Hydrogen bonds between the keto group on one peptide bond and hydrogen on other peptide bond
What are the two types of beta pleated sheet?
Anti parallel beta pleated sheet (stronger)
Parallel beta pleated sheet
What is the secondary structure of silk (fibroin)
Anti parallel beta pleated sheet
What is alpha helix?
It is the spiral structure of the primary sequence forming coiled coils
What bond occurs in alpha helix?
Hydrogen bond between amide group and carboxyl group
How many residues are there in the chain and per turn in a right handed alpha helix?
4 residues along chain
3.6 residues per turn
Where are the side chains orientated in alpha helix?
There side chains protrude from the sides of the helix.
In some cases they are hydrophobic on one side and hydrophilic on the other side
They also may be positive and negative on one side
How does myoglobin have a higher affinity for oxygen than haemoglobin?
Explain using structure of the protein
Myoglobin consists of multiple alpha helixes bonded to a haem group.
Haemoglobin consists of alpha/beta chains.
What are the two main ways to determine protein structure?
X Ray crystallography
Nuclear magnetic resonance (nmr)
Explain the size and shape of water soluble proteins
Water soluble proteins are often globular in shape
- hydrophilic residues are mostly on external surface
- hydrophobic residues are usually buried inside protein
They may assemble into filaments e.g. actin or tubes (e.g. Tubulin)
Describe the organisation of membrane proteins
The membrane spanning regions have externally located hydrophobic residues that interact with the lipid membrane
They may have hydrophilic central channels
Give an example of a fibrous protein
Collagen
Myosin
Keratin
Explain structure of collagen
Collagen has a triple helix
Collagen molecules may assemble into long fibres of sheets
What determines the structure and function of a protein and how?
The protein sequence!
Each protein has a unique sequence of amino acids specified by a gene. The primary sequence determines the fold of the polypeptide into the functional protein structure.
Changes in the sequence caused by mutations result in altered structures and potentially alterations in function
What causes sickle cell anaemia?
It is caused by a point mutation that changes a single amino acid in the beta chain of haemoglobin.
Glu(negative) replaces by val (hydrophobic)
What happens to the red blood cell in sickle cell anaemia?
In the deoxygenated state, of the mutant haemoglobin (HbS) forms insoluble fibres.
Precipitation if the major protein in the cell distorts the normal disc shape to a SICKLE SHAPE.
These sickle shaped cells break and cause anaemia and block capillaries.
