Amino acid, protein and enzymes Flashcards
What is the central dogma of molecular biology theory?
Genetic information flow only in one direction - DNA -> RNA -> Protein
What are the four nitrogenous bases?
Adenine, Guanine, Cytosine, Thymine
How many nucleotides does it take to make a codon?
3
From the 64 different codons, how many different amino acids are coded for?
20
What is the structure of an amino acid?
- Carboxylic acid
- Amine group
- R-Group
- α-carbon
What is the R group?
Unique chemical and biological property of the amino acid
What is the formula of Carboxylic acid?
COOH
What is the formula for amine group?
NH2
What is a Zwitterion?
Internal transfer of H+ from the carboxylic acid to the amine
What does a zwitterion contain?
A positive and negative charge but has a net charge of 0
What is the proportion of amino acids, in their positive, negative and zwitterionic form dependent on?
pH
What is the Zwitterionic structure?
Two groups that are accepting/donating H+
What is Chiral carbon?
A carbon that is bonded to 4 different groups
What does a chiral carbon result in?
2 non-superimposable stereoisomers
What are examples of stereoisomers?
D-amino acid and L-amino acid
What are enantiomers?
D-amino acids and L-amino acids are mirror images of each other
Between D-amino acids and L-amino acids, which amino acid form proteins?
L-amino acids
What can Thalidomide be used as?
- Tranquiliser
- Treating morning sickness
What is the protein structure?
- Primary structure
- Secondary structure
- Teritary structure
- Quaternary structure
What does Aliphatic R groups features have?
- Carbon chains
- non-polar
- Hydrophobic
- Cluster together inside the protein avoiding aqueous environment -> 3D structure
What does Aromatic R groups features have?
- Double bonded carbon rings
- Non-polar
- Hydrophobic
- Cluster together inside protein -> 3D structure
What are the features in polar, uncharged R groups?
- Electronegative heteroatom (N, O or S)
- Hydrophillic (cluster on the enterior of a protein)
- Heteroatoms in hydrogen bonding with water
- Cysteine
What does Cysteine do in uncharged R groups?
Forms disulfide bridges with other cysteines
What are polar, charged R group features?
- Positive or negative charge
- Hydrophillic
- Participate in hydrogen bonding
How is peptides designed for pharmaceutical?
- Select R group that bind to target protein
- Choose hydrophillic R groups that make the peptide more soluble in water
What is needed for amino acid to bind to tRNA?
Energy
How is a peptide bond formed?
Reaction between amine and carboxylic acid, releasing water
What structure is α-helix?
Tightly coiled polypeptide
What structure is β-sheet
pleated sheets
What is the Tertiary structure?
Spatial arrangement of amino acids residues that are far from each other in the linear sequence
What is molecular chaperones?
Catalyse the folding process
What is Monomeric protein?
Single polypeptide chain (only tertiary structure)
What is Oligomeric protein?
2 or more polypeptide chains held together by noncovalent interactions
What is the Conjugated protein?
Has non-amino acid component (prosthetic group)
How to calculate protein weight?
Number of amino acid residues x Average weight of an amino acid residue
What is an enzyme?
Protein that catalyses a biochemical reaction via lowering the activation energy of the reaction
What is the effect of enzymes?
- Draws reactants together
- Ensure right orientation for reaction
- Put strain on the bonds needed to be broken
What does high temperature do to enzymes
Distorts bonding, causes active site to change shape and the enzyme to denature
What does changes in pH cause to enzymes?
Distorts bonding, causing it to denature
What is th Michaelis-Menten equation?
Variation of enzyme activity as a function of the substrate concentration
What is V0 ?
initial velocity of product formation caused by substrate concentration [S]
What is Vmax?
maximum velocity of product formation
What is Km?
Michaelis constant
How to determine V0?
- Plot product concentration over time.
- Calculate gradient of curve at time = 0
- Gives a number with units µM/min
- V0 is dependent on the [S] at time = 0
What are irreversible inhibitor?
Binds strongly to an amino acid R group that participates in substrate binding or catalysis (permantely inactivating the enzyme)
What is the reversible inhibitor?
Inhibitory effects can be reversed by the presence of the substrate
What is a competitive reversible inhibitor?
Form weak covalent bonds with th activ site - substrate can displace the inhibitor
What is a Non-competitive reversible inhibitor?
Inhibitor binds to allosteric site, causing a change to active site
What are the effects of competitive reversible inhibitor on the Vmax?
Vmax of the reaction is unchanged.
- Vmax related to activity of the enzyme
- Enzyme itself is unchanged
- It just needs more substrate
What are the effects of competitive reversible inhibitor on the Km?
Kmof the reaction has increased
What is the effect of Non-competitive reversible inhibitor on Vmax?
Vmax of the reaction has decreased.
- Vmax related to activity of the enzyme
- Active site conformation has changed
- Enzyme cannot work as efficiently
What is the effect of Non-competitive reversible inhibitor on Km?
KM of the reaction is unchanged
- KM related to substrate concentration
- Substrate is not competing for active sites
- Don’t need more substrate
What is the frugal system?
No energy wasted in producing intermediate products whn they are not needed
