Amino Acids Flashcards
What determines how a protein ‘folds’ into its structure?
The amino acid sequence
How do proteins contribute to their function?
3D structure and their chemical reactivity
How many different amino acids are used to build proteins?
20 different amino acids
What is the composition of amino acid?
Central carbon, amino group, carboxyl group, hydrogen, and side chain (R group)
What is consistent and what is variable between amino acids?
The side chain or R group is variable between amino acids. Everything else is consistent.
What does the amino acid R group vary in?
Size and shape, hydrophobicity, hydrogen bond forming ability, charge and chemical reactivity
What are the four categories of amino acids?
Acid, base, non-charged polar and non-polar
What strongly influences the protein folding of amino acids?
Their hydrophobicity
For cytoplasmic protein, where do hydrophilic and hydrophobic amino acids prefer to be?
Hydrophilic amino acids prefer being on the surface (besides water), and hydrophobic amino acids prefer clustering in the center of the protein (away from water)
Are amino acids with nonpolar side chains hydrophobic or hydrophilic?
Hydrophobic
Are amino acids with polar side-chains hydrophobic or hydrophilic?
Hydrophilic
How many amino acids with non-polar side chains are there?
10 in total
How many amino acids with polar, uncharged side chains are there?
5 in total
What is true about the amino acids with polar, charged side chains?
Their R groups contain acidic/basic groups
How many amino acids with polar, charged side chains are there?
5 in total, 2 acidic amino acids and 3 basic amino acids
What is common between optical isomers?
They have identical chemical composition, but they are arranged in 2 different 3D conformations
What does it mean when enzymes are stereospecific?
They can distinguish between D and L forms
What are the two optical isomers called?
L- and D- forms
How are amino acids linked to one another?
Via peptide bonds
What happens while the peptide bond forms?
Two amino acids gets condensed into one molecule
What is the pattern of the peptide backbone?
Repeating pattern of the atoms N-C-C
Where are the R groups linked to?
Central carbon
Why are amino acids technically no longer ‘amino acids’ once they are polymerized?
Because the chemical composition of their amino and carboxyl end has changed.
What are amino acid residues?
The ‘remainders’ of amino acids within a peptide
What is a peptide?
Any chain of amino acids linked to one another
How are proteins different from peptide?
Proteins are usually longer peptide which has folded into a unique 3D shape which has a defined function
How long would a typical protein be?
100-1000 amino acids long
What is N-terminus and C-terminus?
N-terminus is amino terminus and C-terminus is carboxyl terminus
What strongly influences protein folding?
The polarity of the R group
What is the basic strategy to stably fold proteins in an aqueous environment?
- Cluster hydrophobic amino acids together; put them away from water.
- Expose hydrophilic (polar) amino acids on the surface, allow them to interact with water
Where can disulfide bonds form?
Disulfide bonds can form between two cysteine side chains in proteins
What amino acid restricts the flexibility of peptide backbone?
Proline
What can cystines do?
Cystines can form covalent, disulfide bonds to hold polypeptides together
What is conformation?
It is the final folded structure of a protein
What amino acids are on the surface and inside of a conformation?
Polar amino acids are on the surface, and non-polar amino acids are inside.
How can conformation change?
With an interaction with other molecules
Is proper folding guarantee?
No, because sometimes protein misfold, sometimes they require help from chaperone proteins to fold properly
What are the 4 levels of complexity of protein structure?
Primary, secondary, tertiary, and quaternary structure
What is primary structure?
Linear amino acid sequence of the protein
What is secondary structure?
Small segments of peptide backbone form simple 3D structures
What is tertiary structure?
The entire peptide backbone folds into the full 3D structure of the protein
What is quaternary structure?
More than one folded protein combine into a larger structure
What causes the protein to form fiver-like precipitates?
A single amino acid substitution in the beta-hemoglobin
What is E6V mutation?
Glutamic acid to valine mutation at the 6th position
What are the major secondary structures?
Alpha-helix and beta-sheet
How are secondary structures created and stabilized?
By intramolecular hydrogen bonds
What is alpha-helix?
A right hand helix
Where do the R groups in an alpha-helix point to?
Outward
What holds the alpha-helix together?
Hydrogen bonds between the NCC peptide backbone
Where does the hydrogen bond form?
Between every backbone C=O group and N-H group of the amino acid reside located 4 residues downstream of peptide
C=O groups of aa1 forms hydrogen bonds with?
N-H group of aa5
What does the amphipathic alpha-helix look like?
One side of the helix will be hydrophobic and the other side hydrophilic
What is beta-sheet?
Adjacent chains held together by hydrogen bonds between backbone residues
Differentiate between different configurations of beta-sheet.
Antiparallel - backbone run in opposite direction. Parallel- backbone run in same direction.Mixed- combination of parallel and antiparallel.
When viewed from the edge, how does beta-sheet appear?
Rippled or “pleated”
How do the side chains in B-sheet look like?
Side chains alternate pointing up and down
In beta-sheet, how many amino acids are there per strand? How many strands per sheet?
5-10 amino acids per strands, and 2-15 strands per sheet (avg. ~ 6)
How can you determine the direction of each sheet in B-sheet?
By the relative positions of N, central C, and C’
What forms hydrogen bonds in B-sheet?
N-H and C=O of neighbouring amino acids
Where does hydrogen bonding occur in B-sheet?
Hydrogen bonding occurs once every two amino acid pairs
What sequence determines the secondary structure?
Primary structure
What is tertiary structure?
3D arrangement of the polypeptide; folding of all the secondary structures together
What is single domain?
Single structure of proteins that are folded.
Why do some proteins have multiple domains?
Because different regions of a single polypeptide can fold independently.
What is the function of regulatory domains?
Allows for protein / protein interactions
What is quaternary structure?
Multiple protein associates together to form a larger, more complex structure
What are the different X-mer of quaternary structure and how many polypeptide chains are there in each?
Monomer - 1
Dimer - 2
Trimer - 3
Tetramer - 4
Pentamer - 5
Hexamer- 6
Octamer - 8
What is it called when subunits in quaternary structure are different? identical?
Different subunits - heteromer
Identical subunits - homo
In quaternary structures, what could AA be called? Let AA be two identical subunits or protein
Homodimer of two protein A.
(homo because identical, dimer because two polypeptide chains)
