Protein structure and function (wk 1) Flashcards
List four main functions of proteins
Catalysis
Transport e.g. hemoglobin and O2
Structure
Motion e.g. actin
Proteins are linear ______ made of ______
heteropolymers made of alpha amino acids
List the 4 classes of protein structure
Primary
Secondary
Tertiary
Quaterny
T/F:
Only D amino acids can be incorporated into proteins
False
Only L
What is a chiral carbon?
Carbon attached to four different groups
What are the 5 groups used in amino acid classification?
Non polar, aliphatic Aromatic Polar, uncharged Positively charged Negatively charged
What is the isoelectric point?
pH where the amino acid has a neutral charge (pI)
What is pKa?
pH where 50% of the protons are dissociated
What nm do proteins absorb light in?
280nm
Which proteins have the ability to interact with DNA and RNA?
The aromatic ones
Phenylalanine, tyrosine and tryptophan
Which types of amino acids can form H bonds?
Polar amino acids
Which amino acid can form a disulfide bond?
Cysteine
Polar amino acid
Sulfur bond gives some rigidity, important for the folding of the protein
Which group are aspartate and glutamate a part of?
Negatively charged
List three important reactions glutamic acid and aspartic acid are involved in
Amination of R group
Ketone formation
Remove carboxyl group from alpha carbon
What is tyrosine a precursor of?
Dopamine
Noradrenaline
Where is the cut off for polypeptide vs peptide vs protein
Peptide= <10kDa Polypeptide= up to 10kDa Protein= >10 kDa
What type of reaction occurs to make a polypeptide?
Condensation reaction
Water is excluded
The peptide bone allows ______
Resonance
rotation around the bond is restricted because there is a partial double bond
T/F:
The next amino acid of a polypeptide is added on at the C terminus
True
A protein starts with a ____ charge and ends in a ____ charge. Therefore the overall charge is _____.
A protein starts with a positive charge and ends in a negative charge. Therefore the overall charge is neutral.
List some functions of peptides
Hormones/pheremones e.g. insulin, oxytocin
Neuropeptides e.g. substance P
Antibiotics e.g. polymyxin B
Protection e.g. toxins like chlorotoxin in scorpions
What is the native fold of a protein?
Protein molecules adopt a specific 3D conformation that is favourable
The structure is able to fulfill a specific function, it is biologically active
What are some favourable interactions within a protein?
Hydrophobic effect
H-bonds
London dispersion
Electrostatic interactions
The peptide bond has resonance
What does this result in?
The peptide bond is less reactive compared to esters
It is quite rigid and nearly planar
It exhibits a large dipole moment in the favoured trans configuration
In the peptide bond, the carbonyl oxygen has a partial _____ charge and the amide nitrogen has a partial ____ charge
Oxygen= partial negative Nitrogen= partial positive
Phi is the angle between _______
Psi is the angle between ________
Phi= angle between alpha carbon and amide nitrogen Psi= angle between alpha carbon and carbonyl
In a fully extended protein, both phi and psi are ____ degrees
180
A ____ plot shows the distribution of phi and psi dihedral angles found in a protein
Ramachandran
Which two amino acids tend to ‘break the rules’ when it comes to a Ramachandran plot?
Glycine and Proline
What are the two main types of secondary structures?
Alpha helix
Beta Sheet
T/F:
Alpha helixes are usually left handed
False
usually right handed
In an alpha helix, the backbone is held together by _____ bonds between the backbone amides of n and ____ amino acids
held together by hydrogen bonds between the backbone amides of n and n + 4 amino acids
How many amino acids per turn in an alpha helix?
3.6
In an alpha helix, side chains point _____
outwards
T/F:
the inner diameter of an alpha helix is too small to fit many molecules inside and only DNA binds here
False
it is too small to fit anything inside so it is often an empty space
The outer diameter binds with the major groove of dsDNA
What stabilizes the structure of an amino acid?
The carbonyl group of amino acid 1 forms a hydrogen bond with the amide nitrogen of amino acid n + 4
Negatively charged residues in an alpha helix often occur near the ______ end of the helix dipole
positive end
The sheet-like arrangement of a beta sheet is held together by _______ between the _____
hydrogen bonds between the backbone amides in different strands
How are the side chains in a beta sheet arranged?
Protrude from the sheet alternating in an up and down manner
Compare and contrast an anti-parallel and parallel beta sheet
- orientation
- length of the bonds
- strength of the bonds
Anti-parallel:
Amino group is followed by the carboxyl group
H bonds run in opposite directions which results in linear H bonds = stronger
Parallel:
H bonds run in the same direction= bent H- bonds= weaker
Longer H-bonds
What is a beta turn?
Occurs when the strands in a beta sheet change direction
The 180 turn is accomplished over 4 amino acids
It is stabilized by a hydrogen bond from a carbonyl oxygen to amide protein three residues down the sequence
In type 1: proline is in position 2 (breaks the structure to push it to the other side)
In type 2: glycine is in position 3 (provides some flexibility)
What are the two major classes of protein tertiary structure?
Fibrous and globular
List some forces that might be found in protein tertiary structures
hydrophic interactions polar interactions disulfide bonds h bonding between peptide groups metal ion coordination ionic linkages
What is the quaternary structure of a protein?
Formed by the assembly of individual polypeptides into a larger functional cluster
What are some interactions you may find in a quaternary structure?
Hydrogen bonds
Disulfide bonds
What are some benefits for a protein to occur in a quaternary structure?
Stability- reduction of surface to volume ratio
Genetic economy and efficiency
Brings catalytic sites together
Cooperativity
What is denaturation and how can it occur?
Loss of structural integrity with accompanying loss of activity
heat or cold
pH extremes
organic solvents
chaotropic agents
How many strands do you need to form a beta sheet?
2
Describe some diseases related to protein mis folding
refer to written notes cbf to write it all out here sorry future eva
