Chapter 4 Flashcards
what biological macromolecules perform most biochemical functions and catalyze most biochemical reactions?
proteins
what are proteins made of? how linked?
amino acids linked by peptide bonds (aka polypeptides)
what size range are most proteins?
100-1000 amino acids long
what determines the structure of a protein?
the amino acid sequence
what determines the function of a protein?
the structure, determined by the amino acid sequence
what are residues?
amino acids within a polypeptide chain that are linked together
what are amino acids called by themselves?
amino acids (versus residues when they are linked together)
how many common amino acids are there?
20
how do amino acids differ?
by side chain (R group)
how many amino acid side chains are ionizable?
7
what are 3 ways that the side chain can contribute dofferences to an amino acid?
- polarity
- charge
- size
are amino acids chiral or achiral? what does this mean?
they are chiral; means alpha carbon is attached to 4 unique groups
what are the 4 unique groups that the chiral alpha carbon of an amino acid is attached to?
- amino grouo
- carboxyl group
- hydrogen
- side chain
what amino acid is the exception to the chiral rule and why?
glycine has a hydrogen side chain, so its alpha carbon is connected to 2 hydrogens, making it achiral
what are the 2 possible configurations of an amino acid? which one are natural amino acids always in?
L and D; natural amino acids are always in L form
Know the 3 letter and 1 letter names of all 20 amino acids
see flashcards!
what is a special property of aromatic amino acids? name property and the 3 aromatic amino acids
they can absorb and emit radiation
1. phenylalanine
2. tyrosine
3. tryptophan
what is a unique property of cysteine?
in can form disulfide bonds, which helps form tertiary and quarternary protein structures
what is a unique property of proline?
its backbone is fused to its sidechain, makes for kinky polypeptide chains ;)
what is a unique property of glycine?
its alpha carbon is NOT chiral!! (hydrogen is side chain)
give the levels of protein structure from smallest to largest (4)
- primary
- secondary
- tertiary
- quarternary
describe primary protein structure
the amino acid sequence; governs all subsequent structure levels
describe secondary protein structure
3D arrangement of polypeptide backbone into a few common structures
describe tertiary protein structure
folding and arrangement of secondary structures
describe quarternary protein structure
3D arrangement of separate polypeptide chains; the only structure level that involves multiple chains
what kind of reaction forms peptide bonds? give the 2 names
amino-carboxylate condensation aka dehydration synthesis
where does peptide bond formation take place?
in the ribosome
how can peptide bonds be broken? give general process then 2 examples
peptide bond hydrolysis
1. proteases
2. peptidases
what kinds of amino acids are used in acid/base catalysis?
ionizable amino acids
list the 7 ionizable amino acids
- aspartate (aspartic acid)
- glutamate (glutamic acid)
- tyrosine
- cysteine
- histidine
- lysine
- arginine
how many pKas do ALL amino acids have and why?
2; 2 for N terminus and 1 for C terminus
why does the N terminus have a higher pKa than the C terminus?
it has a more basic group than the carboxylic acid end
what is the net charge of an amino acid? what does it depend on?
the overall charge of a molecule; the sum of all charges; depends on pH
what is the isoelectric point?(pI)
the average pH at which a molecule has no net electrical charge
what is the pI governed by?
two pKas that create the neutral species
what does the pI form?
a zwitterion
what is a zwitterion?
electroneutral molecule that contains both positive and negative charges
what are the 3 steps for calculating the net charge of a peptide?
- find the ionizable groups
- determine the charge of each ionizable group at the given pH
- sum charges of all ionizable groups
give the 5 steps for calculating pI?
- find all ionizable groups
- sort pKa’s from lowest to highest
- determine net charges as pH increases (pH=0)
- once the net charge = 0, take pKa above and below current pH
- average the 2 pKas
what is the x axis value for the 1st pKa in a titration curve? how do all other pKas increase?
always 0.5, increase by 1.0 on x axis from there
what are the 3 major types of secondary protein structures?
- alpha helix
- beta sheet
3 beta turn
what is protein folding caused by?
mostly due to noncovalent interactions
are proteins still?
no! proteins are dynamic; always in motion
describe the concept of local versus global conformational changes in proteins
local changes in residues lead to global changes in the whole protein
what causes the secondary structures of proteins?
arrangements of local backbone regions
what is key to the secondary structure of proteins?
hydrogen bonds of the backbone groups
what way do alpha helices turn?
right handed
how many residues are there per turn in an alpha helix (on average)?
3.6
describe the bonds in an alpha helix
n to n+4h; backbone carbonyl oxygen hydrogen bonds with the backbone N-H 4 residues away
give an example of an alpha helix bond
residue 237 and 241
describe the side chain in an alpha helix
extend outward to reduce steric strain
descibe the effects of charged side chains on alpha helices
can help or hurt
1. mix of positive and negative side chains attract and help maintain the helix
2. if all negative or all positive side chains will repel and break the helix
describe the effects of bulky side chains on alpha helices
steric hindrance breaks the helix
describe the effect of proline on an alpha helix and why
helix breaker (side chain fused to backbone)
is glycine a good or bad helix maker? why?
bad helix maker because it has no side chain to interact in any way with other peptides
why does the alpha helix have a dipole moment?
the resonance in the peptide bonds gives them a double bond character and rotation around the double peptide bond is impossible so the peptide backbone has a dipole moment (partial positive on Nterm and partial negative on Cterm), so the alpha helix has an overall dipole moment
what is an amphipathic helix?
an alpha helix with one hydrophobic face and one hydrophilic face
what are amphipathic helices good for? (2)
- gating (keeping the binding site inside and protectec)
- fat hydrolysis
describe the beta strand secondary protein structure
extended polypeptide chains where the side chains extend above and below the backbone
how are beta strand depicted
as an arrow where the point of the arrow points toward the c terminus
describe the beta sheet secondary protein structure
beta strands arranged side-by-side
how are beta sheets joined together?
hydrogen bonding occurs between strands, between the backbone N-H and the carbonyl O
what are the 2 types of beta sheets? describe
- parallel: both strands run same direction
- antiparallel: strands run in opposite directions
what is the beta turn secondary protein structure needed for?
anti-parallel beta sheets only
describe the beta turn secondary protein structure (2)
- connects 2 adjacent segments of antiparallel beta sheets
- 4 residues long
how are beta turns joined together?
residues 1 and 4 interact via hydrogen bonds (between C=O of residue 1 and N-H of residue 4)
where do beta turns occur? what happens to residues 2 and 3?
occur in solvent-exposed regions, residues 2 and 3 hydrogen bond with water (the solvent)
what makes secondary protein structures possible?
phi and psi dihedral angles
what 4 atoms make the phi dihedral angle
amino nitrogen and alpha carbon, then the 2 carbons of each carbonyl
what 4 atoms make the psi dihedral angle?
alpha carbon with carbonyl carbon, then the two amino nitrogens
what 3 factors affect dihedral angles?
- steric interference has to be minimized (larger side chains may clash)
- H-bonding is maximized, as the carbonyl O is H-bond acceptor and amide N-H is H-bond donor
- the side chains present: proline’s phi angle is blocked
what are ramachandran plots?
a plot of all phi and psi angles in a protein
what shade do lower energy regions appear in a ramachandran plot?
darker
what is the importance of a ramachandran plot?
different secondary structures exhibit the same phi and psi angles, so you can plot them to see what secondary structures exist in a peptide
what do you have to know about ramachandran plots?
the general locations of secondary structures, go draw them NOW!!
what is the tertiary structure of a protein?
the 3D shape of a protein including the backbone and side chains (folding); how the secondary structure is arranged
what is the tertiary structure of a protein driven by?
hydrophobic effects
what are the two main shapes of tertiary protein structures?
globular and fibrous
describe globular protein shape
spherical
describe globular protein solubility
soluble in water
describe the core and exterior of globular proteins
hydrophobic core, hydrophilic exterior
what kind of secondary structure types can globular proteins have?
several types
give two common protein types that are often globular
enzymes and regulatory proteins
describe the shape of fibrous proteins
rod shaped
describe fibrous protein solubility
insoluble in water
describe the secondaary structures found in fibrous proteins
usually one repeating element of secondary structure (house of many of the same brick)
give a protein class that is often fibrous
structural proteins
when referring to tertiary protein structures, what does domain mean?
separate structural unit of a protein
when referring to tertiary protein structures, what does denaturation mean? how is this accomplished?
unfolding of a protein; through chaotropic agents and detergents
when referring to tertiary protein structures, what does renaturation mean?
refolding of a protein to native state
describe the beta barrel domain tertiary protein structure
a bunch of beta sheets combined
describe the leucine zipper domain tertiary protein structure
leucines in between alpha helices
describe the alpha/beta domain tertiary protein structure
alpha helices mixed with beta sheets
how are domains held together?
cross-linking
how is cross-linking accomploshed to hold together domains in tertiary protein structures? give 3 ways and describe
- ion pairs (salt bridges) such as acidic/basic side chains
- disulfides: two cysteine residues that interact after oxidation
- coordination around metals: zinc fingers (metal ion in betwene proteins)
what is quarternary proetin structure?
the 3D assembly of all polypeptide chains
what are the 2 prefixes to describe quarternary protein structure? describe
- homo: identical subunits
- hetero: different subunits
how aare quarternary protein structures held together?
the same forces as tertiary (H-bonds, disulfides, ionic)
what do quarternary protein structures allow for?
allow large proteins to be expressed separately
