KH3 Flashcards
what are proteins
linear polymers of amino acids joined by peptide bonds
sometimes referred to as polypeptides
how are proteins made
translation of mRNAs transcribed from genomic DNA
what is the basic biological point of DNA and RNA
allow synthesis of specific proteins that carry out the physical and chemical functions of cells
what is length of smallest proteins
~40 aa in length
what is length of average proteins
~300-400 aa
what is length of largest protein
~30 000 aa
what is the proteins primary structure
specific sequence of amino acids in a protein
do linear polymers form straight rod like structures
NO
they do not fold randomly
they fold into definite 3d structures depending on the sequence of amino acids (determined by shape of backbone)
what are the functions of a proteins determined by
overall shape (specific folding pattern driven by aa sequence) and distribution of aa side chains (with their distinctive chemical properties)
describe the way genome relates to cell biology
genome DNA –> protein primar structure –> protein 3d structure –> function –> cell biology
what are the 2 major classes of amino acid side chains
hydrophilic
hydrophobic
describe hydrophilic
water loving
side chains have a polar electronic charge distribution (tho they can carry a net charge or be neutral)
interact well with polar solvent water
describe hydrophobic
non polar charge distribution
do not interact well with polar solvent water
like oil and water
describe the hydrophobic effect
water molecules surrounding hydrophobic molecules dispersed in water adopt a constrained cage like organization - low entropy
if hydrophobic molecules coalesce - total number of low entropy constrained water molecules is reduced - net increase in entropy drives formation of separate hydrophobic and aqueous phases
what is the coalescence of hydrophobic molecules also favoured by
weak non covalent van der waals intermolecular interactions
describe hydropohic effect informally
2 non polar substances surrounded by water - hydrogen bonded lattice constraining water molecules in cages - water isn’t free to move and degree of randomness is low
then hydrophobic aggregation = 2 non polar bond together and water molecules are released, don’t need as many water molecules, its more efficient to package together, so more random, higher entropy and drives the separation of water and oil
describe oil drop model of protein folding
hydrophobic side chains inside and hydrophilic side chains facing outside
describe why the oil drop model is important
the rule must be respected in any protein structure since cytoplasm is aqueous
define only the crudest level of protein structure
how many structures do proteins adopt
only one or a small number of similar structures called conformations
what are specific protein structures based on
general oil drop model (basic level of chemical topography)
hierarchy of structural elements that define specific elements of substructure
what are the specific and local structural interactions called
secondary and tertiary structure
determine path of peptide backbone through space –> the overall shape of molecule
describe general overview of protein structure/function/folding
primary = sequence
secondary = local folding and h bonding between aas that are close together
tertiary = overall conformation, determines function of protein and all capabilities –> all function OR quaternary
quaternary = complex multimeric structure –> all function OR supramolecular
supramolecular = quite definite large scale assembly–> all function
describe primary structure (generally)
sequence of amino acids
describe secondary structure (generally)
alpha helix = local folding of peptide backbone
beta sheets = add laterally forming a flat sheet like structure
describe tertiary structure (generally)
final structure
elements of secondary come together in specific ways
describe quaternary structure (generally)
made on different ribosomes and they find each other
functional protein has enzymatic function (tertiary could not have enzymatic properties
what are protein structure and function dictated by
amino acid sequence
this dictates 3d structure, so function of protein
DNA indirectly determines protein function
what is a domain (generally)
part of tertiary structure that is independent of molecule
if it is cut off it will float away and hold structure
not every protein has definite domains but many do
what are the important aspects of proteins to remember when thinking about structure or folding
Structure = alpha carbon, h, r group, amino end (linked to cooh of another aa) & cooh end (linked to amino of next aa)
linking = dehydration and formation of peptide bond, amino hydrogens and carbonyl O2
protein translation = amino acid tRNAs
structure of tripeptide = N terminus –> C terminus (5’–>3’), directionality and polarity
what is secondary structure
local conformations of the peptide chain backbone
multiple secondary structure elements
name and describe the 2 major peptide chain backbone conformations of secondary structure
alpha helix = 60% (other 40% = not anything, not alpha or beta but definite path it takes) of length of average polypeptide, chain consists of segments of beta sheet or alpha helix
beta sheet
what are both structures (of secondary structure) based on
H bonding between peptide bond and carbonyl O atoms on aa residue and amino group hydrogens on different aa residue
describe alpha helix structure (periodicity)
periodicity - aa=n and H bonds with aa = n+4
tilted axis of h bonds drives periodicity of 3.6 residues per turn (if h bond aligned =4, but they are tilted, so 3.6 = 36 aa gives 10 turns)
describe alpha helix structure (gross structure)
straight rod
stiff rod with side chains protruding and interaction with other side chains
describe alpha helix structure (surface properties)
dependent on side chains
determine propensity for alpha helix to form and the interactions of alpha helix with other parts of protein (its stability)
can favour or not favour alpha helix - only where side chains do not disturb it
describe beta sheet structure
h bonds link adjacent beta strands
can create large surfaces
strands may be parallel or antiparallel (could be from different polypeptides)
lateral interaction
describe amino acid side chains of beta sheets
protrude above and below the plane of the beta sheet
determines the interactions of the beta sheet with other parts of the protein and the propensity (tendency) for beta sheet to form
what is tertiary structure
overall conformation of the polypeptide
the spatial organization of the multiple secondary structure elements
what is Ras
a small GTPase
GDP binding pocket - side chains reach it and have binding sites for it
describe tertiary structure
can see alpha helix and beta sheet
what do amino acid side chains do in tertiary structure
amino acid side chains mediate interactions between different parts of the protein and its ligand GDP
what are the structure driving interactions among amino acids in a protein
non covalent bonds
describe importance of H bonds in protein structure
h bonds among peptide backbone carbonyl and aa groups support alpha helix and beta sheet secondary structure
h bonds between aa side chains with polar side chains
describe importance of ionic bonds in protein structure
ionic bonds between basic (+) charged and acidic (-) charged side chains
describe importance of van der waals interactions in protein structure
Interactions among hydrophobic side chains
T OR F: covalent bonds are completely useless for proteins
FALSEE
one covalent bond interaction can be important = CYSTEINE BONDS
describe cysteine bonds
side chain of amino acid cysteine contains sulfhydryl group that can covalently from S-S (disulfide) bonds with other cysteine side chains
describe the importance of cysteine bonds
disulfide bonds can be intrachain = contributes to tertiary structure
interchain = contributes to quaternary structure
helps maintain shape
what are motifs
combinations of secondary structures forming distinct local 3D structures with definite properties
have recognizable structure and characteristic aa sequence features
describe coiled coil motif
heptad repeat of hydrophobic - every 7/2 = 3.5, pattern repeats, close to pitch of an alpha helix
involved in protein-protein interactions
strips of hydrophobic side chain showing - how they bind
describe EFhand/helix-loop-helix motif
2 alpha helices with 90 degree angle between
a Ca++ binding motif (allows it to bind to calcium)
describe zinc-finger motif
alpha helix associated with short beta sheet
common in transcription factors - binds to DNA/RNA
describe motifs (compared to domains)
generally small
local structures
do not contain a sufficient number of structure maintaining bonds to hold motif in 3d shape if its cut away from protein
rest of protein contributes to stability of local motif
not structurally independent
describe domains (compared to motifs)
characteristic 3d structures within proteins
larger than motifs
contain a sufficient number of bonds to hold the domain in its characteristic shape if cut away from rest of protein
rest of protein does not contribute much to the stability of the domain
domain = structurally independent entities that are covalently joined to the rest of the protein
name the 4 major structural classes of proteins
fibrous (used in cytoskeleton)
globular (independent, float around)
integral membrane (embedded)
intrinsically disordered
describe intrinsically disordered proteins
proteins or protein segments that exist as random coils under physiological conditions
sequence does not adopt specific structure by itself
what might intrinsically disordered proteins adopt
a specific secondary/tertiary structure upon binding to a well structured partner protein
then can adopt specific configuration
describe tertiary structure domains
> 40 aa long region
compactly folded
can be made of various motifs
describe tertiary structure domains example
globular and fibrous domains of influenza virus hemagglutinin HA2 subunit
HA2 fibrous domain interacts with HA1 subunit
(for quaternary)
heterodimer - ex of quaternary structure, independent polypeptides come together
describe the modular nature of protein domains
similar domains can be found in diverse proteins and as multiple similar copies with any protein
name some modular protein domains
ECF precursor - membrane attachment domain (membrane spanning)
Neu oncogene protein
epidermal growth factor - hormone
tissue plasminogen activator
describe quaternary structure - multimeric proteins (influenza virus hemagglutinin)
trimer of identical subunits - each has HA1 & HA2 chain - held together by noncovalent bonds
= 3 identical 2 protein subunits held together by noncovalent bonds
describe multimeric proteins
can contain any number of identical or different polypeptides
what are supramolecular complexes
> 1MDa
large molecular machines made up of multiple distinct proteins - each may contain multiple subunits
ex: transcription initiation complex
what is more important: the 3d structure of the protein or the amino acid sequence
3d protein structure
many amino acid sequences can make the same shape
shape matters
only point of aa sequence is to drive the structure
evolutions goal is to conserve structure and function of protein
