12 AA and protein structure Flashcards
What is the general structure of an AA?
central carbon attached to:
amino group
carboxyl group
R side chain
What are the 3 general properties of an AA?
- AA are dipolar ions (= at pH 7.4, the AA are protonated and the carboxylic acid groups are in their carboxylate form (neg charge), has both pos and neg charge
- peptide bonds link AA
- AA side chains can be non-polar, polar or charged
what is the most useful way to classify the 20 standard AA?
by the polarities of side chain
What is the classification of these AA?
Non polar hydrophobic
majority of carbon and hydrogen in r side
look out for C and H
what is AA group is glycine classified as?
non polar hydrophobic
its very simple so can be put into different classes, but put here
Non polar vs polar, hydrophobic vs hydrophilic
More non polar - more hydrophobic
More polar - more hydrophilic
What is the classification of these AA?
polar uncharged, hydrophilic
see a lot of hydrogen bonds between H and O (hydroxyl group) = polar
or see amine group, also hydrogen bond between H and N
also no charge on side chain
look out for hydrogen bonds between OH and H and N
What classification is cysteine?
Polar (hydrophilic) uncharged, same case as glycine, can be put in diff groups, but for this class put in this one
What is the classification of these AA?
also polar hydrophilic, and is neg charged in side chain = acidic
polar acidic (= hydrophilic and neg charged)
look out for carboxyl group = hydrophilic = polar
What is the classification of these AA?
Polar (hydrophilic), basic (positive-charged)
look out for nitrogen
pos charge = basic, neg charge = acidic
categories of polar side chains
polar = hydrophilic
but can be uncharged, pos, neg charged
What is GFP? (perspective box)
green fluorescent protein
jellyfish emit green flash when attacked, the fluorescence of GFP is the result of reaction between 3AA - serine, tyrosine and glycine
now GFP is used in many biochem assays and bioimaging
What is the primary structure of protein?
Peptide bond, combines 2 AA
O from carboxyl end and 2H from amino end of another
condensation reaction = produce water molecule
What is the name peptide assigned to?
to short polymers of AA
when do you use the names, dipeptide, tripeptide, oligopeptide and polypeptide?
Dipeptide - 2 AA residues
Tripeptide - 3 AA residues
Oligopeptide - more than 12 less than 20
Polypeptide - exceeds several dozens AA residues
What is the secondary structure of protein?
alpha helix - H bond between carbonyl group of one AA and amide group of another
Beta sheet - H bond between carbonyl group of one AA and amide group further downstream on another backbone chain
What is a loop in secondary structure?
unstructured regions
What determines the shape at secondary level?
H bond
What happens are tertiary level?
protein folding dictated by chemistry of various bonds and interactions
what are the 4 different bonds and interactions involved at tertiary level?
- hydrophobic interactions - between non-polar/hydrophobic AA in the interior of the protein or in transmembrane regions
- ionic bonds - between positively charged basic side chains and negatively charged acidic residues
- disulphide bridge - covalent bond formed between sulfhydryl groups of two cysteine residues
- hydrogen bonds - between polar side chains, usually exterior of the protein (interacting w the aqueous environment)
What aa most likely found in interior?
nonpolar and hydrophobic aa
What aa most likely found in exterior
polar and hydrophilic aa
What is the quaternary structure?
refers to the interaction between multiple polypeptide chains
Do all proteins have quaternary structure?
no, but those that do require this association to be active and functional
What are the 3 classes of protein?
- fibrous
- globular protein
- membrane protein
What are fibrous proteins?
(example, structure, role, solubility)
- i.e. collagen
- relatively simple, regular linear structure
- serve structural roles in cells
- insoluble in water or dilute salt solutions
What are globular proteins?
(structure, aa position, solubility)
- i.e. myoglobin
- roughly spherical and compactly folded
- hydrophobic AA side chains in the interior with hydrophilic side chains on the outside exposed to solvents
- usually very soluble in aqueous solutions
What are membrane proteins?
(example, where found, aa position, solubility)
- i.e. bacteriorhodopsin
- found in association with membrane systems of cell
- hydrophobic aa side chains are exposed in the membrane-associated regions. portions exposed to the aqueous environments are hydrophilic in character
- insoluble in aqueous solutions (characteristically fewer hydrophilic aa than cytosolic proteins)
How does perming hair work?
- reducing agent applied to break disulphide bonds, moist heat applied to break H bond and cause alpha helical conformations to uncoil, make keratin in hair shapeless
- hair is waved or curled to an appropriate shape
- oxidising agents added to establish new disulphide bonds to lock the shape, hair is washed and cooled for polypeptide to return to alpha helical conformation
What is the single aa change between haemoglobin and sickle cell haemoglobin?
glutamate -> valine
at 6th position of the beta chain of haemaglobin - change in primary structure
How does the secondary and tertiary structure differ between normal and sickle cell haemoglobin?
normal: normal alpha and beta globin
sickle: 2 abnormal beta globin, 2 normal alpha globin
what is the quarternary structure of normal vs sickle haemoglobin? and diff in shape?
normal and sickle haemoglobin
sickle: fibres of abnormal haemoglobin deform RBC into sickle shape
what is the difference in function of normal and sickle haemoglobin?
normal: molecules do not associate with one another, each carries oxygen
sickle: molecules stick with one another, reduced capacity to carry oxygen = become a fiber
what is the hierarchical model of protein folding?
- secondary structures form first
- ionic interations near one another guide early steps
- longer range interactions come tgt to form supersecondary structures
- complete domains form and entire pp is folded - each domain can have specific function
What is the second model of protein folding?
- secondary structures form first
- spontaneous collapse of pp into a compact state, mediated by hydrophobic interactions among nonpolar aa i.e. hydrophobic collapse, collapsed state is called a molten globule
- protein undergoes series of comlex motions to attain stability and hydrogen bonding
image explains this model thermodynamically
Which model do protein folding follow?
most proteins probably fold by a process that incorporates features of both models
Do all proteins fold spontaneously?
no, most do not
for proteins that do not fold spontaneously, what do they require?
may require molecular chaperones, proteins that interact with partially folded/improperly folded pp to facilitate correct folding pathways or provide microenvironments in which folding can occur
What is amyloidoses?
protein misfolding
- a protein normally secreted from the cell is in a misfolded state and converted into amyloid fiber
- beta sheet attached to another beta sheet = misfolded, will amplify
formation of disease causing amyloid fibrils
Where can you find amyloidoses?
many conditions like alzheimers disease, huntingtons, parkinsons etc and type 2 diabetes arise from protein misfolding
alzheimer’s disease: amyloid deposited in neurons
type 2 diabetes: amyloid deposited near pancreatic islet beta-cells (responsible for insulin secretion and glucose metabolism)
what are prion diseases?
death by misfolding
- diseases that affect the mammalian CNS (originally thought to be caused by viruses) but actually due to protein misfolding
- prion protein -> disease prion protein
- prion protein is a protein with no known function
- PrP sc induces normal human PrP to adopt the conformations of Prp sc = making more forms of PrP sc
- are transmited by consumption of nerve tissue from infected individual
- i.e. mad cow disease
