Pitch of alpha helix
5.4A
Residues between hydrogen bonds
4
Coil diameter of hydrogen bond
5A
Secondary structure
Spatial arrangement of amino acids near eachother in linear sequence
Tertiary structure
Spatial arrangment of amino acids far apart from eachother in primary sequence
Quaternary structure
Spatial arrangement in protein resulting from polypeptide subunit aggregation
Pauling and grey
Beta pleated sheet
Beta pleated sheets
H bonds stabilise it, residues fully extended, can be antiparallel
Distance of beta pleated sheets
3.5
Antiparallel beta pleated sheets
Goes round
Beta turn
4 residues, glycine 3rd, maintains tight structure
Collagen
3 intertwined helical polymers, steric hindrance means glycine interior
Length and diameter of collagen
3000A, 15A
Keratin
Heptad of 7 residues, 2 intertwined alpha-helices
HIV RT action 1
Viral ss+RNA copied to ss-DNA
HIV rt action 2
Ss-DNA copied to dsDNA
HIV rt action 3
dsDNA trasncribed to viral mRNA
HIV rt action 4
Viral mRNA to ss+RNA
Stages of glycolysis
Investment (3) , cleavage (2) and harvesting (5)
Reactions of investment stage
3
Glycolysis reaction 1 action
Glucose -> glucose-6-phosphate
Glycolysis reaction 1 enzyme
Hexokinase
Glycolysis reaction 1
Irreversible, requires energy from ATP
Glycolysis reaction 2 action
Glucose-6-phosphate -> fructose-6-phosphate
Glycolysis reaction 2 enzyme
Phosphoglucoseisomerase
Glycolysis reaction 2
Reverse, Isomerisation
Glycolysis reaction 3 action
Fructose-6-phosphate -> fructose-6-bisphosphate
Glycolysis reaction 3 enzyme
Phosphofructokinase
Glycolysis reaction 3
Reversible, hydroxy group phosphorylated
Glycolysis reaction 4 action
Fructose-6-bisphosphate to DHAP and GAP
DHAP
Dihydroxyacellate phosphate
GAP
Glyceraldehyde-3-phosphate
Glycolysis reaction 4 enzyme
Aldolase
Glycolysis reaction 5 action
DHAP to GAP
Glycolysis reaction 5 enzyme
Triose phophateisomerase
Glycolysis reaction 6 action
GAP to bisphophoglycerate
Glycolysis reaction 6 enzyme
Glyceraldehyde-3-phosphate dehydrogenase
Glycolysis reaction 6
Dehydrogenation, coupled to phosphorylation, NAD+ reduced
Glycolysis reaction 7 action
Bisphosphoglycerate to 3-phosphglycerate
Glycolysis reaction 7 enzyme
Phosphoglycerate kinase
Glycolysis reaction 7
Anhydride bond hydrolysed, generates ATP
Glycolysis reaction 8 action
3-phosphoglycerate to 2-phosphoglycerate
Glycolysis reaction 8 enzyme
Phosphoglycerate mutase
Glycolysis reaction 8
Phosphate shifts from c3 to c2
Glycolysis reaction 9 action
2-phosphoglycerate to phosphoenolpyruvate
Glycolysis reaction 9 enzyme
Enolase
Glycolysis reaction 9
Dehydration reaction
Glycolysis reaction 10 action
Phosphoenolpyruvate to enolic pyruvate
Glycolysis reaction 10 enzyme
Pyruvate kinase
Glycolysis reaction 10
Irreversible hydrolysis reaction
...
Glucose
Pyruvate
Enolic pyruvate
cac reaction 1 action
acetyl co A + oxaloacetate = citrate
cac reaction 1 enzyme
citrate synthase
cac reaction 1
citryl coA intermediate, enzyme initally can only bind to oxaloacetate
cac reaction 2 action
citrate to isocitrate
cac reaction 2 enzyme
aconitase
cac reaction 2
cis-aconitase intermediate, enzyme has 4Fe, 4S with 3 cysteines
cac reaction 3 action
isocitrate to alpha-ketoglutamate
cac reaction 3 enzymes
isocitrate dehydrogenase
cac reaction 3
produce first pair of high energy electrons, oxidative decarboxylation
cac reaction 4 action
alpha-ketoglutarate to succinyl coA
cac reaction 4 enzyme
alpha-ketoglutarate dehydrogenase complex
cac reaction 4
produces 2nd pair of high energy electrons
cac reaction 5 action
succinyl coA to succinate
cac reaction 5 enzyme
succinyl coA synthetase
cac reaction 5
succinyl coA thioester cleaved, coA displaced by orthophosphate to succinyl phorsphate, phophoryl group removed by His, phosphohistidine transfers P to GDP
cac reacton 6 action
succinate to fumarate
cac reactoon 6 enzyme
succinate dehydrogenase
cac reaction 6
3rd pair of electrons accepted by FAD on histidine
cac reaction 7 action
fumurate to malate
cac reaction 7 enzyme
fumurase
cac reaction 7
hydration reaction
cac reaction 8 action
malate to oxaloacetate
cac reaction 8 enzyme
malate dehydrogenase
cac reaction 8
produces 4th pair of electrons, positive deltaG so driven by fact its product is used by citrate synthase
Step 1 of ethanol fermentation
pyruvate decaroxylase and thiamine pyrophosphate coenzyme convert pyruvate to acetaldehyde
Step 2 of ethanol fermentation
alcohol dehydrogenase reduces it to ethanol, regenerating ATP
Citric acid cycle
further oxidation of organic compounds that yields ATP, ending with complete oxidation to CO2
Oxaloacetate
Citrate
Coenzyme A
Myosin structure
light meromyosin and heavy meromyosin (S1 heads and S2)
Myosin
Track is actin, used in muscle
ATP binding to myosin
decreased affinity for actin
Kinesisn
Track is microtubules, used for transport
Dyneins
Large heavy chain, used in cilia and flagella
ATP binding for kinesin
increased affinity for microtubules
SFT step 1
tropomyosin blocks myosin binding site at rest
SFT step 2
nerve impulse increase calcium ion concentration
SFT step 3
troponin C binds to calcium, conformational change so myosin head can bind
Troponin I
binds actin to complex, preventing contraction in calcium absence
Troponin T
binds to tropomyosin
Head structure
actin binding site, P-loop, nucleotide binding site, regulatory and essential light chain
Step 1 myosin movement
ADP->ATP releases myosin
Step 2 myosin movement
ATP rearranges lever arm
Step 3 myosin movement
ATP->ADP enables myosin to bind to actin
Step 4 myosin movement
phosphate release increases strength of binding, allowing level rest (power stroke)
Actin structure
G actin combines to make F actin, a helical rope structure
Kinesin structure
two heads with extended stalk, head based on P-loop NTPase, light chains bind to carboxyl terminal
Action of kinesin
operate in tandem
Step 1 kinesin movement
ADP bound kinesin binds to mictotubule, ADP disassociates
Step 2 kinesin movement
ATP binds and causes neck linker to zip onto core and 2nd head thrown forward
Step 3 kinesin movement
2nd head binds, 1st hydrolyses and unzips neck linker, 2nd binds to ATP, zips up and 1st thrown forward
Dynein
has microtubules as track, two homologous SOKDA subunits (alpha and beta tubulin), produce helical array, bundle is called axoneme, 9 MT pairs and 2 singlets
P-loop NTPase
proteins that convert ATP into kinetic energy
track
steers the motion of motor assembly
affinity for filament track.....
enables bind, pull and release
Lock and key
Emil Fischer 1890
Induced fit model
Daniel Koshland
Catalytic group
Amino acid chain that makes/breaks bonds
Saturation effect
At constant enzyme concentration, reaction rate increases with substrate until Vmax is reached
Vmax
Maximum velocity or rate at which an enzyme is catalyses a reaction
Enzymes
Biological catalysts that function by stabilising transition states in reactions
Km
Substrate concentration where V0 is equal to 1/2 Vmax
Michaelis-Menten model
Describes kinetic property of enzyme, concentration of enzyne is constant
Michaelis-Menton model equation
E+S=ES=E+P
Michaelis-Menten equation
v = (vmax [S])/(Km + [S])
Michaelis-Menten equation 2
Km = (K-1 + K2)/K1
Lineweaver-burk plot
Plot of 1/V0 against 1/[S] used to calculate Km (gradient) + Vmax (y-intercept)
Uncompetitive inhibitor
Vmax and Km lower
Non-competitive inhibitor
Vmax reduced, Km same
Competitive inhibitor
Increases Km, Vmax same
Post-translational modification types
Ubiquitination, Sumoylation, Hydroxylation, Phosphorylation, Lipidation, Acetylation, Glycosylation
Acetylation
involves acetylation of N-terminal amino acids using acetyl coA and N-acetyl transferase enzymes
Acetylation of lysine in histone
Histones more negative so less attracted to negative phosphate group, loose coil, transcriptionally active
Sumoxylation
Addition of small ubiquitin like modifiers, involving activation, conjugation and ligation
Ubiquitination
Addition of ubiquitin protein to substrate protein, make up of 76 a.as, monoubiquitin K29, involves activation, conjugation and ligation
Lipidation
Covalent modification of proteins with lipids, reversible, can be enzymatic with farnesyl transferase and palmoitoyl transferase
Glycosylation
Attachment of sugar moelcule to residue, can be O linked or N linked
O-glycosylation
Attachment of sugar to O group of threonine and serine, no characteristic sequence
N-glycosylation
Attachment of carbohydrate to asparagine residue, sequeunce N-X-S/T except when X is proline
Oligosaccharide of N-glycosylation
3 glucose, 9 mannose, 2 glucosamine
Hydroxylation
Addition of OH group to residue only proline and lysine, present in collagen
Phosphorylation
Attachment of phosphate group to OH group in side chains
Kinases
Attach phosphate group to OH group
Phosphatases
Remove phosphate group to OH groups
Monosaccharides
Glucose, fructose, galactose
Disaccharides
Sucrose, maltose, lactose
Homopolysaccharides
Used for storage (alpha-glycosidic linkage, helical) and structure (beta-glycosidic linkage, linear)
Cellulose
Beta-1-4 glycosidic linkage, linear, insoluble, layers
Chitin
Beta-1-4 glycosidic linkages, N-acetylglucosamine, long straight chain
Amylopectin starch
Branched, homopolymer, alpha-1-4 ad alpha 1-6 glycosidic linkages, soluble
Amylose starch
Straight chain, alpha-1-4 glycosidic linkages, have maltose, unbranched, spiral shape, chair
Glycogen
Branched, spairingy soluble, forms colloidal solutions, alpha-1-4 glycosidic linkages, branches alpha-1-6 bonds, shorter branches
Heteropolysaccharides
Glycosaminoglycans and glycoproteins
Glycoproteins
Shorter, branched oligosaccharide covalently attached to protein backbone
Glycosaminoglycans
Repeating sequence of 2 monosaccharides, associated with protein non-covalently, form proteoglycans or mucopolysaccharides
Examples of glycosaminoglycans
Chondrotin, keratin, heparin, dermatan sulfate, hyaluronate
Heparin
Sum of total chemical processes occuring that result in growth, energy production and waste removal
Two metabolic activities
Capture and conversion of energy, transformation of organic compounds into others
Chemotroph
Obtain energy by breaking down organic compounds
Anabolism
Biosynthesis of macromolecules, requires energy input, not spontaneous so use enzyme catalysts or couple it to favourable reactions
Catabolism
Biosynthesis, motility, transport and waste, break down molecules, produces energy, spontaneous, increases entropy
Types of metabolic reactions
Ligation, Isomeration, group transfer, oxidation/reduction, hydrolytic reactions and addition/removal of functional groups
Ligation (metabolic)
Form bonds by using free energy from ATP cleavage
Isomerisation
Rearrangement of bonds within a molecule
Group transfer
Movement of phosphate groups etc
Oxidation/reduction
Donation/accepting protons in carbon compounds
Hydrolytic
Bonds cleaved with the addition of water
Addition/removal of functional groups
Forms double bonds e.g. lyases
Metabolism regulation
Amount of enzyme, catalytic activity (inhibition) and substrate accessibility (compartmentalism)
Activated carriers
phosphoryl transfer drives unfavourable reactions, alter proton and protein activity
NAD
Nicotinamide adenine dinucleotide
FAD
Flavin adenine dinucleotide
Kc=
([C]x[D]y)/([A]p[B]q)
If Kc known
Position of equilibrium predicted in closed system
Causes of spontaneous reactions (first law)
Reactions that give out energy, products are of low energy
Causes of spontaneous reactions (second law)
Reactions increase disorder (entropy)
Gibbs free energy equation
DeltaG = deltaH - TdeltaS
High temperature
DeltaG -ve, deltaH +ve, deltaS +ve
Low temperature
DeltaG -ve, deltaH -ve, deltaS -ve
Spontaneous
DeltaG -ve, deltaH -ve, deltaS +ve
Creatine phosphate action
CP + ADP -> ATP + creatine
Formation of ATP
Glyceraldehyde-3-phosphate -> 1-3-bisphosphoglycerate -> 3-phosphoglycerate acid
Endosome-lysosome pathway
Small, stable, non-specific, cysteine serine and aspartic proteases
Endosome-lysosome protease action
Secreted by lysosome -> recognised by phosphotransferase -> N-acetylglucosamine-1-phosphate to mannose residue -> glucosaminidase removes glucosamine (m6P)
Ubiquitin-proteosome pathway
Multidomain, specific, tagrets those marked by ubiquitin, requires ATP, 4 7-membered rings with a cap region and alpha and beta subunit
Serine proteases
Acyl enzyme intermediate, chymotrypsin (aromatic side chain), trypsin (positive lysine/arginine)
Metalloproteases
Zinc, carboxypeptidases, matric MPS used in tissue modelling, cell signalling and growth factors, lysosomal
Cysteine proteases
Involves cysteine-sulfhydryl group, his residue deprotonates cysteine which is then nucleophilically attacked, thioester intermediate
Cysteine proteases example
papain, cathepsin, caspases, calpains (cleave intracellular proteins)
Activation of caspases
cleaved to remove inhibitory sequence or disassociates, activated by apoptosomes