principles biochemistry Flashcards
define catabolism
breakdown of complex molecules into smaller ones to release energy
exergonic and oxidative
e.g. glycolysis - net gain of 2 ATP
define anabolism
synthesis of complex molecules out of smaller ones consuming energy
endergonic and reductive
e.g. gluconeogenesis - 6 ATP used for each 2 pyruvate
what is the formation of collagen
triple helix (3 polypeptide chains- tropocollagen) - form fibrils - form fibres very strong structural bonds
what is the most abundant protein in vertebrates
collagen
what is collagen used for
blood clotting
connective tissue strength
what is the repeating sequence in collagen
amino acid - proline/hydroxyproline - glycine
what is scurvy
lack of vitamin C leading to a lack of hydroxyproline resulting in weakened collagen
what kind of interactions in protein does pH interfere with
electrostatic
what kind of interactions do detergents (urea, guanidine hydrochloride) interfere with in protein
hydrophobic
what kind of interactions do reducing agents and thiol interact with in proteins
disulphide bonds
what is the 1st law of thermodynamics
energy cannot be created or destroyed
what is the 2nd law of thermodynamics
when energy is converted between one form and another some of the energy becomes unavailable to do work
as energy is changed from one form to another, entropy increases
true/false
true
when is a reaction feasible
ΔG < 0
what is ΔG at equilibrium
close to 0
why is an exergonic reaction feasible
ΔG is negative
the products have less free energy than the reactants
gives out energy
why is an endergonic reaction not feasible
ΔG is positive
the products have more free energy than the reactants
requires energy
what is the equation for ΔG
ΔG = ΔH - TΔS
ΔS = entropy change
ΔH = enthalpy change
T is in kelvin
what is ΔG
change in free energy
(energy of products) - (energy of reactants)
kj/mol
what is the function of ribosomal RNA
combines with proteins to form ribosomes where protein synthesis takes place
what is the function of transfer RNA
covalently links to amino acids as a transductor molecule to bring them to the growing protein chain
anticodons - 3 nucleotides
what is the function of messenger RNA
carries genetic information for protein synthesis
what kind of bond is A-T
double hydrogen bond
what kind of bond is C-G
triple hydrogen bond
what 2 bases are purines and what does this mean
A and G
contain 2 carbon-nitrogen rings
what 2 bases are pyrimidines and what does this mean
C T and U
contain 1 carbon-nitrogen ring
what direction does protein synthesis run
5’ - 3’
in DNA structure where do phosphodiester bonds form
between 3’ OH and 5’ triphosphate
what makes up a nucleoside
base + sugar
what makes up a nucleotide
base + sugar + phosphate
what enzyme catalyses DNA replication
DNA polymerases
how is the leading strand replicated
continuously from right to left
how is the lagging strand replicated
slightly slower
in short okazaki fragments
5’ to 3’ synthesis in 3’ to 5’
what enzyme joins okazaki fragments
DNA ligase
what enzyme unwinds DNA
DNA helices
THIIH - pulls a DNA strand down to the RNA polymerase cleft
THIID - holds the other strand in place
what does primase do
makes short RNA sequences (primers) complimentary to the template strand that act as a starting point for the DNA polymerase
what is a coupling reaction
unfavourable and a favourable reaction are coupled to make the overall reaction feasible
what is the henderson hasselbach equation
pH = pKa + log ( [A-]/[HA] ) pH = pKa - log ( [HA]/[A-] )
what is Ka
acid dissociation constant
[H+]{A-]/[HA]
what is the primary protein structure
sequence of amino acids
what is the secondary protein structure
formation of a backbone (hydrogen bonds)
what is the tertiary protein structure
3D structure
fibrous or globular
what is the quaternary structure
spatial arrangement of multiple subunits
disulphide bonds hold proteins together
association of non protein groups e.g. haem group
how many types of RNA polymerases do prokaryotic cells have
1
how many types of RNA polymerases do eukaryotic cells have
3
Pol I, II and III
what do each of the RNA polymerases synthesise
Pol II synthesises all mRNA
Pol I and III synthesise only stable RNA
what direction is RNA synthesised in
5’ - 3’
what is a promoter sequence that marks the start of a new gene
TATA
what is the general transcription factor for all Pol II transcribed genes
TFIID - provides a landing site for other transcription factors e.g. RNA polymerase and allows for formation of pre initiation complex
what are enhancers
short regions of DNA that can be bound by protein activators to increase likelihood of transcription
looping allows them to come into contact with promoter sequences
what kind of graph is the enzyme activity-pH graph
bell curve - relatively sharp decline either side of the optimum pH
what kind of graph is the enzyme activity-temp
increases until optimum temp then decreases sharply
how is the degradation of the mRNA prevented during splicing
5’ capped with GTP
3’ has a poly A tail added allowing for recognition
how is the degradation of the mRNA prevented during splicing
5’ capped with GTP
3’ has a poly A tail added allowing for recognition
how does translation occur
anticodons of tRNA form base pairs with codons of mRNA
what is the start codon for translation
AUG
what is in the P site
the tRNA being translated
what is in the A site
the tRNA waiting to be translated
what enzyme catalyses peptide bond formation between amino acids in P and A sites
peptidyl transferase
how does termination of translation occur
when A site encounters a stop codon
what is held in the E site
the empty tRNA
what do free ribosomes in the cytosol make proteins for
cytosol
nucleus
mitochondria
(post translational)
what do ribosomes on the RER make proteins for
plasma membrane ER Golgi secretion (Co-translational)
what is a polysome
structure formed when multiple ribosomes attach to an mRNA sequence which speeds up translation
what is meant by the genetic code being
unambiguous
degenerate
each codon codes for only one amino acid
many amino acids have more than one codon
do catalysts effect the position of equilibrium
no - they speed up the rate at which equilibrium is achieved
what are apoenzymes
enzymes without a cofactor
what are zymogens
inactive form of enzyme
what are metalloproteins
contain metal cofactors
what is a holoenzyme
enzyme with a cofactor
what are prosthetic groups
tightly bound coenzymes
what enzyme synthesises ACh
ACh transferase
what enzyme breaks down ACh
ACh etherase
what enzymes carry out phosphorylation
protein kinases
what enzymes remove a phosphate
phosphotase
where is GLUT3 found
brain
where is GLUT 5 found
gut
what is Vmax
maximal rate of a reaction at unlimited substrate concentration
all enzymes are fully saturated
what is Km
michaelis constant - 50% Vmax
concentration of substrate that gives a 50% maximal reaction
what does a low Km mean in terms of affinity
low km
only small amount of substrate needed for 50% Vmax
enzyme has a high affinity
what is the name of the graph km and Vmax are read off and how are they read
lineweaver burk plot
X axis = 1/[s]
Y axis = 1/V
gradient = km/vmax
Vmax - where line crosses Y axis = 1/vmax
Km - where line crosses X axis = -1/km
what happens to km and vmax in competitive inhibition
v max is unchanged - can be outcompeted by addition of more substrate
km is increased - more substrate needed to have same impact
what happens to km and vmax in non-competitive inhibition
Vmax is reduced - cannot be out competed as allosteric (bind at different site)
km is unchanged
what kind of relationship do allosteric enzymes show
sigmoidal
e.g. haemoglobin
what kind of relationship do orthosteric enzymes show
follow MM kinetics
hyperbolic
e.g. myoglobin
henderson Haselbach equations are always answered with what
1.
give 3 functions of cholesterol (lipid)
stability in cell membranes
component of myelin sheath
precursor molecule for steroid hormones, vitamin D and bile acids
give 3 functions of triglycerides (lipid)
lipid bilayer membranes
highly concentrated energy stores
how do you differentiate alpha glucose and beta glucose
alpha - H points up, OH points down
beta - OH points up, H points down
where does glycolysis occur
cytosol
what is the net gain of ATP in glycolysis
2 ATP (4 produced, 2 used)
what is the net gain of ATP in glycolysis
2 ATP (4 produced, 2 used)
what are the control points in glycolysis
1st 3rd and final reactions
highly exergonic so irreversible
what enzyme phosphorylates glucose
hexokinase
mediates substrate entry
what enzyme phosphorylates fructose-6-phosphate
phosphofructokinase
mediates substrate movement along pathway
what enzyme converts phosphoenolpyruvate to pyruvate
pyruvate kinase
mediates exit of product molecules
how many NADH + H+ are formed in glycolysis
2
how is NAD+ regenerated
oxidative metabolism of pyruvate
how do the 2 NADH molecules formed in glycolysis get from cytosol to matrix
malate-aspartate shuttle
what happens to pyruvate in anaerobic conditions
alcoholic fermentation
lactic acid formation in humans (H+ dissociates to form lactate in solution)
what happens to pyruvate in aerobic conditions
further oxidised in citric acid cycle
what catalyses the formation of acetyl co A from pyruvate
Pyruvate Dehydrogenase Complex PDC
where are the enzymes of the TCA cycle located
matrix
except succinate dehydrogenase which is integrated in the inner mitochondrial membrane (cristae)
how do cancer cells achieve a high rate of ATP production
possess low Km hexokinase allowing for more rapid entry of substrate
after glycolysis + PDC + TCA how many NADH +H+ are formed
10
after glycolysis + PDC + TCA how many FADH2 are formed
2
after glycolysis + PDC + TCA how many ATP are formed
4
after glycolysis + PDC + TCA how many CO2 are formed
6
what are the steps of glycolysis + PDC + TCA
glucose 2 x pyruvate 2 x acetyl co A joins with 4C acid to form 6C acid in cycle reforms 4C acid 2 cycles of TCA per glucose
what occurs in the PDC
2 x pyruvate to 2 x acetyl co enzyme A
NAD+ –> NADH+ +H+
coenzyme A –> CO2
per pyruvate
in TCA cycle how many pairs of electrons are transferred in the conversion of NAD+ to NADH+ H+
3
in the TCA cycle how many pairs of electrons reduce FAD to FADH2
1
what is most commonly the 4C acid in the TCA cycle
oxaloacetate
what is most commonly the 6C acid in the TCA cycle
citric
what are the steps in glycolysis
glucose
fructose-1,6-bisphosphate
2 triose phosphates
2 pyruvate
what does each TCA cycle generate
3 NADH+H+
1 FADH2
1 GTP
2 CO2
where does the TCA cycle occur
central matrix then cristae
what is the warburg effect
up regulation of anaerobic glycolysis in cancer cells - lactic acid fermentation
where does oxidative phosphorylation occur
in the cristae
what is the electron transfer potential
“standard redox potential”
how readily a compound donates an electron
what is the electron transfer potential
measured by redox potential of a compound
what does a negative standard redox potential mean
reduced form of the compound has a lower affinity for electrons than hydrogen so more likely to donate
what does a positive standard redox potential mean
reduced form of the compound has a higher affinity for electrons than hydrogen so less likely to donate
what is oxidative phosphorylation and what are the two stages
the coupling of respiration to ATP synthesis
electron transport and ATP synthesis
where do electrons from NADH enter the respiratory chain
complex I
where do electrons from FADH2 enter the respiratory chain
complex II
what is the transfer of electrons through the respiratory chain coupled to
H+ transport from mitochondrial matrix to inter membrane space
how many complexes in the ETC pump H+
3/4
1 2 and 4
outline the essence of oxidative phosphorylation
electrons from NADH and FADH2 are used to reduce O2 to H2O
Their energy is used to pump protons (H+) form the mitochondrial membrane to the inter membrane space
the pH decreases in the inter membrane space and increases in the matrix
protons flow back across the membrane following the concentration gradient
energy of the flow is used to phosphorylate ADP to ATP (ATP synthase)
how do CO, cyanide and azide inhibit oxidative phosphorylation
inhibit transfer of electrons to O2 so no proton gradient formed so no ATP formation
Cyanide is a competitive inhibitor and CO is a non-competitive inhibitor
true/false
true
how many H+ ions passing through ATP synthase forms 1 ATP
4
what happens to H+ ions if they don’t enter the ATP synthase protein
they join thermogenin (uncoupling protein) producing heat instead of ATP
what kind of fat is well adapted for thermogenesis
brown fat
how many ATP does the TCA cycle yield
2 (GTP)
how many ATP does one molecule of glucose yield
30-32
cofactors are usually (metal ions/organic molecules)
metal ions
coenzymes are usually (metal ions/organic molecules)
organic molecules
what is the optimum pH of pepsin
low pH
what is the optimum pH of salival amylase
neutral
what is the optimum pH of pancreatic amylase
alkaline
what enzyme is a marker of muscle damage
CK (M form)
(B form in brain)
(MB form in heart)
what enzymes are markers of liver damage
ALT
AST (whole body)
GGT
what enzymes are markers of pancreas damage
amylase
lipase
what enzymes are markers of cardiac damage
CK
AST
LDH
ATP supplies energy to run for how many seconds
4
phosphocreatine supplies energy to run for how many seconds
15
how long does free circulating glucose supply energy for
4 minutes
how long do glycogen stores last
77 minutes
how long do fat stores last
4+ days
what is FiFoATPase
proton pore that utilises the energy yielded from the return of protons along their electrochemical gradient in a condensation reaction with ADP and Pi to yield ATP
why do rapidly contracting human cells start producing lactic acid?
cells have to convert NADH to NAD+
what is a partial agonist
binds to and activates receptor but only partial efficacy t receptor relative to full agonist
