Biochemistry Flashcards
What are the four most common biochemical reactions?
phosphorylation
acylation
carboxylation
esterification
What is the most electronegative species?
oxygen so it is the terminal electron acceptor
What are the main functions of biomolecules?
information storage structure energy generation energy storage recognition/ communication/ specificity
What are the major classes of biomolecules?
peptides/protreins
lipids
nucleic acids
carbohydrates
What is the first law of thermodynamics?
energy is neither created nor destroyed
What is the second law of thermodynamics?
when energy converts forms some of it becomes unavailable to do work
What does delta G equal?
dG= dH-TdS dG= (energy of products) - (energy of reactants) dG= dG(standard conditions) + RTln([C][D]/[A][B])
What is an exergonic reaction?
has a negative dG so free energy of the products is less than the reactants so this will occur spontaneously
What is an endergonic reaction?
positive dG so free energy fo the products is more that the reactants so this won’t occur spontaneously
How are some unfavourable processes achieved?
they are coupled with a favourable process so they are possible together
ATP –> ADP has a very negative dG so can be coupled with an unfavourable reaction
Why is ATP unstable?
negative charges close together so must be regenerated lots tasing creatinine phoshate and ADP
What is catabolism?
breaking down larger molecules into smaller ones releasing energy
What is anabolism?
making large molecules from small ones using energy
What type of reactions are glycolysis and gluconeogenesis?
glycolysis is catabolic with a net gain of 2 ATP
gluconeogenesis is anabolic with a loss of energy
What type of reaction is used as a control point?
large dGs
What is the direction of a peptide?
N –> C bond
What are the majority of amino acids in our body made up of?
20 L amino acids with an alpha carbon
Why are peptide bonds partially double?
the lone pair on N can become a C=N
What is the Henderson-Hasselbalch equation?
pH=pKa + log([A-]/[HA])
What does pH equal in a buffer solution?
pKa
What is the isoelectric point?
the pH where a molecule has no net charge
What are the extra bonds in an alpha helix?
every 4th makes a hydrogen bond
What breaks alpha helices?
proline
What is the structure of a collagen triple helix?
three left-handed twists around each other to form one right-handed super helix
repeating structure is X-Y-Gly
What are the characteristics of fibrous and globular proteins?
fibrous are parallel across one axis so are mechanically strong
globular are folded circularly with exterior that can hydrogen bond with water but interior in hydrophobic
What are the factors that disrupt protein structure?
- heat: vibrations
- pH: electrostatic interactions
- detergents, urea, guanidine hydrochloride (disrupt hydrophobic interactions)
- Thiol agents, reducing agents (disrupt disulphide bonds)
What is a nucleoside?
base and sugar
What is a nucleotide?
nucleoside and one or more phosphate groups
What are the purines?
Adenine and Guanine
What are the pyrimidines?
Uracil, Thymine and Cytosine
What makes up a phosphodiester bond?
between 3’ OH group and 5’ triphosphate
What end are nucleotides added at?
3’
How many hydrogen bonds between the bases?
A two bonds to T
C three bonds to G
What is needed to start DNA replication?
RNA primer
How is DNA replication done with the two strands?
leading strand always has a free 3’ end
lagging strand must be replicated in Okazaki fragments
What makes the RNA primers that are needed for replication?
primase
What is exonuclease activity?
removal of the incorrect nucleotides if an error is made
How many types of RNA polymerase does a cell have?
Eukaryotic have three
Prokaryotic have one
What are telomeres?
repeat sequences of DNA that protect the chromosome ends
What does telomerase do?
extends telomeres (cancer cells reactivate this)
What are the main steps of transcription?
- RNA polymerase binds (transcription factors needed and it detects the promoter region)
- DNA chain separation (uses energy)
- transcription initiation
- elongation
- termination
What is the TATA box?
- promoter region that gets bound to by TBP to give a kink in the DNA which determines the direction of transcription
- other transcription factors and RNA polymerase can bind here
What does newly-formed RNA look like?
stem-loop structure and a stretch of Us when released
What do enhancers do?
bind to DNA sequences near promoter to regulate transcription up or down
What is capping?
the process of properly ending the mRNA chains using ATP for bond formation
What are the three binding sites of a ribosome?
Exit
Peptidyl
Aminoacyl
What happens in initiation of translation?
- GTP hydrolysed for energy
- initiator tRNA is in P site
What happens in elongation in translation?
- next aminoacyl-tRNA to A site by elongation factor
- GTP hydrolysed
- second elongation factor regenerates first one to pick up next aminoacyl-tRNA
What happens in peptide bond formation or translation?
- peptidyl transferase makes peptide bond between amino acids in P and A so peptide is formed in A site
- elongation factors moves ribosome along
- empty tRNA is in E, growing peptide is in P and A is free for next aminoacyl-tRNA
What happens in termination of translation?
when A comes to STOP there is dissociation
What is a point mutation?
a mutation in a single base
What is a missense mutation?
change in amino acid sequence
What is a nonsense mutation?
no change in amino acid sequence so no effect on protein
What happens to a newly made protein?
- targeted so it will move to its final destination
- modified so more chemical groups are added
- degraded so unwanted bits are removed
Where do the proteins that are made by free ribosomes go to?
cytosol
nucleus
mitochondria
(these are moved after translation)
Where do the proteins that are made by bound ribosomes go to?
plasma membrane ER Golgi secretion (moved during translation)
What happens to proteins after translation?
carbohydrates are added
disulphide bonds are formed
multisubunit proteins are formed
cleavage
What do enzymes do to reactions?
stabilise the transition state
reduce activation energy
equilibrium achieved faster
What is a glycogen storage disease?
enzyme deficiency that results in failure of glycogen to enter phosphorylated state eg Von Gierke’s disease
What are cofactors?
metal ions that do redox reactions and stabilise transition states
What are coenzymes?
organic molecules (non-protein) structure that is necessary for the functioning of an enzyme eg from vitamins, redox (NAD), CoA or ATP
What are metalloproteins?
metal cofactors within an enzyme
What are prosthetic groups?
tightly bound coenzymes
What is an apoenzyme?
enzyme without a cofactor
What is a holoenzyme?
enzyme with a cofactor
What is made if you add a cofactor and an apoenzyme?
holoenzyme
What is a cofactor necessary for?
the activity of an enzyme
What is an isozyme?
isoforms of enzymes that catalyse the same reaction but have different properties and structure- these can be used for diagnostic purposes
What are phosphorylation reactions?
carried out by protein kinases and are very fast-switch activity of the enzyme
What are zymogens?
inactive precursors to enzymes that are activated by irreversible covalent modification or covalent bond cleavage
What does Km equal?
(k-1 + k2)/k1
50% of Vmax is moles
What is Vmax?
where the reaction velocity plateaus at a maximal rate at which the enzymes can convert substrate
What is the Michaelis-Menten equation?
describes the rate of catalysis as a function of substrate concentration to give a straight line
What does 1/V equal?
1/V = Km/Vmax . 1/[S] + 1/Vmax
y intercept is 1/Vmax and x intercept is -1/Km
What does a low Km mean?
only a little substrate is needed for half-maximal velocity
What does a high Km mean?
a lot of substrate needed to work at half-maximal velocity
What does competitive inhibition do to Vmax and Km?
changes Km but not Vmax
What does non-competitive inhibition do to Vmax and Km?
changes Vmax but not Km
What do allosteric enzymes have for an M-M curve?
sigmoidal shape that can be controlled by allosteric inhibitors and activators
What can you do to an endothermic reaction to make it feasible?
pair it with an exothermic one
What is a largely negative deltaG reaction likely to be?
irreversible
What does deltaG equal at Keq?
0
What type of rotation is allowed around the nitrogen and the carbonyl group in a peptide bond?
single bond rotation
Does an acid with a higher or a lower pKa dissociate more?
lower pKa dissociates more
higher pKa dissociates less
What happens to pKa values with increasing acid strength?
become smaller
What does collagen contain?
lots of hydroxylated proline residues
What is anabolism?
building larger molecules using energy
What is catabolism?
breaking down into smaller molecules to give out energy
What is formed in anabolism?
oxidised precursor become ad reduce biosynthetic product
What is formed in catabolism?
reduced fuel will become oxidised products
What are the four ways that glucose can be transformed?
- into ribose-5-phosphate by the pentose phosphate pathway
- into pyruvate by aerobic glycolysis
- into glycogen, starch and sucrose for storage
- into lactate by anaerobic glycolysis
What are the differences between each GLUT transporter?
they have a variable Km for glucose
What is the equation for glycolysis?
glucose + 2ADP + 2Pi + 2NAD+ –> 2pyruvate + 4ATP + 2H2O + 2NADH + 2H+
What are the intermediates for glycolysis?
fructose-1,6-biphosphate and 2x triode phosphate
What are the three stages of glycolysis?
- glucose trapped and destabilised
- 2x 3C molecules are formed
- ATP is generated
How many ATP are made in glycolysis?
2 ATP
What are the three enzymes in glycolysis and what are their roles?
- hexokinase (substrate entry)
- phosphofructokinase (rate of flow)
- pyruvate kinase (product exit)
What are the factors that affect glycolysis?
+ AMP
- ATP
- citrate
- H+
What is the ATP/AMP ratio?
the energy charge
if it is all ATP then it is charged
if it is all AMP and Pi then it is discharged
What happens if there is no oxygen for respiration?
NADH converts pyruvate to lactate
NADH is then regenerated in the ETC
this can then be used in glycolysis
How does pyruvate get into the mitochondrial matrix?
H+ gradient
H+/pyruvate symport
facilitated diffusion
How is pyruvate then changed?
pyruvate —pyruvate dehydrogenase complex—> acetyl-CoA + NADH + H+ + CO2
What is the enzyme of the TCA cycle that in the membrane?
succinate dehydrogenase is in the membrane and makes FADH2
What does one molecule of glucose make up until the TCA cycle?
4ATP 10NADH 10H+ 2FADH2 6CO2
What comes out of one turn of the TCA cycle?
3NADH
2CO2
1FADH2
1GTP
What do electrons from NADH and FADH2 do?
convert O2 to H2O and H+ is moved across the membrane
these then flow back to make ATP
What is the malate-aspartate shuttle for?
moves NADH from cytoplasm to matrix
What happens in the malate-aspartate shuttle?
- aspartate –> oxaloacetate -(NADH to NAD)-> malate
- malate transferred to matrix
- malate -(NAD to NADH)-> oxaloacetate –> aspartate
(malate from TCA cycle also used)
What is the phosphoryl transfer potential?
deltaG for the hydrolysis of ATP
What is the electron transfer potential?
the redox potential of a compound so how readily it donates an electron
What does a negative or a positive electron transfer potential mean?
-ve means it will donate electrons
+ve means it will accept electrons
What are the two steps of ETC?
electron transport
ATP synthesis
How are electrons transported in the ETC?
e- from NADH and FADH2 to O2]energy pumps H+ out
How is ATP synthesised in the ETC?
H+ gradient
H+ comes through ATP synthase
How to electrons move across membrane?
complexes eg cytochromes with haem group
3 of 4 pump H+
What is the electrochemical gradient?
+ve inside membrane
-ve in matrix
so electrons move inside the membrane
How is the ETC inhibited?
cyanide, azide, CO = stops electron transfer
no H+ gradient
no ATP made
How many ATP does one glucose make?
30-32 ATP
What is the P/O ratio?
a measurement of coupling of ATP synthesis to electron transport
eg P/O of NADH is 2.5
What does ATP yield depend on?
P/O values
and on which shuttle is used to move NADH into matrix
What is the FiFoATPase?
a proton pore that uses energy from the return of protons along their electrochemical gradient in a condensation reaction with ADP and Pi to make ATP
