Biomolecules Flashcards
Why is ATP a good source of energy?
It contains high-energy bonds that, when hydrolysed, release energy that can be used to drive unfavourable reactions
What is the proton concentration in the mitochondria?
Outside the mitochondria, there is a high proton concentration
Inside the mitochondria, there is a low proton concentration
What drives the synthesis of ATP?
The ‘proton motive force’ - this is the passage of protons through the mitochondria
How many molecules of ATP does anaerobic respiration synthesise?
2 molecules
How many molecules of ATP does aerobic respiration synthesise?
32 molecules
What is myoglobin?
An oxygen storage protein found in the tissues (especially in the muscles)
What is hemoglobin?
An abundant protein present in red blood cells whose function is to transfer oxygen from the lungs to the tissues
It plays a role in the transport of protons and carbon dioxide from the tissues to the lungs
How do you work out the saturation of myoglobin?
The concentration of oxymyoglobin divided by the total concentration of myoglobin
How does the fractional saturation of myoglobin change when the partial pressure of oxygen increases?
The fractional saturation of myoglobin increases rapidly towards 1. When the value nearly reaches one, it plateaus as saturation is reached.
What happens if myoglobin binds too tightly to oxygen?
It won’t be able to release the oxygen when needed
What happens if myoglobin binds too weakly to oxygen?
It won’t be able to pick up the oxygen when needed
What part of myoglobin provides the shape and the structure?
The protein provides the shape and structure
What part of myoglobin provides the oxygen binding site?
Heme is the oxygen-binding site
What structural effect gives myoglobin its stability?
The heme and the interior of the protein is hydrophobic, outside the protein is hydrophilic
The exception is two Histidine groups which are in the centre near the heme group
Why must the iron centre be 2+ and not 3+?
If it was Fe 3+, binding oxygen is not reversible
What is ‘protein dynamics’ in relation to myoglobin?
The protein has to change shape to allow oxygen in, and to allow oxygen out
Why do we have myoglobin against free ferrous heme?
Free ferrous heme cannot bind to oxygen reversibly
The polypeptide chain prevents dimerisation to the oxygen bridge intermediate
Free ferrous heme would bind to CO preferentially (this is the same in myoglobin but to a much lower extent due to hydrogen bonding between histidine and oxygen)
How does hemoglobin bind to oxygen?
It binds to oxygen cooperatively
How does oxygen saturation change in hemoglobin at the lungs compared to the tissues?
Oxygen is saturated in the lungs, and releases half of the oxygen when it reaches the tissue
What is the structure of hemoglobin?
Has four units (two alpha and two beta)
Each subunit has a porphyrin bound to it (four oxygen binding sites)
Strong due to the Hydrogen bonds, van der Waals interactions, hydrophobic interactions and salt bridges
What does oxygen binding ‘cooperatively’ mean?
Oxygen binding at the first site changes the oxygen affinity of the other sites
Does the R state or the T state of hemoglobin bind to oxygen more strongly?
R state binds oxygen with a higher affinity
What changes happen when oxygen binds to hemoglobin?
Iron changes from 5-coordinate to a 6-coordinate species
Iron changes from high spin to low spin
Strain is put on the intersubunit interactions and this promotes the transition to the R state
What is the Bohr effect?
Acidity promotes the release of oxygen release by Hb
When Hb releases four lots of oxygen, it picks two protons up (this keeps the pH of the tissues and the lungs constant)
Carbon dioxide is removed by forming the hydrogen carbonate anion, and this is catalysed by carbonic anhydrase
What is the structural origin of the Bohr effect?
When protonated a salt bridge is formed between histidine and aspartic acid
When it is more acidic, it forces the release of oxygen by moving to the T state in the tissues
When it is less acidic, it forces the uptake of oxygen by moving to the R state in the lungs
What does glucose oxidation to pyruvate yield (glycolysis)?
A net 2 ATP from 2 ADP and 2 Pi
What do we need to oxidise glucose?
We need to reduce NAD+ to NADH (a reverse reaction must occur for sustainability)
What enzyme reduces NADH to NAD+?
Lactase dehydrogenase
What does complete glucose oxidation produce?
2 x ATP, 10 x NADH and 2 x FADH₂
Where does the TCA cycle occur?
It occurs in the mitochondria
What drives the synthesis of ATP?
The downhill flow of protons back across the membrane
How is the proton gradient created?
The downhill electron flow is coupled to the uphill transmembrane transport of protons against a concentration gradient
Do carriers of the sickle-cell trait suffer from the disease?
They do not suffer from the disease
How can we determine between the sickle cell anaemia gene and a ‘normal’ gene?
Electrophoresis - the sickle cell gene doesn’t travel as far as the ‘normal gene’
What is the structural basis of sickle-cell anaemia?
The gene change is on the outside of the protein and is exposed to the polar solvent.
This reduces the solubility of the deoxygenated form but not the oxygenated form.
The R to T transition exposes a complementary hydrophobic patch, which join together with each other to exclude water
How does malaria work?
When malaria attacks hemoglobin, it leaves heme behind (a dangerous molecule that creates free radicals that are very damaging).
The parasite eliminates heme by forming ‘hemozoin’ (a crystalline form of heme)
How does chloroquine work?
It blocks the heme polymerisation steps, killing the parasite
Where is chloroquine stored?
It enters the food vacuole in the parasites cytoplasm
How does chloroquine stay in the digestive vacuole?
It becomes doubly protonated (as the pH is lower in the food vacuole) and cannot escape
What are the benefits of chloroquine?
Safe, effective, targets process unique to parasites, cheap, accumulates at the site of action, the target is not genetically encoded
How did the parasite evolve to develop chloroquine resistance?
It was used too widely without control, and the parasite evolved.
The parasite evolved the ability to pump the drug away from its site of action in the food vacuole (done by an existing efflux pump by a single-point mutation to transport chloroquine)
It binds to the two carboxylate groups in its doubly protonated form, and this prevents the crystallisation
What are the four properties of DNA?
It must have chemical stability
It must have a mechanism for replication
It must have a mechanism for decoding
It must be capable of evolution
Where are the sugar, phosphates and bases located in DNA?
The sugar and the phosphates are on the outside of the double helix, and the bases are located on the inside of the double helix.
What is a gene?
DNA segments containing biological information, coding for proteins and RNA
What is a genome?
The total genetic material of a cell, organism or virus
What does it mean when DNA is said to be ‘antiparallel’?
They run in opposite directions
Why does the double helix have minor and major grooves?
The glycosidic bonds are not diametrically apart
What does it mean when DNA is ‘melted’?
The two strands break apart from each other
What does it mean when DNA is ‘annealed’?
The spontaneous coming back together of two DNA strands
How can we diagnose DNA sequences?
We can add an excess of probes that bind to the single chain DNA when the DNA is melted
What is a probe (when used to diagnose DNA sequences)?
It is a short, synthetic single-stranded DNA complementary to the sequence being sought, with a fluorescent tag for detection
What is semi-conservative replication?
One of the DNA strands is conserved, and one is newly synthesised
What was the Meselson-Stahl Experiment?
Grew cells in N-15, placed in a CsCl solution and ran on a centrifuge. This led to a concentration gradient and was allowed to replicate with N-14. The first generation had a 50:50 split between N-15 and N-14
Which sides do chains always grow from?
They always go from 5’ to 3’
What enzyme completes DNA synthesis?
DNA polymerase
How does DNA polymerase work?
It tightly couples the free energy of the nucleotide triphosphate hydrolysis to phosphodiester bond formation
What are topological isomers?
They have the same structure but have a different number of twists in them
What does it mean to be ‘underwound’ or ‘negatively supercoiled’?
It is the deviation from ideal twisting
How is DNA compacted to fit into cells?
Histones package DNA into structured units called nucleosomes.
Each nucleosome comprises an octameric protein core
It needs to be turned back into a double helix structure for it to be read however
What is a promoter (P)?
It is the start site for transcription
What is a terminator (t)?
The site where transcription stops
What is a coding sequence?
A series of non-overlapping base triplets (codons) coding for amino acids
What is the purpose of AUG (methionine) in a transcription sequence?
It is the start site for protein synthesis
What is the purpose of TGA in a transcription sequence?
It is a STOP codon signalling the end of a protein
What are the two steps in making a protein?
Transcription and translation
What is transcription?
The process by which RNA is made
What is translation?
The process by which proteins are made
What are three differences between DNA and RNA?
Ribose replaces deoxyribose
Uracil replaces thymine
mRNA is single-stranded
Why is RNA less stable than DNA?
It is ribose based, not deoxyribose based
What are the three steps of transcription?
Initiation, elongation and termination
What enzyme carries out transcription?
RNA Polymerase
What is the process of transcription?
RNA polymerase binds to the promoter, and moves along the DNA whilst copying it into RNA.
As the RNA polymerase moves, the mRNA is being copied against the DNA template
The coding strand will look like the mRNA (both complementary to the template strand)
What is a transcription bubble?
The DNA melts into two separate strands in the bubble (one template strand, one coding strand)
What carries out translation?
It is carried out by the ribosome
What is the process of translation?
mRNA travels through the ribosome and gets translated.
When the RNA has the code for the same amino acid as the tRNA, the amino acids get added to the strand
What is tRNA?
Transfer RNA
What are the two parts of tRNA?
One part recognises the RNA
The other part carries the amino acid
What is the importance of the six base pair sequences centred 35 and 10 base pairs upstream of the transcription state site?
These are the promotor sequences - the greater it is to the promotor sequence, the higher the levels of transcription are.
This is varied depending on how much the gene is needed
What are three proteins that are needed for the utilisation of lactose?
Lac permease, beta-galactosidase and beta-galactoside transacetylase
What is the job of lac permease?
It transports lactose into the cell
What is the job of beta-galactosidase?
It cleaves lactose into glucose and galactose
What do these three proteins enable?
They enable survival and growth when lactose is the only available nutrient; they have no function when glucose is in high concentrations
What does the Lac Repressor bind to?
The operator (O)
It stops the production of the proteins (when the lac operator is not needed)
What is the operator (O)?
An operator sequence is a sequence on the DNA to which the regulatory protein binds
What is the job of lactose permease (LacY)?
It transports lactose across the hydrophobic lipid bilayer
The bacterial cell maintains an electrochemical H+ gradient across its cytoplasmic membrane
H+ is pumped out of the cell by respiratory processes
Lactose can be transported against a concentration gradient by co-transport with H+ (proton symport) - these are tightly coupled for efficiency
How is the lac operon turned off when glucose is present?
The concentration of glucose and cAMP are inversely correlated
CRP (cAMP receptor protein) activates the lac operon only when cAMP is bound to it
