Principles Biochemistry Flashcards
What is rRNA?
Ribosomal RNA.
What is the function of rRNA?
rRNA combines with proteins to form ribosomes, where protein synthesis takes place.
Define a redox reaction
A redox reaction is the transfer of electrons from one molecule to another.
Define an oxidation reaction.
An oxidation reaction results in the loss of electrons.
Define a reduction reaction.
A reduction reaction results in the gain of electrons.
Name 3 major classes of molecules.
- Peptides
- Proteins
- Lipids.
- Nucleic acids.
- Carbohydrates.
Give a function of a biomolecule.
- DNA
- Structural (bones, teeth, cartilage).
- Recognition/communication/specificity as hormones/receptors/enzymes.
- Energy currency/storage as ATP.
Give an example of a carbohydrate.
Monosaccharide, disaccharide, polysaccharide (cellulose and glycogen).
What is the First law of thermodynamics?
Energy is neither created nor destroyed.
What is the Second Law of thermodynamics?
As energy is converted from one form to another, some of the energy becomes unavailable to do work.
How may the free energy change (ΔG) be calculated?
Energy of products - energy of reactants.
Describe an exergonic reaction.
An exergonic reaction is one in which the total free energy of the products is less than that of the reactants. ΔG is NEGATIVE.
Can an exergonic reaction occur spontaneously or not?
Yes. Exergonic reactions may occur spontaneously.
Describe an endergonic reaction.
Reactions in which the total free energy of the products is greater than that of the reactants. ΔG is POSITIVE.
Can an endergonic reaction occur spontaneously?
No. they require an input of energy in order to proceed.
ΔG values near zero are characteristic of which type of reaction?
Readily reversible reactions.
What does ΔG = 0 indicate about the system?
It indicated the system is at equilibrium.
Phosphoglucomutase catalyses which reaction?
Glucose-6-phosphate Glucose-1-phosphate.
Glucose-6-phosphate Glucose-1-phosphate.
What are the forward and backward reactions involved in?
Forward: glycogen synthesis.
Backward: glycogen breakdown.
How may unfavourable cellular processes be driven?
By coupling them to highly favourable processes.
What is ATP used for?
It is a universal energy currency for driving many different cellular processes.
Is ATP stored in cells in large amounts?
No, it is constantly regenerated.
How may ATP be regenerated?
Using creatine phosphate.
What type of energy bonds do anhydride bonds possess?
High energy bonds.
Define metabolism.
The sum of all the reactions taking place in the body.
What 2 things can metabolism be divided into?
Catabolism and anabolism.
Define catabolism.
The breakdown of molecules (releases energy).
Define anabolism.
The synthesis of molecules (consumes energy).
Give a brief definition of glycolysis
The initial breakdown of glucose for the generation of ATP.
What is the net gain of ATP per glucose molecule?
net gain of 2 ATP. (2 ATP are initially used, and later steps generate 4 ATP - net gain of 2 ATP).
Define gluconeogenesis.
Production of glucose from non-carbohydrate precursors, e.g. pyruvate.
Does gluconeogenesis produce or consume energy?
It consumes energy.
Is gluconeogenesis the reverse of glycolysis?
No.
What significance do reactions with largely negative ΔG values have in metabolic pathways?
They serve as useful control points.
How is flux through control points in metabolic pathways controlled?
By altering enzyme activity.
Describe a water molecule.
Polar molecule whose electrons are unequally shared.
It is bent, forming a dipole with a tetrahedral shape.
Describe a hydrogen bond.
A polarised covalent bond existing between hydrogen and a more electronegative atom. Individually weaker than covalent bonds. Often linear.
What is an amphipathic (amphiphilic) molecule?
One which is both hydrophilic and hydrophobic.
It has a polar hydrophilic head (choline, carboxylic acid) and non-polar hydrophobic tail (hydrocarbon).
What do amphipathic molecules form when in water?
Micelles.
Describe a peptide bond..
They have partial double bond character.
They are planar, strong and rigid.
What is an acid?
A molecule capable of donating a proton.
What is a base?
A molecule capable of accepting a proton.
What is strength a measure of (in terms of acids and bases)?
Strength of an acid is how readily the substance can donate a proton.
Strength of a base is how readily the substance can accept a proton.
What is the pH of a solution?
A measurement of the number of protons within the solution.
What is a buffer?
A solution controlling the pH of a reaction mixture.
What special property do buffers have that makes them useful?
At their pKa, buffers resist a change of pH on addition of moderate amounts of acid or base.
Are proteins capable of acting as buffers? Explain.
Yes, pH changes can change the ionisation of a protein, leading to structural and functional changes.
What is a primary protein structure?
A sequence of amino acid residues.
What is a secondary protein structure?
A localised confirmation of a polypeptide backbone.
Give an example of a secondary protein structure.
- Alpha helix
- beta strands and sheets
- Triple helix
What may break an α helix?
Proline residues.
what is an α helix an example of?
A secondary protein structure.
Give an example of a triple helix.
Collagen.
What is a tertiary protein structure?
A 3D structure of an entire polypeptide, including all its side chains.
What is a quarternary protein structure?
Arrangement of multiple polypeptide chains in a protein with many (non-/identical) subunits.
Polypeptides can rotate around angles between what?
- α carbon and amino group.
2. α carbon and carboxyl group.
Sickle cell anaemia is the result of what?
A single nucleotide sequence change resulting in an altered protein (valine instead of glutamic acid).
Incorrectly folded proteins may associate with other proteins to cause which conditions?
Alzheimer’s and Parkinson’s etc.
Protein structure may be denatured by what? Give two examples.
- heat
- Extreme pH
- Detergents
- Urea
- Guanine hydrochloride
- Thiol agents
- Reducing agents.
What is the genome?
The total DNA in each cell (the genetic information of the organism).
DNA nucleotide sequences determine what?
Amino acid sequences of polypeptide chains.
What is transcription?
DNA nucleotides are transcribed to RNA nucleotides.
What is translation?
RNA nucleotides are translated to amino acids to form proteins.
What is a nucleoside?
A base + a sugar.
What is a nucleotide?
A nucleoside + a phosphate group.
What is polymerisation?
The formation of a phosphodiester bond between a free 3’ OH group and a 5’ triophosphate.
Nucleotides are added to which end of the DNA strand.
3’ ONLY.
DNA exists as what?
A double helix of base pairs. Two anti-parallel nucleotide strands (5’ to 3’ and 3’ to 5’).
What bond exists between adenine and thymine?
double bond.
what bond exists between cytosine and guanine?
Triple bond.
DNA replication is catalysed by what?
DNA polymerase.
What is required to start DNA replication?
An RNA primer.
Where does replication begin within the genome?
At several points simultaneously to ensure the process is reasonably quick.
What does semi-conservative DNA replication mean?
Both copies of DNA contain one original strand and one new strand.
Is DNA replication uni- or bi-directional?
Bidirectional, ensures quick replication.
Which is the leading and lagging strand in DNA replication?
Leading: 3’ to 5’.
Lagging: 5’ to 3’ and produces Okazaki fragments.
What is the role of helicase in DNA replication?
Helicase unwinds DNA and prevents it from rewinding.
What does primate synthesise?
An RNA primer.
What does DNA polymerase synthesise?
A complementary DNA strand.
What happens at the end of DNA replication?
RNA primers are degrade and DNA polymerase fills in any gaps.
What are the 3 main classes of RNA?
- Ribsomal.
- Transfer.
- Messenger.
What is the function of ribsomal RNA (rRNA)?
rRNA combines with proteins to form ribosomes, where protein synthesis takes place.
What is the function of transfer RNA (tRNA)?
tRNA carries amino acids, enabling them to be incorporated into proteins. They are adapters between nucleic acid and amino acid codes.
What is the function of messenger RNA (mRNA)?
mRNA carries genetic information for protein synthesis, i.e. codes for the synthesis of proteins.
How do RNA and DNA bases differ?
RNA contains uracil instead of thymine.
rRNA makes up what percentage of the total cellular RNA?
60%.
tRNA makes up what percentage of the total cellular RNA?
15%
mRNA makes up what percentage of the total cellular RNA?
5%
Anti-codon consists of how many nucleotides?
3
How is RNA made?
By RNA polymerases. One DNA strand is used as a template to copy the nucleotide sequence into RNA.
Eukaryotic cells have three types of RNA polymerase which are?
Pol I, Pol II, Pol III.
Pol II is responsible for synthesising what?
mRNA
What are the stages of transcription?
- RNA polymerase binding.
- DNA chain separation.
- Transcription initiation.
- Elongation.
- Termination.
What does TBP stand for? What is its function?
TATA-box Binding Protein. It recognises the TATA box and introduces kink into DNA, determines transcriptional start and direction.
Which direction is RNA synthesised? What is its relationship to the template strand.
5’ to 3’. The new RNA sequence is complementary to the template strand and identical to the coding strand.
What is the function of an enhancer?
It binds to specific DNA sequences in the vicinity of a promoter to regulate transcription.
Coordinated gene expression may occur in response to what?
Specific stimuli, e.g. hormones, cellular stress.
Where are steroid receptors located when they are inactive?
In the cell cytoplasm.
How do steroid receptors become active and where are they then located?
By binding a ligand (steroid), they move to the cell nucleus and bind to DNA at steroid-response elements (SREs).
How are steroids transported?
Steroids are transported in the blood bound to albumin or specific transport proteins.
How do free steroids enter target cells?
By diffusion, they then bind to inactive steroid receptors in the cytoplasm, which then translocates to the nucleus.
What are exons?
Regions that code for DNA.
What are introns?
Regions that do not code for DNA.
What happens during translation with regards to codon-anticodon base pairing?
Anti-codons of tRNA molecules form base pairs with codons on mRNA.
What are the energy sources of translation?
ATP and GTP.
What binds amino acids to their corresponding tRNA molecules?
Aminoacyl-tRNA synthesases.
What size is a eukaryotic ribosome?
80S.
Ribosomes have 3 tRNA binding sites, name them.
- Exit.
- Peptidyl.
- Aminoacyl.
What catalyses peptide bond formation between amino acids at the Peptidyl and Aminoacyl sites?
Peptidyl transferase.
What moves ribosomes along mRNA?
Elongation factor (EF-2).
When does termination occur?
When the aminoacyl site of a ribosome encounters a stop codon.
What is a point mutation?
A change in a single DNA base.
What is a missense mutation?
Results in a change of amino acid sequence, and may change protein function e.g. sickle cell anaemia.
What is a nonsense mutation?
Creates a new termination codon, changing the length of the protein due to a premature stop of translation.
What is a silent mutation?
No change in amino acid sequence, is due to degeneracy of the genetic code and has no effect on protein function.
What is a frameshift mutation?
The addition or deletion of a single base (or two) which changes how the DNA sequence is read.
Give examples of chromosomal mutations.
Deletions, duplications, inversions and translocations.
What happens to finished proteins?
- Targeting (moves to final cellular destination).
- Modification (addition of chemical groups).
- Degradation (unwanted or damaged proteins are removed).
Where are proteins produced by free ribosomes in the cytosol destined for?
- cytosol
- nucleus
- mitochondria
- translocated post-translationally.
Where are proteins produced on the rough endoplasmic reticulum destined for?
- Plasma membrane
- Endoplasmic reticulum
- Golgi apparatus
- Secretion
- Translocated co-translationally.
Define glycosylation.
The addition and processing of carbohydrates in the ER and Golgi.
The hereditary form of emphysema results from what?
The misfolding of the protein α1-antitrypsin in the ER.
What is the function of an enzyme?
Speeds up the rate at which a reaction reaches equilibrium.
Describe the action of an enzyme.
They bind and stabilise the transition state, i.e. the reaction intermediate species that has the greatest free energy. They reduce the activation energy by providing alternative reaction pathways.
What is glycogen storage disease?
An enzyme deficiency that results in failure of glycogen to enter the transition phosphorylated state. Causes defective glycogen synthesis/breakdown in muscle, liver and kidney.
Symptoms of glycogen storage disease?
hypoglycaemia, hepatomegaly, skin and mouth ulcers, bacterial and fungal infection, bowel inflammation and irritability.
What properties do cofactors/coenzymes offer to many enzymes?
Catalytic activity.
How are cofactors and coenzymes differentiated?
Cofactors are made of metal ions and are inorganic.
Coenzymes are organic molecules.
What are isozymes?
Isoforms of enzymes that catalyse the same reaction, but have different properties, structure and sequence.
How does lactate dehydrogenase (example of an isozyme) function differ in the heart and in muscle?
In the heart it promotes aerobic metabolism.
In muscle it promotes anaerobic metabolism.
What is Creatine kinase?
A dimeric protein which binds to muscle sarcomere.
Creatine kinase of brain type BB, suggests what?
Stroke or tumour.
Creatine kinase of heart type MB, suggests what?
Heart attack.
What are phosphorylation reactions carried out by?
Protein kinases.
What are zymogens?
Inactive precursors of an enzyme, e.g. trypsinogen and chymotrypsinogen.
What is an apoenzyme?
An enzyme without a cofactor.
What is a prosthetic group?
Tightly bound coenzymes, e.g. haem in haemoglobin.
What is a holoenzyme?
An enzyme with a cofactor.
What is Vmax?
The maximum velocity of a reaction.
What is Km?
The concentration in moles of S which gives 1/2 Vmax.
Km = [S] at 0.5Vmax.
What does a low Km indicate?
A low Km indicates an enzyme only needs a little substrate to work at half-maximal velocity.
What does a high Km indicate?
A high Km indicates an enzyme needs a lot of substrate to work at half-maximal velocity.
What do proline hydroxylates enable?
Proline hydroxylases enable sensing of physiological oxygen ranges.
Define competitive inhibition.
an inhibitor binds to the active site, blocking substrate access.
What is orthosteric inhibition?
Competitive inhibition, binds at the same site.
What is non-competitive inhibition?
An inhibitor binds to a site other than the active site, inhibiting an enzyme by changing its conformation.
What is allosteric inhibition?
Non-competitive inhibition, binds at different sites.
What is irreversible inhibition?
Non-competitive inhibition which cannot be reversed. It usually involves formation or breakage of covalent bonds in the enzyme complex.
What effect does competitive inhibition have on Vmax and Km?
Vmax does not change, but Km varies.
How is methanol poisoning treated?
With 40% ethanol + dialysis + ventilation.
What effect does non-competitive inhibition have on Vmax and Km?
Vmax varies, but Km does not change.
What type of curve do allosteric enzymes produce?
Sigmoidal.
What is V0?
The initial reaction velocity.
Glucose may be converted into what?
- Storage: glycogen, starch, sucrose, conversion to lipid.
- Ribose-5-phosphate.
- Lactate.
- Pyruvate.
What is ribose-5-phosphate used for?
It is a precursor for nucleotide synthesis and DNA repair. It is essential for growth..
Why is lactate important in anaerobic glycolysis?
It enables the rapid, but inefficient production of ATP in the absence of oxygen.
What is pyruvate used for?
Efficient ATP production by oxidative metabolism.
Which glucose symporters allow glucose transport into the brain?
GLUT1 and GLUT 3.
Which glucose symporters allow glucose transport into the Liver?
GLUT2
Which glucose symporters allow glucose transport into muscle and adipose tissue?
GLUT4
Which glucose symporters allow glucose transport into the gut?
GLUT5
What are the 3 control points in glycolysis?
- Hexokinase: controls substrate energy.
- Phosphofructokinase: controls the rate of flow.
- Pyruvate kinase: controls product exit.
What effect does AMP have on glycolysis?
Will increase rate of glycolysis if energy is needed.
What effect does ATP have on glycolysis?
Will slow glycolysis if energy is abundant.
What effect does citrate have on glycolysis?
Slows pyruvate entry to TCA cycle if energy is abundant.
What effect does H+ have on glycolysis?
Slows glycolysis if there is too much lactic acid being produced.
What is the pyruvate produced in glycolysis used for?
Carbon to fuel the TCA cycle in mitochondria.
What is the NADH produced in glycolysis used for?
For the electron transport chain and ATP synthesis.
What happens if mitochondrial metabolism is inhibited by lack of oxygen?
NADH is used to ferment pyruvate to lactic acid (lactate).
NADH is then regenerated.
What is the Warburg effect?
The up-regulation of anaerobic glycolysis in cancer cells.
How do cancer cells produce energy?
By high-rate of glucose metabolism to lactate, i.e. anaerobic glycolysis.
Why is NADH reoxidised?
To enable glycolysis to continue.
How is NAD+ regenerated and why?
Through the oxidative metabolism of pyruvate. Acts as an electron acceptor to maintain Stage 1 and 2 metabolism.
Stage 2 of aerobic respiration has 3 different names, what are these?
- Citric acid cycle.
- Krebs cycle
- Tricarboxylic acid cycle.
Where does the TCA cycle occur?
In mitochondria.
Where are the enzymes for the TCA cycle contained?
The matrix of the mitochondria.
How can pyruvate enter the mitochondrial matrix?
- H+ gradient from the cytosol to the matrix.
- Pyruvate transporter by facilitated diffusion.
3.
When in the mitochondrial matrix, how is pyruvate metabolised to Acetyl-CoA?
Pyruvate dehydrogenase complex catalyses the oxidative decarboxylation of pyruvate to acetyl-CoA.
Can acetyl-CoA be converted back to pyruvate?
No, the reaction is irreversible.
Summarise the TCA cycle.
2C unit from acetyl-CoA condense with a 4C unit to form 6C unit.
