Biochemistry Flashcards
What does delta G say about a reaction.
Negative= reaction is feasible Zero= reaction is at equilibrium Positive= reverse reaction will occur
If many cellular processes are unfavourable and have a positive delta g how do they proceed?
They are driven by coupling to highly favourable processes.
What is a chemical reaction with an associated free energy change that is large and negative likely to be?
Irreversible in the cell
Explain what an exergonic reaction is
Reactions in which the total free energy of the product(s) is less than the total free energy of the reactant(s). So, the free energy change is negative. Such reactions can occur spontaneously.
Explain what an endergonic reaction is
Reactions in which the total free energy of the product(s) is more than the total free. energy of the reactant(s). So, the free energy change is positive. Such reactions cannot occur spontaneously and need an input of energy to proceed.
What sort of reaction is the hydrolysis of ATP
Exergonic- as it yields lots of energy
Why can ATP not diffuse through the cell membrane?
It is highly polar like AMP and ADP
At Keq what is the value of the change in free energy for a chemical reaction?
Zero as it represents the concentrations of products:reactants at which there is no net free energy transfer.
What is a polar molecule?
A molecule with opposite charges at opposite ends
How does water arrange around ions?
The more negative atoms attach to positive ion, the more positive atoms attach to negative ions, water forms a hydration shell.
What do hydrogen bonds involve?
Hydrogen bonds involve a linear arrangement of one hydrogen atom between two electronegative atoms
What do all newly synthesised peptide chains normally start with?
Methionine.
Describe the rotation permitted in a peptide bond
Single bond rotation is permitted between nitrogen and the carbonyl group.
What happens during the formation of a peptide bond?
The α-amino group of one amino acid acts as a nucleophile to displace the hydroxyl group of another amino acid forming a peptide bond.
A strong acid will display a larger Ka but smaller pKa value compared to a weak acid. True or false?
True
When the concentration of acid is equal to the concentration of conjugate base in a buffer what is the relationship between pH and pKa?
pH=pKa
State three things about zwitterions
Zwitterions are dipolar molecules which act as buffers of acids and bases.
Zwitterion ion charge may be positive or negative depending upon prevailing pH.
The overall charge of a zwitterion is neutral at a pH equivalent to the isoelectric point, pI.
Which type of bonding is responsible for the secondary
structure of proteins?
Hydrogen bonding between the C=O and N-H groups of peptide bonds.
Why does proline break an alpha helix?
Proline has an unusual shape for an amino acid because its R-group folds back on itself to form a ring with the amino group of the backbone. That changes the bonding angle of the polypeptide chain and causes a kink. This means the hydrogen bonding process cannot occur.
What does collagen contain?
A high proportion of hydroxylated proline residues.
Which amino acid can form disulphide bonds?
Cysteine
What is a protein domain?
A discrete region of polypeptide chain that has folded into a self-contained three-dimensional structure.
Name four major classes of biomolecules
- Peptides and proteins
- Lipids
- Nucleic acids
- Carbohydrates
Define metabolism, catabolism and anabolism
- Metabolism is all the reactions taking place in the body, divided into
- Catabolism is breaking down complex molecules into smaller ones and releasing energy. Exergonic and oxidative.
- Anabolism is synthesizing complex molecules out of smaller ones in energy-consuming reactions. Endergonic and reductive
What do D and L amino acids refer to?
D and L refers to stereochemistry of amino acids. L is the form in the body.
What are zwitterions?
Compounds with no overall electrical charge. They contain two titratable groups and therefore two pKa values.
What does secondary protein structure refer to?
The localised conformation of the polypeptide backbone. Hydrogen-bonded three-dimensional arrangements of a polypeptide chain are localised and only considers the backbone of the polypeptide.
Describe three types of secondary structure
Alpha helices- rod like and made up of one polypeptide chain.
Beta sheets- Polypeptide backbone almost completely extended, they run flat they don’t twist like alpha helices do. Sheets can run parallel or anti-parallel to each other.
Triple helices- This is a component of bone and connective tissue and is most abundant protein in vertebrates. It is composed of water-insoluble fibres. Three left-handed helical chains are twisted around each other form a right-handed superhelix.
Describe the two types of tertiary structure
Fibrous Proteins- These contain polypeptide chains organized approximately parallel along a single axis. They consist of long fibers or large sheets so they tend to be strong.
Globular Proteins- These are proteins which are folded to a more or less spherical shape. They tend to be soluble in water and salt solutions due to hydrophobic clustering together in the centre and water soluble groups predominating the surface.
Describe the forces stabilising tertiary structure
a. Covalent Disulphide Bonds:
b. Electrostatic interactions (salt bridges): Positive charges attract negative charges
c. Hydrophobic interactions: Weak attractions between water and hydrocarbon and weak attractions between hydrocarbon and hydrocarbon (van der Waals interactions). The hydrophobic effect refers to the fact that amino acids with hydrophobic side-chains tend to cluster in the centre of globular proteins.
d. Hydrogen bonds: In the backbone or side chains.
e. Complex formation with metal ions
Why is the lagging strand synthesised in Okazaki fragments?
DNA Polymerase can only add free nucleotides to the 3’ end of the strand.
What does exonuclease activity do?
Cleaves incorrect nucleotides from the chain resulting in there being less mutations.
What is a telomere?
A region of repetitive nucleotide sequences at each end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighbouring chromosomes.
Describe RNA
It is usually single stranded and contains local stretches of intramolecular base pairing (it folds back on itself), the three main classes are tRNA, mRNA and rRNA.
How is RNA made?
RNA Polymerase. Eukaryotic cells have three types of RNA polymerase (Pol I, Pol II, Pol III), Pol II synthesises all mRNA.
Describe the stages of transcription
- RNA polymerase binding causes detection of initiation sites (promoters) on DNA. This requires transcription factors.
- DNA chain separation occurs with local unwinding of DNA allowing access to the nucleotide sequence.
- Transcription initiation- there is selection of the first nucleotide of the growing RNA.
- Elongation- there is addition of further nucleotides to the RNA chain.
- Termination- finally the finished chain is released.
What is the function of the TATA binding protein
Transcription factor that binds to DNA sequence called the TATA box it is part of the TFIID which is a general transcription factor required for all Poll ll transcribed genes.
Describe termination of transcription
The newly synthesised RNA makes a stem-loop structure followed by a stretch of Us. A specific enzyme will then cleave the (now finished) RNA causing it to be released and the polymerase to dissociate.
How can transcription be regulated?
Transcription factors can be used to activate promoters or enhancers to cause an increase or decrease in the transcription of a specific gene.
Why is the genetic code described as both degenerate and unambiguous?
The genetic code is described as degenerate because a single amino acid may be coded for by more than one codon. The genetic code is also unambiguous as each codon specifies one amino acid or a stop codon only.
What is the function of Aminoacyl-tRNA synthetases?
They bind amino acids to their corresponding tRNA molecule(s).
Describe Initiation of Translation
This requires initiation factors and energy from GTP. Small ribosomal subunit binds to 5’ end of mRNA and moves along the mRNA until start codon is found. tRNA with correct anticodon will bind. Large subunit joins assembly and initiator tRNA is located in P site.
Describe elongation of translation
An elongation factor, brings the next aminoacyl-tRNA to the A site. GTP is hydrolysed, EF is released from tRNA and a second EF picks up the next aminoacyl-tRNA. Peptide bond formation takes place between amino acids in the P and A sites. Elongation factor moves ribosome along the mRNA by one triplet. ‘Empty’ tRNA moves to E site and it can now exit and become reloaded with an amino acid. tRNA with the growing peptide moves from the A to the P site. A site is free for the next aminoacyl-tRNA.
Describe termination of translation
This occurs when the A site of the ribosome encounters a stop codon. No aminoacyl-tRNA base-pairs with stop codons. A release factor RF binds to the stop codon. The finished protein is cleaved off tRNA. The components – rRNA, mRNA and tRNA – dissociate from one another and the whole process starts all over again with the small subunit being bound by IF ready for translation of a new protein.
Describe three things that could happen to the finished protein
Targeting- moving a protein to its final cellular destination.
Modification- addition of further functional chemical groups.
Degradation- unwanted or damaged proteins have to be removed.
What do free ribosomes in the cytosol make proteins destined for?
These are all translocated post translationally
– Cytosol
– Nucleus
– Mitochondria
What do bound ribosomes on the rough endoplasmic reticulum make proteins destined for?
These are translocated co-translationally
– Plasma membrane
– ER
– Golgi apparatus
– Secretion
What do post-translational modifications include?
- Glycosylation- addition and processing of carbohydrates in the ER and the Golgi.
- Formation of disulfide bonds in the ER.
- Folding and assembly of multisubunit proteins in the ER.
- Specific proteolytic cleavage in the ER, Golgi, and secretory vesicles.
What does aminoacyl-tRNA synthesase do?
Enzyme that attaches the appropriate amino acid onto its tRNA.
What are cofactors?
Inorganic metal ions that stabilise transition states.
What are coenzymes?
Organic molecules, they change charge or structure during the course of the reaction, but are regenerated. They may be involved in redox reactions or in group transfer processes.
What is an enzyme without a cofactor called?
An apoenzyme
What is an enzyme with a cofactor called?
A holoenzyme.
Explain what isoenzymes are
• Isozymes are isoforms of enzymes, they catalyse the same reaction but have different properties and structure (and sequence).
• Different isozymes can be:
1) Synthesised during different stages of foetal and embryonic development
2) Present in different tissues
3) Present in different cellular locations
What is a zymogen?
An inactive substance which is converted into an enzyme when activated by another enzyme.
What is Vmax?
The maximum velocity of a reaction
What is KM?
The concentration in moles of S which gives ½ Vmax
What does a low KM mean?
A low KM means that an enzyme only needs a little substrate to work at half-maximal velocity. A low KM will result in the enzyme rate being more sensitive to changes in concentration
What does a high KM mean?
A high KM means that an enzyme needs a lot of substrate to work at half-maximal velocity and enzyme rate will be less affected by changes in concentration
What is competitive inhibition?
Inhibitor binds to the active site and blocks substrate access. Vmax does not change but KM varies.
What is Reversible Non-Competitive inhibition?
Inhibitor binds to a site other than the catalytic centre; inhibits enzyme by changing its conformation (Allosteric Inhibition). Vmax varies but KM does not.
What is Irreversible Non-Competitive Inhibition?
Inhibition cannot be reversed. Usually involves formation or breakage of Covalent bonds in the enzyme complex. Vmax varies but KM does not.
What is feedback inhibition?
Inhibition of rate limiting enzymes by end products and is a common mechanism of allosteric control
What enzymes do not follow Michaelis- Menten kinetics?
Allosteric enzymes
What are the possible fates of glucose?
Storage (anabolic reactions to produce glycogen)
Oxidation by pentose phosphate pathway (catabolism to to proceed ribose-5-phosphate used in DNA repair and synthesis)
Fermentation to produce lactate
Aerobic glycolysis to produce pyruvate
Explain the enzymes involved in the three control points at glycolysis
1) Hexokinase – substrate entry (catalyses first phosphorylation of glucose)
2) Phosphofructokinase – rate of flow (catalyses second addition of phosphate group)
3) Pyruvate kinase (product exit)
Explain control of phosphofructokinase by energy charge
A high ratio of ATP to AMP will inhibit the enzyme and therefore glycolysis
What is the net molar yield of ATP and NADH from the complete metabolism of 1 mole of glucose to pyruvate under aerobic conditions?
2 ATP and 2 NADH
In glycolysis why AMP used to control phosphofructokinase and not ADP?
if ATP is rapidly used up, adenylate kinase can salvage some of the energy in ADP
2 ADP ATP + AMP
So this is not a true representation
Explain lactic acid fermentation
- In the absence of oxygen there will be rapid but inefficient generation of ATP.
- NADH is used to ferment pyruvate to lactic acid (lactate). The NADH will then be regenerated.
Where does the TCA cycle occur?
The matrix of the mitochondria
Where does oxidative phosphorylation occur?
The cristae of the mitochondria
How does pyruvate enter the mitochondrial matrix?
H+/pyruvate symport by facilitated diffusion
What does the pyruvate dehydrogenase complex do and what does it consist of?
Catalyses the oxidative decarboxylation of pyruvate to acetyl-CoA. It does this by removing carbon from the pyruvate. (pyruvate is 3 carbons acetyl-coA is two) PDC consists of 3 enzymes and is allosterically regulated by phosphorylation. The reaction is irreversible Acetyl-coA cannot be converted back to pyruvate.
Explain the malate aspartate shuttle
Allows NADH from glycolysis to indirectly make its way to the oxidative phosphorylation stage. Malate aspartate shuttle is the point which glycolytic rate can be coordinated with TCA:
- NADH from glycolysis is used to generate malate from oxaloacetate in cytosol
- Malate transporters transfer malate to mitochondrial matrix.
- Malate conversion to oxaloacetate in TCA cycle generates NADH in addition to the malate that arises from Fumarate.
Note: Malate is an intermediate of the TCA cycle
What is the electron transport chain made up of?
A chain of electron carriers with increasing redox potential.
- There are four multi-subunit complexes in the inner mitochondrial membrane (cristae)
- Electrons from NADH enter at complex I
- Electrons from FADH2 enter at complex II, this complex II is part of the TCA cycle
- Electrons are handed down from higher to lower redox potentials
- Electrons are ultimately transferred onto O2 to form H2O
Explain ATP generation in relation to ATP synthase
ATP synthase generation of ATP involves a rotating structure outside the inner mitochondrial membrane.
Explain oxidative phosphorylation and how it results in the rotation of ATP synthase.
Transfer of electrons through the respiratory chain is coupled to transport of H+ from the mitochondrial matrix to the intermembrane space
Three of the four respiratory complexes pump H+
This creates a proton gradient and protons through back ATP synthase rotating it.
What would an uncoupler of oxidative phosphorylation most likely lead to?
Operation of the electron transport chain without ATP production
Explain a simple overview of aerobic glycolysis
Glucose goes to fructose-1,6-bisphosphate, this requires 2ATP.
Fructose-1,6-bisphosphate goes to 2 triose phosphates
2 triode phosphates to pyruvate, this produces 2NADH + 2H+ and 4ATP (net gain 2ATP)
Where does glycolysis occur?
The cytoplasm
What is the main purpose of the TCA cycle?
The primary role is to transfer energy to NADH and FADH effectively charging up a store of reducing equivalents.
What is the final balance of respiration?
30-32 ATP, 6CO2 and H20
Go through and learn metabolism cycles
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