Principles Biochemistry Outcomes Flashcards
What is the mass and charge of a:
- proton
- neutron
- electron?
A proton has a mass of 1 and a +ve charge.
A neutron has a mass of 1 and no charge.
An electron has negligible mass and a -ve charge.
What happens to electrons in a covalent bond?
Electrons are shared between atoms in a covalent bond.
Describe an ionic bond.
An ionic bond occurs due to the attraction of opposite charges between ions.
Describe a hydrogen bond.
A hydrogen bond is due to the sharing of a hydrogen atom.
Define hydrophobic interaction.
Hydrophobic interaction is the interaction of nonpolar substances in the presence of polar substances (particularly water).
Define Van Der Waals interaction.
Van der Waals interaction is the interaction of electrons of nonpolar substances
Define electronegativity.
Electronegativity is the attractive force that an atomic nucleus exerts on electrons.
What are condensation and hydrolysis reactions?
Condensation reactions are the removal of water.
Hydrolysis reactions are the addition of water.
what is a redox reaction?
A redox reaction is the transfer of electrons from one molecule to another.
Differentiate between oxidation and reduction.
Oxidation is the loss of electrons.
Reduction is the gain of electrons.
Give 3 functions of biomolecules within the body.
- Information storage (DNA).
- Structure (teeth, bones, cartilage).
- Energy generation (glycolysis, citric acid cycle, electron transport chain).
- Energy currency/storage (ATP).
- Recognition/communication/specificity (receptors, hormones, enzymes)
What are the four major classes of biomolecules?
- Peptides and proteins.
2, Lipids (triglycerides, phospholipids, steroids). - Nucleic acids
- Carbohydrates.
What is an exergonic reaction?
Exergonic reactions are those in which the total free energy of the products is LESS than the total free energy of the reactants. ΔG is NEGATIVE. They may occur spontaneously.
What is an endergonic reaction?
An endergonic reaction is a reaction in which the total free energy of the products is GREATER than that of the reactants. ΔG is POSITIVE. They cannot occur spontaneously as they require an input of energy to proceed.
Account for the central role of ATP in cellular energetics
ATP is used as a universal energy currency for driving many different cellular processes.
How is ATP stored?
ATP is constantly being regenerated as cells do not store it in large amounts.
Define metabolism.
Metabolism is the sum of all of the reactions taking place in the body, and can be divided into: anabolism and catabolism.
Define catabolism.
Catabolism is the breaking down of complex molecules into smaller ones and releasing energy,
Define anabolism.
Anabolism is the synthesising of complex molecules out of smaller ones in energy consuming reactions.
Define glycolysis.
Glycolysis is a catabolic pathway, and the initial breakdown of glucose for the generation of ATP. Produces a net gain of 2 ATP molecules per glucose,
Define gluconeogenesis.
Gluconeogenesis is an anabolic pathway, and the synthesis of glucose from non-carbohydrate precursors, e.g. pyruvate. It requires energy.
What type of bonds exist between water molecules?
Hydrogen bonds exist between water molecules.
Explain the influence of water-water interactions on the organization of amphipathic molecules in an aqueous phase
When in contact with water, amphipathic molecules form micelles.
The polar head interacts well with water.
The non-polar tails do not, and are sequestered from the water.
What is meant by the term hydrophobic effect?
The hydrophobic effect is a term used to describe the behaviour of non-polar substances in water. Non-polar liquids tend to form a two-layer system with water.
Describe the general structure and classification of naturally occurring amino acids found in proteins.
All amino acids contain an α-carbon bonded to: an amino group, a carboxyl group, a hydrogen and a side (-R) chain.
They may be non-polar, polar, acidic or basic.
Describe a peptide bond.
Peptide bonds have partial double bond character, they are planar, strong and rigid. This is important for the folding of proteins.
What is an acid and what is a base?
An acid is a substance capable of donating a proton.
A base is a substance capable of accepting a proton.
What is the strength of an acid and how is it measured?
The strength of an acid is how readily it donates a proton. It is measured by the acid dissociation constant Ka.
What is pH?
pH is a measure of the amount of protons present in a solution.
What is the Henderson-Hasselbach equation?
An equation connecting Ka of a weak acid with the pH of a solution of that acid. It allows the properties of a buffer solution to be calculated.
What is a buffer solution?
A buffer is a solution used to control the pH of a reaction mixture.
At their pKa value, buffers resist changes in pH on addition of moderate amounts of acid or base.
Define isoelectric pH.
The isoelectric pH is the pH at which a molecule has no net charge.
Changes in pH may change the ionisation of a protein, leading to what?
This may lead to changes in structure, and therefore function.
What is the primary structure of a protein?
The primary structure of a protein is the sequence of amino acid residues,
What is the secondary structure of a protein?
The secondary structure of a protein is the localised conformation of the polypeptide backbone.
What is the tertiary structure of a protein?
The tertiary structure of a protein is the 3D structure of the entire polypeptide, including all of its side chains.
What is the quaternary structure of a protein?
The quaternary structure of a protein is the spatial arrangement of polypeptide chains in a protein with multiple subunits.
What are the rotational angles of polypeptides?
Polypeptides can rotate around the angle between: the α-carbon and amino group, and the α-carbon and carboxyl group.
What are the three types of secondary protein structure?
Alpha helix, beta strands and sheets, and triple helix.
Describe an alpha helix(secondary structure)?
An alpha-helix is a rod like one polypeptide chain. It is broken by proline residues.
Describe the structure of beta-strands (secondary structures)?
A beta sheet is a polypeptide backbone that can involve more than one chain. It has two possible directions: parallel and anti-parallel.
Describe the structure of beta sheets?
Beta sheets have a repeated ‘zigzag’ structure that is also known as a beta-pleated sheet.
Describe the structure of a collagen triple helix?
It is protein consisting of 3 left-handed helical chains twisted around each other to form a right-handed superhelix.
They are water-insoluble fibres.
Give examples of tertiary structures.
Tertiary structures include fibrous (e.g. keratin) and globular (e.g. haemoglobin)proteins.
What is the function of collagen?
Collagen influences the strength of connective tissue. It is found in bone and connective tissue,
Describe the function of tropocollagen.
Tropocollagen is a repeating sequence of X-Y-Gly. It is the basic structural unit of collagen.
Give an example of a disease arising from a single nucleotide sequence change.
Sickle cell anaemia.
Give examples of conditions arising from proteins associating with other proteins before they are folded correctly.
Alzheimer’s, Parkinson’s.
Give examples of things that may cause protein denaturation?
Heat, extreme pH, detergents, thiol agents, reducing agents and urea.
Describe the structure of haemoglobin.
Haemoglobin is a quaternary structure consisting of 4 subunits: 2 α and 2 β chains. Each of these contains a haem group able to bind one oxygen molecule.
Describe the structure of DNA.
DNA is a double helix of anti-parallel nucleotide strands containing deoxyribose sugar (sugar-phosphate backbone), and has 4 possible bases: A, C, G, T (paired internally).
Describe the structure of RNA.
RNA contains ribose sugar, and has 4 possible bases: A, C, G, U.
What is polymerisation?
The formation of a phosphodiester bond between a free 3’ OH group and a 5’ triosphosphate. It consumes two high energy bonds.
To which end are new nucleotides added?
New nucleotides may only be added to a free 3’ end.
How many bonds exist between:
- A and T.
- C and G.
A and T have a double bond.
C and G have a triple bond.
Describe the process of DNA replication.
DNA replication is semi-conservative.
Helicase unwinds the DNA. Primase synthesises an RNA primer and DNA polymerase synthesises a complementary DNA strand.
Nucleotides are added to free 3’ ends of the leading strand.
The lagging strand is synthesised in okazaki fragments.
RNA primers are degraded and gaps are filled in by DNA polymerase.
How is replication finished in a reasonable time frame?
Replication starts simultaneously at several points in the genome and is bi-directional.
What are the 3 main classes of RNA?
Ribosomal, transfer and messenger.
What is the function of mRNA?
Messenger RNA carries the genetic information required for protein synthesis, i.e. the codes for protein synthesis.
What is the function of tRNA?
Transfer RNA carries the amino acids to be made into protein.
What is the function of rRNA?
Ribosomal RNA combines with proteins to form the ribosomes where protein synthesis takes place.
Describe a tRNA anticodon.
Three nucleotides with an amino acid dependent upon the anti-codon sequence attached to the 3’ end.
What is the function of RNA polymerases?
RNA polymerases use one DNA strand as a template to copy the nucleotide sequence into RNA.
Describe the process of transcription.
RNA polymerase detects promoters on DNA and binds. The DNA chain separates. Transcription is initiated. Nucleotides are added to the RNA chain. Termination occurs and the release of finished RNA.
What does TBP stand for?
TBP stands for TATA-box binding protein. It recognises the TATA box.
Describe the new strand of RNA in relation to the template and coding strand of DNA.
The new RNA chain is complementary to the template strand, and identical to the coding strand (but with U instead of T).
Describe the physiological actions of steroid hormones in gene regulation.
Steroid receptors are a subset of nuclear hormone receptors.
When inactive, they are located in the cell cytoplasm.
When a steroid binds, the receptor moves to the nucleus and binds to DNA at steroid-response elements.
How are steroids transported in blood?
Steroids are transported in blood bound to albumin or specific transport proteins.
What are exons and introns?
Exons are coding regions of DNA and introns are non-coding regions of DNA.
Which form of RNA is the codon and which is the anti-codon?
Codon: mRNA.
Anti-codon: tRNA.
Both consist of 3 nucleotides.
What is the function of aminoacyl-tRNA synthetases?
Aminoacyl-tRNA synthesases bind amino acids to their corresponding tRNA molecule(s).
How many rRNA molecules make up a ribosome in eukaryotes?
Eukaryote ribosomes contain 4 rRNA molecules.
What are the three tRNA binding sites on ribosomes?
Exit, peptidyl and aminoacyl.
When does termination (RNA) occur?
Termination occurs when the aminoacyl site of the ribosome encounters a stop codon.
What is a point mutation?
A point mutation is a change in a single DNA base.
What is a missense mutation?
A missense mutation causes a change of amino acid sequence and may alter protein function.
What is a nonsense mutation?
A nonsense mutation creates a new termination codon and changes the length of a protein due to a premature stop of translation,
What is a silent mutation?
A silent mutation is due to the degeneracy of the genetic code and causes no change to amino acid sequence or effect on protein function.
What is a frameshift mutation?
A frameshift mutation is the addition or deletion of a base (or two) and changes the reading frame of the translation into protein.
Name the 4 types of chromosomal mutation.
Chromosomal mutations affect larger parts of the genome. 1, Deletion 2. Duplication 3. Inversion 4. Translocation.
Name the 3 things that may happen to the finished protein?
- Targeting
- Modification
- Degradation
Describe the Michaelis-Menten model.
The michaelis menten model described the rate of catalysis as a function of substrate concentration.
Define the term Km,
Km is the Michaelis constant and is the substrate concentration at which the reaction rate is half of its maximal value.
Define the term Vmax,
Vmax is the maximal reaction rate, even at infinite substrate concentrations.
What do a high and low Km indicate about an enzyme?
A high Km indicates that an enzyme requires a high substrate concentration to work at half its maximal velocity.
A low Km indicates that an enzyme only needs a low substrate concentration to work at half its maximal velocity.
What effect does competitive inhibition have on Km and Vmax?
Competitive inhibition causes a variation in Km, but no change in Vmax.
What effect does non-competitive inhibition have on Km and Vmax?
Non-competitive inhibition causes a variation in Vmax, but with no change to Km.
Allosteric enzymes do not follow Michaelis-menten kinetics, what curve do they form on a graph?
Allosteric enzymes form a sigmoidal curve during increasing substrate concentration.
Where are GLUT1 receptors found?
GLUT 1 receptors are found in the brain.
Describe glycolysis, and name its intermediate compounds.
Glycolysis is the pathway for the conversion of glucose to pyruvate.
The intermediate compounds are fructose-1,6-biphosphate, 2 triose phosphates.
What are the 3 control points in glycolysis?
- Hexokinase: controlling substrate entry.
- Phosphofructokinase: controlling rate of flow.
- Pyruvate kinase: controlling product exit.
What is pyruvate used for?
Pyruvate is used as carbon to fuel the TCA cycle in mitochondria.
What is the NADH produced by glycolysis used for?
The NADH produced is used in the electron transport chain and in ATP synthesis.
What is the need for the regeneration of NAD+?-
Only limited amounts of NAD+ are present in cells (derived from niacin). NADH must be reoxidised for glycolysis to occur.
How is NAD+ regenerated?
NAD+ is regenerated through the oxidative metabolism of pyruvate.
Describe the TCA cycle.
The TCA cycle occurs in the matrix of the mitochondria. Pyruvate enters by facilitated diffusion, and is irreversibly catalysed by pyruvate dehydrogenase complex to form acetyl-CoA. Energy is formed as GTP. Four oxidation reactions yield NADH + H+ and FADH2.
All enzymes of the TCA cycle are located in the mitochondrial matrix, except what, which is located where?
Succinate dehydrogenase which is integrated in the inner mitochondrial membrane.
What are lipids?
Lipids are cholesterol, triglyceride, glycerol and fatty acids.
What are the functions of cholesterol in health?
- structure and fluidity of the plasma membrane.
- Cell signalling.
- Precursor molecule of bile/bile acids/bile salts, Vitamin D and steroid hormones.
What are the functions of triglycerides in health?
- structure and fluidity of plasma membrane.
2. Highly concentrated energy stores.
How are cholesterol and triglycerides transported around the body?
Carried by lipoproteins.
What is a case-control study?
A case control study is when two existing groups differing in outcome are identified, and then compared on the basis of some supposed causal attributes.
What is a cohort study?
A cohort study follows a group of people over time, e.g. with reference to risk factors for a disease.
What is a systematic review?
A systematic review is literature focused on a research question.
What is meta-analysis?
Meta-analysis is a statistical technique for combining findings from independent studies.
What is a randomised clinical trial?
A randomised clinical trial is an experiment in which trial participants are randomly allocated to treatment under study.
Explain the term electron transport potential.
In oxidative phosphorylation, the electron transfer potential of NADH+ and FADH2 is converted into the phosphoryl transfer potential of ATP. It is measured by a compounds redox potential.
What are the two stages of oxidative phosphorylation?
- Electron transport: H+ moved out of matrix.
2. ATP synthesis: energy from electrochemical gradient of H+ can be used.
Describe electron transport by the respiratory chain and the associated transport of proteins.
Occurs in the inner mitochondrial membrane. Electrons from:
-NADH: enter at complex I.
-FADH2: enter at complex II.
They are ultimately transferred onto O2 to form H2O
What are cytochromes?
Cytochromes are proteins which contain a haem group as a functional co-factor. Haem contains Fe(II) ion capable of uptaking and releasing electrons.
Describe the electrochemical gradient of electron transport by the respiratory chain.
There are more protons in the intermembrane space than in the matrix, therefore the matrix is more negative, causing protons to want to flow back into the matrix. The protons flowing back through ATP synthase into the matrix is coupled to ATP synthesis.
What may inhibit the process of oxidative phosphorylation?
Cyanide, azide, CO,
How many molecules of ATP are yielded by 1 glucose molecule?
1 glucose molecule yields 30 to 32 ATP molecules.
