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Questions and Answers
Match the following amino acids with their characteristics:
Match the following amino acids with their characteristics:
Glycine = Has a hydrogen atom as R group Proline = Has a secondary amine group Cysteine = Contains a sulfur atom in the side chain Histidine = Has a basic side chain
Match the following protein structures with their descriptions:
Match the following protein structures with their descriptions:
Primary structure = Linear sequence of amino acids Secondary structure = Folding into alpha-helix or beta-pleated sheet Tertiary structure = Three-dimensional arrangement of a polypeptide Quaternary structure = Multiple polypeptide chains together
Match the following enzymes with their characteristics:
Match the following enzymes with their characteristics:
Cofactors = Non-protein helper molecules Isoenzymes = Different forms catalyzing the same reaction Active site = Region where substrate binds Reversible inhibitors = Can be competitive or non-competitive
Match the following proteins with their functions:
Match the following proteins with their functions:
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Match the following phases of enzyme kinetics with their descriptions:
Match the following phases of enzyme kinetics with their descriptions:
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Match the following transport processes with their definitions:
Match the following transport processes with their definitions:
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Match the following types of RNA with their functions:
Match the following types of RNA with their functions:
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Match the following mutations with their consequences:
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Match the following cell structures with their functions:
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Match the following antibiotic actions with their targets:
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Match the following concepts of thermodynamics with their descriptions:
Match the following concepts of thermodynamics with their descriptions:
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Match the following post-translational modifications with their effects:
Match the following post-translational modifications with their effects:
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Match the following types of cell junctions with their functions:
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Match the following components of DNA with their descriptions:
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Match the following types of enzyme inhibitors with their classification:
Match the following types of enzyme inhibitors with their classification:
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Match the following hormones with their derived amino acid:
Match the following hormones with their derived amino acid:
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Match the following enzyme classes with their functions:
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Match the following diseases with their associated deficiencies:
Match the following diseases with their associated deficiencies:
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Match the terms with their definitions in pharmacogenomics:
Match the terms with their definitions in pharmacogenomics:
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Match the following enzymes with their substrates or reactions:
Match the following enzymes with their substrates or reactions:
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Match the following kinetic parameters with their descriptions:
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Match the following scientists' rules with their concepts:
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Match the following drug treatments with their targets:
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Match the following structural features of haemoglobin with their functions:
Match the following structural features of haemoglobin with their functions:
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Match the following classes of enzymes with their actions:
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Match the following conditions with their effects:
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Match the following effects of genetic variations with their outcomes:
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Match the following enzymes with their associated reactions:
Match the following enzymes with their associated reactions:
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Match the following bioenergetic concepts with their descriptions:
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Study Notes
Biochemistry
- Amino acids: There are 20 natural amino acids.
- Each has a primary amino group, carboxyl group, H atom, and a R group (central α-carbon).
- Proline has a secondary amine group.
- Enantiomers: All amino acids except glycine have a chiral center.
- Only L isomers are found in proteins.
- D-amino acids are found in bacterial cell walls and certain antibiotics.
- Different R groups (side chains) lead to different physiochemical properties.
- Glycine has an H atom as its R group.
- Alanine, valine, leucine, isoleucine, and methionine have aliphatic side chains (hydrophobic + inert).
- Phenylalanine, tyrosine, and tryptophan have aromatic side chains (hydrophobic).
- Proline has an aliphatic side chain bonded to its amine group, making it an imino acid.
- Cysteine has a sulfur-containing side chain.
- Arginine and lysine have +vely charged side chains.
- Histidine has a basic side chain.
- Aspartic acid and glutamic acid have acidic side chains.
- Asparagine, glutamine, serine, and threonine are uncharged but polar; they can form hydrogen bonds.
Protein Structure
- Proteins are sequences of amino acids linked by peptide bonds.
- A peptide bond is a covalent bond between the α-amino group of one amino acid and the α-carboxyl group of another.
- Chains of <25 amino acids are called oligopeptides; >25 amino acids are polypeptides.
- Two linked amino acids are called a dipeptide.
- A condensation reaction forms peptide bonds.
- Proteins have different levels of structure (primary, secondary, tertiary, and quaternary).
- Primary structure is the linear sequence of amino acids.
- Secondary structure includes α-helices and β-pleated sheets.
- Tertiary structure is the three-dimensional arrangement of the amino acid chain.
- Quaternary structure describes the arrangement of multiple polypeptide chains.
Enzymes
- Enzymes are catalysts that speed up chemical reactions without being changed themselves.
- They are highly stereo-specific, meaning they only react with certain stereoisomers of a molecule.
- The active site is the region of an enzyme that binds to the substrate and converts it to a product.
- The substrate binds to the active site by weak forces, forming an ES complex.
- Substrate specificity is determined by the properties and spatial arrangement of the amino acid residues forming the active site.
- Enzymes are classified into six main groups based on the type of reaction they catalyze.
- Each enzyme has a unique 4-digit classification number.
- Enzyme assays measure the rate of conversion of a substrate to a product under various conditions.
- Coenzymes transfer groups from one molecule to another(some enzymes need to be able to function).
- Prosthetic groups are non-protein components that are essential to some enzymes’ function.
- Isoenzymes are different forms of an enzyme that catalyze the same reaction but have different physical or kinetic properties.
Thermodynamics
- Gibbs free energy is the energy available to do useful work in a system at constant temperature and pressure.
- If Gibbs free energy is negative, the reaction can occur spontaneously.
- If Gibbs free energy is positive, the reaction requires an input of energy to occur.
- Activation energy is the minimum energy required to initiate a chemical reaction.
- Enzymes lower the activation energy, making reactions occur more quickly.
Enzyme Kinetics
- Enzyme activity is the initial rate at which an enzyme catalyzes a reaction, expressed by its start.
- Low substrate concentration = low reaction rate (fewer collisions with an enzyme).
- Doubling substrate concentration = doubles the reaction rate (proportional).
- Too much substrate, reaction rate plateaus because the enzyme is saturated; reaction rate then depends on how fast the product can dissociate from the enzyme.
- Ideal substrate concentration= the rate is dependent on how fast the product can dissociate from the enzyme.
- Increasing enzyme concentration while maintaining substrate concentration =doubles the reaction rate.
- Temperature: Higher temperatures increase enzyme activity as substrate molecules have sufficient energy to overcome activation energy required to collide with an enzyme = > reaction rate.
- However, very high temperatures denature the enzyme's 3D tertiary structure = < reaction rate.
- pH: Optimal pH is when amino acid functional groups ionize correctly = maintains protein structure's proper conformation, denaturing can occur outside that range = < reaction rate.
Michaelis-Menten Model
- An enzyme (E) combines with a substrate (S) to form an enzyme-substrate complex (ES).
- The complex then releases products (P) and the free enzyme (E).
- Km is the Michaelis constant, a measure of an enzyme's affinity for its substrate.
- A low Km value means a high affinity, and a high Km value means a low affinity for the substrate.
- Vmax is the maximum velocity of an enzyme-catalyzed reaction, which occurs when the enzyme is saturated with substrate.
- Lineweaver-Burk plots are used to graphically determine Km and Vmax values.
Enzyme Inhibition
- Enzyme inhibitors reduce the activity of enzymes.
- Irreversible inhibitors bind permanently to an enzyme, often forming covalent bonds.
- Reversible inhibitors can bind and unbind and include competitive inhibitors.
- Competitive inhibitors structurally resemble substrates, competing for the active site.
- Noncompetitive inhibitors bind to a site away from the active site, causing a conformational change that reduces enzymatic activity.
Cells
- Cells are the basic units of life.
- Organelles are specialized structures within cells with specific functions.
- Cell membranes regulate materials entering and exiting the cell.
- The cytoplasm contains all cellular components, excluding the nucleus.
- The cytosol is the liquid portion of the cytoplasm. The nucleus regulates DNA and RNA actions; it is surrounded by a double-layered membrane.
- The nucleus contains nucleoli.
- DNA, organized into chromatin or chromosomes, controls protein synthesis.
Endoplasmic Reticulum
Highly convoluted single membrane-enclosed compartment = netlike meshwork/tube-like channels. Rough ER: Has ribosomes on outer membrane -> protein synthesis + transport. Smooth ER: No ribosomes -> lipid synthesis + transport, detoxification of drugs.
Ribosomes
- Site of protein synthesis Consist of RNA + protein
- Function is to transcribe and translate genetic information for protein synthesis.
Vacuoles/Vesicles
- Membrane bound organelles involved in storage for water, nutrients, and waste products.
Lysosomes
- Membrane-bound organelles containing digestive enzymes involved in breaking down waste products, pathogens, and worn-out organelles.
Golgi Apparatus
- Structure: 4-6 flattened, smooth membrane-bound compartments associated with vesicles.
- Function: Protein packaging, modification, and transportation.
Mitochondria
- Oxidative phosphorylation, site of ATP production from food energy.
- Has a double membrane -> inner membrane folded into cristae -> matrix inside.
DNA Replication and Protein Synthesis
- DNA replication is the process where DNA produces a copy of itself.
- Protein synthesis involves converting information from DNA into proteins.
- Stages of conversion of chemical food energy to ATP.
- Mitochondrial diseases arise from mutations in the mitochondrial DNA.
- Protein synthesis includes Transcription and Translation.
- Transcription is creating mRNA from the DNA template.
- Translation is reading the mRNA and creating the amino acid chain (protein).
Cytoskeleton and Centrioles
- Cytoskeleton: Provides structure and support to cells, includes actin filaments (shape change) and microtubules.
- Centrioles: microtubules involved in cell division.
Cell Membranes
- Composed of phospholipid bilayer, proteins, cholesterol.
- Proteins include channels (facilitated diffusion), pumps (active transport), and receptors.
- Vesiculation is the process in which materials move in and out of a cell (including endocytosis and exocytosis).
Facilitated Diffusion and Active Transport
- Facilitated diffusion transports substances across a membrane via protein channels that are faster than simple diffusion.
- Active transport uses carrier proteins coupled to an energy source to move substances against their concentration gradient.
DNA Composition and Structure
- Consists of nucleotides (phosphate group, pentose sugar, nitrogenous base).
- Nitrogenous bases in DNA include adenine, thymine, cytosine, and guanine (A-T, G-C pairings).
- Purines (A and G) consist of two fused rings, while pyrimidines (C and T) consist of one ring.
- DNA strands are held together by hydrogen bonds between complementary bases and forms a double helix.
DNA Replication/Mitosis
- Two DNA strands are separated using enzymes (template for new strands).
- These enzymes bring correct nucleotides to existing bases, creating two new DNA double helices (each with one strand from the original strand and one new strand.)
- DNA condenses around histone proteins and forms chromosomes.
Cancer
- Uncontrolled cell division.
- Lifestyle factors and genetics.
- Local disease- restricted to the tissue of origin.
- Metastasis- cancer cells invade and colonize other cell territories (harder to treat).
- Hallmarks: self-sufficiency in growth signals, insensitivity to anti-growth signals, limitless replicative potential, evading apoptosis, sustained angiogenesis, tissue invasion and metastasis.
- Causation- Smoking, body weight, physical activity levels, diet (processed/red meat), alcohol, hormones, UV, genetics, environment.
- Cancer treatments include Surgery, Radiotherapy, Chemotherapy, Targeted therapy.
How Obesity can Increase Cancer Risk
- Fat cells can produce more oestrogen-> affecting tissue growth, increasing the risk of certain cancers.
- Increased levels of insulin and other growth factors can prompt cells to divide more rapidly, which also increases the risk of cancer.
Protein synthesis lecture
- Central dogma = DNA to RNA to Protein
- Proteins composed of Amino Acids.
- 20 AA
- Transcription: DNA to mRNA.
- DNA is too large to leave the nucleus.
- mRNA leaves nucleus to act as a template in the cytoplasm.
- mRNA binds to Ribosomes in the cytoplasm.
- Translation: mRNA to polypeptide.
- Decoding of the mRNA message into polypeptide chain.
- tRNA brings anticodons that are complimentary to the codon on the mRNA and specific attached AA.
tRNA structure
- Amino acid binds to tRNA; anticodons sequence are complementary to the mRNA codon; allow tRNA to bring the correct amino acid to the mRNA.
- Translation: small and large subunit complexes with initiation factors form base pairs with the start codon sequence of the mRNA.
- Start codon (AUG) on the mRNA is positioned in the P site on the ribosome.
- Formyl-methionyl tRNA joins (1st AA)
- Large subunit on the ribosome joins = GTP hydrolyses to GDP+Pi, initiation factors leave the ribosome.
Elongation of translation
- Three binding sites (APE) - usually only two are occupied at a time.
- Aminoacyl acceptor site(A) - aminoacyl-tRNA enters
- Peptidyl site (P) - bonds form between AA's-holds tRNA
- Exit site(E) - tRNA exits
- EFTU catalyzes delivery of AA-tRNA to ribosome.
- EFG catalyses hydrolysis of GTP -> GDP + Pi -> conformational change in EFG.
- Peptide bond forms between AA at A and P sites -> ribosome moves 1 codon forwards = tRNA moves from A site to P site, amino acid on mRNA.
- Unloaded tRNA moves to the E site.
- Process repeats until stop codon reached.
Termination of translation
- Special release factors bind to the A site - stop codon reached.
- Polypeptide in the P site is hydrolysed from tRNA and exits the exit tunnel.
- Ribosomal subunits dissociate = ready to be reused.
Antibiotics and Ribosomes
- Antibiotics target bacterial ribosomes and disrupt their function.
- Streptomycin inhibits initiation.
- Linezolid prevents large subunit binding.
- Tetracycline prevents aminoacyl-tRNA binding to the A site.
- Chloramphenicol inhibits peptide bond formation.
- Erythromycin blocks the exit tunnel.
- Aminoglycosides inhibit initiation, and are extremely effective but toxic.
- Macrolides -> block exit channel on ribosome
- Mutations in rRNA or ribosomal proteins can cause antibiotic resistance.
Genome-Less Complex Than Proteome
- A single gene can lead to multiple RNA transcripts that produce multiple versions of a single protein.
- Post-translational modifications (PTMs) modify amino acids after translation, altering protein structure and function.
- Important for cellular activity regulation (e.g., phosphorylation).
- Kinases and phosphatases are important enzymes that activate or deactivate proteins.
- Crucial for understanding cellular processes, disease, and drug action.
Drugs and Central Dogma
- Drugs can bind to DNA directly (via covalent adducts or intercalating agents) to inhibit DNA replication, transcription, and reverse transcription.
- This affects translation and protein synthesis.
Cancer Lecture 1
- Uncontrolled cell division.
- Lifestyle factors and genetics are major influences.
- Local disease- restricted to the tissue of origin,
- Metastasis- cancer cells invade and colonise other Territories (harder to treat).
- Hallmarks of cancer: self-sufficiency in growth signals, insensitivity to anti-growth signals, limitless replicative potential, evading apoptosis, sustained angiogenesis, tissue invasion and metastasis.
- Causation: smoking, body weight, physical activity levels, diet (processed/red meat), alcohol, hormones, UV, genetics, environment.
Lecture Cancer 3
- Cancer treatments include surgery, radiotherapy, chemotherapy and targeted therapy.
- Surgery may not always be possible, depending on the location and extent of the cancer.
- Radiotherapy depends on the location, and limits toxicity to surrounding tissues.
- Chemotherapy targets rapidly growing cells and works in three main stages: binding to DNA, preventing DNA replication and inhibiting components of cell division.
- Personalized therapy can help predict patients' ability to metabolize and experience adverse effects of treatment, and it uses prognostic markers.
- Targeted therapy interferes with specific molecular pathways involved in cancer growth.
Unexplained/Persistent/Unusual Changes
- Unexplained changes - lumps, swellings, persistent coughs, voice changes, breathing problems.
- Persistent changes - sores that don't heal, digestive problems, unusual bleeding.
- Unusual changes- moles, skin changes, changes in breast size, shape or nipple.
- Weight loss
- Pain that persists.
- Important to consult a doctor if experiencing these changes, especially if they persist for several weeks.
- Tips for checking potential cancer risk factors, including family history, lifestyle, age, ethnicity.
Secondary Protein Structure Lecture
- Polypeptide folding is not random.
- Some conformations are more suitable/favourable due to the structure and rigidity of peptide bonds.
- Secondary structures (alpha helices and beta strands) exist due to hydrogen bonding between peptide bonds.
- Phi and psi angles control protein folding.
- Alpha-helix: A right-handed coil, stabilized by hydrogen bonds between amino acids located four residues apart.
- Beta-sheets: A pleated sheet, stabilized by hydrogen bonds between segments of polypeptide chain running side-by-side.
Tertiary Protein Structure Lecture
- Loops and bends control protein size and shape, and connect other secondary structures.
- Hydrophobic bonding = interactions between hydrophobic amino acids and water.
- Polar/charged interactions are important forces between positively and negatively charged amino acids or polar amino acids in water.
- Important forces in stabilizing tertiary structures, include hydrogen bonds, ionic bonds and disulfide bonds.
Quaternary Protein Structure Lecture
- Haemoglobin is a protein composed of 4 polypeptide chains(2 alpha and 2 beta)
- When O2 binds to hemoglobin, it causes a conformational change in the molecule, allowing for cooperative binding - cooperative binding is where the binding of one ligand increases the affinity for other ligands.
- Movement of corners (of structure).
- Each subunit has a heme group - the heme group contains an iron atom that binds to oxygen.
Allostericity and 2,3 Biphosphoglyceric Acid
- Allosteric regulation describes the change in an enzyme or proteins activity when a molecule (the allosteric effector) binds to a site away from the active site.
- 2,3-biphosphoglyceric acid (BPG) binds to the central cavity of hemoglobin subunits, stabilizing the T-state. BPG binds better to deoxygenated hemoglobin, and reduces hemoglobin affinity.
Enzymes Lecture
- Enzymes are proteins that catalyze biochemical reactions.
- Enzymes have specific properties like rate acceleration, active site, and chirality.
- They require coenzymes for catalytic function (some need metal ions, some are complex organic molecules)
- 6 different classes of enzymes- oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases
- Enzymes have specific mechanisms to speed up chemical reactions, these mechanisms are discussed in enzyme kinetics and dynamics.
Drugs and Diseases
- Aspirin inhibits cyclooxygenase (COX) enzyme, which is involved in prostaglandin synthesis (related to pain reduction and fever).
- Methotrexate inhibits dihydrofolate reductase (DHFR) enzyme critical in nucleotide synthesis.
Pharmacogenomics Lecture
- Pharmacogenomics studies how genetic variations influence a patient response to medicine, which impacts drug efficacy and toxicity.
- Genetic variations like deletions, copy number variants, chromosomal rearrangements, and single nucleotide polymorphisms cause differences in the body's metabolism or response to drugs.
- This lecture explores how different types of genetic variation affects drug metabolism and causes differences in patient's responses (efficacy and toxicity).
- Pharmacogenomics is important as it helps predict patient responses to drugs based on their genetic makeup, which can improve drug efficacy and reduce adverse effects.
Interactions Between Molecules Lecture
- Wallace's rule predicts the temperature at which DNA strands separate based on the base pair content.
- Packing interactions, including pi-pi stacking, influence the way molecules arrange themselves.
- Penicillin mechanism of action: binds with the residue to prevent bacterial cell wall synthesis.
- Oregano-phosphates are implicated in nerve impulse communication and affect acetylcholinesterase enzyme activity.
Health and Disease Concepts
- Health encompasses complete mental, physical, and social well-being.
- Disease involves a disturbance in body function due to some pathology or abnormality.
- Illness is the individual's experience (or perception) of being unwell.
- Health is measured by mortality, morbidity, life expectancy, and quality-adjusted life years.
- Society deals with illness using social norms and approaches to deviance.
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