BABS1201 Lectures - Molecules, Cells and Genes (University of New South Wales) PDF
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These lecture notes cover topics on basic biology, including major elements of life, water's properties, impacts of pH, and how life is classified.
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lOMoARcPSD|16917129 BABS1201 Lectures Molecules, Cells and Genes (University of New South Wales) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Angelin Prabaharan (apra...
lOMoARcPSD|16917129 BABS1201 Lectures Molecules, Cells and Genes (University of New South Wales) Scan to open on Studocu Studocu is not sponsored or endorsed by any college or university Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 LECTURES ydrogen itrogen LIFE E.HQNgeln.sn LO1: Listthe major elements of life. MAJOR ELEMENTS OF LIFE CARBON → CHOs, food sources PHOSPHORUS → DNA, ATP NITROGEN → nucleic acids, amino acids SULFUR → amino acids HYDROGEN OXYGEN COMPONENTS OF LIFE Organic molecules may be synthesised abiotically Stanley Miller (1953) → mimicked conditions of early earth ○ Collected organic compounds in organisms (amino acids, hydrocarbons) ○ Water + electrical water = formation of biological particles LO2: Describesome properties of water that make it essential for life as we know it WATER Water = Presence of life ○ Shapes + function of biological molecules are created from response of solvents ○ Medium for biochemical reactions ○ Reactions that support life → hydration/dehydration WATER = SUPPORTS LIFE POLARMolecule = H2O molecules attract (cohesion & adhesion) to each other → reason for various functions ○ Evaporation of leaves – Water moves up to leaf – Rest of molecules follow due to stronghydrogen bonding from polarity PROPERTIES: WATER TENSION H2O molecules @ surface → interact more to adjacent+ below ○ Strength across as ≠ bonding above SOLVENT Universal solvent ○ Dissolving salt → hydration shell = surrounds each solute ion Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 ○ Dissolves proteins e.g lysozyme Fats + Oils ≠ dissolve in water ○ Hydrophobic → not charged at poles, ≠ attracted DENSITY Water expands and floats when frozen ○ ICE = particles furtherapart → holes = less dense Bottom ocean, colder = less dense = fish can swim not freeze Different state = bonds behave differently LO3: Changes in pH affect living organisms AMPHOTERIC or giving Water can be ionised (taking protons) Control of pH = important = carry out reactions RELEVANCE TO MEDICINE Control of blood pH (respiration, CO2 + H2O) = CO2 dissolve in water in blood ○ pH changing = altering products producing e.g carbonic acid (x_x) pH AND THE BODY ↑ lactic acid (produced in exercise) = ↓ pH in muscles ≠ function of skeletal muscle Untreated diabetes = ↑ ketone bodies (substitute sugar for energy to brain) = coma WATER ACIDIFICATION CO2 dissolves in water ↑ CO2 in atmosphere = dissolved in oceans → ↑ water to be acidic CO2 dissolves → carbonic acids form → hydrogen ion presents → need for carbonate → less of CACO3 produces by marine animals CELLS I LO2 Explain how the diversity of life is classified DIVERSITY OF LIFE = CLASSIFIED → SPECIES CAN DIFFER CLASSIFICATIONS Classified life → species + broader classifications Differed initially→ structure, functions Differed currently → nucleic acids (comparing genes for similarities + differences) Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 THREE DOMAINS BACTERIA Range of morphologies (shapes + size) Cell walls → gram pos/neg Different features → flagella, endospores Vary in metabolism → produce toxins, photosynthetic ARCHAEA Microbes sharing features of bacteria + eukaryotes ○ Size, single-celled similar to bacteria ○ Similar traits to eukaryotes → synthesizes proteins, process DDNA Different features ○ Cell wall ○ Composition of cell membrane ≠ pathogenic Associated w/ extreme environments EUKARYOTES Different kingdoms – plant, animal, fungi, protists LO3 Define what a cell is Smallest unit of life = perform activities essential for life Action of organism is based on activity of a cell ALL CELLS HAVE – DNA – Cell membrane – Ribosomes → proteins = function – Cytoplasm LO4 List some characteristics of life CHARACTERISTICS Reproduce Grow + develop Responds to environment Metabolise to use + generate energy Produce waste DNA NOT LIFE VIRUS PRIONS ○ Smaller than cells + ≠ cells ○ Misfolded proteins ○ Rely on hosts to produce + ○ ≠ replicate = influences other metabolise proteins to misfold Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 LO5 Explain the fundamental differences between prokaryotes and eukaryotes EUKARYOTES PROKARYOTES Membrane bound organelles Smaller 10-100um DNA not bound, can carry extraDNA ○ Plasmids NO membrane bound organelles Bacteria = 1-5 um Plasma membrane → surrounds cytosol ○ Controlling traffic into and out of cell Cytoplasm includes cytosol, ≠ nucleus Ribosome, ≠ organelles ○ Made of ribosomal RNA + proteins, ≠ made of membranes ○ Exist in cytosol, rough ER FACTORS limiting min./max. Size of cells SA:V → supports all processes ○ Eukaryotes ↑ V = allow for different organelles, multiple functions @ a time ○ Prokaryotes ↑ SA = no organelles, processes occur rapidly LO6 Describe the concept of endosymbiosis ENDOSYMBIOSIS THEORY Ancestors of eukaryotes took O2 by using non-photosynthetic prokaryotic cells WHY? ○ Mitochondria similar size to bacteria – Double membrane being engulfed – Genome → compare to bacteria ADVANTAGES ○ Eukaryote capable of living in environment w/ ↑ levels of O2 Eukaryotic taking up photosynthetic cell = take up photosynthesis Looks @ complex cells – chloroplast + mitochondria and how eukaryotic cells developed them Explains how eukaryotic ancestral cells have organelles that eukaryotic cells have today Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 CHLOROPLAST Plant or algae 2 membranes ○ Outer → things passing from cytosol ○ Inner → selectively permeable Chlorophyll = green pigment → enables photosynthesis Thylakoid membranes → inside stroma= chloroplast DNA + ribosomes MITOCHONDRIA Eukaryotic cells 2 membranes ○ Inner → many folds (cristae) = ↑ SA → metabolic activity occurs = selectively permeable – Contains proteins → synthesise ATP Own DNA + ribosome Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 CELLS II LO1 Identify characteristic structures of eukaryotic and bacterial cells, and describe their basic functions PROKARYOTES Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 EUKARYOTES Membrane bound organelles Compartmentalisation → allows different functions to happen in different areas Nucleus = double membrane ANIMAL CELLS Pores in membrane = allow things to go through Nucleus wound by protein → packaged = chromatin (DNA that is packaged, wrapped around proteins) ○ Nucleoli → regions rRNA synthesised – Productive → why? = requires lots of RNA for proteins ○ Nuclear envelope → double membrane enclosing nucleus ○ Pores = transport of RNA leaving PLANT CELL Cell wall = cellulose (fibre) Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 ORGANELLES PEROXISOMES METABOLIC COMPARTMENTS Single membrane Contains enzymes transfer H atoms to O2 = H2O2 → converted to water by catalase LO2 Describe the endomembrane system ENDOMEMBRANE SYSTEM – Regulates protein traffic – Performs metabolic function – Transport network that enables cells to make or break cellular products ENDOPLASMIC RETICULUM (ER) Network of membranes ○ Nuclear envelope + ER interacting w/ e/o Vesicle formation that bud off ○ Part of membrane that moves + merges = allows for TRANSPORT SMOOTH ER Outer, NO RIBOSOMES Metabolic processes Calcium storage Lipid productions → membranes ROUGH ER WITH RIBOSOMES → dots in microscope Associated w/ secreted proteins ○ E.g insulin → produced in pancreas ○ Proteins segregated → transported via vesicles Polypeptide extend from ribosome → threaded into ER pore Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 GOLGI APPARATUS MODIFIES + STORES Vesicles travel here w/ proteins MODIFIES PRODUCTS ○ Foldinginto usable shapes ○ Addingother e.g CHO, lipids Proteins can be STORED → and released when needed ○ E.g insulin released when sugar blood glucose rises Cisternae = flattened membrane sacs → offers directionality = proteins move in one direction New viscles form = leave to new sites LYSOSOMES WASTE DISPOSAL UNIT Metabolising enzymes ○ Hydrolyzing amino acids ○ E.g digestive enzymes ○ BREAKSDOWN → into small molecules that can be used – Lipids – CHO – Proteins Also remove ‘junk’ VACUOLES VESICLES THAT STORE + SURROUND MEMBRANES Derived from ER + Golgi Diff. environment to cytosol LO3 List the main components of the cytoskeleton and briefly describe their roles in the cell Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 CYTOSKELETON DYNAMIC FIBRES Provides: ○ Cell shape ○ Moving things → ‘tracks’ for organelles MICROTUBULES Gives shape Provides tracks Allows cilia + flagella to give motion Made of proteins ○ Tubulin dimer → made of two different molecules (beta, alpha) = hollow tube + circle ends MICROFILAMENTS Twisted double chainsof globular actin proteins Gives cell shape Provides ‘pulling’ forces ○ Polymerising + depolymerising INTERMEDIATE FILAMENTS Present in someanimals → inc. vertebrates ○ E.g Keratin – Present in dead cells – Defective = disorders e.g blisters SUMMARY PROPERTY MICROTUBULES MICROFILAMENTS INTERMEDIATE STRUCTURE – Hollow tubes – 2 intertwined strands of – Fibrous proteins actin coiled into cables DIAMETER – 25nm, 15 lumen – 7nm – 8-12nm PROTEIN – Tubulin – Actin – Several different SUBUNITS proteins MAIN – Cell shape – Maintaining cell shape + – Cell shape FUNCTIONS – Motility changing cell shape – Anchorage of nucleus – Chromosome + – Muscles contraction – Formation of nucleus organelle – Cytoplasmic streaming laming movements – Motility – Division of animal cells Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 SHAPE SCIENTIFIC LITERATURE LO1 Explain the purpose of a scientific journal Journals = cover broad areas → catering to niches COMMUNICATING Scientific knowledge + breakthroughs Medium for articles to be published Narrows categories for science LO2 Identify a primary article and list its features STRUCTURE ○ Abstract ○ Introduction ○ Equipment / Experiment ○ Discussion ○ Conflicts of interest ○ Conclusion ORIGINAL findings LO3 Explain the differences between primary and secondary sources of scientific literature PRIMARY SECONDARY Original findings Review of primary articles Complex No discussion, experiment Targets specific audience Summary Targets wide community audience Peer reviewed Published in scientific journals Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 LO4 Describe the term ‘peer review’ as it applies to scientific literature SCRUTINY OF ARTICLES BY EXPERTS Reviewing the quality ○ Originality ○ Validating ○ Interesting Experts = same research area Decide ○ Is it rigorous? ○ More experiments needed? Submission → seen by editor/editorial team → ‘blind’ = author doesn’t know reviewer → ‘double blind’ = both don’t know each other → review = author responds to recommendations MACROMOLECULES LO1 Provide a broad definition of the term “macromolecule”. POLYMERS (chain like molecules) linked by covalent bonds Polymers = many molecules together Consists of repeating subunits (similar or different) = monomers → individual units LO2 Explain the way in which macromolecules are generally synthesised and broken down by organisms. SYNTHESIS of polymers Lossof water forming a new covalent bond = DEHYDRATION When? → to store polymers Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 SYNTHESIS OF PROTEINS Amino acids linked by PEPTIDE BONDS ○ Formed by dehydration b/w carboxyl group + amino group Proteins have a polarity = has direction ○ Start at alpha amino end – N-Terminus ○ End @ carboxyl end – C-Terminus BREAKDOWN of polymers of water splitting of a covalent bond = HYDROLYSIS Addition When? → breaking food down to absorb PROTEINS: AMINO ACIDS Polymer chain broken = RELEASING amino acids Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 LO3 Briefly describe the general structural features of each of the four major classes of macromolecules. STRUCTURES CARBOHYDRATES SUBUNIT: MONOSACCHARIDES All have a carbonyl group → double bond C = O ○ location varies= change in structure + properties ○ Aldose = group @ the end ○ Ketoses = group within Spatial Diversity ○ Around asymmetric carbons HEXOSES: 6 Carbons, C6H12O6 PENTOSES: 5 Carbons, C5H10O5 MONOSACCHARIDES Ring structure e.g glucose DISACCHARIDES 2 monosaccharides joined by GLYCOSIDIC BOND → covalent bond formed b/w glucoses Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 POLYSACCHARIDES Many monosaccharides joined by GLYCOSIDIC BOND ○ 100-1K e.g starch, glycogen, cellulose, chitin LIPIDS SUBUNIT: FATTY ACIDS DEHYDRATION = ESTER BONDS Glycerol backbone TRIACYLGLYCEROLS (TAGS) 3 formed from 3 fatty acids Can vary in length + no. of double bonds Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 SATURATED NO DOUBLE BONDS Solid @ room temperatures e.g butter UNSATURATED ONE OR MORE DOUBLE BONDS ○ Causes kinksin molecule e.g oils PHOSPHOLIPIDS Similar structure to TAG = phosphate + polar group (choline ) replace one of the 3 fatty acids 2 FATTY ACIDS Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 Kink due to double bond Hydrophilic head ○ Phosphate ○ Glycerol backbone STEROIDS 4 FUSED RINGS e.g cholesterol ○ In animal cell membranes PROTEINS SUBUNIT: AMINO ACIDS Proteins = polymers of AMINO ACID MONOMERSor POLYPEPTIDES ○ Can consist of one or more polypeptides ○ Folded into 3D structure 20 different amino acids Amino acids linked by PEPTIDE BOND ○ Folds = giving 3D structure = gives function AMINO ACID Side chain changes for amino acid → differs in properties and functions ○ Hydrophobic side chains = nonpolar∴ inside of proteins – e.g glycine, proline, methionine (usually first amino acid) ○ Hydrophilic side chains = polar ∴ outside of proteins – Cysteine ○ Hydrophilic electrically charged side chains = ionisable – Take up or give off hydrogen – Acidic = neg. charge – Basic = pos. charge Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 PROTEINS PRIMARY STRUCTURE Sequence of amino acids → order of letters Amino acids linked by peptide bonds = polypeptide chains SECONDARY STRUCTURE Polypeptide chains folding Held by hydrogen bonding ALPHA HELICES BETA SHEETS ○ Different H bonds = stabilising ○ Antiparallel = different polarity (c → n, n → c) TERTIARY STRUCTURE Overall shape of protein Involves interactions between side chains of amino acids ○ Hydrophobic ○ Hydrogen bonds Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 ○ Ionic or electrostatic bonds → first 3 are weak, cumulativelystrong ○ Disulfide bridges = covalent bonds → stronger – Between side chains of 2 cysteine amino acid FIBROUS PROTEINS Long, extended rod like Insoluble in water Mostly alpha helices e.g collagen (tendons) e.g keratin (hair) GLOBULAR PROTEINS Compact and fold back on themselves = complex structure Very soluble Hydrophobic core, hydrophilic surface Alpha + beta structures e.g haemoglobin Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 QUATERNARY STRUCTURE When polypeptide chains assemble into multi-subunit structures ○ One subunit = one polypeptide Proteins w/ 1 or more polypeptide chains Held by non-covalent bonds NUCLEIC ACIDS SUBUNIT: NUCLEOTIDES DNA – Deoxyribonucleic acid Deoxyribose sugar DOUBLE STRANDED ○ Hydrogen bonding = holds double helix → joining nitrogenous bases Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 – 2 H bonds b/w T and A – 3 H bonds w/ C and G – ↑ H bonds = harder to denature, break ○ Anti-parallel – Run in opposite directions → due to polarity – Purpose = during replication → strands apart → one = template SINGLE STRANDED Sugar-phosphate backbones = held by PHOSPHODIESTER BONDS Glycosidic bonds b/w sugar and nitrogenous base Phosphate group = negative charge RNA – Ribonucleic acid Ribose sugar Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 Single stranded 3 parts – phosphate, sugar, base PURINE Doublering Adenine and guanine PYRIMIDINE Singlering Cytosine and thymine LO4 List some examples of members belonging to each of the four major classes of macromolecules. Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 LO5 Describe some of the key functions of members belonging to each of the four major classes of macromolecules. KEY FUNCTIONS + EXAMPLES CARBOHYDRATES STORAGE STARCH Stored by plants Stores energy → used later via hydrolysis Potatoes, plant structures GLYCOGEN Stored by animals e.g liver → stores CHOs as glycogen Hydrolysis = releases as glucose → when demand for energy Exercise/fasting during night, maintain blood glucose levels while sleep STRUCTURAL CELLULOSE Polymer of glucose In cell wall of plants ≠ digest ○ Animals don’t have enzyme to breakdown ○ Herbivores = microbial process (bacteria to breakdown) Important for fibre, ≠ energy CHITIN Exoskeleton of arthropods ○ e.g outside shell of cockroaches Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 LIPIDS ENERGY STORAGE + TRANSPORT TRIACYLGLYCEROLS (TAGS) Fatty acids STRUCTURE PHOSPHOLIPIDS Essential = make up the cell membrane ○ Separating inside and outside environment of cells CHEMICAL MESSENGERS STEROIDS e.g cholesterol PHOTORECEPTORS Lipid parts of proteins in eyes CAROTENOIDS Orange/yellow → carrots ○ Vitamin A derivative from orange veggies ○ Insufficient amount = blindness COVERINGS WAXES On leaves PROTEINS STRUCTURAL Collagen, keratin STORAGE Casein → provides proteins in milk TRANSPORT Haemoglobin, myoglobin HORMONES Insulin MOTAR Actin, myosin → allow movement RECEPTOR Photoreceptors → eye to receive light, tastebuds ENZYMATIC Sucrase DEFENSE Antibodies NUCLEIC ACIDS DNA = stores genetic material → allows to be inherited ○ Organised into chromosomes = compressed ○ Chromatin = chromosomes located in nucleus ○ Histones = proteins that package DNA Chloroplast + mitochondria = own genomes Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 RNA W/ DIFFERENT FUNCTIONS mRNA = ribosomes → ensuring protein translation tRNA = ensures specific amino acid incorporated Other = regulation of gene expression + catalytic activity CELL INTEGRITY LO1 To describe the structure of cell membranes and their function in cell integrity. MEMBRANES Selectively permeable Controlling traffic of molecules into/out of cell Contains proteins Phospholipid bilayer + Proteins AMPHIPATHIC Hydrophilic portions → heads = protrude extracellular Hydrophobic portions → tails = portion in membrane FLUID MOSAIC MODEL FLUID = proteins moving in membrane MOSAIC = combination of different proteins Explains how molecules are spatially arranged in the membrane Proteins not randomly located → can group in areas Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 SIDEDNESS Asymmetrical Distribution of proteins in the membrane Proteins ≠ ‘flip’ → they are amphipathic Position of protein domains relative to the membrane is fixed after protein is inserted into plasma membrane LO2 To describe the different components of the cell membrane that are important in maintaining cell integrity. MEMBRANE COMPOSITION Lipids Proteins Carbohydrates LIPIDS Phospholipids Cholesterol → ↑ stability of bilayer, ↓ fluid PROTEINS Peripheral + integral proteins PERIPHERAL PROTEINS Proteins that interacts w/ surface of lipid INTEGRAL PROTEINS Span membrane w/ different domains at each end 3 DOMAINS EXTRACELLULAR → Soluble in extracellular fluid INTRACELLULAR → Soluble in cytosol TRANSMEMBRANE → insoluble, hydrophobic Cannot move up, down, rotate Can move side to side ∴ position of protein is fixed CARBOHYDRATES GLYCOLIPIDS → Attached to lipid GLYCOPROTEINS → Attached to protein CHO for recognition Diversity of CHOs = large variety of messengers can be placed ○ Pathogens can hijackthis mechanism Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 CELL INTEGRITY PHOSPHOLIPID BILAYER PERMEABILITY BARRIER to most molecules Prevents movement of molecules that are soluble in aqueous environments Hydrophobic molecules = dissolve in hydrophobic core → diffusing across membrane ○ O2, CO2, H2O = diffuse Large molecules, ionised, polar ≠ cross ○ Soluble in aqueous environments ○ Can cross by transporter proteins MEMBRANE PROTEINS Important for cell integrity Connecting peripheral proteins and the cytoskeleton e.g red blood cells ○ Deliver O2 to body tissues via blood flow ○ Take up O2 in lungs and release while squeezing through capillaries ○ Sustain substantial mechanical forces → red blood cells can be easily broken transmembrane proteins connected to cytoskeleton under plasma membrane Functions as a spring → deforms under force → flexible, durable LO3 To explain the non-selective diffusion of some small molecules across cell membranes and osmosis DIFFUSION Occur in presence of concentration gradient Concentration Gradient → unequal distribution of solutes/ions → different in concentration b/w two sides, net movement down gradient to reach equilibrium PASSIVE TRANSPORT = Does not require energy Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 OSMOSIS Passive transport of water Cytosol = water , proteins, ions ○ Concentration of water = low ISOTONIC → concentration of water in/out is balanced HYPOTONIC → less water inside = lysis HYPERTONIC → more water inside = shrivel Isotonic = favoured by animal cells Hypotonic = favoured by plant cells → cell wall = rigid → hypertonic = plasmolysis CELLULAR TRANSPORT LO1 To explain the mechanisms by which small molecules may be selectively transported in and out of cells. FACILITATED DIFFUSION Molecules move down concentration gradient CHANNELS: direct passage CARRIERS: binding of solutes CHANNELS Integral membrane proteins Corridor for specificmolecules/ions to cross ○ Specificity = allows cell to take up/retain – molecules it needs/exclude unwanted H2O = diffuses slowly = due to polarity ○ AQUAPORINS → specific channel for water Importance ○ Corridor opens for specific molecules the cell requires GATED CHANNELS Transports IONS open/close → response to a stimulus e.g binding a specific molecule Do not open at both sides simultaneously e.g neurotransmitter receptors in the brain are neurotransmitter-gated ion channels Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 CARRIERS - TRANSPORTERS Integral membrane proteins Moves solute during shape change Transports solute depending on concentration gradient Have specificity ○ Bind to specific molecules ○ e.g glucose – glucose transporters Slower Easier to regulate – can block other side Alternate b/w 2 shapes CONCENTRATION GRADIENTS – ION CONCENTRATIONS Gradients disappear w/ time if not maintained ○ By active transport againstgradient Steep concentrations = quick movements ACTIVE TRANSPORT AGAINST CONCENTRATION GRADIENT = requires energy → released by hydrolysis Carried out by = specific carrier proteins Transport across membrane = directional Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 ACTIVE TRANSPORT – One molecule at a time ACTIVE COTRANSPORT – 2 molecules at a time ACTIVE EXCHANGE TRANSPORT – 2 molecules in different directions ○ These are irreversible PROTON PUMPS Gives active H+ transport Uses ATP for power to translocate +ve change in form of H+ ions Stores energy by generating voltage WHY? ○ H+ can be used to drive other processes COTRANSPORT (PLANTS) Proton pumps gives active H+ transport ○ Binds to cotransporter (down concentration gradient) – Cotransporter changes shape = sucrose transports to cytoplasm Indirect active transport of sucrose Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 HIGHER ANIMALS Macromolecules = hydrolysedto monomersby enzymes → in digestive tract → monomers taken up by cells lining small intestine ○ Used passive + active transport TRANSPORT EXTERNAL DRIVING MEMBRANE SPECIFICITY MECHANISMS ENERGY FORCE PROTEIN Simple Diffusion No Concentration No Not gradient Facilitated Diffusion No Concentration Yes Specific gradient Active Transport Yes ATP Hydrolysis Yes Specific LO2 To describe the concept of a membrane potential arising from ionic imbalances across cell membranes. MEMBRANE POTENTIAL Voltage difference across a membrane Voltage = created by differences in distribution of positive + negative ions e.g sodium-potassium pump Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 ○ Generates concentration gradients contributing to membrane proteins all animal cells 1. Na+ from cytoplasm binds (Na+ concentration higher outside) 2. ATP phosphorylates 3. Shape change expels Na+ 4. Extracellular K+ binds (K+ concentration higher inside) 5. Phosphate is hydrolyse All cells = voltage differences = unequal distributions of anions + cations Cytoplasm = -ve compared to extracellular ○ (-50 to -200mV) = membrane potential FAVOURS ○ Passive transport cations into cell ○ Passive transport anions out cell ○ ∴ diffusion of ions affected by: – Electrical force: effect of membrane potential – Chemical force: ions concentration – electrochemical gradient Potential acts (voltage difference) → energy source ○ Affecting trafficking ○ Drive other processes from these charges – e.g opening of channels – Neurons → neurons = large cells → transmit signals to active other cells → do this by depolarizing membranes = Na+ channels open → Na+ enters = depolarised LO3 To describe the different types of endocytosis. Small molecules + H2O = enter/leave through bilayer/transport proteins Large molecules = cross membrane in bulk Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 EXOCYTOSIS ○ Releasing molecules through fusion of vacuoles/vesicles ENDOCYTOSIS ○ Molecules entering cell by vesicles Three types – phagocytosis, pinocytosis, receptor-mediated cytosis RECEPTOR-MEDIATED CYTOSIS Receptor proteins on cell surface ○ Recognise + bind to specific molecules e.g cholesterol ○ Clustered in “coated pits” – Function to accumulate molecule in membrane → once accumulated = vesicle Highly selective PINOCYTOSIS CELLULAR DRINKING No receptors Forming of vesicle from random invaginations INVAGINATIONS - Being turned inside out - Folded back forming a cavity NO specificity → any molecules PHAGOCYTOSIS CELLULAR EATING Engulfs → wrapping/packaging = large vacuoles/vesicle Used by macrophages Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 METABOLISM I: METABOLIC CONCEPTS LO1 Explain the terms metabolism, catabolism and anabolism. METABOLISM Chemical Reactions that occur in cell/organism Energy transformations and exchanges b/w living things and environment involves/carried out by enzymes RESPIRATION chemical energy + O2 → H2O + CO2 + ATP PHOTOSYNTHESIS Light energy + CO2 → H2O + O2 + chemical energy CATABOLISM Breakdown (CATABOLIC) reactions releasing energy Storing energy into simple molecules → glucose, amino acids, fatty acids, glycerol ANABOLISM Build up (ANABOLIC) reactions absorb or require energy Producing macromolecules → complex molecules Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 LO2 Explain the basic model for enzyme catalysis ENZYMES Breaking bonds = build up of energy HOW? ○ Level of energy required = ACTIVATION ENERGY Energy supplied to break bond Enzymes = catalysts Reduce amount of activation energy required for a reaction ○ Does not affect products ○ Not consumed ENZYME FUNCTION Binding w/ substrate into active site Where substrate fits/binds Determines specificity Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 WHAT AFFECTS ENZYME ACTIVITY? ENVIRONMENTAL CONDITIONS Optimum temperatures ○ High temps = denature pH Most optimal 6-8pH Can prefer acidicor basic SUBSTRATE CONCENTRATION Rate of reaction ↑ as substrate ↑ (w/ constant enzyme concentration Max activity occur when enzyme is saturated → when all enzymes are occupied COFACTORS + COENZYMES Additional non-protein molecules needed by someenzymes Coenzymes = organic cofactor ○ e.g iron – present in hemoglobin molecule in order to attach O2 Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 ENZYME INHIBITION Inhibitor = similar substrate shape = blocking active site from substrate COMPETITIVE INHIBITORS ○ Prevent substrate binding ○ Inhibitors and substrate competing NON-COMPETITIVE INHIBITORS ○ Inhibitor binds to allosteric site = changes shape of active site Any site other than active ○ ALLOSTERIC REGULATION – Inhibits or stimulates enzyme activity – Allosteric inhibitor changes active site – E.g cyanide → binds to enzyme cytochrome C oxidase → alters shape of active site = electrons cannot be release to O2 Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 – Importance → inhibition feedback → stop a process when end product of a reaction interferes w/ enzyme that helped produce it enzyme = deactivated LO3 Describe the structure and function of ATP ENERGY Moving electrons = MOVEMENT OF ENERGY Bonds Light = energy source ○ Photon strike molecule = energy → electrical energy boosting electron to ↑ energy orbital = reactive Chemical energy ○ Adenosine triphosphate (ATP) → type of nucleotide Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 ○ Capturing energy ADP + phosphate → ATP (ADP = partially charged) ○ Captured by PHOSPHORYLATION adding/removing phosphate group WHAT IS ATP USED FOR? ATP release energy for metabolic processes TRANSPORT WORK - Moving substances across membranes MECHANICAL WORK - Supplying energy for muscle contraction CHEMICAL WORK - Supplying energy to synthesize macromolecules - e.g photosynthesis PHOSPHORYLATION adding/removing phosphate group to synthesize ATP 3 units ○ Substrate-level phosphorylation ○ Oxidative phosphorylation Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 ○ Photophosphorylation SUBSTRATE-LEVEL PHOSPHORYLATION Series of enzymatic reactions Catabolic or anabolic Where? ○ Aqueous environments Transfer phosphate group from a phosphorylated compound (substrate) to ADP using an enzyme e.g glycolysis, TCA cycle, fermentation OXIDATIVE PHOSPHORYLATION Series of REDOX reactions oxidation and reduction processes electron transfer Moving electrons through physical structure Where? → membranes Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 LO4 Describe the terms respiration and fermentation. RESPIRATION Process involved the PRODUCTION OF ENERGY Cellular respiration/aerobic respiration + photosynthesis CELLULAR RESPIRATION Breaking down food molecules to capture ATP Organisms take broken down molecules → release the chemical energy stored in the bonds → energy release is stored as ATP Glucose + O2 → H2O + CO2 + ATP Bacteria → occur in cytosol, cell membrane Eukaryote → occur in cytosol, mitochondrial matrix + inner membrane ESSENTIALS FOR GROWTH 3 basic ○ Energy source ○ Source of electrons for cellular respiration ○ Source of matter – carbon ENERGY SOURCE – PHOTOTROPHS Photo = self, trophs = nutrition Photon capture → energy Plants Produces complex organic molecules from inorganic ENERGY SOURCE – CHEMOTROPHS Obtain energy from oxidation of electron donors Donor molecules → organic/inorganic ○ Proteins ○ Fats ○ CH2O ELECTRON SOURCE Lithotrophs ○ Inorganic substances as electron source ○ ≠ C-H bonds ○ e.g H2O, minerals, metals, salts Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 Organotrophs ○ Organic substances as electron source ○ Has C-H bonds ○ e.g H2O, proteins, lipids, nucleic acids CARBON REQUIREMENTS Heterotrophs ○ Eat preformed organic molecules as carbon source e.g glucose Autotrophs ○ Self feed → make own food MAJOR NUTRITIONAL TYPES Photolithotrophic autotrophs Photoorganotrophic autotrophs Chemolithotrophic heterotrophs Chemoorganotrophic heterotrophs FERMENTATION Respiration w/ absence of oxygen redox redox reactions to RE-OXIDIZE NADH to NAD+ Pyruvate - input substrate Occurs in cytosol Yeast, bacteria → product = alcohol (TOXIC) Muscle cells of mammals → product = lactic acid (TOXIC) Used in industry → produces cheese, ethanol, acetic acid Ultimately, allows glycolysis to continue w/o O2 RESPIRATION VS FERMENTATION Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 LO5 Describe the importance of redox reactions in metabolism, including the common cofactors. REDOX REACTIONS oxidation and reduction processes electron transfer Metabolism → respiration ○ Generates CO2 + H2O + ATP ○ This is done in oxidative phosphorylation = series of redox reaction ○ Requires the movement of electrons = redox reactions REDUCTION Atom becomes reduced undergoing chemical reactions ○ GAINS electrons = more potential energy ○ By bonding to ↓ e;ectronegative atom ○ Often to a H OXIDISATION Atom becomes more oxidised undergoing chemical reaction ○ LOSES electrons ○ Bonding to a ↑ electronegative atom ○ Often to a O METABOLISM II: EXTRACTING ENERGY FROM FOOD LO1 Describe the catabolism of different macromolecules. RESPIRATION Energy (food source) + O2 → H2O + CO2 + ATP Food source = proteins, lipids, CHO Proteins, fat, CHO → broken down by catabolic pathways w/ aerobic respiration Monomers → entry points to glycolysis → citric acid Oxidised w/ electrons Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 LO2 Describe the central features of glycolysis, the TCA cycle and oxidative phosphorylation GLYCOLYSIS SPLITTING of glucose Occurs in cytosol, 10 enzymes Breakdown of glucose → 2 molecules of pyruvate Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 INVESTMENT STAGE ‘Investing’ energy to break glucose → 2 ATP Results in 2 3-carbon units (glyceraldehyde-3-phosphate) HARVESTING STAGE 4 ATP, 2 NADH produced ○ Result of substrate-level phosphorylation End result = 2 molecules of pyruvate Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 TCA CYCLE acety Conversion of pyruvate → acetyl-CoA For each pyruvate → 2 NADH release, 2CO2 released 3 enzymes + Coenzymes A, NAD+ Also ○ Tricarboxylic acid cycle ○ Citric acid cycle ○ Krebs cycle Produce reducing agents → give electron power of ETC ○ NADH ○ FADH2 Occurs in matric 8 enzymes Acetyl-CoA oxidises (loses electrons) Reduces ○ NAD+ → NADH ○ FAD → FADH2 CO2 = expelled = wasted OXIDATIVE PHOSPHORYLATION Series of redox reactions Movement of electrons from ↑ electronegativity to ↓ ○ Allows protonsto be pumped across inner mitochondrial membrane → against concentration gradient ○ This builds up electrical potential = allows synthesis of ATP through protein complex, ATP SYNTHASE Overall process → fuels (eg. glucose) are oxidized and phosphorylation yields ATP (through the actions of the electron transport chain and chemiosmosis). Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 LO3 Explain the process of chemiosmosis ELECTRON TRANSPORT CHAIN + CHEMIOSMOSIS Located ○ Cytoplasmic membrane (prokaryotes) ○ Cristae → inner mitochondrial membrane folds (eukaryotes) 4 complex proteins + ATP Synthase Higher concentration of H+ in inter membrane space Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 LO4 Compare the advantages and disadvantages of fermentation and aerobic respiration. FERMENTATION AEROBIC RESPIRATION - ATP produced by substrate level - ATP produced by oxidative phosphorylation r phosphorylation - Rapid production - 32 ATP produced per glucose - 2 ATP per glucose - NADH reoxidised in electron transport - NADH reoxidised involving the final chain electron acceptore.g pyruvate → - Occurs in mitochondria lactate - Occurs in cytosol LO5 Explain the control of cellular respiration via feedback Demand for ATP changes ○ Resting = less ○ Exercising = more Supply + demand influences fuels used REGULATION BY PHOSPHOFRUCTOKINASE Exercise → ATP levels drop ○ ∴ prompts increase in enzyme activity controlling the rate of catabolism reaction Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 1 Resting → ATP levels rise CHOPS ○ ∴ enzymes are important for control of catabolism are inhibited Phosphofructokinase = allosteric enzyme in glycolysis ○ Has a number of sites for activator + inhibitors PHOTOSYNTHESIS CHOPS LO1 To explain the functions of the different stages in photosynthesis; light harvesting, the conversion of light energy into chemical energy, and carbon dioxide fixation. CARBON CYCLE 40 Reciprocal process of of oxygenic photosynthesis and respiration C H All AEROBIC RESPIRATION 00 Energy (food) + O2 → CO2 + H2O + ATP (energy) 9 8 OXYGENIC PHOTOSYNTHESIS Energy (solar) + H2O + CO2 → O2 + sugar (food) ENCO LIGHT REACTION - HILLS REACTION Light harvesting in thylakoid membranes = light dependent Conversion of light energy into chemical energy (ATP + NADPH ○ Anaerobic form of metabolism → does not require oxygen Anesliationo GHTAT xygen.org energy Oygenic Downloaded by Angelin Prabaharan ([email protected]) reas.ishesis'ECHOS EnergytcopHydrogen lOMoARcPSD|16917129 Oxygen 1 CALVIN CYCLE sugar Light independent ○ Fixation of CO2 to make glucose ○ Using ATP and NADPH PHOTOSYNTHESIS Physio-chemical used by plants, algae, photosynthetic bacteria Uses light to drive synthesis of organic compounds → glucose, starch IMPORTANCE ○ Liberation of oxygen, consumption CO2 ○ Provides food requirement create d ○ Stores energy in coal, gas etc ○ Supplies needs for clothes, building materials gmcgq.gr LO2 To explain the overall organisation of the light reactions in photosystems I and II. PHOTOPHOSPHORYLATION Using energy of light to phosphorylate ADP to gain phosphate = ATP Photon strikes chlorophyll pigment molecule ○ Energy from light → electrical energy ○ Exciting electrons of chlorophyll in a higher orbital – energy electrical energy is ‘packaged’ as chemical energy = ATP – And another ‘energy courier’ molecule called = NADPH Occurs in thylakoid membrane Performed by photosystems (protein complex) ADP ATP Downloaded by Angelin Prabaharan ([email protected]) chroypyll pigments photosten 1 lOMoARcPSD|16917129 photostenz where PY topump 700mm PHOTOSYSTEMS which fatuongignm low hydrogen Collection of chlorophyll pigment molecules → get excited by photons Pigments = bound to proteins formed in antenna complexes→ transfers to reaction center Hits photosystem II first ○ WHY? – II shorter wavelengths, 680nm – I 700nm Flow from high electron donors to low ○ This movement of electrons allows energy to pump H+ against concentration gradient hits reactivates photon proton Phi 68,81Eelengths H ikigh ELECTRON TRANSFER Electrons lost need to be replaced election out pump ○ WHY? Ht against – Become more positive Electrons moved from PSII → PSI gradient replaces electrons lost from photons in PSI Proton gradient generating = this will drive the synthesis of ATP Electron transfers in protein complex in PSI w/ H+ ions and NADP+ = NADPH electrons and replacing PS PS2 PSI Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 LO3 To describe, in overview, the fixation of carbon dioxide and synthesis of glucose in the Calvin cycle. CALVIN CYCLE Occurs in stroma INGREDIENTS ○ Ribulose-1,50biophosphate carboxylase oxygenase RuBisCO Enzyme – Catalyses the carbon fixation ○ Ribulose-1,5-bisphosphate RuBP – 5-CARBON SUGAR JOINING TO CO2 IN FIXATION ○ CO2 – Enters stroma ○ Adenosine-5-triphosphate ATP ○ Nicotinamide adenine dinucleotide phosphate NADPH 3 steps → carbon fixation, reduction, regeneration CARBON FIXATION Taking CO2 and attach to RuBP → using RuBisCO Making 6 carbon intermediate → breaks down to 2 3-carbon molecules 3-PG 6 CO2 + 6RuBP → 12 3-PG REDUCTION 3-PG = phosphorylated using ATP = second intermediate (1,3-bisphosphoglycerate) NADPH provides energy by reducing second intermediate to G3P 12 3-PG = 12 G3P CALVIN CYCLE OUTPUT Continuously repeating → each time making carbon atom avail for G3P G3P = ultimate goal → decomposed of the simplest sugar 3 cycles of G3P = fructose → rearranged = glucose Downloaded by Angelin Prabaharan ([email protected]) lOMoARcPSD|16917129 REGENERATION G3P phosphorylate w/ ATP to regenerate more RuBP 5G3P → 3RuBP 12 G3P → 2 molecules to make sugar → 10 G3P = 6 RuBp LO4 To compare and contrast the generation of energy from photosynthesis and oxidative phosphorylation. GENERATION OF ENERGY OXIDATIVE PHOSPHORYLATION PHOTOSYNTHESIS DNA REPLICATION LO1 Explain the semi-conservative model of DNA replication SEMI-CONSERVATIVE: The two parental strands separate as a template to each form with a complementary strand (parental are joined with complementary strand) Downloaded by Angelin Prabaharan ([email protected])
