Download Hss2305a notes and more Study notes Cellular and Molecular Biology in PDF only on Docsity!
Prof Notes:
Midterm # Read full articles Figure out scope Look at figures (will guide you)
Midterm
All chapters (1, 2, 3, 5, 7, 10, 11) Especially 10 and 11
Abbreviations
w/: with w/o: without
prok: prokaryote euk: eukaryote HP: Human Perspective EP: Experimental Pathways FA: fatty acid NB: nitrogenous bases
HSS2305A-Chapter 1-Sept. 8, 2014
(1.1) The Discovery of Cells
Who invented the microscope? Robert Hooke: double lens. This was refined by Leewenhoek’s single lens. Which three scientists developed the cell theory?
Schleiden, Schwann, Virchow.
What does the cell theory consist of? 1. organisms composed of one or more cells
- structural unit of life
- cells exist through division of pre- existing cells
(1.2) Basic Properties of cells
What are HeLa cells? Cultured tumour cells isolated from cancer patient (Henrietta Lacks) by George Gey in 1951 First cultured human cells kept alive in culture for long time Name some basic properties of cells. • They are highly complex and organized
- possess genes that encode how cells perform all their functions
- Reproduce themselves
- get and use energy (ex. Photosynthesis, glucose ATP)
- carry out chem rxns
- mechanical activities
- respond to stimuli
- self regulates (adapts to changes)
- cellular activities=chain rxn (one event automatically triggers another)
- (^) evolve
(1.3) Two Fundamentally Different Classes of Cells
What does the earth’s biogeological clock reveal?
- Prokaryotes arose ~3.7 billion years ago
- Complex animals (shelly invertebrates) and vascular plants are recent.
- Photosynthetic bacteria may have arisen much earlier Comparison of prok and euk cells
What is bacterial conjugation? • Bacteria cells share DNA through F pilus (tube) What characteristics distinguish prok. And euk. Cells from each other?
- (^) Complexity (structure and function)
- Cytoplasm (euk. has membrane bound organelles and complex cytoskeletal proteins. Both have ribosomes, but differ in size)
- Cell reproduction: eukmitosis, prok. Simple fission.
- Locomotion: euk use both cytoplasmic movement and
Why are mice important? Can accept graft of human without rejection
What are the two common measurements of cells?
Micrometers (1um=10^-6m) Nanometers (1nm=10^-9m)
Why is cell size important? Size is limited to cytoplasm content, larger is not better since
requires more energy for diffusion to regulate inside cells due to large SA Small more advantageous, exposed to more nutrients and can absorb more effectively
What is synthetic biology? Field aims to create living cells in the lab with nucleic acids, proteins, and lipids
HP: Why are stem cells so important?
Undifferentiated cells, can divide and reproduce into different types of cells Self renewal replace damaged and disease adult tissue Ex. Hematopoietic can replace blood related cells and marrow, neural stem cells replace nerve related cells such as glial cells and such
What is an embryonic stem cell and how are they obtained for cell replacement therapy?
- Removed from a blastocyte with a micropipette. Isolate and grow in culture
- Piece of tissue taken from patient, fused with donor oocyte (nucleus removed)results in donor oocyte with patient cell nucleus, which is developed into early embryo stage. Cell is then induced to transform into required cell and then transplanted into patient to restore organ function. These ES cells are triploid and pluripotent (capable of giving rise to many different cell types)
What are induced pluripotent (iPS)
cells?
Reprogramming fully differentiated cell into pluripotent stem cell Ex. Sickle cell anemic mice. Skin cells collected and reprogrammed in culture by ferrying 4 required genes into cell by viruses and then cells begin to undifferentiate. Cells treated to differentiate into blood stem cells. New cells injected back in culture and proliferate and differentiate into normal blood cells. Disorder cured.
EP: What new idea about origin of Euk cells did Woese propose?
Because of rRNA sequence similarities among organisms, thre are 3 major cell lineages: Bacteria: gram pos, gram neg, cyanobacteria Archaea: halophiles, thermophiles, ,methanogens and acidophiles Eucarya: plants animals, fungi, protists EP: How can you tell when cells have evolved together?
Nucleotide sequence similarities Different kingdoms EP: What is lateral gene transfer (LGT)?
Organism with both parental DNA and DNA from other organisms in environment (bacteria and eucarya show evidence of LGT)
HSS2305A-Chapter 2: Chemical Basis of Life-Sept 8, 10, 2014
Describe the structure-function of the four groups of macromolecules.
Carbs: sugars, sugar polymers Lipids: nonpolar molecules
- Fats are glycerol linked by 3 ester bonds to 3 fatty acids (FAs) Proteins: polymers of amino acids
Nucleic acids polymers of nucleotides: Store/transmit genetic info
What’s the difference between ketose and aldose?
- Ketose: carbonyl on an internal carbon (fructose is a ketohexose carbonyl is internal
- Aldose: carbonyl on terminal carbon (glucose is aldohexose bc carbonyl is located terminally)
What are the properties of a stereoisomerism?
- stereoisomers or enantiomers
- Stereoisomerism: carbon placed in center of tetrahedron
- glyceraldehyde is only aldotriose (aldose+3 carbons)
- 4 groups bonded to carbon different then 2 configurations possible: D and L
- D-isomer if OH group projects right, L-isomer projects from left
Describe the shape of aldotetroses
and pyranose.
- Aldotetroses: 2 symmetric carbon atoms, exist in 4 configurations
- Pyranose: glucose undergoes self rxn to form pyranose ring (6 membered ring), 2 stereoisomers generated: alpha when OH projects below, beta when hydroxyl projects upwards
What are the different types of
saccharides?
- Disaccharides: readily available nrg
- (^) Oligosaccharides: bound to lipid or protein surfaces, used for recognition
- Polysaccharides: made up of identical monomers but possesses diff. properties. Ex. Glycogen (animals, highly branched), starch (plant, helical), cellulose (highly extended)
How are sugars linked together? • Glycosidic bonds (–C-O-C- links between sugars)
What is sucrose made up of? • Glucose and fructose
What sugars I s lactose made up
of?
Name 3 polysaccharides with identical sugar monomer but different properties.
- Glycogen: highly branchedenergy store
- Starch: helicalenergy store
- (^) Cellulose: unbranched and extendedstructure
Name the 3 structural polysaccharides.
- a) Cellulose: tough fiber
- b) Chitin: invertebrate exoskeleton
- (^) c) GAGs: 2 different sugars found in extra cellular space
Explain the structure of fatty acids and their saturation properties.
- FAs=unbranched hydrocarbons+1 carboxyl group (amphipathic, means has both hydrophilic and hydrophobic parts)
- Saturated=lack carbon double bonds, solid @ room temp
- Unsaturated=one or more carbon double bond, liquid @room temp
What are the properties of steroids? • Steroids: 4 ring, animal lipid, implicated in atherosclerosis
Break down the structure of a phospholipid (phosphatidylcholine).
- (^) Phospholipids: amphipathic, major component of cell membrane. Glycerol backboneshydroxyl groups covalently bonded to 2 fatty acids and a phosphate
maintained by many types of non covalent bonds (van der Waal, hydrogen, ionic), protein domains are functional regions, dynamic changes within proteins are conformational changes that are triggered by binding of specific molecules
- Quaternary: Polypeptides interacting with each other. Proteins composed of subunits (how these subunits interact), multiprotein complexprotein-protein interactions, hub proteins have many interaction partners and tend to be more important
What are the different factors of
protein folding?
- Protein folding: unfolding due to denaturation caused by various agents, once gents are eliminated, spontaneous refolding occurs, return to native form requires intermediate steps to form secondary structure first
- HP- protein misfolding deadly consequences: A) Creutzfeld-Jakob Disease misfolded protein in the brain (normal brain has PrP(c), CJD brain has PrP (Sc) B) Alzheimers’s diseaseaccumulation of misfolded proteins in brain, amyloid precursor protein (APP) cleaved off from brain neurons by two secretase enzymes, genetically predisposed to AD have A(beta)42 (one of the cleavage proteins which misfolds and self associates into amyloid plaque), neurofibrillary tangles (NFTs) composed of misfolded tangles of protein called tau. Soluble A(beta) prone to aggregation. (cluster together)
- Molecular Chaperones: transport protein that helps proteins ensure proper folding, prevent interference of protein assembly, isolate polypeptide from rest of environment
What is proteomics? • Proteome: inventory of all organism’s proteins
- Proteomics: separation of mixtures of proteins (gel electrophoresis and mass spectrometry
What is structure-based drug design?
- Structure-based drug design: proteins made from computer that target viral proteins
Walk through the development protein targets drug
- Development of protein targeting drug: 1) protein target.
- screen large chem library 3) identify effective compounds 4) info used to make compound with greater binding affinity. 5)tested in vivo compound and mice. 6) clinical testing
How do protein adapt? • Adaptation and Evolution: natural selection, different
versions of proteins are called isoforms What are 3 of the most important nucleic acid molecules?
- Ribozymes=RNA has catalytic activity
- ATP: cellular metabolism
- GTP: activate proteins What is the heat shock response? • Heat shock response: synthesis of heat shock proteins prevent denaturation of existing proteins
Highlight the similarities and differences between macromolecules. Explain the importance of polymerization in the production of macromolecules. Emphasize the importance of shape in biological chemistry. What are the four types of biological molecules and how are they different from each other? What is yeast two-hybrid technique?
Used to test whether proteins are related
HSS 2305A-Chapter 3: Bioenergetics, Enzymes & Metabolism-Sept. 10, 15, 2014
What is the First Law of Thermodynamics? • Law of conservation of energy=energy can neither be created or destroyed
- Equation: (delta)E=Q-W
- E=internal energy of system
- Q=Heat energy
- W=work energy What is transduction? Give some examples. • Conversion of energy form
- Ex. Electrical to mechanical, chemical to light What are the 2 possible thermodynamic outcomes from (delta)E?
- Exothermic: lose heat
- Endothermic: gain heat What is the second law of thermodynamics? • State of higher energy lower energy
- Spontaneous What is entropy? • Measure of randomness
- Loss of available energy=T(delta) What does free energy entail in respects to entropy?
- Free energy=(delta)G
- Equation: (delta)H=(delta)G+T(delta)S
- Exergonic=(delta)G<
- Endergonic=(delta)G>
- @equilibrim: (delta)G= What is the standard free energy changes? • Variable for each rxn under specific conditions How do non-standard conditions of free energy changes work? (slide 13)
What are the roles for ATP hydrolysis? • Charge across membrane
- Concentrate solute
- Drive chem rxn
- Slide filaments
- Donate phosphate
What is the difference between potential and
kinetic energy? Explain the significance of the First and Second Laws of Thermodynamics.
First Law: law of conservation. No energy can be created nor destroyed. Delta E= Q-W. (internal nrg, heat nrg, work nrg) Delta E>0=endothermic (gain heat) Dealta E<0=exothermic (lost heat) Transduction convert energy from one from to another (ex. Electrical to mechanical energy when we plug in a clock. Chemical to mechanical with heat release when contracting mucles. Chemical to light in firelies and luminous System (focus)[energy in system is called internal energy and Surroundings (everything else) Second Law:events proceed form higher nrg state to low nrg state Spontaneous occurs without something external trigger Loss of nrg during process happens due to randomness increase (nrg goes in all directions) when nrg transfer occurs Entropy=measure of randomness/disorder Loss of available nrg =T(delta)S Every event accompanied by increase in entropy of universe
Define free energy and its relationship to the spontaneity of processes.
What is the difference between steady state and equilibrium?
How do coupled rxns operate?
What is the difference between enzymes and inorganic catalysts?
Explain activation energy and transition state.
Describe the enzyme kinetic principles and define terms (Km, Vmax)
What’s the difference between competitive and non competition enzyme inhibitors?
Explain mechanisms of metabolic regulation.
What are redox rxns?
What are enzymes?
What are the properties of enzymes?
Explain the mechanisms of an enzyme catalyst and it’s types
What is the Lineweaver-Burk plot?
Name and explain the different types of enzyme inhibitors.
Irreversible inhibitors Reversible inhibitors
Competitive inhibitors Why is antibiotic resistance a problem? Some genes are similar and bacteria learn to adapt to antibiotic What is an antibiotic? Strain taken from bacteria and applied to others List the quantities of each molecule (ATP, NADH, co-factor) generated through the process of metabolism Describe glycolysis. What general steps cofactors are involved in the process of glycolysis? What is transfer potential?** Higher energy, less affinity, better donor
HSS 2305A-Chapter 5: Aerobic Respiration and the Mitochondrion-Sept. 15, 2014
What does the balance between mitochondrial fusion and fission determine about the cell?
Mitochondrial number, length, and degree of interconnection What proteins regulate mitochondrial fission? ER tubules and Drp How do cristae communicate inside mito? Through narrow tubular openings in intermembrane space What is the structure and function of porins? Beta sheet barrel, allows moderate sized molecules to pass Generate an overview of carb metabolism in euk cells.
In cyto: Glycolysis generates pyruvate and NADH, when O2 is absentpyruvate reduced by NADH to lactate (or ethanol in yeast) and the NAD formed is used for the continuation of glycolysis In mito matrix: when O2 is present pyruvate moves into matrix to be decarboxylated and linked to CoA this generates NADH, NADH produced helps molecules pass inner memb by giving high energy electrons, acetyl CoA passes through TCA cyclegenerates NADH and FADH2, electrons of NADH and FADH2 passed through electron transport chain which reacts with O presence36 ATP (1 molecules of glucose What is the net rxn in glycolysis? Glucose+2NAD+2ADP+2Pi2 Pyruvate+2ATP +2NADH+2H+2H What molecules are involved in the TCA/Krebs cycle?
Oxaloacetate, acetyle CoA, CO2, NADH, FADH2, ATP, GTP What catabolic cycle helps feed TCA cycle? What molecules are involved?
Fatty acid cycle. Generates mostly NADH, FADH and acetyl CoA What does the glycerol phosphate shuttle help transport?
Electrons from NADH to FADH2 via DHAP
Chemiosmosis Proton coupling through ATP synthase pump to produce ATP
enzymes due to defects in translocation of proteins from cytoplasm to the peroxisomal enzymes Adrenoleukodydstrophy: lack of peroxisomal enzymefatty accumulation in brain leads to destruction of myelin sheath
HSS2305A-Chapter 7: Interactions Between Cells and Their Environment-Sept. 17, 22,
2014
Glycocalyx Cell coat, formed from carb projections from plasma membrane What is the extracellular matrix? Organized network beyond plasma membrane, determines shape/intracellular activities Basement membrane (basal lamina) Continuous sheet that underlies epithelial tissue and surrounds blood vessels What are the functions of the basement membranes?
Cell attachment Substratum (foundation) for cell migration Macromolecule barrier Collagen Fibrous glycoprotein Most abundant protein in body Trimer of polypeptide (alpha helix) wound around each other Difference between corneal stroma and basement membrane collagen?
Corneal stroma collagen fibrils uniform diameter and spacing Basement have type IV non fibrillar show irregular polygon lattice (interlaced structure) List the collagen based diseases Fibril collagens Type I: osteogenesis imperfect-fragile bone Type II: dwarfism Ehler-Danlas syndromes: hyperflexibility Fibrosis: overproduction of collagen in lung (pulmonary fibrosis) or liver (cirrhosis) Non-fibrillar (type IV) Alpert syndrome: kidney disease of the glomerular basement membrane Distinguish the structure of a proteoglycan complex.
Protein-polysaccharide complex (core protein attached to GAGs Repeating disaccharides Negatively charged GAGs attract cations and waterforms hydrated gel Acts as cushion Has binding sites for growth hormones
Explain the structure of fibronectin. Linear array of polypeptides
Binding sites for other ECM components Guides migrating cells during embryogenesis
Review slide 12, 14, 16
Laminins Extracellular glycoproteins 3 polypeptide chains linked (via disulfide bonds) cell migration during development domains for interaction with other proteins (ex. Collagen in basement membrane via entactin molecules)
Matric metalloproteinases (MMPs) Degrade ECM materials Involved in tissue remodeling, embryonic cell migration , wound healing, form blood vessels Associated diseases: arthritis, tumor, blood clot, heart attacks Regulated by tissue inhibitor of metalloproteinases (TIMPs)
Integrins Membrane proteinheterodimer of alpha and beta Bent: inactive Upright: active (ligand binding) Integrate extracellular and intracellular environments Inside out signaling: becomes active through binding of protein (ex. Talin) to cytoplasmic tail
What is RGD needed for? Platelet aggregation (via fibrinogen/integrin interaction) Anti-clotting drugs: RGD peptide (Aggrastat) acts as competitive inhibitor to fibrinogen/integrin interaction
Focal adhesions Scattered sites for cell adhesion to substratum Act as sensory structure Cell locomotion (by deforming collagen substratum)
Hemidesmosomes. What are some diseases that can occur when defected?
Basal attachment to basement membrane of epithelial cells Dense plaque with keratin filaments linked to ECM by integrins Disease Bullou pemphigoid: autoimmune disease (antibodies against plaque) Epidermolysis bullosa: genetic
Review slide 23
What are the different types of collagen and what can happen if they become defected?
Homologous Chromosomes Chromosome = linkage group Genes on same chromosome do not assort independently, they are part of the same linkage group
Drosophila as a genetic tool Morgan First one to use wild fruit flies Mutationprimary tool and mechanism for variation in populations Confirmed genes reside on chromosomes
Crossing over in Drosophila Crossing Over and Recombination Linkage between alleles is incomplete Maternal and paternal chromosomes exchange pieces Recombination percentage in a pair of genes constant % Recombination in different pairs of genes can be different Gene’s position along chromosome (loci) can be different Frequency of recombination: indicates distance, increases as distance increases, this is bc when spread farther apart, there is more of a chance that the two genes (ex. One for eyes and another body) become unlinked by recombination Chiasmata When homologues are crossed
Polytene chromosomes
Mutagenesis and Giant Chromosomes Useful to observe specific bands “puffs” in polytene chromosomesDNA being very actively transcribed, allow visualization of gene expression
10.3 The Chemical Nature of the Gene Structure of DNA Nucleotide=a phosphate, a sugar, and either pyrimidine (thymine (T) and cytosine (C)) or purine (adenine (A) and guanine (G)) nitrogenous base
The chemical structure of DNA
Chargaff’s rule #A=#T #C=#G
Nucleotides structure Polarized where ends are: 5’ and 3’ Phosphodiester bonds link sugar and phosphate NB project out
The double helix
Watson-Crick Proposal DNA double helix Right-hand helices Antiparallel: chains run in opposite directions Sugar-phosphate backbone outside molecule NB inside helix 2 chains held together by H bonds 2nm wide major grooves and minor grooves makes turn every 10 residues 2 chains are complimentary to each other
Three functions of the genetic material
Importance of Watson-Crick Proposal 1. Storage
- Replication and Inheritance
- (^) Expression and genetic message
DNA supercoiling
Supercoiled DNA More compact Negatively supercoiled Underwound DNA, helps fit within cell nucleus Positively supercoiled Overwound DNA
DNA topoisomerases
DNA supercoiling Enzyme topoisomerase change level of DNA supercoiling Type I: create transient break in one strand Type II: make transient break in both strands See slide 22. DNA topoisomerase II functional steps
10.4 The Structure of the Genome
Complexity of genome Denaturation: separate into 2 strands Renaturation (or reanneling) Single strand reassociate Nucleic acid hybridization: complementary strands from different sources can form hybrid molecules Complexity of Viral and Bacterial Genomes Rate of renaturation of bacterial/viral DNA depends on size of genome (larger genome, lower concentration of complementary fragments, more time for renaturation to complete) Complexity of Eukaryotic Genome Reanneling of eukaryotic genomes3 classes of DNA:
- highly repeated
- moderately repeated
- nonrepeated
Highly repeated reanneling types (DNA fingerprinting)
