Midterm Notes.pdf

BIO-1 Course pack I OBI This course pack covers material for the midterm Cellular Biology NOTES AND SUMMARIES Biology is a science – __________________________________ Scientific method: 1. ________________________ 2. ____...

BIO-1 Course pack I OBI This course pack covers material for the midterm Cellular Biology NOTES AND SUMMARIES Biology is a science – __________________________________ Scientific method: 1. ________________________ 2. ________________________ 3. ________________________________________________________________________________ 4. ________________________ 5. ___________________________________________ ____________________________ ____________________________ 6. ____________________________________ Biostatistics: a group of procedures used by biologists to interpret data ✓ Descriptive ✓ Inferential Introduction - chapter 1 1. Properties of life: There is unity in the living world, for all organisms-cells have the following properties in common. a. All organisms are made of cells; cells are the smallest unit of life. (Cell theory see point 4 below) b. Cells exhibit _________________ made of parts/organelles with specific functions c. They are assembled from the same kinds of atoms and __________________________________________________ (see point 3 below) d. They are capable of processing energy and obey the same laws of energy. 1° law of thermodynamics: Law of conservation of energy: Energy cannot be created or destroyed; it can only be converted from one form to another 2° law of thermodynamics: The total amount of entropy or disorder tends to increase in the Universe and this correlates with release of heat an unusable form of energy, and small molecules (carbon dioxide and water). Cells need to constantly counteract this tendency and therefore require continual energy input from food (cellular respiration) or from sunlight (photosynthesis). These two laws help explain: ____________________________________________________________ d. Cells metabolize (perform chemical activities). Cells need to regulate these chemical activities in order to maintain a balanced internal environment, called _______________________________ e. They can respond to specific conditions in the environment, by changing their metabolism, patterns of behavior. f. Cells are adapted to their environment through _____________________________________________________________________________________________. g. Most importantly they are able ________________________________ and pass on their characteristics or traits to offspring based on the heritable instructions encoded in the molecular structure of their DNA h. They have the capacity for ____________________________________ determined by their genes 1 Cellular Biology NOTES AND SUMMARIES 2. In this course we study cells. Cells are positioned within the hierarchical levels of biological organization: ______________________________________________________________________________________________ ______________________________________________________________________________________________ Organs and organ systems: studied in Bio 3 Human Physiology Population – community – ecosystems: studied in Bio 2 Ecology and Evolution 3. All organisms are made of the same macromolecules: a. carbohydrates b. lipids c. proteins d. nucleic acids 4. The cell theory – chapter 6: ✓ All organisms consist of cells which are the smallest units of life. ✓ Cells can only be made from pre-existing cells, the basis of biogenesis ✓ The purpose of cellular division is: a. _____________________________in uni -and multi-cellular organisms b. growth and repair of multicellular organisms. ✓ Two types of cells exist: prokaryotes (bacteria and archaebacteria) ________________________________________ eukaryotes (protists, fungi, plants and animals_________________________________ 2 Cellular Biology NOTES AND SUMMARIES ✓ Virus: considered non-living because they are not capable of reproducing without a host cell small: _____________________________________ retain some properties of life: ✓ consists of genetic information (DNA or RNA); o The nucleic acid has the information for replicating more viral particles (capsid and other viral proteins). ✓ contained within a protein shell called _______________ ✓ specialized enzymes – proteins allow host specific infection and replication ✓ The capsid of some viruses is surrounded by additional membranous envelope derived from the host cell. 3 Cellular Biology NOTES AND SUMMARIES Carbon Compounds - Macromolecules in Cells - chapter 5 Organic compounds consist of H hydrogen covalently bonded to C carbon atoms that commonly form linear and ring-shaped backbones. The following most common elements, O, N, P and S are also linked to the carbon backbone of cellular organic compounds. CHNOPS ✓ CO2 is not considered an organic carbon compound. It is inorganic. ✓ Functional groups attached to the carbon backbone impart diverse properties to organic compounds that are the characteristics of life. ✓ In nature, only living cells can assemble the large organic compounds called macromolecules or polymers: ✓ 1. complex carbohydrates, 2. lipids, 3. proteins and 4. nucleic acids. ✓ Organisms draw from small pools of organic compounds - monomers - The accompanying Table on page 14 summarizes the major categories of these compounds and their functions. 4 Cellular Biology NOTES AND SUMMARIES Metabolism : sum total of the chemical reactions that occur in the cell and as a result within the organism. ✓ Metabolism describes the transformation of substances into energy or materials that the cell can use or store. ✓ Anabolism : ______________________________________________ o Ex: Cells link monomers to form polymers by dehydration synthesis – condensation. In this process, water __________________________ o Protein synthesis – chapter 17 ✓ Catabolism : _______________________________________________ o Ex: Macromolecules are broken down [digested] to their component monomers by hydrolysis. In this process, water ___________________________ o Digestion – hydrolysis of food in the intestines of animals; hydrolysis of macromolecules by the lysosome in white blood cells – chapter 6 o cellular respiration – chapter 9 is overall a catabolic process but does not involve hydrolysis reactions 5 Cellular Biology NOTES AND SUMMARIES 1. carbohydrates ✓ Most abundant macromolecules; general composition: CHO (N in chitin) ✓ Monosaccharides or sugars generally (CH2O)n; n being the number of C in the sugar ✓ Glucose, fructose, galactose, glucosamine ✓ disaccharides (2 sugars) store energy: ___________________________________________________________ ✓ Complex carbohydrates – Polysaccharides are true polymers: o They are made of multiple monomers by dehydration synthesis. They function either in storage of energy or have a structural role in the cell. o Energy and chemical storage: __________________________ ▪ ______________________________________________ ▪ ______________________________________________ o Structural: ________________________ o ___________________________________________________________________________ o chitin (chain of glucosamine found in cell wall fungi) 6 Cellular Biology NOTES AND SUMMARIES 2. lipids ✓ Not true polymers but considered macromolecules due to their size ✓ Heterogeneous group of macromolecules; _______________________ - water fearing; not soluble in water ✓ Composition: CHO, (N and P in phospholipids) ✓ Monomers: fatty acids and glycerol (for fats, oils and phospholipids) ✓ Energy storage: triacylglycerides – triglycerides o ____________________________________________________________ o ____________________________________________________________ ✓ Structural : _______________________________________________________ o Amphipatic : ________________________________________________ ________________________________________________ ✓ Multiple functions: cholesterol see Table on page 14 for functions ✓ Regulatory: steroid hormones ✓ Cofactors required for absorbing light: retinal, carotenoids 7 Cellular Biology NOTES AND SUMMARIES Properties of fatty acids: Saturated Unsaturated Cell membrane Relationship between cell membrane and cell wall 8 Cellular Biology NOTES AND SUMMARIES 3. Proteins - polypeptides ✓ Most diverse macromolecules – diverse functions ✓ Composition: CHNOS ✓ Monomer: ___________________________________________________________________________________ ✓ Each aa has a side chain that imparts specific chemical properties to the overall function of the protein ✓ Bond between aa : _________________________________________________ ✓ Number of different proteins is infinite; depends on: o Number of aa o Composition of aa o Sequence of aa ✓ different sequences → different proteins with different functions; ✓ The shape of the protein is obtained by folding of the amino sequence into secondary, tertiary and quaternary structures Primary structure: __________________________________ __________________________________ Secondary structures: __________________________________ __________________________________ __________________________________ Tertiary structure: __________________________________ __________________________________ Quaternary structure: __________________________________ __________________________________ 9 Cellular Biology NOTES AND SUMMARIES ✓ Functions depend on shape; shape depends on aa sequence ✓ Enzymes: __________________________________________________________ ✓ Structural: __________________________________________________________ ✓ Storage: nourish embryo; ovalbumin ✓ Transport: __________________________________________________________ ✓ Transport across membranes of cells ✓ Hormones: ______________________________________________________ ✓ Receptors: sense and transduce environmental signals - synapse ✓ Contractile and motile: muscle contraction and cell movement; actin and myosin ✓ Defensive: fight diseases and foreign molecules; antibodies – immunoglobulins 4. nucleic acids ✓ Important informational macromolecules; composition: CHNOP ✓ Monomers: nucleotides ✓ Bond between nucleotides:__________________________________________________ ✓ Two forms of nucleic acids: ✓ DNA – Deoxyribonucleic acids made of 4 different deoxyribonucleotides ____________________________ ✓ RNA – Ribonucleic acids made of 4 different ribonucleotides _______________________________________ ✓ Some nucleotides, including ATP – adenosine triphosphate – have central roles in metabolism as energy carriers (see page 12-13) 10 Cellular Biology NOTES AND SUMMARIES criteria DNA RNA Overall structure monomers Pentose sugar base function Location in cell Chromatin: 11 Cellular Biology NOTES AND SUMMARIES ✓ Base pair rules: DNA:DNA A – T; C – G Exercises: 1. Find how many combinations of amino acids are possible in a 10 aa polypeptide. 2. Find the nucleotide sequence of the complementary strand of DNA: 5’ GAATCATCGACTT3’ 12 Cellular Biology NOTES AND SUMMARIES ATP hydrolysis is a favorable – spontaneous reaction associated with the release of Gibbs (G) free energy useful to power cellular work Cellular work includes: Chemical work: anabolic reactions Mechanical work: cellular movement; muscle fiber contraction Transport: molecular transport across the cell membrane – chapter 7 The ATP cycle 13 NYA – General Biology I A tour of the cell: Cell Structure and Function - chapter 6 1. Three generalizations constitute the cell theory - Biogenesis: a. All living things are composed of one or more cells. Cells are made of the same macromolecules. b. The cell is the smallest unit that retains the properties of life (remember the properties of life that we have seen in the introduction). That is, it either lives independently or has a built-in genetic capacity to do so. c. New cells arise only arise from ___________________________________________________________: ✓ ____________________________________________________ ✓ ____________________________________________________ 2. Cell size: ________________________________________(with a few exceptions; for example a chicken egg is 5 cm in diameter and some nerve cells can be close to a meter long). ✓ Observed with the microscope o Light: visible light optics (lenses); observe live specimens, limited resolution and magnification ▪ Fluorescence microscopy o Electronic: electron optics (magnets); observe fixed specimens, better resolution and magnification o Resolution: ____________________________________________________________________________________ o Magnification: ____________________________________________________________________________________ ✓ Limits to cell size o Lower limit: ____________________________________ o upper limit: _____________________________________ o If a cell is very large (large volume), the surface of the plasma membrane may not be large enough to allow efficient exchange of the cell with its environment (absorption of nutrients and release of cellular wastes). o Solutions to upper limit: ▪ 1. compartments which store and manage wastes and nutrients ▪ 2. adopt elongated shapes or structures (microvilli) o Larger organisms have more cells 3. The minimal cell: Minimal cell: __________________________________ __________________________________ __________________________________ __________________________________ a. The plasma membrane (PM) maintains the cell as a distinct, separate entity. ✓ 9nm thick, phospholipid bilayer + ______________________________ ✓ ________________________________________________________________________(see chapter 7 notes) o Impermeable to hydrophilic substances (ions, polar molecules water, sugars…) o Permeable to hydrophobic, non-polar substances (gases, lipid soluble molecules cholesterol) 15 NYA – General Biology I ✓ Presence of membrane transport proteins allow the passage of hydrophilic substances b. prokaryotic cell: ________________________________________ ✓ Prokaryotes have no membrane bound cytoplasmic organelles, i.e. no nucleus, no mitochondria, no Golgi etc. Prokaryotes are also on average 10X -100X smaller than eukaryotic cells ✓ Nucleoid: similar to nucleus, area for DNA; not membrane bound ▪ DNA is a single circular chromosome ✓ Cell wall: ____________________________________________________________ ✓ Capsule: sticky polysaccharide for attachment; found in pathogenic bacteria ✓ pili: extensions for attachment; found in pathogenic bacteria ✓ Flagella: locomotion 16 NYA – General Biology I 17 NYA – General Biology I plant animal Mitochondria Cellular respiration Chloroplast photosynthesis Cell wall Centrosomes Cell division Centrioles no (*) yes Junctions Storage & treatment of wastes Flagella-cilia no (*) yes 18 NYA – General Biology I 4. Eukaryotes: __________________________________________________________________________ Eukaryotes have organelles that can be classified as: a. nucleus: Is enveloped by a double membrane (2 phospholipid bilayers) called the nuclear envelope ✓ Contains genetic information (chromosomes made of chromatin: proteins called histones + DNA) ✓ Site of transcription and DNA replication ✓ The nucleolus, a denser structure within the nucleus: ▪ ___________________________________________________________________ ▪ ___________________________________________________________________ ✓ The nuclear envelope consists of pores which allow the passage of molecules in and out – from the cytoplasm into the nucleoplasm and vice versa (ex: mRNA and ribosomes leave the nucleus) b. endomembrane system: This system includes all membranes and organelles that communicate or are connected with each other; starting from the outside to the inside: PM, vesicles & phagosomes, lysosomes, vacuole, Golgi, endoplasmic reticulum (ER) and outer membrane (OM) of the nucleus. ✓ The major role of the endomembrane system is to produce, fold, modify, sort and transport proteins to their destination (exterior, membrane, lysosomal/vacuolar or SER). ✓ RER:____________________________________________________________ o ________________________________________________________________________________________ o Glycoproteins – blood antigens – are proteins modified by carbohydrates in the RER ✓ SER: ____________________________________________________________ o _________________________________________________________________________________________ o Site of detoxification of drugs and natural wastes (liver - hepatocytes) o Storage of Ca2+(muscle fibers) ✓ Golgi: o completes protein folding, proteins are further modified (carbohydrates, phosphate, lipids, protein cleavage), o sorting and shipping o « ZIP code » 19 NYA – General Biology I ✓ Lysosomes – found in animal cells only: o hydrolytic enzymes ______________________________________________________________________ o ________________________________________________________________________________________ o ________________________________________________________________________________________ o « stomach » of cell o Example: macrophages (immune cells which combat bacterial infections) ✓ Large central vacuole – found in plant cells only has multiple functions: o Storage of wastes, ions, pigments o Water homeostasis: Turgor pressure & cell growth ENDOMEMBRANE SYSTEM – SUMMARY FLOW CHART DNA → mRNA c. organelles that have a role in metabolism: ▪ mitochondria (cellular metabolism and production of ATP) ▪ chloroplasts (photosynthesis). ✓ Double membrane bound organelles (IM and OM); ✓ Contain their own ribosomes and DNA; ✓ Endosymbiont theory*: ___________________________________________________________________ 20 NYA – General Biology I d. Peroxisomes: ✓ Site of detoxification of oxygen radicals; O2- ✓ Detoxify alcohol in liver cells ✓ Fatty acid catabolism 5. Cell shape: a. Cell wall: ✓ Plants: cellulose (-glucose polymer) ✓ Fungi: chitin (N-acetylglucosamine polymer) ✓ Bacteria: peptidoglycan: polymer made of sugars, and linked by short peptides. ✓ Bacteria DO NOT have a CYTOSKELETON. 21 NYA – General Biology I b. Cytoskeleton: ✓ maintain cell shape and anchoring of organelles in eukaryotic cells. ✓ plays a dynamic role during cellular division, transport of proteins and organelles, and cell movement. ✓ Filaments that constitute the cytoskeleton are made of proteins: o Microfilaments: also called actin filaments, 7nm fibers, made of actin protein subunits; dynamic filaments (can grow and shrink) ✓ Microfilaments are associated with the PM → cortex ✓ Multiple functions: Shape:________________________ Motility (pseudopod of amoeba or for phagocytosis) Muscle contraction: _____________________________ cell division: ____________________________________ o Intermediate filaments: 10nm fibers; ex: keratin in skin cells ✓ Multiple functions: strength and shape of cells anchor organelles (like nucleus and mitochondria) form nuclear lamina o Microtubules (MTs): 25nm hollow filaments, made of tubulin protein dimers; dynamic. ✓ They grow at centrosomes, microtubule organizing centers (MTOs – equivalent of centrosome in plant cells) and basal bodies (flagella and cilia) ✓ Multiple functions: Cell shape Cell movement: ____________________________________________ Cell division, chromosome movement: ________________________ Organelle movement: tracks for transport of vesicles during protein secretion 22 23 25 Membrane Structure and Function – Chapter 7 1. Properties of membranes: Membranes are flexible: they can take almost any shape as long as there is an underlying cytoskeleton to support it or a cell wall to constrain it. Membranes are self-sealing: the chemical properties of phospholipids that make up the membrane are such that they will automatically interact to form an enclosed environment. A membrane does not have open-ends. Membranes are fluid: o Factors that affect fluidity: temperature; saturation of hydrophobic tails; in animal cells, cholesterol serves to lower gelling temperature of membranes and increase melting temperature (cholesterol acts as a fluidity buffer). o The Fluid Mosaic Model: o Lateral movement of phospholipids and membrane proteins embedded within (not flipflop movement) o Integral membrane proteins have hydrophobic sections that directly interact with the hydrophobic core of the phospholipid bilayer Membranes can fuse with one another as well as bud off new vesicles. Endocytic vesicles arise because the membrane invaginates – bulges inward. Secretory vesicles fuse with the plasma membrane releasing their contents to the exterior. Membranes exhibit selective permeability. o permeable (let pass) to hydrophobic/non - polar molecules (need to be still soluble in water and not too large): gases, steroids o impermeable to hydrophilic (polar or charged) such as water, glucose, ions; and/or large molecules such as macromolecules, unless specialized proteins allow their passage through the membrane. o This selective permeability makes it easier for cells to maintain homeostasis. Membranes work like capacitors: opposite charges (ions, for example Na+, and counterions, Cl-) that separate and align along membranes result in a membrane potential. 2. Membrane associated proteins – integral membrane proteins: ✓ The topology or orientation of membrane associated proteins within the bilayer is asymmetric. The types of proteins associated with a particular membrane give it its properties. ✓ Functions: Attachment-anchoring proteins, ie integrin: these serve to anchor cells to the surrounding connective tissue (extracellular matrix) Transport: Passive transport: channels, transporters, pores Active transport: pumps Enzymes: synthesis or modification of fatty acids; metabolic enzymes 26  Receptors and signal transduction and: homeostasis and response to the environment Junctions and CAM Recognition proteins: “antigens” on bacteria for example are recognized by antibodies 3. Transport of small molecules across the membrane _____________________________________________________________________ ✓ Factors that affect transport: ___________________________________________________________________________ ____________________________________________________________(see selective permeability) Passive transport ✓ Movement of water by osmosis occurs through channels called “aquaporins” → facilitated osmosis o Water moves from _____________________________________ see diagram below o Ex: Red Blood Cells hemolyse in hypotonic solutions o Ex: Water moves into paramecia in fresh water (hypotonic environment) ▪ In order to avoid bursting, paramecia use contractile vacuoles to expel water out ✓ Movement of lipid soluble – non polar molecules across the membrane by simple diffusion; down their concentration gradients (from high to low) ✓ Movement of hydrophilic molecules via channels and transporters by facilitated diffusion; down their concentration gradients (from high to low) o Channels: ___________________________________________ ___________________________________________ ___________________________________________ ___________________________________________ ___________________________________________ o Transporters: ___________________________________________ ___________________________________________ ___________________________________________ ___________________________________________ 27 Passive transport cont. ✓ Movement is favorable (spontaneous if appropriate channels and transporters are present) – no input of energy required ✓ Diffusion of one solute is independent of another solute Osmosis water movement Diffusion of solutes Active transport: ✓ Solutes move against their gradients (from low to high) ✓ Requires energy – in the form of ATP hydrolysis or equivalent ✓ Active transport per se: o Na+/K+ ATPase pump – in the PM of animal cells o H+/ATPase pump – in the PM of plant cells or across lysosome (animal) / vacuole (plant) o Electrogenic Pumps: ________________________________________________________________________________ ✓ Co-transport (also called secondary active transport): ______________________________________________________________________________________ o Na+/glucose co-transporter (animal) o H+/sucrose co-transporter (plant) 28  The Na+/K+ pump 4. Movement of large macromolecules (for example proteins) in and out of cell: bulk transport ✓ These are energy requiring processes; ___________________________________ ✓ Balance between exocytosis and endocytosis out of cell or exocytosis; also called secretion: - using endomembrane system, from rough ER →Golgi→secretory vesicle→PM, proteins are secreted to the exterior, eg release of insulin by beta-cells of the pancreas. - via fusion of synaptic vesicles with the PM with the subsequent release of neurotransmitters into the synapse (junction between neurons) - via fusion of secretory vesicles containing wastes (from intracellular digestion of food within food vacuoles and lysosomes) with the PM. Into the cell or endocytosis: - phagocytosis: _________________________________ ingestion of large food particles or bacteria. Phagocytosis involves pseudopod formation around food/bacteria by specialised cells in body (macrophages or immune cells) - pinocytosis: __________________________________ cell drinking of dissolved materials, no pseudopods involved but vesicles pinch off from folds of PM. - receptor-mediated endocytosis ___________________________________________ for example uptake of LDL-cholesterol particle; highly specific means of concentrating a large molecule inside a cell 2 Table of comparison Passive versus Active transport mechanisms The cell cycle – Mitosis – Chapter 12 1. Functions: a. asexual reproduction in eukaryotic unicellular organisms (and a few multicellular organisms.) b. _______________________________________________________ c. _______________________________________________________ ✓ Two identical daughter cells are formed ✓ Each receives an identical set of chromosomes as well as cytoplasm. ✓ The number of chromosomes is constant from one generation to the next. 2. 3 events: 1) DNA is replicated/copied ✓ ____________________________________________________________________ ✓ Sister chromatids: __________________________________________________ 2) Nuclear division or mitosis: chromosomes are divided 3) Cytoplasmic division or cytokinesis 3. 4 phases of the cell cycle: G0: quiescence, cells do not grow or divide; metabolism; most cells G1: Gap phase 1 ✓ Cells grow in size and metabolize ✓ _________________________________________________________________ ✓ Genes are transcribed and proteins are made in preparation for S phase ✓ G1 checkpoint: ___________________________________________________________________________________________ ___________________________________________________________________________________________ ✓ commitment to complete cell division. S: synthesis ✓ DNA synthesis; duplication of chromosomes: ____________________________________________ ✓ In humans, this would be 46 duplicated chromosomes with each chromosome having 2 sister chromatids (total of 92 chromatids). ✓ duplication of centrosomes or MTOCs (plant cells) – poles of the mitotic spindle G2: Gap phase 2 ✓ cells produce more proteins and a critical surface area / volume ratio is reached 31 ✓ preparation for Mitotic phase G1, S and G2 phases form the INTERPHASE: ________________________________________________________________________________________________ M phase: Mitotic; _______________________________________________________________________________ ✓ Mitosis: ______________________________________________________________________________________ ✓ Cytokinesis: __________________________________________________________________________________ 4. M-subphases: a. prophase: ✓ Chromosomes condense ____________________________________________________________________ and appear X-shaped; condensation facilitates movement and division of chromosomes; ✓ Chromosomes are made of chromatin - DNA wrapped around histones - and further compacted and attached to a protein scaffold. 32 ✓ Chromosomes in non-dividing cell are not fully condensed and not easily visible. ✓ Nucleolus disappears ✓ _______________________________________________________________________ b. prometaphase: nuclear envelopes disappears centrosomes at opposite poles mitotic spindle complete (chromosomes become captured) The distinction between prophase and prometaphase is not clear cut. c. metaphase: ____________________________________________________________________________________ d. anaphase: ✓ sister chromatids separate to opposite poles ✓ overlap of polar MTs reduces (spindle elongates) ✓ kinetochore MTs attached to centromeres of chromosomes become shorter e. telophase: ✓ nuclear envelope reforms → two nuclei appear ✓ chromosomes decondense; spindle disappears; nucleolus reappears ✓ cytokinesis: o animals: formation of a ____________________________ or pinching of the cell membrane by the contraction of the actomyosin ring (microfilaments). o plant cells: formation of a ___________________________________ which is created by vesicles originating from the Golgi that align and fuse at the equator of the dividing cells. Eventually, one large vesicle fuses with the PM and separates the two cells. New cell wall is then deposited between the cells. 3 3 5. Cell division in bacteria (prokaryotes) also called ____________________________________________ ✓ The single circular chromosome of bacteria is replicated at a single origin called the origin of replication. ✓ The two origins separate at either end of the dividing bacterium. During replication the bacterium elongates. ✓ The cells physically separate by inward growth of the cell membrane; new cell wall is deposited ✓ DNA replication is not synchronized with physical separation of the cells. ✓ In rapidly dividing bacterial cells, the next round of DNA replication initiates before the previous cell separation is complete. This may lead to improper separation of chromosomes. 6. Checkpoints: ✓ There are 3 basic checkpoints that monitor the progression of the cell cycle: G1 (restriction) checkpoint in late G1; G2 checkpoint and M checkpoint ✓ These checkpoints “control” that the preceding phases are completed before cells proceed with the next phases. The G1 checkpoint __________________________________________________________________________________________________ __________________________________________________________________________________________________ _________________________________________________________________________________________________ The following are examples of conditions in which the G1 checkpoint is involved : ✓ Anchorage dependence: cells only divide if attached to a surface; if not the G1 checkpoint kicks in to stop cell division ✓ Density dependent inhibition: cells stop dividing once the entire surface is covered with cells – 1 layer. Once the surface is covered, the G1 checkpoint kicks in to stop further cell division ✓ DNA damage: cells stop dividing to repair the damage. The G1 checkpoint prevents cell division for as long as DNA remains damaged. When DNA damage is beyond repair, cells may undergo programmed cell death – apoptosis Apoptosis is a genetically controlled multistep process: A signal (internal or external) triggers mitochondria to activate a series of caspases. Caspases are proteins that act as proteases and initiate the apoptotic response. 1) Chromatin condenses and nucleus fragments – DNA fragmentation 2) Apoptotic bodies form – the cell blebs – cellular fragmentation 3) Phagocytosis of apoptotic bodies 3  Release of cell contents Internal signals: DNA damage; protein misfolding in ER External signals: Death signals from neighboring cells; immune cells (T cytotoxic cells) bind to viral infected cells and trigger apoptosis Apoptosis is important in brain development, immune system, and development of fingers and toes. 3 When the G1 checkpoint fails to work, cells may divide even when conditions are not optimal. This may result in transformation of cells through accumulation of DNA mutations and formation of cancer cells. 3 Meiosis and sexual life cycles – chapter 13 1. Advantages of sexual reproduction: Increases genetic variability (variation in traits) of offspring Increases potential of survival of a population in ever changing environment 2. Homologous chromosomes One copy is inherited from mother; the other from father _____________________________________________________ _____________________________________________________ _____________________________________________________ ____________________________________________________________________________________ Karyotype: ________________________________________________________________________ human diploid number is 46; display of metaphase chromosome showing banding patterns, number of chromosomes and ploidy 23 pairs; 22 somatic pairs (autosomes) + 1 pair sex chromosomes; XX = female, maternal, ovum always carries 22 + X; XY = male, paternal, sperm carries 22 + Y or X The human haploid genome is the sum of all genes (30 000) found in one set of 23 chromosomes 3. Human sexual reproduction proceeds through three events: meiosis (formation of gametes), fertilization (unites sperm and egg to form a zygote), and mitosis & development (creates a multicellular functional organism from one starting cell, the zygote). Meiosis that produces sperm and egg (oocyte) is called spermatogenesis and oogenesis respectively. 38 ✓ Meiosis divides the chromosomes number by half for each forthcoming gamete. ✓ Thus, if both parents are diploid (2n), the gametes that are formed are haploid (n). ✓ Later, the union of the two gametes at fertilization restores the diploid number in the new individual ( n + n = 2n ). 39 3. Meiosis consists of 2 nuclear divisions, Meiosis I and Meiosis II, but DNA replication occurs only once in S of interphase ______________________________________________ ______________________________________________ ______________________________________________ ______________________________________________ ______________________________________________ ______________________________________________ ______________________________________________ ______________________________________________ ______________________________________________ ______________________________________________ ______________________________________________ 40 Meiosis I: First division. Prophase I chromosomes condense Synapsis: ___________________________________________; synaptonemal complex (glue) crossing over: ___________________________________________________________________ Metaphase I ________________________________________________________________________________ Homologous chromosomes are held by chiasmata, former crossing over sites Independent assortment: _____________________________________________________________________________________ _____________________________________________________________________________________ Anaphase I separation of homologous chromosomes but not of sister chromatids. Telophase I chromosomes decondense (spindle disappears, nuclear envelope reforms) Cytokinesis does not necessarily occur. →resulting nuclei are haploid Meiosis II: Second division. This division resembles mitosis Prophase II Chromosomes recondense; _______________________________________________ Metaphase II Chromosomes align at equator Anaphase II “Sister” chromatids separate – at this point the chromatids are no longer truly sisters because of crossing over Telophase II chromosomes decondense and cytokinesis occurs →resulting in 4 different haploid cells →4 different haploid nuclei reform 4. Variation in traits among offsprings: Variation is due to the following reproductive events: 1. Production of unique gametes by meiosis: Homologous but not identical parental chromosomes in germ cell Crossing over during prophase I Independent assortment during metaphase I 2. « random » fusion of egg (female) and sperm (male) cells. ✓ crossing over: During meiosis, each pair of chromosomes may exchange segments, a process called crossing over. Each time they do, they exchange hereditary instructions or genes. 41  ✓ independent assortment: Meiosis assigns one of every pair of chromosomes to a forthcoming gamete - but which gamete is its destination is matter of chance. This random assignment of chromosomes during Meiosis I is called independent assortment. 5. Comparison mitosis meiosis Cell types #divisions: Crossing over (prophase I) Ind. assortment (metaphase I) #DNA synthesis # cells produced Ploidy of cells produced: 42 43 DNA REPLICATION – Chapter 16 One of the most important discoveries of last century was the identification and characterization of the Genetic Material. Scientists were interested in this question with the rediscovery of Mendel’s work and with newer work by Thomas H. Morgan and colleagues on the inheritance of traits in the fruit fly. It became clear that the molecule considered as the genetic material would have the following characteristics: 1. Must contain the information necessary to construct the entire organism. 2. Must be passed unaltered from parent to offspring. 3. Must be copied since parents can produce more than one offspring. 4. Significant phenotypic variability--genetic material must have variation within a species to account for phenotypic variation. Suffice it to say that the discovery of DNA as the genetic material by numerous scientists followed by the elucidation of its structure in the early 1950s opened the era of molecular biology and development of DNA technologies that continue to this day. DNA replication = ______________________________________________________________________________ ✓ ___________________________________________________________________ ✓ ___________________________________________________________________ ✓ formation of phosphodiester bonds between nucleotides (nt) of a daughter strand, complementary and antiparallele to a template strands ✓ requires a free 3’OH on the newly synthesized daughter strand (otherwise a primer is needed to initiate DNA replication ✓ _____________________________________________ (synthesis is always 5’→3’ for DNA and RNA) ✓ Endergonic process, requires input of energy ✓ Requires numerous enzymes Replication fork: ✓ Y shaped structure where synthesis of 2 complementary daughter strands occurs simultaneously (almost); 5’ → 3’ synthesis for both; primer needed to initiate synthesis ✓ ______________________: provides the initial 3’OH without which DNA replication is NOT possible Replication towards the fork: _______________________________________ Replication away from the fork: ________________________________________ ✓ many short DNA segments called __________________________________________ (1000-2000nt in ✓ E. coli and 100-200nt in eukaryotes). These fragments form the lagging strand. 44 Semi conservative DNA replication Direction of replication → 45 The events of DNA replication, based on the bacterial system, occur as follows: (Notice that each step requires the assistance of an enzyme) 1) recognition of the origin of replication 2) melting- unzipping of the parental strands by ___________________________________; ✓ All the while, ____________________________ reduces the strain (supercoiling) produced by unwinding the parental strands. DNA topoisomerase acts ahead of the replication forks by cutting the DNA strands, releasing the tension and religating the strands. ✓ The initial bubble grows bi-directionally as replication proceeds and the two replication forks on either side of the bubble move away from each other. 3) ___________________________________ keep the parental strands apart and prevent their reannealing. 4) ________________ produces a short RNA primer complementary to a sequence of the template strands. The primer has a free 3’ OH group necessary for the synthesis of DNA by DNA polymerase 5) DNA is synthesized by ___________________________________ in the 5’ to 3’ direction; sliding clamp pushes DNA polymerase III along the template strand. _________________________________ 6) RNA primers are degraded and replaced by DNA. This step is catalysed by _____________________. * ✓ Linear chromosomes typically will have an overhang of ssDNA because the last primer when removed cannot be filled in for lack of an anchor. This is a problem because it leads to shortening of chromosomes, and to the loss of coding information with each round of DNA replication, as cells continue to divide. The problem is solved by telomerase – see below* 7) Okasaki fragments of the lagging strand are joined by _________________________. 46 Eukaryotes Prokaryotes When: S phase ongoing and uncoupled from cytoplasmic division Replication origins: Problems: replication of ends of linear improper segregation of replicated/ing chromosomes chromosomes SOLUTION: ____________________________ In eukaryotes, numerous control mechanisms exist within the cell to block cell cycle progression in case that DNA replication is incomplete or inaccurate. 1. Telomeres: are sequences at both ends of linear chromosomes that consist of hexanucleotide repeats (AGGGTT). Telomeres are about 1000 – 1700 nucleotides long. Telomeres are added to the chromosomes of a zygote (diploid, formed by fertilization) by _____________________early during development. But most cells of a mammalian (somatic – body cells; ex: neurons) lose the ability of maintaining telomere length sometime during development. 2. Role of telomeres: Telomeres protect the coding region of chromosomes from being lost with each round of DNA replication. Overall, if telomere length is not maintained, mammalian cells can divide about 50 times before losing important genetic information (from the coding region). ✓ Absence of telomerase: shortening of telomeres ✓ shortening is associated with aging cells ✓ Hayflick limit : cells stop dividing as the chromosomes reach a critical shorter length 3. Telomerases: Germ cells, precursor cells, called stem cells, and embryonic cells divide more than 50 times to produce an adult organism and to regenerate damaged tissues. In these cells, the telomerase enzyme is present to maintain telomere length. 4. Telomeres and cancer: Cancer cells have high levels of telomerase activity and do not exhibit telomere shortening seen in normal differentiated cells. It is thought that the extended life of cancer cells is due to telomerase activity. 47