Chapter 3: Cell Biology & Genetics

Intro

1/17/2012 10:35:00 AM

Most of earths cells are unicellular Most ancient cells are bacteria 3 main types of microscopes o Light o Transmission Electron o Scanning Electron Cell Theory: o New cells are formed from other existing cells, and that the cell is a fundamental unit of structure, function, and organization in all living organisms Cellular Activity is both individual and collective o Dictated by sub-cellular structures Continuity of life has cellular basis Humans are composed of 70 trillion cells Diversity: Not all cells look alike Dont perform identical roles 70 trillion cells in the human body

Cellular

260 different types of cells vary in size & shape size/shape determined by the proteins made Cell differentiation is how cells become other cells Types of Cells: Stem Cells: have the ability to renew themselves through mitotic cell division and differentiate into a diverse range of specialized cell types; can replicate indefinitely o Embryonic Stem Cells: Can become any type of cell (totipotent); o Adult stem cells are found in breast tissue & umbilical cord blood Progenitor Cells: partly specialized daughter cells of stem cells o Commited cells/ specific type of cell o Can divide a limited number of times o Repair system for the body- replenish special cells, but also maintain the blood, skin & intestinal tissues

Cell Aging: Wear & tear theory: chemical insults, free radicals (cumulative effects) Genetic theory: cessation of mitosis, pre-programmed genes (apoptosis) All cells of the body contain the same DNA Embryos exposed to chemical signals that hinder development Genes of specific cells turn on or off Cell Characteristics: mini protein factories Smallest part of an organism Plasma (cell membrane): forms outer boundary of the cell through which cell interacts with its external environment Nucleus: centrally located; directs cell activities (mostly take place in cytoplasm); genetic library; dictates the kind & amount of proteins to be made Cytoplasm: located between the plasma membrane and the nucleus. 80% water Organelles: perform specific functions o Mitochondria: power plant of cell; aerobic respiration Functions of the Cell Cell Metabolism & Energy use: o chemical reactions are metabolic reactions (cell metabolism) o energy released from reactions is used for cellular activities (synthesis of molecules & muscle contraction); other energy released is used for heat to maintain body temp Synthesis of Molecules: o Cell makes diff types of molecules (proteins, nucleic acids, and lipids) o Functions of cells determined by type of molecules produced Communication: o Cells produce/respond to chem and electrical signals (allow them to communicate to one another)

Nerve cells produce chem signals which allows communication with muscle cells (respond by contracting or relaxing) Reproduction & Inheritance o Cells contain complete copy of all genetic info of individual (determines structural & functional characteristics of cell) o During growth, cells divide to produce new cells (with same genetic info) o Gametes (specialized cells of the body) are responsible for transmitting genetic information to the next generation

Plasma Membrane

Lipid bilayer (phospholipids & cholesterol) with proteins embedded in either surface Function: Controls entry & exit of substances; receptor molecules function in intercellular communication; marker molecules enable cells to recognize one another Selectively Permeable: o Some materials freely pass (small hydrophobic molecules, CO2 AND O2, and small lipids, and small polar molecules (H20) o Some materials are excluded (large molecules)

o Some materials enter or leave the cell only by the using cell energy/protein channels (Ions and nutrient molecules) Cytosol (fluid part) Water w/ dissolved ions & molecules; colloid with suspended proteins (catalyze decomposition & synthesis reactions) Cytoskeleton (internal skeleton) o Composed of microtubules (large), intermediate filaments, microfilaments (small- centrioles, cilia/flagella, basal bodies) o Support cytoplasm (anchors organelles/maintains shape) & form centrioles, spindle fibers, cilia, & flagella o Responsible for movement of structures in cell Actin filaments/Microfilaments (smallest) Composed of actin (protein); spider web like Provide structure to cytoplasm Mechanical support to microvilli Support plasma membrane & define shape of cell (reconstruct to help cells move) Responsible for muscles contractile capabilities Cyclosis: movement of cytoplasm contents within the cell Amoeboid movement and phagocytosis Mitosis: cleavage furrow in cytokinesis Intermediate filaments Composed of keratin (protein) Mechanical strength to cells Cell Attachments

Microtubules (largest) Hollow; composed of tubulin (protein) Support & structure to cytoplasm Help transport intracellular materials Form key parts of centrioles, spindle fibers, cilia, and flagella Mitosis: Form the spindle apparatus (separates chromosomes during cell division) Cytoplasmic Inclusions o Stored nutrients, secretory products, and pigment granules

o Function depends on molecules Energy storage (lipids, glycogen) Oxygen transport (hemoglobin) Skin color (melanin) Pigments that incr with age (lipochromes) Nucleus: contains/stores DNA; determines how cell will function & basic structure of cell; manufactures all RNA; duplicates DNA b/f cell division; largest organelle; Nuclear Envelope o Double membrane o Nuclear pores that contain RNA and protein that provide channels for exchanging substances with the cytoplasm of the cell Proteins lining pores determine which molecules enter/leave the nucleus o Outer surface coated with ribosomes o Endoplasmic reticulum is connected to the nuclear envelope Chromatin o Combination of all DNA and histones in nucleus o Threadlike strands of DNA used to form chromosomes Condenses to form chromosomes during cell division DNA and histones (protein important for structural organization) o Condenses into chromosomes (x) during mitosis o After DNA replication, chromosomes have two chromatids (one of the lines in the x)

DNA: blueprint for protein synthesis o found in the cells nucleus o Genes are the instruction carrying units of DNA o DNA combines with RNA to make a protein o Chromosomes condensed nuclear DNA and proteins (histones); consists of two chromatids o Chromatids: attached at centromeres Kinetochore: protein structure in centromere; provides point of attachment for microtubules during cell division o Establishes structure of protein by specifying the sequence of their amino acids o Ribonucleic acid (RNA): intermediate for DNA that can leave the nucleus DNA determines structure of messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA) o Gene: sequence of nucleoties in a DNA molecule that specifies the structure of a protein or RNA molecule Nucleolus o Small concentrated masses DNA, RNA, and protein o Synthesis of ribosome subunits Ribosomes are the site for protein synthesis Ribosomes have 2 subunits (large/small) & are composed of RNA & protein Ribosomal subunits move into cytoplasm for functioning (attached to rough ER or free in cytoplasm) Free ribosomes: synthesize proteins used inside the cell Ribosomes attached to endoplasmic reticulum produce proteins that are secreted from the cell

Cytoplasmic Organelles: structures within cells specialized for particular functions; secretion of proteins = ER & Golgi Rough Endoplasmic Reticulum: synthesizes, transports, and isolates intracellular contents o Membranous tubules and flattened sacs with attached ribosomes o Connected to nuclear envelope

o Protein synthesis: produced and modified for secretion o Vesicles formed at ER migrate to the Golgi bodies, merge & pass through the Golgi & are packaged and labeled for export in Golgi vesicles Smooth Endoplasmic Reticulum o Membranous tubules and flattened sacs with no attached ribosomes o Abundant in cells that produce many lipids o Make lipids and carbs and steroids via enzymes o Stores calcium trigger muscle contraction o Detoxifies harmful chemicals (alcohol) o Increases surface area for action/storage of enzymes Golgi Apparatus: secrete large amounts of protein (glycoproteins), such as cells in the salivary glands & the pancreas o Composed of stacks of cisternae (isolated from cytoplasm) o Processing center for materials to be packaged up & distributed in organelles or exported/secreted from the cell in vesicles pinched off of the tips of the Golgi membranes Digestive enzymes packaged for lysosomes Hormones are packaged into vesicles for secretions o Modifies packages (protein & lipid packaging) made by the rough/smooth ER before export Carb portion of glycoproteins are added in the Golgi body Polysaccharides are made in the Golgi o Proteins become more concentrated and chemically altered o Distributes protein & lipids for secretion of internal use Vesicular transport model: vesicle (forms membrane of ER) moves to the Golgi apparatus, fuses with its membrane, & releases the protein into its cisterna; The Golgi concentrates/chemically modifies the proteins by making/attaching carb molecules to proteins to form glycoproteins or by attaching lipids to proteins to form lipoproteins; proteins are then packaged into vesicles that pinch off from the margins of the Golgi and are distributed

Some vesicles carry proteins to the plasma membrane, where proteins are secreted from the cell by exocytosis Other vesicles contain proteins that become part of the plasma membrane Other vesicles contain enzymes that are used within the cell Secretory Vesicle o Membrane-bound sac pinched off Golgi apparatus o Carries protein and lipids to cell surface for secretion (membranes fuse w/ plasma membrane & released by exocytosis; membranes of vesicles then are incorporated into plasma membrane) Lysosome (vesicles) o Contains enzymes that can breakdown carbs, proteins, nucleic acids, & many lipids (intracellular digestive system) o Made from enzymes/membranes of the rough ER and packaged in the Golgi (pinched off) o Contains digestive enzymes; digest pathogens & destroy nonfunctional organelles (cell maintenance & renewal); Autophagia: process where lysosomes digest organelles of cell that arent functional o Lysosomes move to plasma membrane & enzymes are secreted by exocytosis (ex) bone remodeling: breakdown of bone tissue by specialized bone cells; enzymes responsible for that degradation & are released into extracellular fluid from lysosomes produced by those cells

Peroxisome o Smaller than lysosomes o Detoxify and neutralize/break down free radicals by transferring hydrogen in reactions to oxygen (peroxide H202) via the enzyme catalase Breaks down hydrogen peroxide into water & oxygen o Detoxification for liver & kidney cells (many peroxisomes) o One site of lipid and amino acid degradation

Proteasomes o Large protein complexes (recycle proteins within the cell) o NOT surrounded by membranes o Tubelike protein complexes in the cytoplasm o Destroy unneeded, damaged or faulty proteins Mitochondria: provide energy for the cell (ATP production) o Spherical rod-shaped, or threadlike structures o Enclosed by double membrane o Inner membrane forms cristae (projections) Enzymes found in cristae: enzymes of citric acid cycle (inner membrane) & of electron transport chain (matrix) o Major site of ATP synthesis when Oxygen is available Contains enzymes needed to get energy from the carbs. That energy forms ATP o The larger the energy requirements of the cell, the more mitochondria o Contain their own DNA and ribosomes & can self-replicate Not as many strands of nuclear DNA as nucleus

Does not have histone associated proteins Centrioles (microtubules) o Pair of cylindrical organelles in the centrosome Centrosome: specialized zone of cytoplasm close to the nucleus & is the center of microtubule formation Contains 2 centrioles o Consists of triplets of parallel microtubules Microtubules: influence distribution of actin & intermediate filaments Extend from centrosomes o Centers for microtubule formation o Determine cell polarity during division in mitosis o Form the basal bodies of cilia and flagella o Determine cell shape & movement Spindle Fibers (microtubules) o Microtubules extending from centrosome to chromosomes & other parts of the cell (ex) aster fibers

o Cilia o o o

Assist in the separation of chromosomes during cell division Project from surface of cells Move small particles across the cell Move materials across cell surfaces Movement of microtubules past each other (requires ATP) responsible for movement of cilia Dynein arms: proteins connecting adjacent pairs of microtubules (push microtubules past each other) Basal body (modified centriole) located in cytoplasm at

base of cilium o Formed from microtubules o Small in length; many in a cell Numerous on surface cells that line the respitory tract and the femal reproductive tract Cilia in the trachea move mucus w/ dust particles away from the lungs (keeps lungs clear of debris) Flagellum o Tail-like projection used to propel the cell o Responsible for movement of sperm cells (entire cell) Only human cells with flagella (only 1 per cell) o Long length & a cell has very few Microvilli o Extension of plasma membrane containing microfilaments o Increase surface area of the plasma membrane for absorption & secretion o Modified to form sensory receptors Elongated microvilli in hair cells of inner ear respond to o o o o sound Smallest (smaller than cilia No movement Supported with actin filaments (not microtubules) Found in intestine, kidney, & other area in which absorption is important Model of Plasma Membrane

Fluid Mosaic

Bilayer of phospholipids & cholesterol with proteins floating in the membrane Nonpolar/hydrophobic region of each phospholipid molecule is directed toward the center of the membrane o Phospholipid heads Polar/hydrophilic region is directed toward the water environment either outside or inside the cell o Phospholipid tails Proteins In the Plasma Membrane Marker Molecules: intercellular communication o Allow cells to identify one another or other molecules o Glycoproteins o Cadherins: proteins that attach cells to other cells o Integrins: proteins that attach cells to extracellular molecules Attachment Proteins: Intracellular Joining o Anchor cells to other cells (cadherins) or to extracellular molecules (integrins) Transport proteins: carriers o Channel Proteins Form passageways through the plasma membrane (allowing specific ions or molecules to enter/exit the cell) May be gates or nongated o Carrier Proteins (transporters) Move ions/molecules across the membrane Binding of specific chemical to carrier proteins causes changes in the shape of the carrier proteins (requires ATP- active transport) The carrier proteins then move the specific chemical across the membrane o ATP- powered pumps: transport proteins Move specific ions or molecules across the membrane Require ATP molecules to function Receptor Proteins: Recognition o Function as binding sites for chemical signals in the extracellular fluid (guide cell attachments/adhesions)

o Exposed receptor site which attaches to specific chemical signals o Binding of chemical signals to receptors triggers cellular responses o Immune system: distinguish foreign cells Enzymes o Catalyze chemical reactions either inside or outside cells Passive Transport: moving biochemical and atomic or molecular substances across the cell membrane Osmosis: movement of water across a partially permable membrane from an area of low solute concentration to an area of high solute concentration. It is a physical process in which solvent moves, without input of energy, across a semipermeable membrane (permeable to the solvent, but not the solute) separating two solutions of different concentrations. (water follows stuff) Simple Diffusion: H20, CO2, O2, & small lipid-solubles (alcohol) o net movement of substances from a region of high concentration to a region of low concentration o Substances are diffused across the membrane between the phospholipids. o Rate of diffusion is slow & cant cover much distance Facilitated Diffusion: the spontaneous passage of molecules/ions across a biological membrane passing through specific transmembrane transport proteins o Glucose, many small ions, amino acids Filtration: movement of solute molecules and water across a membrane by normal cardiovascular pressure. The size of membrane pores dictate the molecule that may pass

Active Transport: some transport proteins (carrier proteins) use energy to move molecules against the concentration gradient Requires two carrier protein active sites o One to recognize the substance to be carried o One to release ATP to provide the energy for the protein carriers or pumps Concentration gradients of ions (H or Na ions) o used to provide energy

Exocytosis: moves substances (solid particles) out of a cell Endocytosis: moves substances in a cell Phagocytosis: cell eating; larger vesicles formed; solid particles ingested (bacteria, cell debris & foreign particles); eliminates harmful substances from the body (white blood cells phagotyze) Pinocytosis: cell drinking; smaller vesicles are formed; engulfs molecules dissolved in liquid (not particles) engulfs extracellular fluid Transcytosis: substances are drawn into, across and out of a cell (in one side, out the other side). Common for pathogens (viruses) Vesicular Transport: moves large particles across a membrane REVIEW Intracellular: inside the cell Extracellular: outside the cell Intercellular: between cells Plasma Membrane potential: charge difference across the plasma membrane (outside is positive & inside negative)- polarized; caused by regulation of ion movement by cells; Sodium ions & Postassium ions Sodium Ions are responsible for making the outside of the cell Large proteins inside the cells are responsible for net negative Glycocalyx: collection of glycolipids, glycoproteins, & carbs on outer surface of plasma membrane; contains molecules absorbed from extracellular environment Function of Cholesterol in plasma membrane 1/3 of total lipids in plasma membrane regulates fluidity and permeability Cholesterol limits the movement of phospholipids, providing stability to plasma membrane Integral vs peripheral proteins in the plasma membrane Integral: passing through the width of the membrane; acts as transport channels Peripheral: acts as recognition sites; contains carbs to help cell recognition o Glycolipid: lipids attached to carbs; blood type (antigens)

o Glycoproteins: proteins attached to carbs; blood type Two Functions of marker molecules Intracellular communication- glycoproteins Recognition (no foreign objects enter cell) Three Types of cell communication Contact Signaling: cell touching via sugar chains Electrical signaling: via ion gates Chemical signaling: via neurotransmitters & hormone G-protein receptors: via second messenger Cadherins vs Integrins: cell adhesion and cellular communication Cadherins: proteins that attach cells to other cells; homophilic o Epithelial, placental, neural Integrins: proteins that attach cells to extracellular molecules; heterophilic; function in pairs of integral proteins which interact with intracellular & extracellular molecules Three Classes of Transport Proteins Channel Proteins Carrier Proteins ATP powered pumps Nongated ion channels: channel protein; always open; permeability to ions Ligand-gated ion channels: channel protein; open or close in response to chemical signals (small molecules that bind to the proteins/glycoproteins) Voltage gated ion channels: channel protein; open/close when there is a change in charge across the plasma membrane Uniport: movement of one specific ion or molecule across membrane Symport: movement of two different ions or molecules in the same direction across plasma membrane Antiport: movement of two diff ions or molecules in opposite directions across the plasma membrane Carrier Proteins (transporters) move ions/molecules from one side of plasma membrane to the other by using specific binding sites at which ions/molecules attach & the protein changes shape to move the bound ions to the other side of plasma membrane where they are released.

Facilitated diffusion (doesnt require energy- moves from higher concentration gradient to a lower one) passive transport

ATP Powered Pumps : movement of ions or molecules across the membrane is fueled by the breakdown of ATP. There are binding sites for the protein & binding site for ATP. The breakdown of ATP into ADP releases energy which changes the shape of the protein to move ion across membrane Active transport Receptor molecule: chemical signal attaches to receptors on the cell surface. When chemical signals (ligands) bind to the receptors, the channels either open or close Changes permeability because receptors offer a selectively permeable interface o the receptors check for a ligand (structure on entering molecule that has a structure complementary to its own) o if the appropriate ligand is present, the molecule gains entry into the cell Receptors alter activity of G protein complexes G proteins on inner surface of plasma membrane & acts as intermediate between a receptor and other cellular proteins Alpha, Beta, & Gamma proteins G protein complex only associates with a receptor that has a chemical signal bound to it Activated (alpha) subunits stimulate cell response in 3 ways: o Intracellular chemical signals o Opening of ion channels in the plasma membrane o Activation of enzymes associated with the plasma membrane Action of enzyme in the cell membrane Breaks the peptide bond of a dipeptide to produce 2 amino acids for enzymes on the surface of cells

MOVEMENT THROUGH THE PLASMA MEMBRANE

Molecules/ions Can Pass Through Plasma Membrane in 4 Ways: Directly through the phospholipid membrane o Molecules that are soluble in lipids (O, CO2, steroids) dissolve in lipid bilayer o Bilayer is a barrier to substances that are not lipid-soluble Membrane Channels o Protein channels for size, shape, & charge o Rapid movement of water across cell membrane Transport Proteins o Large polar molecules (not lipid soluble)- glucose & amino acids o Transported by mediated processes o Specific molecules bind to specific transport proteins that carry them across plasma membrane Vesicles o Large nonlipid-soluble molecules, small pieces of matter & whole cells o Membranous sacs involved in transport o Vesicle & plasma membrane fuse because of fluid nature of

membranes, allowing contents of vesicle to cross plasma membrane Diffusion: movement of solutes from an area of higher solute conecentration to an area of lower solute concentration Concentration gradient: the concentration difference between two points, divided by the distance between two points o Solutes diffuse down concentration gradients (from higher to lower solute concentration) until equilibrium is achieved o Decreasing concentration difference or increasing distance Rate o o o o between 2 points lower concentration gradient of diffusion influenced by: Temperature (Higher temperature, faster molecule movement) Molecule size (smaller molecules move more easily) Concentration (Initial rate faster with higher concentration) Viscosity of the solvent (Diffusion rate decreases with more viscous solvents)

Osmosis: diffusion of water (solvent) across a selectively permeable membrane (allows water, but not all solutes to enter) Aquaporins: water channel proteins o Increase membrane permeability to water in kidney cells Water diffuses from less concentrated solution (fewer solutes, more water) into more concentrated solution (more solutes, less water) Importance: large volume changes caused by water movement disrupt normal cell function Osmotic Pressure: force to move water through membrane; osmotic refers to concentration of the solutions o The greater the concentration of a solution, the greater the osmotic pressure of the solution & the greater the tendency for water to move into the solution o Isosmotic: solutions with same concentration of solute have the same osmotic pressure o Hyperosmotic: more concentrated solution with higher osmotic pressure o Hyposmotic: The more dilute solution with lower osmotic pressure -tonic refers to tendency of cells to swell/shrink o Isotonic: osmotically balanced (tonicity); equal proportions of solutes to water on both sides of the membrane; artificially made to resemble body fluid (Gatorade) o Hypertonic: water moves out of cell by osmosis causing cell to shrink (crenation); solution is hypertonic because solution has a higher solute concentration (less water) than the cell (ex) food preservation o Hypotonic: water moves into cell by osmosis, causing the cell

to swell (lysis); solution is hypotonic because it has a lower solute concentration (more water) than the cell (ex) distilled water Filtration: process of separating suspended particles from the fluid through a porous material in which the fluid can pass while the suspended particles are retained Depends on pressure difference on either side of the divider o Liquid moves from greater pressure to lower pressure

Occurs in kidneys as a step in urine formation Occurs when blood pressure moves fluid from the blood (water, ions, and small molecules pass through, but most proteins and blood cells remain in the blood) Mediated Transport Process by which transport proteins (carrier, ATP-powered pumps, and channel proteins) assist in the movement of large, watersoluble molecules or electrically charged molecules/ions across the plasma membrane (ex) amino acids and glucose & proteins Characteristics o Specificity: each transport protein binds to and transports only a single type of molecule or ion; determined by the chemical structure of the binding site For Channel protein (ion channels), specificity is determined by size and charge within a channel o Competition: similar molecules binding to the transport protein; the substance in the greater concentration or that binds more readily is passed through membrane o Saturation: the rate of movement of molecules across the membrane is limited by the number of available transport proteins; occurs when all carrier proteins/channels are occupied As concentration of a transported substance increases, more transport proteins have their binding sites occupied (maximum rate) Rate of transport: o As the concentration differences increase, the rate of transport increases and then levels off When concentration of molecules outside cell is low, the transport rate decreases More molecules outside the cell more molecules being transported/ transport rate increases (if transport proteins are available) When the number of molecules outside the cell outnumbers the transport proteins, the system is saturated & transport rate cannot increase.

Three Kinds: o Facilitated Diffusion: carrier/channel mediated; moves substances in & out of cells from a higher to lower concentration; rate of transport is directly proportional to their concentration gradient up to the point of saturation, then the rate of transport is constant at its max rate o Active Transport: requires energy provided by ATP to move substances against concentration gradients (low to high); rate depends on number of pumps & availability of ATP; Sodium-potassium pump: moves Na out of cells and K

into cells; ATP is broken down o Secondary active transport: does not require ATP molecule; gets energy from existing concentration gradient (sodium); one molec moves out of cell with the energy from other molecule moving in the cell Glucose is moved from the lumen of the intestine into epithelial cells by this process Endocytosis & Exocytosis Endocytosis: internalization of substances (phagocytosis & pinocytosis) o Uptake of material through the plasma membrane by the formation of a vesicle (membrane-bound sac found within the cytoplasm of a cell) o Receptor-mediated endocytosis: specific molecules are ingested into the cell, as a result of a receptor-ligand interaction; specificity & saturation Increases rate at which substances enter cell Cholesterol and growth factors are molecules accepted by the receptor Exocytosis: substances contained in vesicles are discharged from cell o (ex) secretion of digestive enzymes by the pancreas and secretion of mucus by the salivary glands Cytoplasm: half cytosol and half organelles Cytosol: fluid portion, cytoskeleton, and cytoplasmic inclusions

o Fluid portion = dissolved ions and molecules and a colloid with suspended molecules (proteins, which catalyze breakdown of molecules for energy) o Cytoskeleton= supports cell & holds the nucleus/other organelles in place responsible for cell movements three groups of proteins: microtubules, actin filaments & intermediate filaments Genes & Gene Expression Heredity: genetic transmission of characteristics (traits) from parents to their offspring Genes: functional units of heredity; responsible for the characteristics of cells (inherited- traits of the entire organism) o Each gene is a segment of a DNA molecule DNA molecules (w/ proteins) form chromosomes o Gene: All the triplets necessary to make functional RNA molecule or protein o 2 types of Genes Structural: DNA sequences that determine specific amino acid sequences in proteins (enzymes, hormones, or structural proteins like collagen) Regulatory: segment of DNA involved in controlling which structural genes are expressed in a given tissue Sequence of nucleotides in a DNA molecule is a method of storing information that is based on a triplet code o Triplets: Three consecutive nucleotides that form the words of the triplet code Used to construct other DNA molecules, RNA molecules, & proteins Gene Expression: production of proteins (made in the cytoplasm) from the info stored in DNA; region of a DNA molecule between the promoter & terminator o 2 Steps Transcription: copy DNA from genes (DNA stays in nucleus)

mRNA = copy of DNA that travels from the nucleus to ribosomes in the cytoplasm Translation: converting copied information into a protein Information in the copy (mRNA) constructs protein Amino acids are key to making proteins o Transfer RNA (tRNA): specialized transport molecules that carry amino acids to the ribosomes 2 Sections of protein-coding regions of RNA o exons: code for parts of a protein & sections o Introns: do not code for parts of a protein Transcription o Synthesis fo mRNA, tRNA, and rRNA based on the nucleotide sequence in DNA o Occurs when a section of a DNA molecule unwinds and its complementary strands separate One of the DNA strands is the template strand for transcription (DNA transcribed into RNA) Nucleotides that form RNA align with the DNA nucleotiedes in the template strand by complementary base pairing Thymine (from DNA) with Adenine Adenine with a Thymine (from DNA) Cytosine with a Guanine (from DNA) Guanine with a Cytosine (from DNA) Uracil (from RNA) with Adenine (from DNA) RNA polymerase: enzyme that makes the complementary RNA molecule from DNA o Attaches to a DNA nucleotide sequence (promoter) To attach: RNA polymerase associates with transcription factors (other proteins) so that it can interact with DNA o Attachment of polymerase to promoter causes a portion of DNA to unwind (exposing nucleotide sequence) Complementary RNA nucletides then align with DNA nucleotides of the template strand

RNA nucleotides combined by dehydration reactions (catalyzed by RNA polymerase) to form mRNA o RNA polymerase detaches from DNA (releasing the new form of mRNA) when it encounters a terminator (DNA nucleotide sequence) Genetic Code: information contained in mRNA Codons: sets of three nucleotide units which carries genetic code o Specifies an amino acid during translation o Start codon: signals beginning of translation o Stop codon: signals end of translation Do not specify amino acids Translation: synthesis of a protein at the ribosome in response to the codons of mRNA Requires ribosomes and tRNA o Ribosomes consist of ribosomal RNA (rRNA) and proteins mRNA, tRNA, and rRNA are produced in the nucleus by transcription o tRNA: matches specific amino acid to a specific codon of mRNA one end of each kind of Trna COMBINES WITH A SPECIFIC AMINO ACID anticodon: consists of three nucleotides and is complementary to a particular codon of mRNA; only can combine with its matched codon

REVIEW 1. Difference between Start Codon & Promoter and between Stop Codon & Termination Site? The start codon is located on the mRNA strand (it signals TRANSLATION to start by recruiting the large ribosomal unit to the small one). The promoter is located on the DNA strand (it signals TRANSCRIPTION to start). The stop codon is located on the mRNA strand (it signals TRANSLATION to stop, via the Release Factor). The termination sequence is located on the DNA strand (it signals TRANSCRIPTION to stop)

2. Where are codons and anticodons found and how is their relationship crucial to protein synthesis? Codons are the mRNA triplets of nucleotides (i.e. AUG, CUG, etc) that are made by DNA (transcription). DNA is in the nucleus and makes a strand of mRNA. This mRNA leaves the nucleus and goes out into the cytoplasm and binds to a ribosome. These mRNA codons are complementary to triplets of nucleotides in a tRNA molecule (anticodon) which is out in the cytoplasm of the cell. This tRNA anticodon brings the amino acid that it codes for into the ribosome (translation) to join with other amino acids to eventually become a protein. These relationships - DNA to mRNA (transcription) and mRNA with tRNA (translation) are what direct the process of protein sythesis. The base pairing of the nucleotides from a DNA codon to a mRNA codon and from mRNA to a tRNA anticodon are what determine the sequence of amino acids in the protein. 3. Describe the role of mRNA, rRNA, and tRNA in the production of a protein at a ribosome. What is a polyribosome? mRNA carries genetic information copied from DNA in the form of a series of three-base code words which specifies a particular amino acid tRNA is the key to deciphering the code words in mRNA. Each type of amino acid has its own type of tRNA, which binds it and carries it to the growing end of a polypeptide chain if the next code word on mRNA calls for it. The coorect tRNA with its attached amino acid is selected at each step because each specific tRNA molecule contains a 3 base sequence that can base-pair with its complementary code word in the mRNA rRNA associates with a set of proteins to form ribosomes. These complex structures (physically move along an mRNA molecule) catalyze the assembly of amino acids into protein chains. They also bind tRNAs and various accessory molecules necessary for protein synthesis. Ribosomes are composed of a large & small subunit, each of which contains its own rRNA molecule or molecules Translation is the whole process by which the base sequence of an mRNA Is used to order and to join the amino acids in a protein.

4. What are Exons & Introns? How do they related to Post-Transcriptional RNA processing and mrNA? Prokaryotic DNA transcription produces messenger RNA, which is necessary for transfer from the cell nucleus to the cytoplasm where translation occurs. In contrast, eukaryotic DNA transcription takes place in a cell's nucleus and produces what is called a primary RNA transcript or pre-messenger RNA. Before eukaryotic products of transcription can be moved into the cytoplasm, they must undergo modifications that allow them to become mature messenger RNA. Splicing is the name given to the reaction that removes unnecessary segments of the primary RNA transcript, called introns. The removal of the introns produces mRNA (see the figure, below). Messenger RNA contains only exons, those portions of the primary RNA transcript that will be translated into a protein. 5. Relationship among centrosomes, spindle fibers and kinetochores of chromosomes during cell division? CELL LIFE CYCLE: changes a cell undergoes from the time it is formed until it divides to produce two new cells 2 stages: o Interphase: phase between cell division; 90% or more of life cycle cell carries out metabolic activities performs specialized functions (ex) secretion digestive enzymes cell prepares to divide increase in cell size (b/c many cell components double in quantity) replication of the cells DNA: 2 new strands of DNA are made (using two existing strands as templates) replication of the centrioles within the centrosome Three Subphases G1, S, and G2 G1 (gap phase)- cell carries out routine metabolic activities

S (synthesis phase)- DNA is replicated G2 (second gap phase)- cell prepares for cell division G0 phase: resting cells exit cell cycle o Cell Division stage Division of the nucleus to form two new nuclei Division of the cytoplasm to form 2 new cells Each of the new cells contains one of the newly formed nuclei division of nucleus occurs by mitosis division of cytoplasm is cytokinesis Mitosis: Division of nucleus into two nuclei (each with same amount and type of DNA as original nucleus) DNA (replicated during interphase) is dispersed as chromatin o Chromatin becomes very densely coiled to form compact chromosomes (each chromosome consists of two chromatids attached at the centromere) Each chromatid contains a DNA molecule As daughter cells are formed, chromatids separate and are now called a chromosome

4 phases: o Prophase o Metaphase o Anaphase: Cytokinesis begins; formation of a cleave furrow (indentation of the plasma membrane-forms midway between centrioles); actin filaments pull plasma

membrane inward, dividing cell into halves o Telophase Genetics: study of heredity Mendelian Genetics: study of how certain genetic traits are passed from parent to offspring (used to determine risk of disease inheritance) o During the production of gametes (sex cells), each gamete receives one hereditable factor

o Genotype: genes an organism has for a given trait o Phenotype: expression of the genes as traits o Genes (alleles) occur in dominant and recessive forms Dominant: mask effects of recessive allele for a trait Human genome: all of the genes in a human chromosome Modern Use of Genetics Chromosomes o Made up of DNA and proteins found in the nuclei of somatic cells(all cells of the body except for the gametes)- (ex) epithelial cells, muscle cells, neurons, fibroblasts, lymphocytes, and macrophages Diploid: # of chromosomes in somatic cell; humans=46 Humans have 23 paired chromsomes Haploid: # of chromosomes in a gamete Haploid number of chromosomes is 23 o Gametes Males sperm cells Females oocytes o Autosomal Chromosomes: all chromosomes but sex chromosome (22 pairs) o Sex Chromosomes: determine sex of individual (1 pair) Female = XX in each somatic cell Male = XY in each somatic cell o Karyotype: display of chromosomes of a somatic cell during metaphase of mitosis Homologous: chromosome pairs Genome: all the genes found in the haploid number of chromosomes from one parent Combined genomes from parents responsible for all genetic traits Multiple Alleles: dominant and recessive o 2 alleles for each given gene (one on each homologous chromosome) o differences in alleles caused by mutation (DNA nucleotide sequence is altered) Gene Dominance

o Complete dominance: homozygous dominant and herozygote had the same phenotype o Codominance: two allesles at the same locus are expressed so that separate, distinguishable phenotypes occur at the same type (ex) ABO blood types o Incomplete Dominance: dominant allele does not completely mask the effects of the recessive allele in the heterozygote Heterozygote produces less of the protein product than the homozygous dominant & has intermediate phenotypic characteristics (ex) beta thalassemia: disorder of a gene on chromosome 11 (affects synthesis of beta globulin polypeptide chains- which are part of hemoglobin in red blood cells) hemoglobin=protein that transports oxygen anemia: deficiency of hemoglobin in the blood blood transfusions key to maintain hemoglobin levels

Polygenic Traits o Many genes determine phenotype o (ex) height, intelligence, eye color, skin color Sex Linked Traits o Traits affected by genes on the sex chromosomes X linked traits = on x chromosome Y linked traits = on y chromosome o Most are x-linked because y chromosome is very small Hemophilia A ability to produce certain blood clotting

factors is not present Clotting impaired & persistent bleeding Meiosis and Transmission of Genes Gametes are produced that have one homolog from each of the homologous pairs of chromosomes o Gametes have the number of chromosomes and the alleles of the original diploid cells

Gametes are haploid cells that are derived from diploid cells o Punnett Square: probability of the transmission of alleles to the next generation (if the genotypes of parents are known) Carrier for a recessive trait is a person who is heterozygous for that trait (one normal allele and one disorder-causing allele) Genetic Disorders Failure of structure, function, or both as a result of abnormalities in a persons genetic makeup (his/her DNA) Mutagens: agents that cause mutations Nondisjunction: one of the daughter cells receives both chromosomes and the other receives none o Aneuploidy: 47 chromosomes vs 45 chromosomes in daughter cells (instead of normal 46) Downs Syndrome (trisomy 21): 3 chromosomes 21 are present Syndrome = set of signs and symptoms occurring together as the result of a single cause (ex) single

mutation or one extra chromosome (a trisomy) 2 Purposes of Cell Division body growth tissue repair Mitosis: process by which a cell separates the chromosomes in its cell nucleus into two identical sets in two nuclei 4 Phases of Mitosis Prophase Metaphase Anaphase Telephase Cytokinesis: division of cytoplasm Control of Cell Division: Surface to Volume Ratio Chemical Signals Growth Factors

Hormones Contact Inhibition

Some tissues lose the ability to divide Hyperplasia: increased number of cell divisions (often a cause for abnormal pap smears in women) Diseases characterized by uncontrolled cell proliferation create tumors or neoplasm Cancerous Neoplasm (malignant tumor or malignancy) can turn into metastasis which is the spread of a disease from one organ or part to another non-adjacent organ or part. Causes of Cancer Carcinogens (chemicals) Radiation Viruses/Mutation (ex) HPV

Types of Cancer & location: Carcinomas- epithelial cells Melanomas- melanocytes (skin) Sarcomas- muscle cells or connective tissues Leukemia- blood forming organs (bone marrow) Lymphoma- lymphatic tissue Angiogenesis: formation of new blood vessels triggered by cancer cells dividing rapidly and continuously Carcinogenesis: multistep process involves mutation of oncogenes and anti-oncogenes Many mutations may have to accumulate before it becomes cancer Treatment of cancer is difficult because it is not a single disease

 Cancer

Cells in a tumor do not all behave the same way treatments Surgery Chemotherapy Radiation therapy

ATP Production Glycolysis (in cytoplasmglucose goes in) Krebs Cycle (citric acid cycle) Electron Transport Chain (in mitochondriaATP comes out)

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1/17/2012 10:35:00 AM Importance of Physics Deals with matter, energy & interactions Humans like to ask why? We are curious & want to understand Universe is mysterious Importance of Units Give meaning to the numbers we calculate 1 mi= 1609 m Vectors vs Scalar Vector: position, velocity, & acceleration & displacement o Magnitude (size) & direction o (ex) 5 meters to the right o displacement is vector quantity o velocity = m/s in direction Scalars: speed, distance o Only Magnitude (size of vector) or distance Magnitude of velocity is speed o (ex) 5 meters o distance is scalar quantity

o speed = m/s (rate of motion/change in position) o rate (speed)=distance/time o can be positive or negative Acceleration Rate of change of velocity over time (changes velocity) slope in velocity vs. time graph o Slowing down if velocity and acceleration are opposite signs o Speeding up if velocity and acceleration are the same signs In position vs time graph, acceleration=0 when: o there is a change in concavity and o when velocity is constant In position vs time graph, acceleration is speeding up if its concave up & slowing down if concave down Vector quantity For constant acceleration: v/t= v(final)-v(initial)/ t o m/s^2 o if doesnt change=constant acceleration

Constant acceleration is like a compound interest o space ship at launch: a lot of acceleration; sustains acceleration for a short time b/c limited supply of energy & fuel (dot-com portfolio) o Balanced portfolio Consistent returns sustained over a long period Starts slow- but acceleration starts building 1. Which of the following is vector? Velocity (specify number & units & direction): rate at which an object changes position Displacement 2. Which is scalar? (specify number & units) Distance Speed 3. Speed=distance/time interval units: m/s always positive 4. Velocity= displacement/time interval (x/t) units: m/s or mph/s can be negative/positive at same speed= uniform speed; constant velocity

4 types of motion: Linear: straight line Circular: revolving Rotational: spinning about itself Projectile Motion: elliptical; 2 dimensional (up & down- basketball) The Particle Model: Numbers show order of frames Single dot represents the object Coordinate System: Towards right (horizontal)= positive displacement along x axis Towards left (horizontal) = negative displacement along x axis Moving up (vertical) = positive displacement Moving down (vertical) = negative displacement Motion Diagram

Ball: at rest/stationary Skateboard: constant speed (more same amount in each time interval) Girl: Speeding up Car: Slowing Down Basketball: move along 2 dimensional (vertical & horizontal) o Vertical: distance shrinking going up (negative) or accelerating going down (positive) o Horizontal: constant speed Displacement= final position initial position Position Direction matters Vector Can be negative One dimensional vs. Time Graph Point: specifies position at a given instant of time Path: between 2 points describing the motion Slope: indicates speed or velocity (rise/run) Direction: (slope) indicates direction of motion Steeper slope = faster speed o Positive slope = moving in positive direction o Negative slope = moving in negative direction o If slope is decreasing, object is slowing down o If slope is increasing, velocity is speeding up X (final) = x (initial) + Velocity (x) t o Position Equation for an object in uniform motion (velocity of x is constant) o x =v (x) t Concave down: acceleration decreasing (neg) Concave up: acceleration is increasing (positive) vs. Time Graph Displacement/distance = area under curve (m) Acceleration = slope (change in velocity/change in time) o Constant acceleration = constant slope (magnitude 0, horiz line) o Acceleration= change in distance/change in time

Velocity

If sign for acceleration is same as sign for velocity, it is speeding up. If different, its slowing down. Uniform Motion No acceleration Motion with Acceleration