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EXAM II EXAM II is on MARCH 15 Covers Weeks 4, 5 and 6 What is a substrate? • A substrate is a reactant for an enzymatic reaction. • A substrate attaches to an enzyme at the active site. • The substrate is the reactant in that the enzymatic reaction only occurs once the substrate attaches with the enzyme that is specific for that particular substrate. • Remember, we are talking about molecules here. All of the big blobs you see that I've drawn are representations or cartoons of what are actual molecules. • These molecules undergo a reaction to produce a PRODUCT. Then, that product can be used as the reactant or SUBSTRATE for the next enzymatic reaction. Enzyme Active Site In general only the “active site” of the enzyme binds to the substrate I. II. Active Site of the Enzyme III. A slight change at the active site allows for the attachment of the substrate WEEK 5 Continued Adenosine Triphosphate (ATP) ATP is a nucleotide The base of the nucleotide is adenine The sugar of the nucleotide is ribose Tri refers to the 3 phosphate groups attached to the ribose sugar - The last two Phosphate bonds are UNSTABLE, easily broken - In cells, the end phosphate is hydrolyzed to release energy which results in ADP, adenosine diphosphate and a Phosphate molecule ATP and the Electron Transport Chain ATP is produced via the electron transport chain (ETC) Chloroplasts in plant cells use solar energy to generate ATP using ETC Mitochondria in animal cells use glucose to generate ATP using ETC The ETC is a series of transfers of electrons whereby high energy electrons are transported through a series of steps to release energy for the synthesis of ATP Energy comes from the transfer of electrons WEEK 6 Chpt 18 (pg320-327)- Cell Evolution and multicellularity Chpt 20 (all)- Viruses, Bacteria and Archaea Chpt 4 (pg68-84)- The Eukaryotic Cell Chpt 5 (all)- Membranes and Transport Mitochondria and Chloroplasts Energy is created in the Mitochondria in animal cells and in the Chloroplasts of Plant cells How do we know this? Using Microscopy, scientists have discovered the organelles and molecular structures responsible for cell structure 1- All organisms are composed of cells 2- Cells are the basic units of structure and function in organisms 3- Cells come only from preexisting cells because cells are self-reproducing Fig. 4.2 Cell Size Cells are small- approximately 1 micron (µm) This is 1,000th of a millimeter Cells are the smallest unit of living matter SURFACE AREA TO VOLUME RATIOS Fig. 4.3 Why are cells so small and Why is having a large surface area so important? 1. A Smaller cell has more surface area per volume than a large cell 2. Small cells have more surface area for exchanging wastes for nutrients because of its greater surface-area-to-volume ratio. Two Types of Cells Bacteria and Archaea YOU ARE RESPONSIBLE FOR UNDERSTANDING THE DIFFERENCE BETWEEN PROKARYOTIC AND EUKARYOTIC CELLS AND HOW ANIMAL CELLS DIFFER FROM PLANT CELLS Chpt. 18 CELLULAR EVOLUTION Protocell containing DNA Genes true cell Plasma membrane forms Polymers aggregate within the plasma membrane= protocell Monomers joined to form Polymers (proteins, RNA) Abiotic Synthesis created Small organic molecules (ex. Amino acids, nucleotides) 4.6 BYA Chpt. 18, page 325 First Prokaryotes arose 3.5 BYA Eukaryotic cells arose 2.1 BYA Eukaryotes contain Mitochondria which are believed To have been independent , free living aerobic bacteria The endosymbiotic theory states that a nucleated cell Engulfed these free living aerobic bacteria which later Became organelles or ‘MITOCHONDRIA’ Heterotrophs cannot produce Own food and practice Sexual reproduction The eukarya arose from ARCHAEA Heterotrophic protists arose when eukaryotic cells engulfed aerobic bacteria THE EUKARYOTIC CELL http://www.wisconline.com/Objects/ViewObject.aspx?ID=AP11403 ANIMAL CELLS HAVE A PLASMA MEMBRANE THE NUCLEUS Chromosomes Nuclear Envelope Nucleolus Condensed Chromatin Surrounds Nucleus Contains genetic information/ Genes Composed of two layers Contains ribosomal RNA which aids in production of protein Composed of DNA Set number per species (humans Have 23 pairs or 46 Chromosomes) http://library.thinkquest.org/12413/structures.html Has nuclear pores to permit The passage of ribosomal Subunits and mRNA out of the nucleus THE CYTOPLASM Centrioles Involved in Cell division Chloroplasts (Plants ONLY) Contains Green Chlorophyll where Photosynthesis occurs Cytoskeleton Composed of microtubules Supports cell and Gives shape http://library.thinkquest.org/12413/structures.html Endoplasmic Reticulum Fused to Nuclear Membrane 2 types-Smooth Rough Produces protein Lysosome Digests Proteins Lipids, Carbs Transports waste to cell membrane Made by Golgi Mitochondria Produces ATP Has 2 membranes Folds are cristae CHAPT 4 Golgi Apparatus Packages Protein Near Nucleus Cell division Vacuoles Store, digest and Removes cell Waste Plants have a Large Central Vacuole Ribosomes Particles where protein synthesis Occurs Composed of 2 Subunits (large and small) THE CYTOSKELETON Intracellular protein Matrix Ropelike fibrous polypeptides Now called ACTIN filaments= Actin monomers, twisted in a helical manner Made of tubulin- a globular protein http://www.wisconline.com/Objects/ViewObject.aspx?ID=AP11403 ANIMAL CELLS HAVE A PLASMA MEMBRANE PLANT CELL (eukaryote) PLANT CELLS HAVE A CELL WALL AND CHLOROPLASTS THE PROKARYOTIC CELL PROKARYOTES HAVE A CELL WALL, NO NUCLEUS! Prokaryote fossils date to 3.5 BYA Extremely diverse in structure and metabolic capabilities Some prokaryotes move with the use of ‘FLAGELLA’ Flagella= strands of flagellin protein wound in a helix Many prokaryotes adhere to cells with the use of ‘FIMBRIAE’ Fimbriae = short bristlelike fibers on the surface Prokaryotes DO NOT HAVE A NUCLEUS Prokaryotes have a dense area called a NUCLEOID where a Single chromosome of circular DNA exists Some prokaryotes also have accessory rings of DNA called Plasmids Prokaryotes reproduce ASEXUALLY via BINARY FISSION Generation time can be as little as 12 minutes Prokaryotes are HAPLOID- one copy of each gene Mutations are highly vulnerable to Natural selection! Prokaryotes can exchange genetic information via CONJUGATIONwhen two bacteria are temporarily linked together, genetic information is passed from one to the other = Transduction Pg. 364 in text BACTERIA ARCHAEA Found practically in every environment on earth Became a distinct domain in 1977 because ribosomal RNA of Archaea differs from Bacteria Protected by a cell wall that contains PEPTIDOGLYCAN-polysaccharides linked by amino acids Bacteria are classifed by whether they are: 1-Gram +, thick layer of peptidoglycan 2-Gram -, thin layer of peptidoglycan 3 shapes: Spirilli (spiral shaped), Bacilli (rod) Cocci (round/spherical) Some bacteria are: 1- Obligate anaerobes- unable to grow in the Presence of O2 2- Facultative anaerobes- able to grow in the Presence or absense of O2 Bacteria and Arachaea can be: 1- Photoautrotrophs 3- Chemoheterotrophs 2- Chemoautotrophs Eukarya are more closely related to archaea than to bacteria Archaea contain lipids that allow them to Exist in high temperatures Cell walls do NOT have peptidoglycan Types of Archaea: 1-methanogens, 2- halophiles, 3- thermoacidophiles Methanogens- Methane makers Halophiles- need high salt concentration to grow, ex. The Dead Sea Thermoacidophiles- found in hot springs, Highly acidic conditions Photoautotrophs- Are photosynthetic and use light energy to assemble the organic molecules they require -Primitive photosynthesizing bacteria us only photosystem I and DO NOT GIVE OFF O2 -Advanced photosynthesizing bacteria (ex. Cyanobacteria) use photosys. I and II And give off O2 Chemoautotrophs- Make organic molecules by using energy derived from the oxidation of inorganic compounds in the environment -Ex. Methanogens can be found at the deep hydrothermal vents, H2S -They can produce methane from hydrogen gas and CO2 -Nitrifying bacteria oxidize ammonia (NH3) to nitrites (NO2) and nitrites to nitrates (NO3) Chemoheterotrophs- Most free-living bacteria are chmoheterotrophs, they take up Pre-formed organic nutrients -Bacteria produce chemicals such as ethyl alcohol, acetic acid, butyl alchol, acetones -Bacteria action produces butter, chees, sauerkraut, rubber, cotton, silk, coffee CELL MEMBRANE STRUCTURE AND FUNCTION Fig. 5.1 Chpt 5 pg 86 Plasma Membrane of an Animal Cell -Proteins inserted into plasma membrane are INTEGRAL proteins -PERIPHERAL proteins are on the cytoplasmic side of the membrane The membrane is ‘fluid’ Current model to describe fluidity= Fluid-Mosaic Model Cells must be fluid and pliable, rigidity can be caused by cholesterol Glycoprotein- a phsopholipid with a carbohydrate or sugar chain attached Protects cell, facilitates adhesion btwn cells TYPES AND FUNCTIONS OF PROTEINS (chpt 5 pg 88) The Plasma Membrane The plasma membrane is permeable and regulates the passage of molecules in and out of the cell The plasma membrane is ‘SELECTIVE’ or ‘Differentially Permeable’ or ‘Selectively Permeable’ Some molecules passively cross the plasma membrane (NO ENERGY REQUIRED) while others are actively transported across the membrane (ATP IS REQUIRED) Small, non-charged particles freely pass the membrane barrier: Carbon Dioxide (CO2) Oxygen (O2) Glycerol Alcohol (These molecules follow their concentration gradient) Water passively moves across via a protein called AQUAPORIN Ions and polar molecules like glucose and amino acids slowly cross membrane, BUT often need assistance by carrier proteins PASSIVE TRANSPORT Concentration gradient- Movement of material from an area of high concentration to an area of low concentration Diffusion- the movement of molecules from a higher to a lower concentration Fig. 5.5 page 91 OSMOSIS Diffusion is the movement of molecules from an area of high to low concentration OSMOSIS is the movement of WATER across a membrane due to concentration differences of solutes OSMOTIC PRESSURE is the pressure that develops in a system due to osmosis ISOTONIC SOLUTION Solute and water concentration inside and outside of the cell are equal No gain or loss of water HYPOTONIC SOLUTION Solutions that cause cells to swell and burst The net movement of water is from the outside to the inside of the cell HYPERTONIC SOLUTION Solutions that cause a cell to shrink or shrivel due to loss of water The net movement of water out of the cell More Solute inside cell swells as water moves in to dilute solute Equal solute inside and out More Solute outside cell Shrivels as water moves out to dilute solute Fig. 5.8 page 93 Gases and small non-polar molecules can easily diffuse across the membrane Larger molecules like glucose and amino acids need protein assistance ACTIVE TRANSPORT Movement of molecules or ions across the membrane AGAINST their concentration gradient CHEMICAL ENERGY or ATP is required for active transport Carrier proteins are needed for active transport Proteins that assist in the active transport of molecules across the membrane are called ‘PUMPS’ The most studied PUMP is the ‘SODIUM-POTASSIUM PUMP’ + Na K+ Moves Moves Outside Inside Cell Cell IMPORTANCE OF Na+ - K+ PUMP -Essential in maintaining the electrochemical gradient across the cell membrane. -The electrochemical gradient generated by transporting Sodium OUT and Potassium IN is used in secondary active transport -Maintanence of osmotic balance, and most importantly -Action potential generation and propagation in muscle and nerve cells/ Cell signalling. http://wiki.answers.com/Q/Why_is_a_sodium_potassium_pump_important_in_organisims#ixzz1FwvJ9yD6 Fig. 5.10 page 95 BULK TRANSPORT- TRANSPORT OF LARGE MACROMOLECULES Very specific form of pinocytosis Vitamins, peptide hormones and lipoproteins can bind to the receptors Ex. Cholesterol is taken into the cell by a coated pit THE EXTRACELLULAR MATRIX (ECM) AND CELL JUNCTIONS Provides protection Collagen and Elastin -Proteins in the ECM -Provide structure Integrin - Protein connected to fibronectin - Plays a role in cell signaling - Influences shape and activities of the cell ANIMAL CELL JUNCTIONS HOW ARE CELLS CONNECTED TO EACH OTHER?? Tight Junction Membrane proteins attach to each other Desmosome Cells joined by Intracellular filaments Gap Junction Occurs when identical plasma membrane proteins join together HOW DO PLANT CELLS COMMUNICATE? Plasmodesmata- narrow, membrane-lined Channels that pass through the cell wall. http://www.mcb.uct.ac.za/tutorial/virusentplant.htm VIRUSES VIRUSES Viruses are found in plants, animals and bacteria and are Associated with diseases in all 3. Viruses have an RNA or DNA genome, but THEY ONLY REPRODUCE BY USING THE METABOLIC MACHINERY OF A HOST CELL Viruses cannot reproduce on their own Viruses are noncellular Virus= poison, (Latin root) Family= Viridae Subfamily= Virinae Suffix= Virus Species hard to classify due to high mutation rates LOUIS PASTEUR (1822-1895) French Chemist Believed something smaller than a bacteria was the cause of rabies First coined the term, “virus” DIMITRI IVANOWSKY (1864-1920) Russian Microbiologist Studied viral diseases in tobacco leaves Filtered infected extract of tobacco leaves through a porcelain filter that retains bacteria leaves still got disease something smaller than bacteria was causing disease 1950’s - ELECTRON MICROSCOPY Uses a particle beam of electrons to magnify specimens. Avian flu virus, shown in this scanning electron microscope image from 3DScience.com VIRAL STRUCTURES VIRAL STRUCTURE Size- 10-400 nm. About the size of a large protein Genome- 3-100 genes Envelope - Covers capsid (not all viruses have an envelope, viruses w/o are “naked - Is usually a piece of the host cell’s plasma membrane, contains viral glycoprotein spikes Outer Capsid- Composed of protein subunits Inner Core- Contains nucleic acid, either DNA or RNA - Contains Various proteins (ENZYMES) Bacteriophage HIV Human Papillomavirus Non-enveloped DNA Virus Double stranded circular DNA Infects skin and mucosal tissue Some forms of HPV are cancer causing or cause genital warts and are sexually Transmitted Other forms cause warts on the skin Ex. Plantar warts Only known host for HPV is human TYPES OF VIRUSES Enteric Viruses -Viruses that infect the GI tract Respiratory Viruses -Viruses that infect the respiratory system -Obtained by inhalation ex. Orthomyxoviridae (influenza) Arboviruses -Viruses from insects -Arthropod-born (mosquitos, flies etc. ex. Bunyaviridae Oncogenic Viruses -Cell transforming viruses -Target specific tissues -some are zoonotic (from animals) ex. Herpesviridae, papoviviridae FAMILIES OF VIRUSES Herpesviridae- dsDNA, lytic cycle, replicates in Nucleus Ex. Chickenpox, shingles, cytomegalovirus, Epstein Barr Virus and Herpes Simplex 1&2 Retroviridae- ssRNA, integrates into host genome in nucl., Has own reverse transcriptase gene, Ex. HIV Papovaviridae- dsDNA, ex. HPV Adenoviridae- dsDNA, lytic, human and horse hosts Paramyxidae- ssRNA, replicates in cytoplasm, nonLytic/budding ex. MUMPS and MEASLES Orthomyxoviridae- ssRNA, replicates in nucleus and Cytoplasm, non-lytic/budding ex. INFLUENZA Rhabdoviridae- ssRNA, replicates in cytoplasm, Lytic and buds from membrane. Ex. Rabies Bunyaviridae- ssRNA, replicates in cytoplasm, nonLytic ex. Hantavirus (rift valley fever) Arenaviviridae- ssRNA, replicates in cytoplasm, nonLytic ex. Lassa Virus (West African fever) Parvovaviridae- ssDNA, replicates in nucleus, ex. B-19 virus=Human hemolytic anemia Poxvirdidae- dsDNA, replicates in cytoplasm, Budding and lytic ex. Smallpox, monkeypox Example of how Zoonotic Viruses are transferred to Humans Fig. 20A page 360 in your text VIRUSES ARE PARASITIC Viruses are ‘OBLIGATE INTRACELLULAR PARASITES’ *They can NOT reproduce outside of a living cell A virus canNOT duplicate its own genetic material A virus must infect a living cell to reproduce When the infected cell duplicates, the viral genetic material is also duplicated Viruses are HOST SPECIFIC – They infect many kinds of cells, but certain viruses only infect certain kinds of cells! Ex. Bacteriophages only infect Bacteria Rabdinoviridae (Rabies Virus) only infects mammals Human Immunodeficiency Virus (HIV) only enters certain blood cells Scientists can study viral behavior and infection in the laboratory by: - Using live chicken eggs- inoculating eggs with live viral particles - Infecting ‘CELL LINES’ (ex. From the ATCC-American Type Culture Collection) VIRUSES ARE CONSTANTLY MUTATING Viral reproduction is highly imperfect Many ‘mistakes’ are reproduced leading to mutation The mutation rates in eukaryotes and in bacteria are Around 1 mutation per 100,000,000 base pairs or 10-8 per generation The mutation rate in DNA viruses is approx. 1/1,000,000 (10-6) to 1/100,000,000 (10-8) The mutation rate in RNA viruses is approx. 1/1,000 (10-3) to 1/100,000 (10-5) BREAKOUT SESSION #1 Every year, the Influenza or Seasonal Flu virus infects thousands of people Of the thousands of people who get the flu, an average of 36,000 people actually die from flu associated symptoms!! Although we are vaccinated every year, some people still get the flu. WHY DO PEOPLE STILL GET THE FLU AND WHY MUST WE GET VACCINATED EVERY YEAR?? VIRAL REPRODUCTION- Bacteriophages Bacteriophages or phages- VIRUSES THAT PARASITIZE BACTERIA Bacteriophages have two life cycles 1) Lysogenic 2) Lytic STEP 1 Bacteriophage attaches to a Bacterial cell, ex. E. coli The bacteriophage injects Its DNA into the bacterial cell Fig. 20.3 VIRAL REPRODUCTION- Bacteriophages Prophages can be toxic ex. Scarlet Fever VIRAL REPRODUCTION- Animal Viruses 1- Attachment and fusion of virus to animal host cell or Viruses taken in by endocytosis 2- Virus is uncoated-capsid and envelope removed 3- The viral genome is released and biosynthesis/duplication of genome occurs 4- Newly synthesized viruses are released via budding or lysis of the cell 3. 1. 4. 2. This is a non-lytic Budding virus example The viral genetic material is Duplicated in the cytoplasm Fig. 20.4 page 361 Ex. of Retrovirus Replication (ex. HIV) 1. Attachment 2. Entry 3. Virus uses its own Reverse Transcriptase to create copy DNA from ssRNA 4. ss Copy DNA (cDNA) become ds cDNA and is incorporated into the host’s DNA 5. The host cell replicates its DNA AND THE VIRAL DNA!!! 6. The viral DNA is transcribed from the host DNA 7. The new viral DNA is re-packaged and the virus is released from the cell VIROIDS AND PRIONS Viroids- Naked strands of RNA not covered by a capsid VIRUS VIROID Prions- Proteinaceous Infectious Particles (a misshapen protein) Causes TSEs (transmissible Spongiform encephalopathies) Disease found in tribal members who practice cannibalism (eat brain of deceased) in small Tribe in Papua New Guinea Viroids infect crops, ex. Potatoes, Coconuts, Citruses Misshapen prion interacts with normal protein causing change in shape STILL UNDER INVESTIGATION EXAM REVIEW Chpt 3 (pages 37-58)-Macromolecules Chpt 6 (pages 104-105top, 106,108-112) Chpt 18 (pg320-327)- Cell Evolution and multicellularity Chpt 20 (all)- Viruses, Bacteria and Archaea Chpt 4 (all)- The Eukaryotic Cell Chpt 5 (all)- Membranes and Transport EXAM REVIEW