exam ii
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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. - PowerPoint PPT PresentationTRANSCRIPT
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
Active Site of the Enzyme
A slight change at theactive site allowsfor the attachment ofthe substrate
I. II. III.
WEEK 5 Continued
Adenosine Triphosphate (ATP)
ATP is a nucleotide
The base of the nucleotide is adenineThe sugar of the nucleotide is riboseTri 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 ETCMitochondria 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 ArchaeaChpt 4 (pg68-84)- The Eukaryotic CellChpt 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 cells2- Cells are the basic units of structure and
function in organisms3- 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
Fig. 4.3
SURFACE AREA TO VOLUME RATIOS
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
CELLULAR EVOLUTIONChpt. 18
4.6 BYA
Abiotic Synthesis createdSmall organic molecules (ex. Amino acids, nucleotides)
Monomers joined to formPolymers (proteins, RNA)
Plasma membrane formsPolymers aggregate withinthe plasma membrane= protocell
Protocell containing DNAGenes true cell
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 cellEngulfed these free living aerobic bacteria which later Became organelles or ‘MITOCHONDRIA’
Chpt. 18, page 325
Heterotrophs cannot produceOwn food and practiceSexual reproduction
The eukarya arose from ARCHAEAHeterotrophic protists arose when eukaryotic cells engulfedaerobic bacteria
THE EUKARYOTIC CELL
http://www.wisconline.com/Objects/ViewObject.aspx?ID=AP11403
ANIMAL CELLS HAVE A PLASMA MEMBRANE
http://library.thinkquest.org/12413/structures.html
THE NUCLEUS
Chromosomes
Condensed Chromatin
Contains genetic information/Genes
Composed of DNA
Set number per species (humansHave 23 pairs or 46 Chromosomes)
Nuclear Envelope
Surrounds Nucleus
Composed of two layers
Has nuclear pores to permitThe passage of ribosomalSubunits and mRNA out of thenucleus
Nucleolus
Contains ribosomalRNA whichaids in production ofprotein
http://library.thinkquest.org/12413/structures.html
THE CYTOPLASM
CentriolesInvolved inCell division
Chloroplasts(Plants ONLY)Contains GreenChlorophyll wherePhotosynthesis occurs
CytoskeletonComposed of micro-tubulesSupports cell and Gives shape
Golgi ApparatusPackages ProteinNear NucleusCell division
LysosomeDigests ProteinsLipids, CarbsTransports wasteto cell membraneMade by Golgi
MitochondriaProduces ATPHas 2 membranesFolds are cristae
EndoplasmicReticulumFused to NuclearMembrane2 types-SmoothRoughProduces protein
VacuolesStore, digest andRemoves cellWastePlants have aLarge CentralVacuole
RibosomesParticles whereprotein synthesisOccursComposed of 2Subunits (largeand small)CHAPT 4
THE CYTOSKELETON
Now called ACTIN filaments=Actin monomers, twisted in a helical manner
Intracellular proteinMatrix
Ropelike fibrous polypeptides 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 BYAExtremely diverse in structure and metabolic capabilities
Some prokaryotes move with the use of ‘FLAGELLA’ Flagella= strands of flagellin protein wound in a helixMany prokaryotes adhere to cells with the use of ‘FIMBRIAE’Fimbriae = short bristlelike fibers on the surface
Prokaryotes DO NOT HAVE A NUCLEUSProkaryotes have a dense area called a NUCLEOID where a Single chromosome of circular DNA existsSome 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 CONJUGATION- when two bacteria are temporarily linked together, genetic information is passed from one to the other = Transduction Pg. 364 in text
BACTERIA ARCHAEAFound practically in every environment on earth
Protected by a cell wall that contains PEPTIDOGLYCAN-polysaccharides linkedby amino acids
Bacteria are classifed by whether they are:1-Gram +, thick layer of peptidoglycan2-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 thePresence of O2
2- Facultative anaerobes- able to grow in thePresence or absense of O2
Bacteria and Arachaea can be:1- Photoautrotrophs 3- Chemoheterotrophs2- Chemoautotrophs
Became a distinct domain in 1977 becauseribosomal RNA of Archaea differs from Bacteria
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- halo-philes, 3- thermoacidophiles
Methanogens- Methane makersHalophiles- need high salt concentration togrow, ex. The Dead SeaThermoacidophiles- 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 IIAnd 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 FUNCTIONFig. 5.1Chpt 5 pg 86Plasma Membrane ofan Animal Cell
-Proteins inserted into plasma membraneare INTEGRAL proteins
-PERIPHERAL proteinsare on the cytoplasmicside of the membrane
The membrane is ‘fluid’Current model to describe fluidity=Fluid-Mosaic ModelCells must be fluid andpliable, rigidity can be caused by cholesterol
Glycoprotein- a phsopholipid with a carbo-hydrate or sugar chain attachedProtects 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)GlycerolAlcohol(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
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
PASSIVE TRANSPORT
Fig. 5.5 page 91
OSMOSISDiffusion 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 differencesof 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 equalNo gain or loss of water
HYPOTONIC SOLUTION
Solutions that cause cells to swell and burstThe 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 waterThe net movement of water out of the cell
Equal solute insideand out
More Solute outsidecell Shrivels as water moves out to dilute solute
More Solute insidecell swells as water moves in to dilute solute
Fig. 5.8 page 93
Gases and small non-polar molecules can easily diffuse across the membraneLarger molecules like glucose and amino acids need protein assistance
ACTIVE TRANSPORT
Movement of molecules or ions across the membrane AGAINST their concentrationgradient
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 arecalled ‘PUMPS’
The most studied PUMP is the ‘SODIUM-POTASSIUM PUMP’
Na+
Moves Outside
Cell
K+
Moves
Inside
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 pinocytosisVitamins, peptide hormones and lipoproteins can bind to the receptorsEx. 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 JUNCTIONSHOW ARE CELLS CONNECTEDTO EACH OTHER??
Tight JunctionMembrane proteins attachto each other
DesmosomeCells joined by Intracellularfilaments
Gap JunctionOccurs when identical plasmamembrane proteins jointogether
HOW DO PLANT CELLS COMMUNICATE?
http://www.mcb.uct.ac.za/tutorial/virusentplant.htm
Plasmodesmata- narrow, membrane-linedChannels that pass through the cell wall.
VIRUSES
VIRUSESViruses 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 ownViruses are noncellular
Virus= poison, (Latin root)
Family= ViridaeSubfamily= VirinaeSuffix= Virus Species hard to classify due to high mutation rates
LOUIS PASTEUR (1822-1895)
French Chemist
Believed something smaller thana 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 tobaccoleaves through a porcelain filter thatretains bacteria leaves still gotdisease something smaller thanbacteria 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 STRUCTURESize- 10-400 nm. About the size of a large proteinGenome- 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)
HIVBacteriophage
Human Papillomavirus Non-enveloped DNA Virus
Double stranded circular DNA
Infects skin and mucosal tissue
Some forms of HPV are cancer causingor cause genital warts and are sexuallyTransmitted
Other forms cause warts on the skinEx. Plantar warts
Only known host for HPV is human
TYPES OF VIRUSESEnteric 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
Herpesviridae- dsDNA, lytic cycle, replicates inNucleus Ex. Chickenpox, shingles, cytomegalovirus,Epstein Barr Virus and Herpes Simplex 1&2Retroviridae- ssRNA, integrates into host genome in nucl.,Has own reverse transcriptase gene, Ex. HIVPapovaviridae- dsDNA, ex. HPVAdenoviridae- dsDNA, lytic, human and horse hostsParamyxidae- ssRNA, replicates in cytoplasm, non-Lytic/budding ex. MUMPS and MEASLESOrthomyxoviridae- ssRNA, replicates in nucleus andCytoplasm, non-lytic/budding ex. INFLUENZARhabdoviridae- ssRNA, replicates in cytoplasm, Lytic and buds from membrane. Ex. RabiesBunyaviridae- ssRNA, replicates in cytoplasm, non-Lytic ex. Hantavirus (rift valley fever)Arenaviviridae- ssRNA, replicates in cytoplasm, non-Lytic ex. Lassa Virus (West African fever)Parvovaviridae- ssDNA, replicates in nucleus, ex.B-19 virus=Human hemolytic anemiaPoxvirdidae- dsDNA, replicates in cytoplasm, Budding and lytic ex. Smallpox, monkeypox
FAMILIES OF VIRUSES
Fig. 20A page 360 in your text
Example of how Zoonotic Viruses are transferred to Humans
VIRUSES ARE PARASITIC
Viruses are ‘OBLIGATE INTRACELLULAR PARASITES’
*They can NOT reproduce outside of a living cellA virus canNOT duplicate its own genetic materialA 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 imperfectMany ‘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 pergeneration
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 actuallydie 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 EVERYYEAR??
VIRAL REPRODUCTION- BacteriophagesBacteriophages or phages- VIRUSES THAT PARASITIZE BACTERIABacteriophages have two life cycles 1) Lysogenic 2) Lytic
STEP 1Bacteriophage attaches to aBacterial cell, ex. E. coli
The bacteriophage injectsIts DNA into the bacterialcell
VIRAL REPRODUCTION- Bacteriophages
Prophages can be toxic ex. Scarlet Fever
Fig. 20.3
VIRAL REPRODUCTION- Animal Viruses1- Attachment and fusion of virus to animal host cell or Viruses taken in by endocytosis2- Virus is uncoated-capsid and envelope removed3- The viral genome is released and biosynthesis/duplication of genome occurs4- Newly synthesized viruses are released via budding or lysis of the cell
1.
2.
3.
4.
This is a non-lyticBudding virus exampleThe viral genetic material isDuplicated 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
Viroids infect crops, ex. Potatoes,Coconuts, Citruses
Prions- Proteinaceous InfectiousParticles (a misshapen protein) Causes TSEs (transmissible Spongiform encephalopathies)
Disease found in tribal memberswho practice cannibalism (eatbrain of deceased) in smallTribe in Papua New Guinea
Misshapen prion interacts withnormal protein causing changein shapeSTILL UNDER INVESTIGATION
EXAM REVIEW
Chpt 3 (pages 37-58)-MacromoleculesChpt 6 (pages 104-105top, 106,108-112)Chpt 18 (pg320-327)- Cell Evolution and
multicellularityChpt 20 (all)- Viruses, Bacteria and ArchaeaChpt 4 (all)- The Eukaryotic CellChpt 5 (all)- Membranes and Transport
EXAM REVIEW