EXAM II

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