LEC EXAM 2 REVIEW

• Last Common Ancestor

  • there is evidence that supports the claim that all eukaryotes come from one common answer, as they all have similar genetic makeup

• Cillia and Flagella

  • eukaryotic flagella ia different from bacterial flagella - 10x thicker

  • eukaryotic flagella are similar to flagella in structure but are smaller and more numerous, found only in a single group of protozoa and certain animal cells

• Glycocalyx

  • A waxy protective coating made up of polysaccharides

  • contributes to protection, adherence, and signal reception

  • appear as

    • a network of fibers

    • a slime layer

    • a capsule

• Phospholipid bilayer

  • a bilayer that has polar heads and fatty acid tails

• Structures and functions of cell

  • Nucleus

    • most prominent organelle

    • separated by a nuclear envelope

    • has a lipid bilayer with small pores for macromolecules to enter/exit

  • E.R.

    • for transport and storage

    • rough - transports materials from nucleus to GA via transitional vesicles

      • has ribosomes 

    • smooth - synthesized non protein nutrients like lipids

      • does not have ribosomes

  • Golgi Apparatus

    • responsible for transport and modifying material from ER to cell wall/membrane via condensing vescles

  • EXPLAIN Nature’s Assembly Line 

  • Mitochondria

    • produce ATP/energy for the cell

    • extracts chemical energy contained in nutrient molecules and stores it as ATP

  • Chloroplasts

    • found in algae and plant cells

    • capable for converting energy from sunlight into chemical energy via photosynthesis

  • Ribosome (80s)

    • made up of subunits 40s and 60s

  • Cytoskeleton – functions

    • holds organelles in place and also helps move RNA and vesicles 

    • permits shape and movement

  • EXPLAIN endosymbiosis

    • big ate little, big cant live without little, work together

• Fungi

  • Yeast vs. Hyphae

    • Yeats - round/oval shape, asexual, budding, soft uniform texture and appearance

    • Hyphae - breadmold, long/threadlike cells found in bodies of filamentous fungi, cottony/hairy velvety texture

  • Nutrition

    • Heterotropic

      • acquire nutrients from a wide variety of organic substrates

    • Saprobic

      • acquire nutrients from dead plants and animals in soil or aquatic habitats

    • Parasitic

      • grow on bodies of living animals or plants, few require a living host

      • penetrate substrate and secrete enzymes that reduces it to small molecules that can be absorbed by the cells

      • often found nutritionally poor or adverse environments, with high salt or sugar content

  • Morphology

  • Asexual mold spores

    • Sporangiospores - cleavages with a saclike head (sporangium) and a stalk (sporangiophore)

    • Conidiospores/Condia - free spores (no sac)

• Protozoa

  • Nutrition

  • Life Cycles – EXPLAIN when active and dormant

    • Trophozoite - active/feeding stage -> drying due to lack of nutrients-> cells round up, loses motility (early cyst wall formation) -> mature cyst (dormant, resting stage) -> moisture and nutrients restored -> cyst wall breaks open -> trophozoite reactivated

  • Recognize the ones from lab 

• Helminths

  • Flatworm vs. Roundworm

    • Flatworm - thin, segmented body (tapeworms or flukes)

    • Roundworms - aka nematodes, elongated, cylidnrical, unsegmented body

  • Morphology

    • reproductive tract is the most developed organ

  • Life Cycles

    • Egg->intermediate (larvae)->definitive(adult)->transport

    • EXPLAIN Pinworm lifecycle

Chapter 5

• Filterable Virus

  • early researchers found that when putting a pathogenic solution through a porcelain filter (to ger rid of bacterial pathogens) the solution was still pathogenic, resulting in a pathogen smaller than bacteria

• Active and Inactive

  • a viral debate on whether viruses are alive or not

  • they are able to reproduce and decide when they want to do these stages, but do not have all the machinery to live independently

• Properties of Viruses

  • parasitic to all cells

  • 10^31 viral particles (more than 10x the number or archaea and bacteria combined)

  • are ubiquitous to nature

  • basic structure (capsid and nucleic core)

  • have special appendages to attach to host

  • take over hosts genetic material and regulate synthesis to assemble new viruses

  • lack enzymes for most metabolic processes

  • lack machinery for synthesizing proteins 

• Classified and named

• Virus size

  • 10x smaller than bacteria

• Components

  • capsid - protein shell that protects nucleic acid

    • most prominent feature of virus

    • nucleocapsid (only on naked viruses)

  • envelope - external covering over capsid (part of host cell membrane to go undetected)

  • spikes - project from the nucleocapsid or the envelope that allow viruses to dock with host cells 

  • viron - a fully formed virus that us able to establish an infection in a host cell

• Capsid

  • Helical

    • rod-shaped capsomers that bond together to form a series of hollow discs resembling a bracelet

    • discs link with other discs to form a continuous helix into which the nucleic acid strand is coiled

  • Icosahedral

    • 3D 20 sided figure with 12 evenly spaced icosahedrons

    • structure vary from virus to virus

    • can construct from one or more capsomeres

  • Complex

    • only found in viruses that infect bacteria

    • may have multiple types of proteins

    • not symmetrical or enveloped

• Viral envelope

  • uses parts of cell membrane to disguise self 

  • more flexible than capsid (pleomorphic)

  • can bud from

    • cell membrane

    • nuclear envelope

    • endoplasmic reticulum

• Nucleic Acids

  • RNA or DNA not both

  • Variety

  • Examples of DSDNA, SSDNA, SS-Sense, SS-sense, SSRNA+reverse transcriptase

    • Positive sense RNA - can be translated

    • Negative sense RNA - needs to be converted before translation

    • segmented - individual genes that can exist on separate pieces of RNA

    • retrovirus - carry own enzymes to create DNA out of their RNA, borrow the host tRNA molecules

  • Enzymes

    • polymerase - synthesize DNA to RNA

    • replicase - copy RNA

    • perverse transcriptase - synthesizes DNA from RNA (used bc majority of viruses do not have enough genes for synthesis of metabolic enzymes)

    • arenavirus - pack along host ribosomes

  • Adsorption

    • virus invades host cell by fitting into specific molecules of host

    • if cells lack compatible virus receptors, cells are resistant to invasion of that virus

  • Penetration

    • virus penetrate host cell through cell membrane 

    • direct fusion of viral envelope and host cell membrane

  • Uncoating

    • explained above

  • Synthesis

    • DNA VIruses - enter host cells nucleus and are replicated and assembled there

    • RNA viruses - replicated and assembled into cytoplasm

    • Retroviruses - turn their RNA genomes into DNA

  • Assembly

    • viruses is put together using “parts” manufactured during synthesis process

  • Release

    • number of viruses released by infected cells controlled by size of virus, health of host cell (if viruses are big, break cell, if cell is weak, virus can break open easier)

• Damage to the host cell

  • CPEs

    • virus induced damage to cell that alters is macroscopic appearance

      • gross changes in shape and size

      • development of intracellular changes

      • inclusion bodies - compacted masses of viruses or damaged cell organelles in the nucleus and cytoplasm

      • syncytia - fusion of multiple damaged host cells into single large cells containing multiple nuclei (giant cells)

  • Persistent infections

    • cells maintaining carrier relationship: cell harbors virus while still being alive

    • can last a few weeks till remainder of host life

    • can remain latent in cytoplasm

    • provirus - viral DNA incorporated in DNA of host (measles)

    • chronic latent state - periodically become activated under influence of various stimuli (herpes simplex and herpes zoster)

  • Oncogenic

    • cancer causing viruses

    • Transformation - effect of oncogenic viruses

    • either by viruses that cary genes that directly cause cancer or they produce proteins that induce a loss of growth regulation, leading to cancer

      • increase rate of growth

      • change in chromosomes

      • change in cells surface molecule

      • capacity to divide indefinitely 

    • papillomaviruses, herpes virus, Hep B, HTLV-1

• Bacteriophage

  • bacterial eating virus

  • mainly DS DNA but some RNA exist

  • specific to a specific bacteria 

  • often more pathogenic for humans

  • Be able to explain, compare and contrast the Lytic and Lysogenic cycles!

    • Lytic

      • phage attaches to host cell and infects cell with DNA

      • DNA from the phage replicates and naked proteins

      • New phage particles are created and released from cell

    • Lysogenic

      • Phage infects cell and becomes integrated into host DNA

      • cell divides along with mix of DNA (from phage and original cell)

      • DNA from the phage replicates and paled proteins 

      • new phage particles are created and released from cell

• Cultivating techniques

  • In vivo and in vitro

    • in vivo - laboratory bred animals and embryotic tissues

    • in vitro - cell/tissue culture methods

• Prions, satellite virus

  • Prions

    • composed primarily of proteins (no nucleic acid)

    • exact more of infection is still being investigated

    • deposited as long protein fibrils in the brain tissue of humans and animals

• Viruses and Human Health

  • Common causes of acute infections - colds, hepatitis, chickenpox, influenza, herpes, warts

  • prominent viral infections worldwide - dengue fever, rift valley fever, yellow fever

  • infections with high mortality rates - rabies, AIDS, ebola

  • connections to chronic infections - type 1 diabetes, MS< various cancers, alzheimers, obesity

• Explain why antibiotics have no effect on viruses

  • antibiotics have no effect on viruses (just bacterial infections)

  • drugs damage both host cells and host cells 

  • viruses disguise themselves using host cell membrane 

  • easier to develop vaccines than to treat viral diseases

Chapter 6

• Essential nutrients, micronutrients and macronutrients

  • Essential nutrients - any substance that must be provided to an organism

  • Macronutrient - required in relatively large quantities and play principal roles in cell structure and metabolism (C,H,O)

  • micronutrient aka trace elements - present in much smaller amount are involved in enzyme function and maintenance of protein structure (Mg, Zn, Ni)

• Difference between organic and inorganic

  • organic as C and H

  • inorganic has the other stuff??

• Chemical composition of cytoplasm

• What microbes eat (slides 11-12)

  • heterotroph - an organism that must obtain its carbon in an organic form

    • Chemoheterotrophs - derive both carbon and energy from organic compounds, process these molecules through cell respiration or fermentation

    • saprobes - free-living organisms that feed on organic detritus from dead organisms, decomposers, recycle organic nutrients

    • parasites - derive nutrients from the cells or tissues of a living hosts, range from viruses to helminths

      • pathogens - cause damage to tissues or even death

      • ectoparasites - live on the body

      • endoparasites - live in the organs and tissues

      • intracellular parasites - live within cells 

      • obligate parasites - unable to grow outside of a living host

  • autotroph - an organism that uses inorganic CO2 as its carbon source

    • can convert CO2 into organic compounds

    • not nutritionally dependent on other living things

    • photoautotroph - uses CO2 that can be used by themselves and by heterotrophs

    • chemoautotrophs

      • chemoorganic autotrophs - use organic compounds for energy and inorganic compounds as a carbon source

      • lithoautotroph - rely totally on inorganic minerals and require neither sunlight or organic nutrients

  • phototroph - microbe that photosynthesizes

  • chemotroph - microbe that gets its energy from chemical compounds

• Energy sources (slide 13-15)

• CHONPS 

  • What element they are

    • Carbon: Makes up all you macromolecules (building blocks) of life - proteins, carbohydrates, lips and nucleic acids

    • Hydrogen: Important for hydrogen bonds, source of free energy in cell respiration (NAD --> NADH) , maintains pH

    • Oxygen: Major component in all macromolecules! structural and enzymatic function. Aerobic cell respiration stops without it!

    • Nitrogen: Major component in Proteins, DNA, RNA, and ATP.  synthesizes amino acids, amphibolism

    • Phosphate: ATP (cellular energy transfers)!!! Nucleic Acid backbone (essential for genetics)

    • Sulfur: Disulfide Bonds (protein structure and shape), essential component to some vitamins 

  • Key role in a cell

  • Other nutrients (K, Na, Ca, Mg, Fe and Zn) – why they are helpful

    • potassium (K) - essential to protein synthesis and membrane function

    • sodium (Na) - important for certain types of cell transport

    • calcium (Ca) - stabilizer of cell wall and endospores of bacteria

    • Magnesium (Mg) - component of chlorophyll and stabilizer of membranes and ribosomes

    • Iron (Fe) - important component of cytochrome proteins of cell respiration

    • Zinc (Zn) - essential regulatory element for eukaryotic genetics

• Diffusion, Osmosis, Facilitated diffusion and Active transport

  • diffusion - atoms or molecules that move in a gradient from an area of higher concentration to an area of lower concentration

    • facilitated diffusion - use of a protein channel to bring in larger molecules

    • active transport - use energy, go from low to high concentration

  • osmosis - diffusion of water through a selectively permeable membrane

• Endocytosis slide

  • cell encloses the substance in its membrane

  • simultaneously forms a vacuole and engulfs the substance

• Min, Max and Optimal temperature

  • minimum temp - lowest temp that permits a microbes continued growth and metabolism

  • maximum temp - highest temp at which growth and metabolism can proceed before proteins are denatured

  • optimum temp - an intermediate between the min and max that promotes the fastest rate of growth and metabolism

• Oxygen usage slides 

  • aerobes

  • Aerobes: need oxygen to live - think most fungi, protozoa and bacteria

  • Microaerophiles: need small amounts of oxygen (but full amounts will harm it)  - think soil microbes 

  • Facultative microbes: don't care about oxygen (could take it or leave it) - think some gram -negative intestinal bacteria

  • Anaerobes: die in the presence of oxygen (don't have the enzyme to break down oxygen) -  think most other intestinal bacteria

  • Aerotolerant anaerobes: don't need oxygen but wont die if exposed to small amounts of oxygen - think streptococci bacteria

• pH

  • you know pH

• halophiles

  • prefer high concentrations of salt

• Symbiosis

  • Mutualism - organisms that live in obligatory mut mutually beneficial relationship

  • Parasitism - a relationship in which the host organism provides the parasitic microbe with nutrients and a habitat, host suffers from the relationship

  • Commensalism - the partner called the commensal received benefits while its partner is neither harmed nor benefited

• Binary Fission slide! 

  • one cell becomes two

  • parent cell enlarges

  • duplicated its chromosomes

  • starts to pull its cell envelope together to the center of the cell

  • cell wall eventually forms a complete septum

• Growth Curve (slides 8-14)

  • a predictable pattern of bacterial population growth in a closed system

  • lag phase - flat

    • newly inoculated cells that require a period of adjustment, enlargement, and synthesis

    • pop of cells are so sparse or dilute that sampling misses them

  • exponential growth phase - growth curve increases geometrically

    • will continue as long as cells have adequate nutrients and the environment is favorable

  • stationary growth phase - flat

    • cell birth and death rates are equal

    • cell division rates slow down

    • caused by depleted nutrients and oxygen

  • death phase - decline (slower than growth phase)

    • cells begin to die at an exponential rate due to the buildup of wastes

    • speed at which death occurring depends on the resistance of the species and how toxic the conditions are 

• Turbidity

  • greater turbidity, larger pop size of microbes

Chapter 7

• Metabolism slide

  • Metabolism - pertains to all chemical reactions and physical working of the cell

  • Anabolism 

    • any process that results in synthesis of cell molecule sand structures

    • a building and bond-making process that forms larger macromolecules from smaller ones

    • requires the input of energy

  • Catabolism - breaks the bonds of larger molecules into smaller molecules, releases energy

• Enzymes and how they work

  • serve as physical site upon which substrate can be positioned for various reactions

  • larger in size than the substrate

  • presents a unique active site that matched only that particular substrate

  • binds to substrate

  • participates directly in changes to the substrate

  • does not become part of the products

  • not used up by the reaction

  • can function over and over again

  • Structure

    • holoenzyme - a combination of protein and one or more cofactor

    • apoenzyme - protein portion of a holoenzyme

    • cofactors - either organic molecules called coenzymes or inorganic elements (metal ions)

  • Enzyme substrate reaction

    • answered above

  • Naming

    • classified and named according to characteristics such as site of action, type of action, and substrate

    • end in -ase

  • Regulation of Enzyme action

    • changes in normal conditions can cause enzymes to be unstable, distort or become denatured which prevent substrate from attaching to the active site

      • temp, pH, osmotic pressure

  • Explain the difference between Competitive and Non competitive inhibition

    • competitive - multiple substrates compete for active site of enzyme, only the correct substrate produces a product, or reaction is blocked

    • noncompetitive - substrate binds to active site and produced a product, if reaction is blocked due to regulatory molecule, active site changes shape, and no reaction occurs 

  • E. coli  enzyme induction

    • if a particular strain if E. coli is inoculated into a medium whos principal carbon source is lactose it will begin to produce the enzyme lactase to hydrolyse the disaccharide into its component parts, glucose and galactose

    • if the bacterium is subsequently inoculated into a medium containing only sucrose, as a carbon source, it will cease synthesizing lactase and begin synthesizing sucrase

    • this response enabled the organism to utilise a variety of nutrients and it also prevents a microbe from wasting energy making enzymes for substrates that are not present

  • Metabolic pathways

    • linear, cyclic, divergent, convergent

• Energy (see my notes posted in the module)

  • Redox reactions

    • OIL RIG

    • oxidation is lost

    • reduction is gained

  • Phosphorylation

    • oh its just ADP + P -> ATP

  • ATP

  • Aerobic, Anerobic and Fermentation

    • Glycolysis, Oxidative phosphorylation, Krebs Cycle, ETC

    • Where is happens

    • Input and outputs

    • ATP created

• Amphibolism - the ability of a system to integrate catabolic and anabolic pathways to improve cell efficiency

Why only 2 NET ATP in Glycolysis

Although you yield 4 ATP (2 per pyruvate), it takes energy to break you 6 carbon molecule, so the net yield is only 2ATP once that stage is complete. Use 2 and have 2 remaining.