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UA / Biology / BSC 242 / How are specific genus and species names properly formatted?

How are specific genus and species names properly formatted?

How are specific genus and species names properly formatted?

Description

School: University of Alabama - Tuscaloosa
Department: Biology
Course: Microbiology and Man
Professor: Daryl lam
Term: Winter 2016
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Cost: 50
Name: Exam 1 study guide
Description: ch 1-5 study guide
Uploaded: 02/02/2016
19 Pages 67 Views 3 Unlocks
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Study Guide exam 1 2/2/16 11:57 AM


How are specific genus and species names properly formatted?



Ch1

• Facts to know

o Microbial individuals are too small to be seen with the naked  eye

• Linnaeus system

o How to correctly “format” scientific genus and species names ???? Italicized or underlined 

???? Genus is capitalized

???? Specific epithet is lower case

???? Ex: Escherichia coli

• Viruses vs Cellular organisms  

o Viruses

???? Acellular

???? Consist of DNA or RNA care

✂ Surrounded by protein coat


What does pasteur's experiment demonstrate?



• Maybe be enclosed in lipid envelope

???? Only replicated when they are in living host cell

• 3 Domain system of classification (for cellular organisms)

o bacteria

o archaea

o eukarya We also discuss several other topics like Which war is the bloodiest war in american history?

• Cell theory

o All living things are composed of cells and come from  

preexisting cells

o “biogenesis” living organisms arise from preexisting life

• Spontaneous generation

o Living organisms arise from nonliving matter

• Pasteur’s experiment

o Demonstrated:  


What refers to the study of fungi?



???? microorganisms are present in air and can contaminate  

sterile solutions

???? heat can kill microorganisms

o experiment

???? Nutrient broth placed in S-shaped flask, heated,  

✂ not sealed

• Microbial growth

✂ Sealed

• No microbial growth

o Aseptic (sterile) technique/ Contamination

???? Heat kills microorganisms Don't forget about the age old question of What are some examples of applied anthropology?

???? Used to prevent contamination by unwanted microbes • Fermentation

o Conversion of sugar to alcohol to make beer and wine • Pasteurization

o Application of a high heat for a short time

• Vaccine

o The protection is called immunity

o Agent or virus is given to patient to build antibodies,  Don't forget about the age old question of What do occupational and relational roles pertain to?

immunities to fight that virus as well as the original virus ???? Inoculating person with cowpox virus, person is then  

protected from smallpox

• Antibiotic  

o Chemicals produced by bacteria and fungi that inhibit or kill  other microbes

• Define If you want to learn more check out What are examples of abiotic organisms?

o Bacteriology

???? Study of bacteria

o Mycology

???? Study of fungi

o Parasitology

???? Study of protozoa and parasitic worms

o Immunology

???? Study of immunity

o Virology

???? Study of viruses

• Bioremediation  

o Microbe involvement

???? Ex: microbes (bacteria) degrade organic matter in  

sewage such as oil and mercury

Ch 2

• 3 subatomic particles of atom

o proton

o neutron

o electron

• atomic number

o number of protons

• atomic mass

o number of protons + neutrons We also discuss several other topics like How does incentive influence a person's action?

• covalent bond vs. ionic bond

o covalent: 2 atoms share 1 or more pairs of electrons o ionic: attractions between ions of opposite of opposite  charges

???? 1 atom loses (-) and another gains (+)

• hydrogen bond

o forms when

???? hydrogen atom covalently bonds to O

???? N atom is attracted to another O or N

• strength of  

o covalent, ionic, hydrogen

???? strongest= hydrogen

???? ionic

???? weakest=covalent

• elements of organic compounds

o carbon

o hydrogen

• elements 95% of organisms weight

o carbon

o hydrogen

o nitrogen

o oxygen

• basic properties of water

o inorganic

o polar

???? acts as solvent

???? used in chem reactions

???? temp buffer

o hydrophilic

o high specific heat If you want to learn more check out What do linking verbs connect?

o surface tension

o dissociation or ionization

• physical states of water

o solid

o liquid

o gas

• acids and bases

o acid substance that dissociates into 1 or more H+ and an  anion

???? HCl ✁ H+ + Cl

o Base substance that dissociates into 1 or more OH- and a  cation

???? NaOH ✁ Na+ + OH

o ph value amount of H+ in a solution= pH

???? pH=-log[H+]

???? increasing H+

✂ increase acidity, decrease pH

???? increasing OH-

✂ increase alkalinity, increase pH

• salt substance that dissociates into cations and anions, neither of  which is H+ or OH

o NaCl ✁ Na+ + Cl-

???? Table salt, held together by an ionic bond

• biological macromolecules

o carbohydrates

???? monomer: glucose

???? biological ex: starch, glycogen, chitin, cellulose ✂ important for use in structures and energy  

sources

✂ (CH2O)n 

o lipids

???? monomers: glycerol, 1-3 fatty acids

???? biological ex: fats or triglycerides

✂ primary components of cell membranes

???? characteristics

✂ C, H, and O

✂ Nonpolar, uncharged

✂ Hydrophobic, insoluble in water

• proteins

o monomers: amino acids

o biological ex: proteins, enzymes

???? essential in cell structure and function

???? transporters, flagella, bacterial toxins, antibodies, and  some hormones are proteins

o bonds= peptide bonds

• nucleic acids

o monomers: nucleotides

???? pentose, phosphate group(s), N-containing base

o biological ex: DNA, RNA

???? DNA:  

✂ Deoxyribose

✂ double helix

✂ hereditary material

✂ order forms genetic instructions for RNA and  

proteins

???? RNA:

✂ Ribose

✂ Single stranded

• hydrophobic vs. hydrophilic

o hydrophobic= repel water

o hydrophilic= attracted to water, form ionic or H-bonds • dehydration synthesis

o removal of water  

o joins 2 monosaccharides

• saturated vs unsaturated lipids

o saturated: no double bonds, all C are saturated with H o unsaturated: 1 or more double bond in fatty acid

• protein importance to cellular metabolism

o speed up chemical reactions

o some (transporter proteins) move chemical across  membranes

• protein structure

o primary

???? chain of amino acids

o secondary

???? chain folds and coils into helix or pleats

✂ due to H-bonds

✂ local and repetitious

✂ shape: α-helix or β-pleats

o tertiary

???? helix folds irregularly forming

✂ disulfide bonds

✂ H-bonds

✂ Ionic bonds

✂ Between anion acid R-groups in chain

o Quaternary

???? 2 or more polypeptides

• protein denaturation

o unfolding

o protein loses function

o causes

???? high temp, hostile pH, improper salt conc.  

• Importance of ATP

o Energy molecule for life

o Structure

???? Ribose, adenine and 3 phosphate groups

???? Made by dehydration

???? Broken by hydrolysis

✂ Liberating energy

Ch 4

• Prokaryotes vs. Eukaryotes

o Pro= before nucleus

???? 1 circular chromosome DNA, no membrane

???? no histones

???? no membrane-bound organelles

???? binary fission

???? peptidoglycan cell walls

✂ peptidoglycan: polymer of NAG and NAM

o Eu= true nucleus  

???? Paired linear chromosomes, nuclear membrane

???? Histones

???? Membrane-bound organelles  

???? Simple polysaccharide cell walls when present

???? Mitotic spindle, meiosis

• Basic shapes of bacterial cells

o Coccus: spherical

o Bacillus: rod shaped

o Spiral: twisted

• Define  

o Monomorphic

???? One shape (most bacteria fall under this category) o Pleomorphic  

???? Many shapes (few bacteria are this)

• Glycocalyx

o Outside cell wall

o Sticky polysaccharide  

???? Extracellular polysaccharide allows cell to attach

o Required by many pathogens

o Slime layer vs. capsule

???? Slime layer: unorganized and loose

???? Capsule: neatly organized

• Flagella

o Motility  

???? Rotate flagella to run (go straight) or tumble (change  direction)

???? Move toward or away from stimuli (taxis)

✂ Chemotaxis

• Occurs when whole organism travels up or  

down a chemical conc. gradient

✂ Phototaxis

• Occurs when whole organism moves  

towards or away from stimulus of light

o Define

???? Monotrichous

✂ 1 flagellum on 1 side

???? Iophotrichous

✂ A few (3) flagella on both sides

???? Amphitrichous

✂ 1 flagellum on each side, 2 total

???? Peritrichous  

✂ Many flagella all over

• Define

o Endoflagella  

???? Special flagella of spirochetes that spiral tightly around  the cell

???? Anchored at one end of cell

???? Rotation causes cell to move in corkscrew motion

o Fimbriae

???? Allow attachment

o Pili  

???? Used to transfer DNA from 1 cell to another

• Prokaryotes

o Cell wall

???? Materials: peptidoglycan (in bacteria)

???? Purpose: prevents osmotic lysis

o gram-positive vs gram-negative bacteria

???? gram-positive

✂ thick peptidoglycan

✂ teichoic acids (negative charge)

• lipoteichoic acid links to plasma membrane  

• wall teichoic acid links to peptidoglycan

✂ no outer membrane

✂ contains mycolic acid in acid-fast cells

✂ looks like layers of peptidoglycan sitting on top of  

membrane

???? gram-negative  

✂ thin peptidoglycan

✂ no teichoic acid

✂ outer membrane

• lipopolysaccharides, lipoproteins,  

phospholipids

• forms periplasm between outer membrane  

& plasma membrane

• protection from phagocytes, complement,  

and antibiotics

• LPS (lipopolysaccharide)

o O-polysaccharide antigen, e.g. E. coli

o Lipid A is an endotoxin (characteristic  

symptoms)

• Porins (proteins) form channels through  

membrane

• Net negative charge on cell surface

✂ Looks like double layer membrane

o cell (plasma) membrane

???? materials: phospholipid bilayer (=1 membrane),  peripheral proteins, integral proteins (some are  

transmembrane)

???? purpose: selective permeability allows passage of some  molecules

???? enzymes for ATP production located here for bacteria o define

???? diffusion

✂ simple diffusion: movement of solute from area of  high conc to low conc

✂ no ATP needed

???? facilitative diffusion

✂ solute combines with transporter protein in  

membrane

✂ no ATP needed

???? active transport

✂ low conc ✁ high conc  

✂ requires

• energy

• transporter protein

• ATP

???? Osmosis

✂ Movement of water across selectively permeable  

membrane from area of high conc to area of low  

water conc

✂ Osmotic pressure pressure needed to stop  

movement of water across membrane  

aquaporins

o difference

???? isotonic

✂ no net movement of water

???? hypotonic

✂ water moves into the cell and may cause the cell  

to burst if the wall is weak or damaged

???? hypertonic

✂ water moves out of the cell, causing its cytoplasm  to shrink  

o cytoplasm

???? substance inside of plasma membrane

o nucleoid  

???? different from nucleus

???? not a true nucleus

???? no nuclear membrane

o endospore

???? resting cells (not reproductive)

???? for survival  

???? no metabolism occurs (dehydration)

???? resistant to desiccation, heat, chemicals

???? bacillus, clostridium

✂ ex: anthrax and botulism

???? sporulation endospore formation process

???? germination the return to vegetative (normal) state o fact to know

???? prokaryote ribosomes are smaller than eukaryotic  

ribosome

• eukaryotes

o cell wall

???? materials: simple polysaccharides

???? plants, algae, fungi

???? carbohydrates

o pellicle

???? flexible outer protein covering on some protozoa o glycocalyx

???? carbohydrates extending from animal plasma  membrane

???? bonded to proteins and lipids in membrane

o define

???? cytoplasm

✂ substance inside plasma and outside nucleus ???? cytosol

✂ fluid portion of cytoplasm

???? cytoskeleton

✂ microfilaments, intermediate filaments,  

microtubules

???? cytoplasmic streaming

✂ movement of cytoplasm throughout cells

o Function of organelles

???? Membrane-bound

✂ Nucleus

• Contains chromosomes (DNA)

✂ ER

• Transport network

✂ Golgi complex

• Membrane formation and secretion

✂ Lysosome

• Digestive enzymes

✂ Vacuole

• Brings food into cells and provides support

✂ Mitochondrion

• Cellular respiration, ATP production

✂ Chloroplast

• Photosynthesis

✂ Peroxisome

• Oxidation of fatty acids; destroys H2O2 

o Endosymbiotic theory

???? Explains the origin of eukaryotic cells from prokaryotes

Ch 5

• Metabolism: sum of chem reactions in an organism

o Catabolism vs. anabolism

???? Catabolism: breakdown molecules to generate ATP

???? Anabolism: use ATP to build molecules

• Molecule used as an energy source for all biological organisms o ATP

• Enzymes

o Decrease activation energy needed for reaction to occur o Speed up chem reactions by putting reactants closer together  and in a proper orientation

???? Effectively increases collision frequency

o Biological catalysts

???? Specific for a chem reaction

???? Not used up in that reaction

???? “___ase” (see pg 113)

???? parts

✂ apoenzyme protein portion

✂ cofactor nonprotein component

• Fe, Mg, Ca, Zn

✂ Coenzyme organic cofactor

• NAD, FAD

• Important coenzymes

o NADH, NAD+

o NADPH, NADP+

o FADH2, FAD

o Coenzyme A

✂ Holoenzyme apoenzyme + cofactor (coenzyme)

• Collision theory: chem reactions can occur when atoms, ions, and  molecules collide

o activation energy

???? needed to disrupt electronic configurations so a reaction  can occur

o reaction rate

???? Frequency of collisions with enough energy  

???? Can be increased by

✂ Enzymes

✂ Increasing temp or pressure

• Heat= faster

• Cold= slower

• Higher pressure: harder, faster

• Lower pressure: less

• active site  

o where the substrate binds

• factors influencing enzyme activity

o pH

o temp

o substrate conc

• competitive inhibitor vs. noncompetitive inhibitor  

o competitive

???? binds to active site blocking substrate

o noncompetitive

???? binds to allosteric site

???? alters active site blocking substrate

• feedback inhibition

o allosteric regulation

• oxidation vs. reduction

o oxidation

???? removal of electrons

???? OIL= oxidation is loss

o Reduction

???? Gain of electrons

???? RIG= reduction is gain

• methods of ATP generation

o Substrate-level phosphorylation (SLP)

???? Transfer of high-energy PO4- directly to ADP

???? C-C-C ~ P + ADP ✁ C-C-C + ATP

o Oxidative phosphorylation (OP)

???? Energy released from the transfer of electrons  

(oxidation) of 1 compound to another (reduction) is  

used to generate ATP by chemiosmosis

o Photophosphorylation

???? Plants, algae, cyanobacteria

???? Light causes chlorophyll to give up electrons

✂ Energy released from transfer of electrons  

(oxidation) of chlorophyll through a system of  

carrier molecules is used to generate ATP

• carbohydrate catabolism

o Glucose has electrons that can be removed (by oxidations)  and carried (by coenzymes) to system that stores energy in  ATP

o Breakdown of carbohydrates to release energy involves • glycolysis  

o cost: 2 ATP

o products: 4 ATP, 2 NADH, 2 pyruvate

o net gain: 2 ATP

o cell part where it occurs

???? cytoplasm

• fermentation  

o aerobic vs anaerobic

???? anaerobic= oxygen NOT present

✂ Pyruvate is converted into

• Lactic acid, ethanol, mixed acids, 2,3  

butanediol, propionic acid, acetone-butanol  

Via fermentation

???? aerobic= oxygen present

✂ Pyruvate is converted to Acetyl CoA

✂ Via

• Pyruvate Oxidation in Mitochondria of  

eukaryotes or cytosol of prokaryotes: Kreb’s  

Cycle (CO2) and Electron Transport (H2O)

???? types named after end product

✂ lactic acid fermentation

• lactic acid= end product

✂ alcohol fermentation

• ethanol= end product

• CO2= end product

• Krebs cycle (CAC or TCA)

o Where does it occur in eukaryotes

???? Mitochondrial matrix

o How many reactions in cycle

???? 9 reactions

o Carbohydrates ✁ CO2

???? Carbons in pyruvate (product of glycolysis) are oxidized  to CO2

o Aerobic or anaerobic?

???? aerobic

• facts to know

o pyruvate oxidation joins glycolysis with the Krebs (CAC) o NADH and FADH2 products from the Krebs cycle are used to  drive (power) the electron transport chain

o Electron transport chain makes the 36 ATP (eukaryotes) or 38  ATP (prokaryotes)

o ATP production in electron transport chain is called  

chemiosmosis and it involves oxidative phosphorylation

Example Questions

• A prokaryotic cell

o Lacks a nucleus

o Lacks membrane bound organelles

o Is an organism in either domain Archaea or Bacteria

o All the above 

• In a single molecule of water, the H and O atoms are held together  with by ____

o Ionic bonds

o Covalent bonds 

o Hydrogen bonds

o None of the above

• Enzymes

o Are biological catalysts

o Can be denatured by changed in temp

o Can be denatured by changes in pH

o All the above 

• Which 2 organelles were specifically discussed in regards to  endosymbiotic theory

o Mitochondrion and chloroplasts

2/2/16 11:57 AM

2/2/16 11:57 AM

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