MCB2000 UF Exam One Asghari

Name a compound used as solidifying agent is culture media.

Agar

What is the purpose of an amphibolic pathway?

Amphibolic pathways bridge the reactions that lead to the breakdown (catabolism) and synthesis (anabolism) of carbohydrates, lipids, proteins, and nucleotides.

What is biofilm? What is its significance?

Biofilm: A microbial community that usually forms as a slimy layer on a surface. Biofilms form coordinated functional communities.

What the cell wall, cell membrane, and ribosome of bacteria are made of? What are their functions in the cell?

Cell wall: peptidoglycan/ structure for the cell, keeps it from bursting Cell membrane: phospholipids/ selective barrier Ribosomes: protein + RNA/ protein synthesis

What is the basic difference between chemotrophs and phototrophs?

Chemotrophs use oxidation-reduction reactions as their primary energy source, and phototrophs use light.

Describe the important features of plasma (cytoplasmic, cell) membrane? What is meant by fluid-mosaic model, semi-permeable or selective permeability? Which molecules can easily pass through cell membrane without help of carriers?

Controls the flow of chemicals • Semipermeable/Selective Permeability: selective on what enters/leaves • Made of phospholipid bilayer • Things with charge (ex:sugars) cannot get through the hydrophobic inside layer

Describe the role of microbes in making designer jeans? (Page 3)

Genetic engineering allows you to insert the gene that makes indigo into a bacterium that will do it for you.

What are the central pathways to metabolism? What is their role molecule is at top of this pathway? How other molecules may enter the pathway? What are the differences between anabolism and catabolism?

Glycolysis + Krebs cycle. glucose Anabolism is the synthesis of complex organic compounds using simpler ones, catabolism is the breakdown of organic molecules into simpler ones.

Give examples of different gram reactions, morphology and arrangement for bacterial cells.

Gram positive bacteria are a purple color, whereas gram negative cells are pink. Coccus (spherical), bacillus (rod-like), and spiral are primary. They can then be divides into diplococci, streptococci, staphylococci, tetrads, and sarcinas for coccus; coccobacillus, diplobacillus, and streptobacilli for bacillus; and spirilla, spirochetes, or vibrios for spiral.

What is the role of lipases?

Lipases break down fats into fatty acids and glycerol

What is the difference between magnification and resolution?

Magnification is the degree to which the size of an image is larger than the image itself. Resolution is the degree to which it is possible to distinguish between two objects that are very close together.

How molecules are transported across the cell membrane. Compare passive diffusion/active transport and simple/facilitated diffusion.

Molecules are transported across the cell membrane through diffusion, osmosis, or transport. • Passive Diffusion: molecules go from area of high concentration tot are of low concentration until equilibrium is reached. Force of concentration only. Net movement=0 • Facilitated Diffusion: goes from high to low concentration until equilibrium is reached but requires help from proteins across the membrane. No energy required. • Active Transport: consume energy (ATP). Can go from area of low concentration to one of high concentration. Bacteria use this to concentrate nutrients inside. Work against concentration gradient.

Describe different variation oxygen requirements. How come some organisms do not need oxygen? What do they use instead? Why some are obligate anaerobes? (page 151, table 6.5)

Obligate anaerobes need air to survive, facultative aerobes grow best where there is oxygen but can survive without it, obligate anaerobes only grow where there is no oxygen, aerotolerant anaerobes grow anywhere without regard to oxygen and microearophiles grow where there is a small dissolved oxygen concentration. Some organisms do not need oxygen because they are unable to use it. They use anaerobic respiration to obtain energy. Some are obligate anaerobes because they require molecular oxygen to live.

What are phospholipids are made of? What is the important feature of these molecules?

Phospholipids are made up of two fatty acids (long chains of hydrogen and carbon molecules), which are attached to a glycerol 'head.' The important feature is that the tails are hydrophobic and the heads are hydrophilic.

Compare pili and flagella structure and function. Where in the cell one can find them?

Pili are normally shorter, straighter, and thinner than flagella and number only one or two a cell, they are used in twitching and gliding motility and they are found distributed around the cell membrane. Flagella are long filamentous appendages used to propel bacteria. Flagella may be peritrichous (distributed over the entire cell) or polar (at one or both poles or ends of the cell).

Which groups of organisms have cell wall? What are they made of? What is bacterial cell wall made of? Its function?

Plants, fungi, and bacteria have cell walls. Plants are made of cellulose, fungi are made of chitin, and bacteria are made of peptidoglycan. It functions as a form of structure for the cell and the major function of the cell wall is to prevent bacterial cells from rupturing when the water pressure inside the cell is greater than that outside the cell.

Compare positive and negative types of stain.

Positive stains result in a stained specimen and a colorless background. Negative stains results in colorless bacteria against a stained background.

Compare the prokaryotes/eukaryotes for the composition/presence of cell wall/cell membrane?

Prokaryotes and eukaryotes both have a cell membrane. Most prokaryotes also have a cell wall, whereas most eukaryotes do not. Bacterial (prokaryote) cell walls are composed of peptidoglycan, other than gram negative cells. Most eukaryotic cell membranes are composed of of a phosopholipid bilayer.

Compare prokaryotes and eukaryotic structures.

Prokaryotic structures lack membrane enclosed organelles and a nucleus, but usually contain a cell wall. Eukaryotic stuctures contain membrane enclosed organelles and a nucleus, but lack a cell wall.

Define sporulation, germination and vegetative stage of life. Importance of endospores?

Sporulation is the formation of nearly dormant forms of bacteria. Germination is the development of a plant from a seed or spore after a period of dormancy. Vegetative bacteria are the bacterial cells that are metabolizing and undergoing binary fission. Endospores form to keep the bacteria alive in extreme conditions or environmental stress.

How temperature and pH may affect the cell. Define max, min and optimum growth temperature? (Figure 4.18)

Temperature and pH can hinder or stop cell growth if it is above or below the prime temperatures. • Max- The highest temperature growth is possible • Min- the lowest temperature where the species will grow • Optimum: the temperature at which the species grows best.

Define final (terminal) electron acceptor? Give examples of final e acceptors for aerobic and anaerobic respiration.

Terminal Electron Acceptor: the final acceptor in the electron transport chain that gets the electron after you liberate energy • Electron Acceptors in Aerobic Respiration: Oxygen • Electron Acceptors in Anaerobic Respiration: Nitrate & Sulfate

Why is it difficult to define psychrophile, mesophile, and thermophile?

The ranges and temperatures that determine these are not rigidly defined.

What features of lipids make them and excellent molecule to make membrane with? What most hormones are made of?

They are nonpolar and semipermeable. Proteins

What is the primary use of lipids in cells?

They are used as a structural component of membranes.

Describe the following media. Indicate if they are selective, differential, either or both. a. Blood agar b. Mannitol salt agar c. MacConkey agar

a. Differential b. Both c. Both

What Bacteria are capable of doing if they possess: a. Plasmid b. Capsule c. Pili

a. Passing along important genes, such as disease causing or antibiotic resistant genes. b. capsules are important in contributing to the degree to which a pathogen causes disease, and protect pathogenic bacteria from phagocytosis by the cells of the host. c. Pili provide motility.

Fatty acid and phospholipids are very important for the formation of

cell membrane

List the structures present on a typical bacteria cell. List the structures every bacterium MUST have.

cell wall, glycocalyx, cytoplasmic membrance, cytoplasm, ribosomes, cytoskeleton, a one (or a few) chromosome(s)

During which phase of fermentation is ATP generated?

glycolosis

What is the difference between homolactic and heterolactic fermentation?

homolactic fermentation produces only lactic acid, heterolactic fermentation produced lactic acid + other acids/alcohols

What is the most abundant compound in cell? Note: It is not water.

proteins

What is decarboxylation?

removal of carboxyl group

Why is sugar added to fruit to make jams and jellies?

the high salt or sugar concentrations draw water out of any microbial cells that are present and thus prevent their growth.

What are the three domains of microorganisms, what are the five kingdoms of living organisms? Which ones are prokaryotes? Which domain or kingdom do viruses belong to? Explain.

• 5 kingdoms: plants, animals, fungi, protista, monera (first 4 are eukaryotes) • 3 domains: Bacteria, Archaea, Eukarya • Bacteria and Archaea are prokaryotes and belong to kingdom monera • Eukarya are eukaryotes and belong to Protista • Eukaryotes have organelles • Viruses do not belong to these 5 kingdoms: they are acellular and only reproduce

Define microbes. What is the unit of life? What are the hallmarks (minimum requirements of life) of a cell? Why viruses do not fit in this picture. Name three acellular infectious agents.

• A structure that cannot be seen by the unaided eye • Cells are the units of life • Hallmarks of a cell: o Cell membrane o Cell membrane controls what goes in and out (flow) o Must have chromosome made of DNA (not RNA) o Must be able to self replicate • Viruses are acellular structures

Compare Respiration/Fermentation/anaerobic (Table 5.5)

• Aerobic Respiration: o Oxidation-molecule loses electrons o Energy is liberated o Reduction-electron is gained o Glycolysis: glucose (6C)2 Pyruvate (3C) o Glucose is oxidized into pyruvate, electrons are releasedATP is produced o NAD accepts the electron and becomes NADHNADH now reduced o Krebb's Cycle: PyruvateAcetyl CoA (2C)Krebb's converts pyruvate to CO2Energy ProducedMore electrons dumped on NADH o NADH migrates to cell membrane and drops electrons off to electron transport chainNADH is reoxidized o Oxygen is the final electron acceptor o Oxygen turns into water • Anaerobic Respiration: o No oxygen available-sulfate or nitrate used as the final electron acceptor • Fermentation: you don't go through the electron transport chain, you stop with glycolysis. GlucosePyruvateMake acids and alcohol o You still generate NAD and get rid of the electron, but the final electron acceptor is Ethyl alcohol or Lactic acid (from the inside) o This also produces ATP (much less than respiration)

Define and give examples of microorganisms that are considered primary producers.

• An organism that produces organic from inorganic by using energy from sunlight-photosynthetic organisms • EX: Plants and Bacteria

List and compare four major polymers with respect to their: a. Building blocks b. Examples c. Role/functions/where found in cell

• Carbohydrates sugar peptidoglycan energy source/ cell wall • Lipids fatty acids waxes and hormones structure/ cell membrane • Proteins Amino Acids polypeptide Regulate what goes in and out, enzymes/ transport proteins, ribosomes • Nucleic Acid Nucleotides DNA and RNA make up genetic information/ DNA in nucleus, RNA in cytoplasm

What are the six major bio elements? Where in cell (polymers) you find these elements?

• Carbon: lipids, carbs, proteins, ad nucleic acids • Hydrogen: lipids, carbs, proteins, nucleic acids • Oxygen: carbs, proteins, nucleic acids • Nitrogen: proteins, nucleic acid • Phosphorous: Nucleic acid • Sulfur: Proteins Lipids: CH Carbohydrates: CHO Proteins: CHONS Nucleic Acids: CHONP

Define different forms of chemical reactions: endergonic, exergonic, synthetic, decomposing, dehydrating, and hydrolytic reactions

• Chemical Reaction: a change of energy occurring during any chemical reaction • Endergonic reactions: require energy • Exergonic reactions: release energy • Synthetic: multiple reactants combine to form a single product. • Decomposing: a product breaks down into multiple reactants. • Dehydrating: a molecule of water is released • Hydrolytic: a molecule of water is added.

Define chromosome, gene, and genome. Where in animal/bacterial cell one can fine DNA? Who has plasmid, and what is its significance (page 76)?

• Chromosome: an extremely long molecule of double stranded DNA that is tightly coiled around special basic protein molecules so as to fit inside the cell compartment • Gene: genetic units arranged along the length of the chromosome that carry information about maintenance and growth • Genome: the complete set of genes in a cell or organism • DNA in animals: nucleus and mitochondria • DNA in bacteria: in the bacterial chromosome that with RNA and other proteins, forms the nucleoid • Bacteria have plasmid: nonessential pieces of DNA o Carries antibiotic resistant genes o Genes that cause diseases o Can be shared to other bacteria and spread the resistance and infection causing genes to others

Define and give examples of bacterial morphology. What are the relative sizes of different cells?

• Coccus (round) o Gram positive cocci=strep, staph (staph is cluster, step is chain) • Bacillus (cylinder) • Vibrio (curved) o Cholera • Spirium (squiggle) • Spirochete (corkscrew) o Syphilis, Lime disease • Filamentous (branching) • Most bacteria fall between 1 and 10 micrometers in size

List three chemical bonds and their role in chemical reactions.

• Covalent: allows molecules to share electrons • Ionic: Allows molecules to reach prime number of electrons, creates ions • Hydrogen: weak bond formed between hydrogens

Compare defined vs. undefined (complex) culture media, selective vs. differential media.

• Defined Media: all of the components are known (exact chemical makeup) • Complex Media: exact components are not known • Selective Media: suppress growth of unwanted bacteria and encourage growth of desired microbes • Differential Media: makes it easier to distinguish the desired colonies from others growing

Define chemiosmosis theory.

• Energy comes in the form of a reduced molecule, you convert this molecule into CO2 and water and extract energy, this requires the electron transport chain and a supply of an electron acceptor.

What are enzymes? The characteristics/function of enzymes, their roles in chemical reactions (section 7.1)

• Enzymes are biological catalysts or biological couplers that couple two reactions together • They catalyze chemical reactions by lowering the activation energy required and are not used up in the process

Compare the germ theory of disease and the concept known as spontaneous generation.

• Germ Theory: diseases are caused by germs, too small to see with the human eye. • Spontaneous Generation: life can come from nonliving, disproved by Louis Pasteur.

Compare cell envelope of G- vs. G+ (differences in cell wall/cell membrane/etc).

• Gram Negative: o Thin peptidoglycan cell wall o Lipopolysaccharide is part of the outer membrane o Two membranes (outer membrane and cell membrane) make them more resistant to chemicals and antibiotics o Outer layer: Porins (selective protein channels) Partly LPS (toxic compound called endotoxin) that causes toxicity to the human body o Space between two membranes is called the periplasmic space: additional storage for enzymes o Rigid or flexible shape • Gram Positive: o Techoic acid embedded in thick peptidoglycan cell wall o One membrane o Always rigid shape o More sensitive to penicillin (b/c penicillin attacks peptide bridges in the cell wall)

Where in the cell components of Electron transport system are located. What is their function?

• In bacteria, in the cell membrane • In human cells, in the inner membrane of the mitochondria (powerhouse of the cell-provides ATP) • Accept the electron from NADH and transfer it to Oxygen

What is role of interactions between electrons in ionic, hydrogen, and covalent bonds?

• Ionic: electrons exchanged • Covalent: Electrons shared • Hydrogen: electron attracted to electronegative ion

What are different variations of light microscope? What is the difference between electron microscopy and light microscopy? Compare the two with respect to magnification, resolution, and source of illumination. Compare the two forms of electron microscopy. What is the significance of fluorescent microscopy?

• Light Microscopes: o Bright field Microscope: specimens are stained, light passes through and you can see them o Dark Field Microscope: the light doesn't hit the specimen directly, it is illuminated under a dark background o Phase-Contrast Microscope: you hit the specimen at different angles and see different details o Fluorescent Microscope: attach fluorochrome (a type of luminescent dye that glows under UV light) to specific antibodies to lead us to bacteria (great diagnostic tool) • With light microscopes o Resolution: in the order of micrometers (smaller the better=clearer) o Magnification: in the order of 1000x • Electron Microscopes: o Transmission Electron Microscope (TEM): Shows the details of the inside of the specimen o Scanning Electron Microscope (SEM): Shows surface details of the specimen • With electron microscopes, no light is used. Use electron beams for illumination source and cover the specimen with gold, which binds to the specimen. These microscopes cover almost half of a room. o Much smaller resolution (nanometers) o Magnification in the order of hundreds of thousands

List the three units that are used to measure microbes? How long is a micrometer?

• Millimeter: one thousandth of a meter 10^-3 • Micrometer (micron): one millionth of a meter 10^-6 • Nanometer: one billionth of a meter 10^-9

Define osmosis, hypotonic, isotonic, and hypertonic solutions. (Page 147)

• Osmosis: diffusion of water across a selectively permeable membrane • Isotonic solution: the concentration is similar on both sides of the cell membrane • Hypotonic solution: the solute concentration is lower than that of the cells environment. Water moves toward the higher concentration and rushes into the cell. In bacteria, cell wall prevents the cell from exploding. (EX: pure water) • Hypertonic solution: more contents outside of the cell than inside, so water leaves the cell and it shrivels and dies. Cell has no control over this (ex: pickled environments)

What are the differences between photosynthesis and other forms of metabolism?

• Photosynthesis uses energy from light and is used by autotrophs • Other forms of metabolism use energy from chemicals via oxidation/ reduction.

Define pili, fimbriae, glycocalyx, capsule, slime layer, and importance of formation of biofilm.

• Pili: An appendage on a bacterial cell used for conjugation and gliding motility. • Fimbriae: An appendage on a bacterial cell used for attachment. • Glycocalyx: substances that surround the cell • Capsule: An outer, viscous covering on some bacteria composed of a polysaccharide or polypeptide. • Slime layer: A glycocalyx that is unorganized and loosely attached to the cell wall. • Biofilms can harbor human infectious agents in the environment, but they also can promote remediation of contaminated groundwater and soils. They assist in metals mining and they play an important natural role recycling matter on Earth.

List important contributions to microbiology made by Koch and Pasteur. List contributions made by others discuss in lecture.

• Robert Koch: o Koch's Postulate 1884: used today to establish the link between a particular microorganism and a particular disease (isolate microbe from sick, give to second person-must exhibit same disease-isolate microbe from second person and observe-must be the same) one microbe, one disease. o Introduced use of pure culture (contains only one kind of bacteria) techniques for handling bacteria in the lab o Demonstrated that anthrax is caused by a bacterium • Louis Pasteur: father of microbiology o "Swan Neck" flask experiments o Spontaneous Generation: life arises from nothing o Germ Theory of Diseases: life arises only from the living (check) o Demonstrates yeast can degrade sugar to ethanol and carbon dioxide as they multiply o Develops pasteurization as a method to destroy unwanted organisms in wine (takes away the harmful bacteria)

List the importance of protein molecules. Define a polypeptide. List the Forces and bonds involved in primary, secondary, tertiary, and quaternary structure of proteins? What is the significance of H bonds in the function of proteins and DNA/RNA molecules?

• The most versatile and abundant polymer in the cell (55% of body) • As enzymes, catalyze chemical reactions • Regulate cellular processes (control what genes are expressed) • Provide structural support (collagen) • Polypeptide: contains an unspecified number of amino acids (usually more than 20) and is often a smaller subunit of a protein • Primary Structure: linear • Secondary Structure: hydrogen bonds contribute to this structure-two types o Helical (alpha helix) o Pleated (beta sheet) • Tertiary Structure: more hydrogen bonds (when the protein becomes fully functional) o Globular o Fibrous • Quaternary Structure: Several pieces become one big molecule o EX: hemoglobin (carries for oxygen with it-multiplies function by 4 times) • Hydrogen bonds keep DNA/RNA and protein together

.List the end products of glycolysis/Krebs cycle? Define and give examples of amphiboloic pathway.

• two Pyruvate, two NADH, and two ATP • 6 NADH + H+ molecules, two FADH2 molecules, four carbon dioxide molecules, and two ATP molecules • A biochemical pathway that involves both anabolism and catabolism. Krebs cycle & glycolosis.

List the top ten cause of death in the US. Which ones are called infectious diseases?

1. Heart disease 2. Cancer 3. Chronic lower-respiratory disease 4. Cerebrovascular disease 5. Accidents 6. Alzheimer's 7. Diabetes 8. Influenza and pneumonia* 9. Kidney disease 10. Suicide

Draw a typical growth curve and label different phases of growth. Define generation time. Which stage of growth curve is used to measure generation time? How one may define/measure bacterial growth. What is Optical Density (OD). How one measures OD. Define binary fission.

1. Lag 2. Log 3. Stationary 4. Death • The time it takes for a cell to reproduce (and its population to double) • Log • Cell numbers or total mass • the degree to which a refractive medium retards transmitted rays of light. • Spectrophotometer • Binary fission is how bacteria reproduce, it involves the cell splitting in half.

Compare simple and differential stains. What are the important features of Gram stain?

A simple stain is an aqueous or alcohol solution of a single basic dye. Differential stains react differently with different kinds of bacteria and thus can be used to distinguish them. Gram stain distinguishes into gram positive and gram negative cells.

What are Steroids? Give two examples.

A specific group of lipids, including cholesterol and hormones. Cholesterol and testosterone.

What is the significance of acid-fast staining procedure?

Acid-fast staining is a differential stain used to identify bacteria that are not decolorized by acid-alcohol. This includes Mycobacteria and Nocardia, who have waxy outer membranes.