Bio 328 Exam 1

Multicellular algae: red algae

-Large, plantlike seawear -Found in deeper ocean water than brown algae -One type of red algae (gelidium) is the source of agar

Multicellular algae: brown algae

-Large, plantlike seawear -Usually found in ocean water -Are a source of algin, which is a thickener in ice cream

pH: alkalinophiles

-Line in alkaline soil and water up to pH 11.5

What causes fermentation?

-Linked to debate over spontaneous generation -Spoiled wine threatened the livelihood of vintners -This created funding for research into how to promote production of alcohol but prevent spoilage by acid production during fermentation -Some believed air caused fermentation reactions, while others insisted living organisms caused fermentation

Why might mutations not affect phenotype?

-A mutation may be silent -A mutation may occur in a noncoding region -A mutation may not affect protein folding or the active site

Why might mutations affect phenotype?

-A mutation may cause a premature stop codon -A mutation may change protein shape or the active site -A mutation may change gene regulation

Heterotrophs

-Catabolize reduced organic molecules (proteins, carbohydrates, amino acids, and fatty acids) as source of carbon

Mutations: frameshift mutation

-Insertion or deletion of nucleotide in DNA sequence -Changes everything downstream

Enzymes: ligases

-Join molecules together

Phage therapy

-A small group of scientists discovered that they could use bacterial viruses to cure bacterial infections -Popular until antibiotics became more popular -Now that we have antibiotic resistance, phage therapy is becoming more popular again

Cellular respiration: Krebs cycle

-Acetyl-CoA is used to initiate the Krebs cycle -Each step of the Krebs cycle involves the removal of a carbon molecule, which produces NADH -End product is CoA, one molecule of GTP (one ATP equivalent), one molecule of FADH2 (two ATP equivalent), three molecules of NADH (nine ATP equivalent) and two molecules of CO2 -Produces 12 ATP equivalents -For the cycle to continue, NAD+ is required

Chemotrophs

-Acquire energy from redox reactions involving organic and inorganic chemicals

Active transport: group translocation

-Active process whereby substance is chemically modified during transport

Microaerophiles

-Aerobes that require oxygen levels from 2-10% and have a limited ability to detoxify hydrogen peroxide and superoxide anion -Must have oxygen in order to live but too much oxygen kills them because they don't have the enzymes to detoxify oxygen's poisonous forms

Prokaryotic cell reproduction

-All reproduce asexually -Binary fission most common -Reproduce using spores or buds

iCHIP

-Allows microorganisms to more readily grow when researchers try to cultivate them -Used to discover new antibiotics -Put agar onto really tiny wells in an iCHIP -Dilute bacteria and put them in each individual well and then seal the well with a semipermeable membrane -Place iCHIP into soil -A lot of microorganisms aren't used to growing as colonies or in the lab media that we use -Perhaps there is something in the soil that the microorganisms need

Translation

-Amino acids are coded by mRNA base sequences -Translation converts mRNA messages into polypeptides -A codon is a sequence of three nucleotides that codes for an amino acid -RNA could code for 64 different combinations -Many amino acids coded by more than one codon (redundancy built into the system) -Special codons also coded for: start codon signals start of translation, top codon signals end of amino acid chain -This code is universal (same in almost all organisms) -Suggests common ancestor -Means scientists can insert gene from one organism into another to make functional proteins -Amino acids are linked to become a protein -Two important "tools" needed to translate a codon into an amino acid 1. Ribosome, as its the site of protein synthesis 2. tRNA, which carries free-floating amino acids from cytoplasm to ribosome -tRNA attaches to specific amino acid -Has three-letter anticodon that recognizes specific codon -Occurs in cytoplasm of cell Process -mRNA binds to ribosome -Ribosome pulls mRNA strand through, one codon at a time -Exposed codon attracts complementary tRNA bearing an amino acid -Amino acids bond together and tRNA molecule leaves to find another amino acid -Ribosome moves down mRNA attaching more amino acids until reaches stop codon

Five kingdoms: protista

-Any eukaryote that is not an animal, plant, or fungus -60,000 protist species -Most are single-celled -Include algae and protozoa

Fungi: diseases

-Are responsible for diseases in humans, animals, and plants -In humans, infections could be superficial, affecting the skin, hair, fingernails, toenails -Some of these fungal infections can be more internal and thus be more severe

Flagella: internal flagella

-Axial filaments are anchored to the spirochete and as it tries to move, because it is anchored to the bacteria, the entire bacteria rotates in a corkscrew shape and moves forward

pH: acidophiles

-Bacteria and fungi that grow best in acidic habitats -Acidic waste products can help preserve foods by preventing further microbial growth

pH: neutrophiles

-Bacteria and protozoa that grow best in ph 6.5-7.5

Woese's three domains based on genomic data

-Bacteria, Archaea, Eucaryotes

Protozoa: classification

-Based on method of locomotion Major groups -Amoebae: pseudopodia -Flagellates: possess flagella -Ciliates: possess cilia -Nonmotile protozoa: called sporozoa

Louis Pasteur

-Boiled his infusion in a swan-neck flask that allowed the air to move in and out of the flask, killing any existing microbes -After months the infusion remained sterile because dust from the air settled in the bed of the flask where it can't contaminate the infusion -Once the flask was tilted and the sterile infusion came into contact with the dust, microbes appeared in the infusion

Inhibitors: noncompetitive/allosteric inhibitors

-Bond to an allosteric site (a bonding site other than the active site), which distorts the active site's shape and prevents a substrate from binding to it -The opposite of these are allosteric activators, which are molecules that must be bonded to the allosteric site in order for a substrate to successfully bond to the active site

Cellular respiration: ETC

-By undergoing a series of reactions, the electron carriers (NADH and FADH2) shuttle electrons through ETC while pumping out more hydrogen ions into the exterior of the prokaryote (or the intermembrane space of the mitochondrion), forming a proton gradient -For every molecule of NADH, three molecules of ATP are produced -Every FADH2 molecule produces two ATP molecules -The hydrogen ions re-enter the cell through the ATP synthase and the electrons, coupled with oxygen, produce water -As this occurs, ATP synthase produces ATP -Oxygen is only present in aerobic organisms; anaerobic organisms can have nitrogen, sulfur, or ion compounds as primary terminal electron acceptors -A total of about 36 net molecules of ATP are formed from one molecule of glucose in most eukaryotic cells -A total of about 38 net ATP are formed in prokaryotes, and some eukaryotic cells

Osmotic pressure: facultative halophiles

-Can tolerate high salt concentrations

Osmotic pressure: nonhalophiles

-Cannot grow when salt is present

Capsid morphology

-Capsids are protein coats that provide protection for viral nucleic acid and means of attachment to host's cells -Capsid composed of proteinaceous subunits called capsomeres -Some capsids composed of single type of capsomere; others are composed of multiple types -The arrangement of the capsomere proteins gives different structures to the viruses: polyhedral viruses, helical viruses

Viruses

-Cause many infections of humans, animals, plants, and bacteria -Cannot carry out any metabolic pathway -Rely on host to carry out all metabolic pathways for them -Neither grow nor respond to the environment -Cannot reproduce independently -Obligate intracellular parasites (means they cannot grow or live on their own)

Characteristics of viruses

-Cause most diseases that plague industrialized world -Minuscule, acellular, infectious agent having one or several pieces of either DNA or RNA -No cytoplasmic membrane, cytosol, or organelles -Have extracellular and intracellular states Extracellular state -Called virion -Protein coat (capsid) surrounding nucleic acid -Nucleic acid and capsid together are called the nucleocapsid -Some have phospholipid envelope -Outermost layer provides protection and recognition sites for host cells Intracellular state -Capsid removed -Virus exists as nucleic acid

Replication of animal viruses: attachment

-Chemical attraction leads to attachment -Animal viruses do not have tails or tail fibers; have glycoprotein spikes or other attachment molecules that mediate attachment

Inhibitors: competitive inhibitors

-Compete with substrate to bond to the enzyme's active site -Once in the active site, substrate cannot bind -Increasing the substrate concentration will make competitive inhibitors less efficient

Glycocalyces: capsule

-Composed of organized repeating units of organic chemicals -Firmly attached to cell surface -Protects cells from drying out -May prevent bacteria from being recognized and destroyed by host

Fungi: multicellular molds

-Consists of many types of multicellular fungi -Have great commercial importance -Consists of many antibiotic producing molds like Penicillium -Used to make many different kinds of cheese -Potato blight mold caused the famine in Ireland in the mid-19th century

Peroxidase

-Consumes hydrogen peroxide and oxidizes NADH

Catalase

-Consumes hydrogen peroxide and produces oxygen gas

Bacterial cell walls: acid fast cell walls

-Contain layers of wax-like lipid, in addition to a Gram-positive cell wall -Up to 60% of cell wall can be mycolic acids -Porins present to let things through the lipid layers

Catabolism and anabolism

-Controlled biochemical reactions that take place within cells -Metabolism is the combination of anabolism (making larger molecules) and catabolism (breaking down into smaller molecules, which releases heat/energy) -The ultimate function of metabolism is reproduction

Structure of DNA

-DNA is long polymer composed of monomers called nucleotides -DNA is composed of four types of nucleotides -Each nucleotide has three parts: a phosphate group, ring-shaped sugar called deoxyribose, nitrogen-containing base -Nucleotides always paired in the same way -Backbone formed by covalent bonds that connect sugar of one nucleotide to phosphate of another -Weak hydrogen bonds between bases hold the strands together -Base pairing rules: A with T and C with G

Microbial growth

-Defined as an increase in a population of microbes rather than an increase in size -Result of microbial growth is a discrete colony-an aggregation of cells arising from a single parent cell -Reproduction results in growth

J.B. van Helmont

-Developed a recipe for making mice in that involved combining dirty undergarments and wheat for 21 days to produce a fully formed mouse -Believed in spontaneous generation

Streak plates

-Dilutes microorganisms down enough to get individual CFUs -Each streak dilutes the microorganisms more and more

Pour plates

-Dilutes the microorganism each time you pour -Eventually you pour the diluted sample into an agar plate where you can see fewer colonies

What causes disease: observations on contagion

-Disease can be spread to others (seen in lepers) -Aristotle and Alexander the Great both understood the importance of hygiene and water contamination -This was compared to how other people though planetary conjunctions and supernatural forces led to diseases like influenza and poisonous miasmas/gasses -Girolamo Fracastoro identified three different forms of contagion in 1546 -Direct contact: disease spreads by touching infected person -Fomites: disease spreads by touching contained objects -Distance: disease spreads by contaminated air and water

Differential media

-Distinguishes one microorganism type from another growing on the same medium -Add a component to the media that let's you distinguish between two different types of microorganisms -Can be done by adding acid that changes the color of the media, which can let you differentiate certain microorganisms based on their characteristics -MacConkey agar is a differential medium: there is a pinkish glow around E. Coli that indicates that E. Coli can ferment lactose, whereas salmonella has a yellowish glow around it because it cannot ferment lactose -Blood agar is also a differential medium: on blood agar, organisms are able to have a differential feature

Archael cell walls

-Do not have peptidoglycan -Cell walls contain variety of specialized polysaccharides and proteins -Gram-positive archaea stain purple -Gram-negative archaea stain pink

Anaerobes

-Do not use aerobic metabolism

Aerotolerant anaerobes

-Do not use aerobic metabolism but have some enzymes that detoxify oxygen's poisonous forms -Prefer to use nitrogen or sulfur compounds instead of oxygen as the primary oxygen source

Viral replication of bacteriophages: lysogeny

-During entry, the virus can incorporate its DNA into the host's DNA and that host will replicate and reproduce the viral DNA -When the host's conditions become unfavorable for the bacterial replication (or more favorable for the bacterial replication depending on the virus), induction occurs and the viral DNA is signaled to separate from the host DNA and reenter the lytic cycle at the synthesis phase

Cellular respiration: synthesis of acetyl-CoA

-Each pyruvic acid is converted into acetate and combined with Coenzyme A (CoA) to form two acetyl-CoA molecules -Results in two molecules of acetyl-CoA, two molecules of CO2, and two molecules of NADH

Cellular respiration: energy yields

-Each turn of the Krebs cycle results in 12 ATP equivalents, starting with acetyl-CoA -Each turn of the Krebs cycle results in 15 ATP equivalents, starting with pyruvate -Four net ATP equivalents are produced from the complete oxidation of one molecule of glucose, substrate-level phosphorylation only

Replication of animal viruses: synthesis

-Each type of animal virus requires different strategy depending on its nucleic acid -Must consider how mRNA is synthesized and what serves as template for nucleic acid replication -Positive-sense single stranded RNA (+ssRNA) enters the host cell and must make complementary negative-sense single stranded RNA so that it can make copies of the +ssRNA --ssRNA enters the host cell and must make complementary +ssRNA to act as a template for making copies of -ssRNA -dsRNA unwind: one strand is used to make proteins and the other is used to make new viruses

DNA replication

-Enzymes (helicases) unzip double helix, breaking hydrogen bonds and exposing bases as the molecule separates -Free-floating nucleotides pair up one-by-one forming complementary strands to template -DNA polymerase ligates each new nucleotide to the growing strand -Two identical molecules of DNA formed, each with one new strand and one original strand -Fast and accurate -Process takes just a few hours -DNA replication starts at many points in eukaryotic chromosomes, but at only one point in prokaryotes that proceeds in both directions -DNA polymerases can find and correct errors -How is it possible that it takes 40min to replicate the E. Coli chromosome but E. coli can divide every 20min? -One round of replication does not necessarily have to finish before a new round can begin (multi-fork replication)

Factors affecting enzyme activity: ionic strength

-Enzymes have optimum range of ionic strength

Factors affecting enzyme activity: pH

-Enzymes have optimum range of pH -Pepsin functions best at pH 2; trypsin operates best at pH 8

Chargaff's Rule

-Erwin Chargaff discovered that different organisms have different ratios -Found same four bases of DNA in all organisms and proportions of four bases were different in organisms Rule: amounts of adenine equal thymine and amounts of cytosine equal guanine (A = T and C = G)

Leeuwenhoek categories for microorganisms: fungi

-Eukaryotic -Consists of molds (multicellular, have hyphae, reproduce by sexual and asexual spores) and yeasts (unicellular, reproduce asexually by budding, some produce sexual spores) -Diseases: ringworm, athlete's foot, yeast infections

Chromosomal mutations: gene duplication

-Exchange of DNA segments through crossing over during meiosis (eukaryotes) or through transformation (horizontal gene transfer in prokaryotes) -This is how antibiotic resistance happens

John Needham

-Experiments with beef gravy and infusions of plant materials in order to reinforce the idea of spontaneous generation, as microorganisms would still spontaneously generate in the boiled gravy even when it was covered with gauze clothe (like the meat experiment)

Lipid catabolism: beta-oxidation

-Fatty acid chains are broken down two carbon molecules at a time and shuttled off into glycolysis or the Krebs cycle -Carbon-carbon bonds hold a lot of energy

Desmids: spirogyra

-Filamentous algae

Flagella arrangement: peritrichous

-Flagella are all over the place that coordinate movement

Flagella arrangement: amphitricous

-Flagella runs through the cell

Selective media

-Formulated to support the growth of one group of organisms, but inhibit the growth of another -Selecting against certain microorganisms from growing by having certain components that prevent other microorganisms from growth -MacConkey agar is a selective medium: E. coli can grow but staphylococcus cannot, whereas both were able to grow on a nutrient agar

Frederick Griffith

-Found a "transforming principle" between rough and smooth streptococcus pneumoniae -Smooth streptococcus pneumoniae has a capsule and rough do not -Used two forms and injected them into mice -The S, or smooth, form (deadly) and R, or rough, form (not deadly) -When he heat-killed the S form of bacteria, the mice survived -But when he injected mice with a combination of heat-killed S bacteria and live R bacteria, he mice died -Griffith concluded that a transforming material passed from the dead S bacteria to live R bacteria, making them deadly

Fungi: unicellular yeast

-Found in soil and water and on skin of many fruits and vegetables -Reproduce by an asexual process called budding -Results in the production of a type of asexual spore called a blastospore -Responsible for beer, wine, leavened bread -Some species are human pathogens (Canadida albicans)

Viral envelope

-Found more on animal viruses -Acquired from host cell during viral replication or release; envelope is portion of membrane system of host -Membrane forms when the virus leaves a cell via exocytosis and membrane rejoins a cell when it the virus merges with the cell via endocytosis -Composed of phospholipid bilayer and proteins; some proteins are virally-coded glycoproteins (spikes) -Envelope's proteins and glycoproteins often play role in host recognition

Unicellular algae: diatoms

-Freshwater and marine environments -Cell walls contain silicon dioxide (glass) -Used in filtration systems, insulation, nail polish, and abrasives (like toothpaste

Beta-oxidation: energy yields

-From each fatty acid, you produce eight acetyl Co-A, seven NADH, seven FADH2 -It costs two ATP to initiate the process -Glycerol is converted to DHAP using one ATP; DHAP yields one NADH, two ATP, and one pyruvate -129 (96+21+14-2) from each fatty acid produces 406 ATP equivalents (387+19)

External structures of prokaryotic cells: glycocalyces

-Gelatinous, sticky substance surrounding the outside of the cell -Composed of polysaccharides, or rarely, polypeptides, or both -Composed of organized repeating units of organic chemicals -Firmly attached to cell surface -Protects cells from drying out -May prevent bacteria from being recognized and destroyed by host

Anaerobic media

-Lacks oxygen in it, so anaerobic microorganisms can grow in it -You can use anaerobic containers to create an anaerobic environment -You place pouches in the container that soaks up all the oxygen from it -You can also use large chambers to create anaerobic environment to house the media

What causes disease: correlation between disease and microorganisms

-Germ theory developed by Pasteur -Koch studied causative agents of disease -Developed famous postulates from studying anthrax -Examined colonies of microorganisms on solid media (agar and Petri plates) -Because of his achievement, Koch is considered the father of the microbiological laboratory -His work let to the development of simple staining techniques, first photomicrograph of bacteria, first photomicrograph of bacteria in diseased tissue, techniques for estimating CFU/ml, use of steam to sterilize media, use of solid media and Petri dishes, aseptic techniques, bacteria as distinct species

Antoni van Leeuwenhoek

-Glassmaker who found that he could combine different lenses together to make microscopes -"Father of microscopy" -Began making and looking through simple microscopes -Often made new microscope for each specimen -Examined water and visualized tiny animals like fungi, algae, and single-celled protozoa

Unicellular algae: desmids

-Group of green algae -Can photosynthesize

Osmotic pressure: extreme halophiles

-Grow in highly concentrated salt environments

Osmotic pressure: halotolerant microorganisms

-Grow in low salt concentrations

Osmotic pressure: halophiles

-Grow when some salt is present

Desmids: euglena

-Has algal and protozoan characteristics -Has a primitive mouth -Does not have a cell wall -Has an eyespot -Has flagellum

Fungi: slime molds (cellular and acellular)

-Have both fungus and protozoal characteristics -May be cellular or acellular -Found in soil and on rotting logs Cellular slime molds -Begin life as ameba-like organisms -If harsh conditions ensure, individual organisms will fuse together to form a motile, multicellular form that is called a slug -Slug becomes a fruiting body which consists of a stalk and spore cap -Spores released and are airborne -If suitable habitat is found, a spore becomes an ameba Acellular slime molds (plasmodial slime mold) -Also produce a stalk and spores -Haploid cells fuse to form diploid cells -Forms large masses of motile, multinucleated protoplasm

Bacterial cell walls: Gram-negative

-Have only a thin layer of peptidoglycan sandwiched between two membranes -Two membranes allow bacteria to be selective about what comes in and out of the cell -Periplasmic space between outer membrane and plasma membrane contains peptidoglycan; periplasm; and water, nutrients, and substances secreted by the cell, such as digestive enzymes and metabolism proteins -Outer bilayer membrane composed of phospholipids, channel proteins (porins) and lipopolysaccharide (LPS) -Mutated porins allow even fewer things to come in and out of the cell, including certain antibiotics (leads to antibiotic resistance) -Following Gram staining procedure, cells appear pink -Will appear blue after an acid-fast stain

Francisco Redi

-He observed that meat left out in the open will "spontaneously" produce maggots -When meat was placed in a sealed flask, no maggots or flies appeared -People claimed that this was because there was no oxygen and so you need oxygen to spontaneously produce life -In response, Reid placed the meat in a flask covered with gauze that still allowed oxygen to enter the flask -Flies were attached to the flask and laid eggs that hatched into maggots

Factors affecting enzyme activity: reactant concentration

-High concentration of substrate allows for faster enzyme activity -A high enough substrate concentration will eventually lead to the enzyme becoming saturated (saturation point), meaning all active sites are occupied and the reaction will not speed up no matter how much additional substrate is added

Factors affecting enzyme activity: temperature

-Higher temperatures increase activity (to a point) -Temperatures that are too high denature and inactivate the enzyme

Watson and Crick

-Hypothesized that DNA might also be a helix -Declared that DNA was double helix and strands are complimentary

What causes disease: proving a certain microbe causes a particular disease

-If a certain microbe causes a certain disease, you should always be able to find that microbe whenever a person has that particular disease -This could be a correlation, though, not a causation -Take the microbe and infect a person or animal with it and see if that causes a disease -And, do you see the microbe in the diseased tissue of the person you just infected? Koch's postulates -Suspected causative agent must be found in every case of the disease and be absent from healthy hosts -Agent must be isolated and grown outside the host -When agent in introduced into a healthy, susceptible host, the host must get the disease -Same agent must be re-isolated from diseased experimental host

Oncogene theory

-In a DNA's normal state, when the cell is done growing, protooncogenes are repressed a repressor produced by specific mRNA made from the gene for the repressor -This results in no cancer -When the first "hit" occurs, a virus inserts its promoter by the oncogene, which is still being repressed by the repressor -Results in no cancer, even though the oncogene is being exposed to a promoter -When a second "hit" occurs, the virus inserts into the repressor gene, meaning no repressor protein can be produced because the gene is segments, and the oncogene is allowed to produce mRNA and proteins that cause cell division -This results in cancer because there are no repressors present to turn off cell division

Viral replication of bacteriophages: lytic replication

-Infection of cell occurs right away -Replication cycle usually results in death and lysis of host cell Stages of lytic replication cycle 1. Attachment: receptors attach virus to host cell 2. Entry: virus either enters as a capsid protein (an entire virus) or by injecting its viral genome into the cell 3. Synthesis: once in the cell, the virus must synthesis new parts (new capsid protein, new nucleic acid) 4. Assembly: all the newly synthesized parts are assembled together to form a new virus 5. Release: virus is released either by lysing or budding from the cell

Hydrostatic pressure: barophiles

-Live under extreme pressure -Their membranes and enzymes depend on this pressure to maintain their three-dimensional, functional shape -Because barophiles are used to extreme pressure and low depths under water, growing barophiles in higher depths closer to the surface will be ineffective because their enzymes won't work/won't function properly

Glycocalyces: slime layer

-Loosely attached to cell surface -Water soluble -Protects cells from drying out -Sticky layer that allows prokaryotes to attach to surfaces

The makeup of enzymes

-Many composed entirely of protein that have a number of different features to them that help break down or build up molecules in a very specific fashion -Some are RNA molecules called ribozymes -Others are holoenzymes, composed of protein portions (apoenzymes) that are inactive if not bound to non-protein cofactors (inorganic ions or organic molecules called coenzymes) -Binding of apoenzyme to its cofactor(s) yields the active holoenzyme

Protista: algae

-Many produce energy by photosynthesis (hence their usually green color) -Most algal cell walls contain cellulose (also found in plants) -May be unicellular or multicellular

Transport media

-Media used to store and transport microorganisms

ETC: chemiosomsis

-Membrane maintains electrochemical gradient by keeping one or more chemicals in higher concentration on one side (during ETC, there are more hydrogen ions outside than inside) -Cells use energy released in redox reactions of ETC to create electrochemical gradient known as proton gradient, which has potential energy known as proton motive force -Hydrogen ions, propelled by the proton motive force, flow down the electrochemical gradient through ATP synthases (transmembrane channels) that phosphorylate ADP to ATP (oxidative phosphorylation)

Physical requirements for growth: osmolarity

-Microbes require water to dissolve enzymes and nutrients required in metabolism (water is important reactant in many metabolic reactions -Most cells die in absence of water because the cells lose their ability to maintain critical metabolic reactions -Some have cell walls that retain water -Endospores and cysts can cease most metabolic activity for years when their environment lacks water

Facultative aerobes

-Microorganisms that can maintain life via fermentation, aerobic respiration, or by anaerobic respiration

Endosymbiotic theory

-Mitochondria and chloroplasts are semiautonomous -They divide independently of the cell but are dependent on the cell for many of their proteins -They contain their own circular DNA molecule and 70S ribosomes, with which they make their own proteins -Lynn Margulis proposed that eukaryotes formed from the phagocytosis of small prokaryotes by a larger prokaryote -Small cells became organelles

Replication of animal viruses: assembly and release

-Most DNA viruses assemble in and are released from nucleus into cytosol; most RNA viruses develop solely in cytoplasm -Number of viruses produced and released depends on type of virus and size and initial health of host cell -Enveloped viruses can cause persistent infections -Do not need to lyse the host cell in order to get out -Viruses can just continuously produce more virus inside of the same cell and bud out in order to create the envelope -Virions released slowly over time (instead of the sudden busts of virion release from bacteriophages)

Protista: protozoa

-Most are unicellular -Most are free-living organisms that live in soil and water -Ingest other organisms or organic material -Do not have a cell wall Life cycle -Usually have two stages in their life cycle: trophozoite and cyst -Trophozite: motile, feeding, dividing stage -Cyst: dormant, survival stage -Can be found in a variety of environments -Symbiotic relationship between termites and protozoan -Termite's guts can contain protozoans that help the termites digest wood -Parasitic relationships (malaria, giardiasis, African sleeping sickness, amoebic dysentery)

Bacterial cell walls

-Most bacteria have cell walls composed of peptidoglycan; a few lack a cell wall entirely (i.e. Mycoplasma) -Peptidoglycan composed of sugars, NAG and NAM -NAG-NAM polymers are connected by tetrapeptide crossbridges -Bridges may be directly linked to one another, or bridges may be joined by short connecting chains of amino acids -Three basic types of bacterial cell walls: Gram-positive, Gram-negative, acid fast cell walls

Prokaryotic cell reproduction: binary fission

-Most common -Bacteria replicate their chromosomes, grow and enlarge, cell wall invaginates and separates into two daughter cells -Before the cell separates completely, it must rearrange its peptidoglycan -This gives a lot of Gram-positive organisms their different morphologies

ATP production and energy storage

-Most molecules in a cell use ATP as a form of getting energy to do some type of process, like breaking bonds or inhibiting a reaction from happening -Organisms release energy from nutrients; can be converted to high-energy phosphate bonds of ATP -Cells phosphorylate ADP to ATP in three ways 1. Substrate-level phosphorylation 2. Oxidative phosphorylation 3. Photophosphorylation -Use the energy from photons and light to create ATP

Hosts of viruses

-Most only infect particular kinds of host's cells -Due to affinity of viral surface proteins or glycoproteins (anti-receptors) for complementary proteins or glycoproteins on host cell surface (receptors) -Cell must have everything the virus needs in order to infect that cell; if something is lacking, the virus won't be able to infect that cell -Generalists infect many kinds of cells in many different hosts -Example: a bacteriophage (bacterial virus) doesn't attack and infect human cells because it is specific to receptors found only on bacterial cells, not human cells

Chromosomal mutations: transposition

-Movement of genes through "jumping genes"

Chromosomal mutations: transduction

-Movement of genes through bacteriophage (horizontal gene transfer in prokaryotes)

Flagella arrangement: lophotrichous

-Multiple flagella at one pole

Fungi: lichens

-Mutualistic relationship between an alga and a fungus -Are tough and self-sufficient -Can inhabit inhospitable habitats such as deserts, newly formed volcanic islands, the Arctic, bare rock -Grow slowly -Arctic colonies grow 1-2 inches every 1000 years -Some thought to be over 4000 years old

Control of substances crossing the cytoplasmic membrane

-Naturally impermeable to most substances -Proteins allow substances to cross membrane -Occurs by passive or active processes -Maintains a concentration gradient and electrical gradient; collectively known as electrochemical gradient -Substances concentrated on one side of the membrane or the other -Voltage/electric potential exists across the membrane -Outside of cell is usually positively charged in comparison to the usually negatively charged insides -A lot of cells couple a negatively charged ion with a sodium or hydrogen ion and bring them both in together via an integral protein, or an integral protein will only allow certain ions into the cell -This facilitated diffusion is done using the electrochemical gradient

Why is oxygen deadly for anaerobes?

-Neither gaseous O2 nor oxygen covalently bound in compounds is poisonous -The forms of oxygen that are toxic (superoxide, hydrogen peroxide, hydroxyl radical, water) are excellent oxidizing agents -Resulting chain of oxidations causes irreparable damage to cells by oxidizing compounds such as proteins and lipids -Microbes use enzyme systems to detoxify oxygen -Such enzymes include catalase, peroxidase, superoxide dismutase, superoxide dismutase/catalase in combination, superoxide reductase -Obligate anaerobes lack these enzyme systems

Neoplasia

-Neoplasia occurs when there is uncontrolled cell division in multicellular animal; mass of neoplastic cells is a tumor

Chromosomal mutations: plasmid transfer

-Non-chromosomal DNA passed from bacteria to bacteria

External structures of prokaryotic cells: pili

-Nonmotile extension -Long, hollow tubules composed of pilin -Longer than fimbriae but shorter than flagella -Bacteria typically only have one or two per cell; function as grappling hooks -Join two bacterial cells and mediate the transfer of DNA from one cell to another (horizontal gene transfer/conjugation) -How antibiotic resistance is spread -Also known as conjugation pili or sex pili

External structures of prokaryotic cells: fimbriae

-Nonmotile extension -Sticky, proteinaceous, bristle-like projections -Used by bacteria to adhere to one another, to hosts, and to substances in environment -May be hundreds per cell and are shorter than flagella -Serve an important function in biofilms

Oncogenes

-Normally, animal's genes dictate that some cells can no longer divide and those that can divide are prevented from unlimited division -Genes for cell division "turned off" or genes that inhibit division "turned on" (oncogenes) -Factors involved in activation of oncogenes: ultraviolet light, radiation, carcinogens, viruses

Ignaz Semmelweis

-Noticed that doctors coming from the morgue, where they were inspecting patients who died from an infectious disease, to the maternity ward had patients who would die from the same patient as the one in the morgue -Concluded that some microbe was being transferred from the morgue to the maternity ward -Knowing that certain things can kill microorganisms, Semmelweis suggested doctors wash their hands when going between different areas of the hospital (but not necessarily between patients) -Doctors pushed back and forced Semmelweis out of the hospital -He went crazy and died in an insane asylum

Cellular respiration: glycolysis

-Occurs in cytoplasm of most cells -Involves splitting of a six-carbon glucose into two three-carbon sugar molecules -Direct transfer of phosphate between two substrates (substrate level phosphorylation) occurs four times (at 2 steps) -Net gain of 2 ATP molecules, 2 molecules of NADH, and 2 molecules of pyruvic acid

Inhibitors: feedback (negative) inhibitors

-Once enough products are made, the final products inhibits early steps in its own synthesis (i.e., the precursors for making the product)

Mutations: point mutation

-One nucleotide is substituted for another

Temperature: mesophile

-Optimal temperature is 39ºC

Temperature: psychrophile

-Optimal temperature is 4ºC

Temperature: thermophile

-Optimal temperature is 60ºC

Temperature: hyperthermophile

-Optimal temperature is 88-106ºC

Morphology of prokaryotic cells: coccobacillus

-Oval-shaped bacteria

Enzymes: hydrolases

-Perform hydrolysis of polymers

Glycolysis: substrate-level phosphorylation

-Phosphate from phosphoenolpyruvate (PEP) is bound to ADP to produce ATP and pyruvic acid

Fungi: multicellular (hyphae, reproduction)

-Possess hyphae (a tube-like cell) -A mass of hyphae forms a mycelium -Septate hyphae have cross walls or septations -Non-septate hyphae lack cross walls or septations Reproduction -Can reproduce sexually or asexually -Can produce sexual or asexual spores -Sexual spores form by the fusion of two gametes -Asexual spores form in many different ways

Genetic material of viruses

-Primary way scientists categorize and classify viruses -Show more variety in nature of their genomes (nucleic acid) than do cells -Much smaller than genomes of cells -Genetic material is very compact -May be DNA or RNA; rarely both -Can be dsDNA, ssDNA, dsRNA, ssRNA -May be linear and composed of several segments or single and circular

Endospores

-Produced by Gram-positive rods like Bacillus and Clostridium species -Each vegetative (actively growing) cell transforms into one endospore -Each endospore germinates to form one vegetative cell -Constitute a defensive strategy against hostile or unfavorable conditions; not a reproduction mechanism -This action is triggered by being in an unfavorable environment, like when there is a change in temperature or moisture content -This is not a method of reproduction but instead of method of maintaining a non-metabolic environment where the organism is still alive so it can grow when new, more favorable conditions become available -Spores are easy to transmit from one patient to the next -This is avoided by washing hands with soap and water and wearing proper PPE (coats, gloves, goggles) -Alcohol gels will not destroy the spores because they have a thick outer coat that protects the spore -Can remain viable for tens to thousands of years

Aristotle

-Proposed spontaneous generation (living things can arise from nonliving matter) as long as water is present

Fluid mosiac model

-Proteins and phospholipids are interacting with each other in an open environment where they are free to move along inside of the lipid bilayer -Some structures can still to each other and float around in the membrane Certain proteins can go to one area of the cell versus another based off the shape of the liid bilayer

Physical requirements for growth: temperature

-Proteins are designed to be effective at a certain temperature -Temperatures above or below this setpoint affects protein function -Low temperatures make lipid-containing membranes become rigid and fragile, meaning the membrane can breal -High temperatures make membranes become too fluid and cannot contain the cell or organelle, making it a poor barrier and leading to potential cell death -At a minimum temperature, membrane gelling occurs and transport processes slow so growth cannot occur -As the temperature increases from the minimum, enzymatic reactions occur at increasingly rapid rates -When an optimum temperature is reached (37ºC for humans), enzymatic reactions occur at the maximal possible rate -When temperature reaches a maximum value, protein denaturation and thermal lysis occur and the cytoplasmic membrane collapses (cell dies)

Protein catabolism

-Proteins are hydrolyzed using proteases and shuttled off into the Krebs cycle

Alfred Hershey and Martha Chase

-Provided conclusive evidence that DNA was the genetic material in 1952 -Studied viruses that infect bacteria (bacteriophage) -Bacteriophage is a simple-protein coated surrounding DNA core -Proteins contain sulfur but very little phosphorous -DNA contains phosphorus and very little sulfur First experiment -Grew phages in radioactive sulfur and added them to a batch of culture where they could inject their "whatever" into the bacterium -They then blended the bacterium, knocking off the empty protein shells and leaving only the bacterium with the injected phage DNA -They found that all the radioactivity stayed inside the phage particles that came off of the bacterium -This told them that all the material the phages are injecting into the cell is most likely not protein Experiment two -Grew phages in radioactive phosphorous and added them to cultures where they could inject their "whatever" into the bacterium -They then blended the bacterium, knocking off the empty protein shells and leaving only the bacterium with the injected phage DNA -They found that the bacteria itself contained all the radioactivity and the phage shells (the protein coat) was not radioactive -Shows that phages are injecting DNA in the bacteria and its that DNA that allows the virus to create new viruses

Gram-negative: lipopolysaccharide (LPS)

-Provides protection to the cell -Union of lipid with sugar -Also known as endotoxin (and is toxic to animals) -Lipid portion known as lipid A -Released from dead cells when cell wall disintegrates and when you're using antibiotics -Can trigger fever, vasodilation, inflammation, shock, and blood clotting -Often released when antimicrobial drugs kill bacteria -Used to serotype bacteria E. Coli O157 H7 -The O number in the E. Coli name refers to what oligosaccharide the bacterium uses to produce its LPS

Prokaryotic cell walls

-Provides structure and shape and protects cell from osmotic forces -Eukaryotes can control their environments and therefore don't need a cell wall, whereas prokaryotes cannot necessarily control their environment and whether its aqueous or not -Assists some cells in attaching to each other -Can function as a barrier to certain antimicrobial substances -Animal cells have no cell walls; can use different antibiotics that target cell wall of bacteria -Bacteria and archaea have different cell wall structure and chemistry

Transcription

-RNA carries DNA's instructions -RNA acts as messenger between nucleus and protein synthesis in cytoplasm -In prokaryotic cells processes take place in cytoplasm -In eukaryotic cells, processes are separated: replication and transcription (splicing) occur in nucleus and translation occurs in cytoplasm -Produces three major kinds of RNA -Messenger RNA (mRNA) codes for translation -Ribosomal RNA (rRNA) forms part of ribosome -Transfer RNA (tRNA) brings amino acids from the cytoplasm to a ribosome to help make growing protein

How do RNA and DNA differ?

-RNA has the base uracil in place of thymine -Nucleotides in RNA are ribose, not deoxyribose -RNA is single stranded, not double

Enzymes: isomerases

-Rearrange atoms in a molecule

Charls Avery

-Reasoned that something from the S bacteria was being taken up by the R bacteria and making it basically an S bacteria -Fractionated cells (separated the components of cells) and added them back one at a time to the rough bacteria -When Avery added DNA back to the R bacteria, it transformed into the S strain -Concluded that DNA is the molecule that carries the heritable information -Avery then performed tests with enzymes -When he added enzymes to break down proteins, transformation still occurred -When he added enzymes to break down RNA, transformation still occurred -When he added enzymes to break down DNA, transformation failed to occur -Concluded from this that DNA was the transforming factor

Prokaryotic cytoplasmic membrane functions

-Referred to as phospholipid bilayer; composed of lipids and associated proteins -Controls passage of substances into and out of the cell; selectively permeable -Water can freely enter a cell but other molecules cannot and must use integral proteins in order to pass through the membrane -A molecule's charge makes it least permeable when crossing a membrane -Size, concentration, and polarity also plays a role -Mitochondria have lipid bilayers that create a proton gradient across the membrane that allows the cell to produce energy -Harvests light energy in photosynthetic prokaryotes

Bacterial cell walls: Gram-positive

-Relatively thick layer of peptidoglycan above a single cell membrane -Contains unique polysaccharides called teichoic acids (-phos-ribitol-)n -Some covalently linked to lipids, forming lipoteichoic acids that anchor peptidoglycan to cell membrane -Retains crystal violet dye in Gram staining procedure; appear purple -Will appear blue after an acid-fast stain

Enzymes: oxidoreductases

-Remove or add electrons

Superoxide reductase

-Removes O2(-) and produces hydrogen peroxide

Superoxide dismutase/catalase in combination

-Removes O2(-) and produces oxygen gas

Superoxide dismutase

-Removes O2(-), produces hydrogen peroxide, and produces oxygen gas

Complex media

-You know about what's in the media but not exactly the specific components -Blood agar is a complex medium because you don't know the components of the blood used, down to the molecules

Peptidoglycan

-Repeating units of NAG and NAM -Peptide crossbridges of amino acids link different strands of peptidoglycan together -Amino acids are chiral, which provides structure and protection from certain enzymes that break down the bacterial cell wall

Osmotic pressure: obligate halophiles

-Require salt in order to grow and can grow in up to 30% salt

External structures of prokaryotic cells: flagella

-Responsible for movement -Long, propeller-like structures that extend beyond surface of cell -For prokaryotes, these are rigid, protein helices that rotate Structure -Composed of filament, hook, and basal body -Flagellin protein (filament) arranged in chains and forms helix around hollow core -Base of filament inserts into hook -Basal body anchors filament and hook to cell wall by a rod and a series of either two or four rings -Filament capable of rotating 360º

Chromosomal mutations: gene translocation

-Results from the exchange of DNA segments between non-homologous chromosomes (eukaryotes)

Morphology of prokaryotic cells: bacillus

-Rod-shaped bacteria -Can be oval-shaped (coccobacilli), in chains (streptobacilli), or in clusters (mycobacteria)

Flagella function

-Rotation propels bacterium through environment -Flagella are able to recognize chemical gradients in their environment and rotation can be clockwise or counterclockwise based on this recognition (reversible) -Prokaryotes move in response to stimuli (taxis) For cells with multiple flagella... -Runs: movements of cell in single direction for some time, towards a favorable environment; increase with favorable stimuli (positive chemotaxis, positive phototaxis) -Tumbles: abrupt, random, changes in direction; increase with unfavorable stimuli (negative chemotaxis, negative phototaxis)

Morphology of prokaryotic cells: coccus

-Round, circular bacteria -Grow and divide straight down the middle -Can be in pairs (diplococci), in chains (streptococci) or in clusters (staphylococci)

Replication of bacteriophages vs. animal viruses

-Same basic replication pathway as bacteriophages but more complicated Differences result from... -Presence of envelope around some viruses -Eukaryotic nature of animal cells -Lack of cell wall in animal cells

Leeuwenhoek categories for microorganisms: protozoa

-Single-celled eukaryotes -Similar to animals in their nutritional needs and cellular structure -Typically live freely in water; some live inside animal hosts -Classified by mechanism of motility -Diseases: malaria, amebiasis

Oncogenes: viruses

-Some carry copies of oncogenes as part of their genome -Some stimulate oncogenes already present in host -Some interfere with tumor repression by inserting into host's repressor gene -Some inactivate tumor suppressor genes -Several DNA and RNA viruses are known to cause ~15% of human cancers (Burkitt's lymphoma, Hodgkin's disease, Kaposi's sarcoma, cervical cancer)

Mutations

-Some mutations affect a single gene, while others affect an chromosome -Mutation is a change in an organism's DNA -Mutations that affect a single gene usually happen during replication -Mutations that affect group of genes or chromosome happen during meiosis (eukaryotes)

Physical requirements for growth: pH

-Something with a pH of 7 (like pure water) indicates that there are equal concentrations of hydroxide ions and hydrogen ions in that solution -As pH increases, the solution has fewer and fewer hydrogen ions and more hydroxide ions; as pH decreases, the solution has fewer and fewer hydroxyls and more hydrogen ions -pH is really a log scale -Orange juice at pH 4.0 is 10^4x (or 10,000x) more acidic than seawater, which is pH 8.0 -pH changes affects the hydrostatic interactions that proteins needs in order to maintain their structure (and function

Enzymes: lyases

-Split molecules without adding water

Joseph Lister

-Surgeries in the late 1800's had a poor success rate -Lister used a machine to spray the surgery room with carbonic acid, which largely increased Lister's success rates -Other doctors modified his technique and sprayed their surgery instruments too, which lead to aseptic (but not necessarily sterile) surgeries

Edward Jenner

-Tested the idea that people with cowpox or horsepox do not develop smallpox by infecting his parner's son with cowpox and then smallpox -The son did not become infected with smallpox, supporting this idea -Led to the invention of vaccinations

John Snow

-The father of epidemiology -Investigated the origin of the cholera outbreak in London in 1854 -By asking people where they have eaten, shopped, drank, and traveled to before becoming infected with cholera, Snow was able to narrow down the origin to a single water pump in London that was downstream to a major sewer outlet -Snow removed the handle from the pump, making it unusable, and the cholera outbreak ended -People adapted Snow's ideas to track diseases like E. Coli etc.

Osmolarity: osmotic pressure

-The pressure exerted on a semipermeable membrane by a solution containing solutes that cannot freely cross membrane -Related to concentration of dissolved molecules and ions in a solution Tonicity -Hypotonic solutions have lower solute concentrations; cells (without walls) placed in these solutions will swell and burst -Hypertonic solutions have greater solute concentrations; cells placed in these solutions will undergo crenation/plasmolysis (shriveling of cytoplasm) (this effect helps preserve some foods) -Placing cells in an isotonic environment does not change the shape of the cell because the inside of the cell and the cell's external environment have an equal concentration of solutes -Salt, which lacks water, restricts organisms to certain environments -Microorganisms create compatible solutes for the environments that they're in in order to create isotonic environments -Allows them to grow in high-sugar and high-salt environments

Microbiology

-The study of microorganisms, how they work, interact with the environment, and interact with us -Body is mostly bacterial

Oxidation and reduction reactions

-The transfer of electrons from a molecule that donates electrons to a molecule that accepts electrons -The oxidation step involves losing electrons while a molecule gains electrons during reduction -Energy is released because electrons are losing potential energy as they move away from a molecule like carbon and onto more electronegative atoms such as oxygen -Cells use electron carrier molecules to carry electrons (often in H atoms)

Culture

-To culture (culture here is used as a verb) something means you're introducing inoculum with microorganisms into a broth or solid medium -Such microorganisms include environmental specimens, clinical specimens, stored specimens -Culture also refers to the act of cultivating microorganisms or the microorganisms that are cultivated (culture here is used as a noun) -If you plate these microorganisms dilute enough and allow them to grow, they will eventually grow into another culture -Cultures composed of cells arising from a single progenitor (progenitor is termed a colony forming unit (CFU)

Enzymes: transferases

-Transfer functional groups on/off molecules

Aerobes

-Undergo aerobic respiration -Oxygen is essential, as its the final electron acceptor in ETC -Can use oxygen from the air to respire -Breathing is a higher order function and the process of taking air into the lungs -Respiration is at the cellular function and is based on how you get your energy (from oxygen)

Leeuwenhoek categories for microorganisms: prokaryotes

-Unicellular and lack nuclei -Much smaller than eukaryotes -Found everywhere there is sufficient moisture; some found in extreme environments (archaea) -Reproduce asexually Two kinds: -Bacteria: cell walls contain peptidoglycan (though a few lack cell walls), most do not cause disease and some are even beneficial -Archaea: cell walls composed of polymers other than peptidoglycan, do not cause diseases -Diseases: TB, diphtheria

Leeuwenhoek categories for microorganisms: algae

-Unicellular or multicellular organisms -Photosynthetic -Simple reproductive structures -Categorized on the basis of pigmentation, storage products, and composition of cell wall -Non-pathogenic except for their role in red tides and shellfish poisoning

Active transport: uniport, antiport, and coupled transport (uniport/symport)

-Uniport: brings one molecule in or out of the cell -Antiport: brings one molecule in while expelling another molecule -Coupled transport (uniport and symport): ATP is used to expel a molecule out of a cell via a uniporter and that molecule is used to bring multiple things into the cell via a symporter

Chemoautotrophs

-Use CO2 as a carbon source and chemical compounds (mostly inorganic chemicals) as an energy source -Hydrogen, sulfur, and nitrifying bacteria -Prokaryotes only

Photoautotrophs

-Use CO2 as a carbon source and light as an energy source -Plants, algae, and cyanobacteria use H2O to reduce CO2, producing O2 as a byproduct -Photosynthetic green sulfur and purple sulfur bacteria do not use H2O nor produce O2

Autotrophs

-Use inorganic carbon source (CO2) as source of carbon

Phototrophs

-Use light as their energy source

Chemoheterotrophs

-Use organic compounds as a carbon source and chemical compounds (mostly organic chemicals) as an energy source -Aerobic respiration: most animals, fungi, and protozoa and many bacteria (Humans!) -Anaerobic respiration: some animals and bacteria -Fermentation: some bacteria and yeasts

Photoheterotrophs

-Use organic compounds as a carbon source and light as an energy source -Green nonsulfur and purple nonsulfur bacteria -Prokaryotes only

Anaerobic respiration: fermentation

-Used because sometimes cells cannot completely oxidize glucose by cellular respiration -Utilizes glycolysis and then converts pyruvic acid into other compounds (organic waste products) -Cells require constant source of NAD+ (in order to absorb hydrogens not broken down by glycolysis) that is not regenerated by simply using glycolysis -Fermentation is the process of taking reduced NADH and oxidizing it back into NAD+ so NAD+ can be reused for glycolysis -Fermentation pathways provide cells with another way of regenerating NAD+ -Partial oxidation of sugar (or other metabolites) to release energy using an organic molecule as an electron accept rather than ETC (NADH oxidized to NAD+ while organic molecule is reduced) -Essential function-regeneration of NAD+ for glycolysis, so that ADP can be phosphorylated to ATP -Not as energetically efficient as respiration -Most of the potential energy remains in the bonds of fermentation products -Fermentation products are wastes to cells that make them, many are useful to humans (ethanol, acetic acid, and lactic acid)

Unicellular algae: dinoglagellates

-Usually photosynthetic -Some produce light and are often called fire algae -Responsible for "red tides"

Osmolarity: hydrostatic pressure

-Water exerts pressure in proportion to its depth -For every additional 10m of depth, water pressure increases 1atm

Modern age of microbiology

-We currently investigate how genes work through microbial genetic, molecular biology, recombinant DNA technology, and gene therapy -We investigate the role microorganisms play in the environment through environmental microbiology -We defend against disease through immunology and chemotherapy

Lazzaro Spallanzani

-When Spallanzani boiled gravy and left the flask open, the gravy was teeming with microorganisms, but when Spallanzani boiled gravy and sealed the flask, the gravy was free of microorganisms Concluded that... -Needham failed to heat vials sufficiently to kill all microbes or had not sealed vials tightly enough -Microorganisms exist in air and can contaminate experiments -Spontaneous generation of microorganisms does not occur -Critics said sealed vials did not allow enough air for organisms to survive and that prolonged heating destroyed the "life force"

Replication of animal viruses: latency

-When animal viruses remain dormant in host cells -May be prolonged for years with no viral activity, signs, or symptoms -Some latent viruses do not become incorporated into host chromosome (exist as episomes) -When provirus is incorporated into host DNA, condition is permanent; becomes permanent physical part of host's chromosome

Five kingdoms: fungi

-World's largest organism is a honey mushroom (a microorganism) -Unicellular or multicellular eukaryotes -Reproduce asexually and sexually -Five phyla based on their mode of sexual reproduction -Lack chlorophyll -Have a cell wall made of chitin -Are saprophytes -"Garbage disposers" of nature

Leeuwenhoek categories for microorganisms: small animals (helminths)

-Worms that live inside your body -Diseases: tapeworms, flukes, and roundworms

Gene expression and regulation

-Your cells can control when gene is "turned on or off" with promotor regions -Different in prokaryotic and eukaryotic cells -Because cells are specialized in multicellular organisms, only certain genes are expressed in each type of cell

How viruses are distinguished

1. Type of genetic material they contain -Double stranded or single stranded DNA? Double or single stranded RNA? Plus or minus sense? Do they undergo reverse transcription? 2. Kinds of cells they attack (host range) -Strictly animal host? Strictly plant host? Does it infect bacteria? 3. Size of virus 4. Nature of capsid coat 5. Shape of virus 6. Presence or absence of envelope

Protozoa: reproduction

Asexual reproduction -Binary fission: produces two daughter cells -Schizogony: multiple nuclear divisions before cytoplasmic divisions, results in more than two daughter cells Sexual reproduction -Gametocyte production: two haploid gametes which fuse to form a diploid zygote

Effects of solutions on organisms (tonicity)

Cells without a wall (animal cells) -In isotonic solutions, water enters and leaves the cell at a constant, equal rate -In hypertonic solutions, water leaves the cell and the cytoplasm shrinks (crenation) -In hypotonic solutions, water enters the cell and the cell bursts/lyses Cells with a wall (plant, fungal, and bacterial cells) -In isotonic solutions, free water enters and leaves the cell -In hypertonic solutions, water leaves the cell and the cell wall stretches (and lyses) because it is anchored to the shrinking cell membrane (plasmolysis) -In hypotonic solutions, water enters the cell but the cell membrane cannot grow and burst because the cell wall around it is rigid (this makes for a happy bacteria)

Replication of animal viruses: entry and uncoating

Direct penetration -Naked viruses with glycoproteins on the capsid itself; capsid recognizes the receptors on the host cell -Capsid stays on the outside of the cell and inserts its viral genome into the cell Endocytosis -Enveloped viruses use spiked glycoproteins on the outside to attach and enter into host cells -The entire virus cell enters the host cell and form there, the nucleocapsid leaves the viral cell and the uncoated capsid then releases its viral genome Membrane fusion -Viral glycoproteins recognize and bond to receptors on the cytoplasmic membrane of the host -The enveloped virus fuses with the host membrane -Viral glycoproteins remain in the cytoplasmic membrane but the uncoated capsid enters the host cell and releases the viral genome

Morphology of prokaryotic cells: pleomorphic

Do not necessarily have any defined shape

Glycolysis: steps

Energy-Investment Stage -Glucose is phosphorylated by ATP to form glucose-6-phosphate -The atoms of glucose-6-phosphate are rearranged to form fructose-6-phosphate, which is phosphorylated by ATP to form fructose-1,6-biphosphate Lysis Stage -Fructose-1,6-biphosphate is cleaved to form glyceraldehyde-3-phosphate (G3P) and dihydroxyacetone phosphate (DHAP) -DHAP is rearranged to form another G3P Energy-Conserving Stage -Inorganic phosphates are added to the two G3P molecules and two NAD+ are reduced -Two ADP are phosphorylated by substrate-level phosphorylation to form two ATP -The remaining phosphates are moved to the middle carbons and a water molecule is removed from each substrate -Two ADP are phosphorylated by substrate-level phosphorylation to form two ATP; two pyretic acid are formed

Eukaryotes vs. prokaryotes

Eukaryotes -Have membrane surrounding DNA; have a true nucleus -Have internal membrane-bound organelles -Membrane-bound organelles (ribosomes) are 80S -Call walls made of chitin, silicates, etc. -Larger; 10-100 μm in diameter -Large because they have vesicles that are able to move things throughout the cell -More complex, diverse structure -Eukaryotic flagella are a '9+2' arrangement of microtubules encased in the cell membrane and undulate -Examples: algae, protozoa, fungi, animals, and plants Prokaryotes -Do not have membrane surrounding their DNA; no nucleus -Lack various internal membrane-bound structures -Prokaryotic ribosomes are 70S -Small; ~1.0 μm in diameter -Smaller because everything occurs in the cytoplasm and because the small size is easy for diffusion to transfer molecules -Simpler structure -Prokaryotic flagella are rigid protein helices with a hollow core that rotate -Two types of prokaryotes: bacteria and archaea

Morphology of prokaryotic cells: spirillum

Have a wave form; coiled

Effects of animal viruses on cells: lytic infection, latent infection, persistent infection

Lytic infection -Viruses enter a host cell, replicate, and lyse the cell in order to get out (this kills the host cell) Latent infection -Virus present but doesn't cause harm to the cell until later, when it emerges in lytic infection Persistent infection -Virus enters host cell and slowly releases virions without killing the host cell -Transformation of normal cells to tumor cells, leading to cancer -Occurs from either latent or persistent infections

Defined media

Media where you know every single molecule in that media

Structure of viruses: naked vs. enveloped virus

Naked virus -Inside consists of nucleic acid -Outside consists of single capsomere subunits that together are called capsid -Capsid and nucleic acid together are called nucleocapsid Enveloped virus -Naked virus surrounded by envelope

Morphology of prokaryotic cells: spirochete

Skinny and tightly wound like a corkscrew; spiraled

Morphology of prokaryotic cells: vibrio

Slightly bent in the middle; curved rod