Lecture Exam 1 Flashcards
Hepatitis C
Hepacivirus (HCV)
Hepatitis B
Orthohepadnavirus
Human Herpesvirus 1
Simplexvirus (HHV-1)
Fever blisters, oral herpes. More common.
Human Herpesvirus 2
Simplexvirus (HHV-2)
Common genital herpes
Human Herpesvirus 3
Varicellovirus
Chicken pox
Flu
Influenzavirus
Aids/HIV
Lentivirus
Measles
Morbillivirus
Gastroenteritis
Norovirus
Papillomavirus
Papillomavirus
Rubella (German Measles)
Rubivirus
Mumps
Rubulavirus
Pertusis (whooping cough)
Bortadella pertussis
Acute gastroenteritis
Campylobacter jejuni
Chlamydia
Chlamydia trachomatis
Colitis
Clostridium difficile
Gangrene, enteritis
Clostridium perfringens
Diptheria
Corynebacterium diphtheriae
Tuberculosis
Mycobacterium tuberculosis
Gonhorrhea
Neisseria gonorrhoeae
Gastroenteritis
Salmonella enterica
Boils, impetigo, sinusitis
Staphylococcus aureus
Pneumonia
Streptococcus pneumoniae
Rheumatic fever, necrotizing fasciitis, strep throat
Streptococcus pyogenes
Candidiasis (oral thrush, vaginitis) (fungi)
Candida albicans
Flu (fungi)
Coccidioides immitis
Pneumonia (fungi)
Pneumocystis jirovecii
Diarrhea (protist)
Cryptosporidium parvum
Giardia
Giardia lamblia (protist)
Malaria
Plasmodium falciparum (protist)
Taeniasis (tapeworms)
Tania solium
How many types of viruses are there?
2, naked and enveloped
What are viruses?
- nonliving entities, not cells
- rely on enzymes/substrates of a host cell
- don’t replicate outside out of a host
- outside a host are completely inert, do not grow or develop
- much smaller than bacteria!
What is a naked virus?
Nucleic acid in a capsid. (Nucleocapsid).
What is an enveloped virus?
Nucleocapsid in a phospholipid envelope. Membrane derived from host membrane or organelles of host membrane.
Glycoprotein spikes
- Function in attachment to host cell
- Found in naked and enveloped virus
- So that virus infects the right cell. Viruses very specific!
What are the 5 types of DNA/RNA that viruses can have, and how quickly can they synthesize proteins?
- dsDNA (immediate)
- ssDNA (immediate)
- dsRNA (needs enzyme)
- +ssRNA (immediate, functions as mRNA)
- -ssRNA (needs enzyme)
What is a bacteriophage?
Viruses that infect bacteria. Found everywhere.
Stages of lytic replication
- Attachment
- Entry - via protein needle
- Synthesis - make RNAs, which are read to make proteins
- Assembly - viruses are assembled
- Release - via lysis of host cell
Plaques on agar due to lytic replication.
What is a temperate phage?
A bacteriophage that can choose between lytic and lysogenic replication?
What is a prophage?
When the temperate phage is within the bacteria’s chromosome. With reproduction both cell DNA and prophage are replicated.
What is induction?
The process by which a dormant prophage detaches from the DNA of a bacterium and switches from lysogenic to lytic replication.
Bacteriophage vs Temperate phage
Bacteriophage is virulent, can infect host cell. Temperate phage injects a dormant prophage, which can use lysogenic or lytic replication.
What is lysogenic conversion?
Presence of a lysogenic phage (or multiple) alters the phenotype of the cell. Viruses do not produce toxins, but cause the bacteria to produce toxins.
What does animal virus replication depend on?
- Virus type
- Type of genetic material
- Same basic steps as bacteriophage
+RNA/-RNA
+RNA contains genetic code
-RNA complement to the code
Attachment in Animal Virus Replication
Glycoproteins/other molecules attach to host cell receptors due to chemical attraction between virus and cell receptors.
Entry of enveloped viruses in Animal Virus Replication
Endocytosis or membrane fusion
Entry of naked viruses in Animal Virus Replication
Endocytosis, or injection of nucleic acid into cell
Steps of Animal Virus Replication
- Attachment
- Entry/penetration
- Uncoating
- Synthesis
- Assembly
- Release
Where does RNA replicate?
Cytoplasm, dsRNA and -ssRNA must carry their own enzymes
Where does DNA replicate?
Nucleus, using host enzymes
First to observe microorganisms
Antonie VanLeeuwenhoek
Used a magnifying glass w/excellent optics, not a compound microscope. Saw “animalcules”
Endosymbiotic theory
Theory that eukaryotic cells developed from prokarkyotic cells
Fluid mosaic model
Structure of a cell membrane is a double layer of phospholipids with protein molecules
Chromosome
Thread-like structure of nucleic acids and proteins that carries genetic information
Organelle
Specialized structure within a cell
Meiosis
Division into 4 daughter cells
Eukaryotic mitochondrion
Ribosome is 70s. Circular DNA. Double membrane.
Cristae - folds created by the inner membrane
Matrix - inside of inner membrane
Chloroplasts
2 membrane, where photosynthesis takes place
Thylakoids
Sites where photosynthesis occurs. Small discs.
Grana
Stacks of thylakoids
Stroma
Surround grana/thylakoids. 70s ribosomes, suggesting that chloroplasts came from bacteria.
Cytoskelteon functions and contents
Maintains cell shape, motility, anchors organelles, vehicle transports, cytokinesis(division)
- Microtubules
- Microfilaments
- Intermediate filaments
Ribosomes
Organelle that synthesizes proteins. Made of rRNA and protein, same function in both bacterial and eukaryotic ribosomes.
Lg - 60s
Sm - 40s
Together - 80s
Golgi body
Packages proteins
Nucleus
2 membrane, 2 phospholipid bilayers. Things go in/out via nuclear pores. Holds DNA, which determines function. Different gene expressions produce different phenotypes
Nucleolus
Site of ribosome biogenesis
Rough ER
protein synthesis
Smooth ER
Calcium storage, lipid synthesis
First to view cells
Robert Hooke, under compound microscope
What are cilia and flagella?
Microtubules. No bacteria have cilia!
Antonie Van Leeuwenhoek
First to observe microorganisms. Used magnifying glass w/excellent optics
Genome
Complete set of genes in an organism
Plasmid
Extra-chromosomal molecule of DNA that replicates independently of the chromosome. Typically circular, typically not in eukaryotes but common in bacteria. Contains non-essential, accessory genes, such as those for antibiotic resistance.
Endoflagellum
Flagella inside the structure of the cell, also called axial filaments.
Taxis
Movement in response to a stimulus (bacterial cells)
Fimbriae vs Pili
Appendages on bacterial cells.
Fimbriae: bristle like proteins used for adhesions. More numerous, often attach to microvilli of intestines.
Pili: long protein appendages, less numerous, used for adherence, some used for motility (reeling in), used for conjugation
Glycocalyx (2 layers)
Layer of complex carbohydrates covering the bacterial cell.
- Capsule: dense, firmly attached, helps escape digestive system by binding to antibodies
- Slime layer (biofilm): loosely attached to the cell, very protective.
Peptidoglycan
Forms bacterial cell wall, consists of amino acids and carbohydrates. Protects from osmotic forces, maintains cell shape.
- Made of NAGs and NAMs
- Thick layer with Gram-positive bacteria
Periplasmic space
The bacterial cell wall is not totally solid, things can flow through the peptidoglycan without transport proteins
Lipopolysaccharide (LPS)
Outer membrane of gram-negative bacteria, comprised of Lipid A, a core polysaccharide, and an O-side chain. (Phospholipids and proteins)
Gram-pos vs Gram-neg membranes
G-pos: plasma membrane, peptidoglycan. Contains teichoic acid/lipoteichoic acid, not found in G-neg
G-neg: plasma membrane, thin peptidoglycan, outer LPS
Acid-fast bacteria
Subgroup of Gram-positive bacteria that has mycelia acid in the cell wall, which is a wax that prevents the gram stain from working properly. Have to use acid-fast stain to visualize. Example: tuberculosis
Flagella purpose
Motility. Rotate from H+ to propel through the environment.
Chemotaxis
Bacterial movement in response to food
Phototaxis
Bacterial movement in response to light
Side by side bacillus arrangement
Palisade
Endospores
Form via sporulation. Metabolically inactive, resistant to drying, UV light, heat, cold. Form when conditions are unfavorable, dormant until conditions improve for vegetative growth.
Cytoskeleton in bacteria
Simpler than in eukaryotes. Helical/linear proteins force bacteria to take a bacillus shape.
Vibrio
Comma shape for bacteria
Bacterial cells that take many shapes
Pleomorphic
The field of naming organisms
Taxonomy. Organized based on evolutionary similarities.
Carolus Linnaeus
“Linnean system” First system of taxonomy/classification. It had 3 kingdoms: plants, animals, minerals. It was the first to establish a “binomial nomenclature” wherein all animals were give a unique genus/species combo.
Inventor of current system of taxonomy
Carl Woese. Domains: Eukarya, Bacteria, Archea
Protist
Animal that is not a plant/animal/fungus
Mold morphology
Multicellular. Cells form long filaments called hyphae. A mat of hyphae=mycelium
Yeast morphology
Multicellular, oval-round in shape
Pseudohyphae
A “filament” of yeast cells that do not attach after budding. (Candida albicans)
Dimorphic fungi
Switch from mold (environment) to yeast (inside a person) depending on temperature
Protozoa characteristics
Unicellular/no cell walls. Complex life cycles, use sexual and asexual reproduction. Cholesterol
Fungi characteristics
Uni or multicellular. Asexual or sexual. Parasites or saprobes (live off death).
Cell wall = chitin
Cell membrane = ergosterol
Fungi cell wall/cell membrane
Cell wall = chitin
Cell membrane = ergosterol
Protozoa lifecycle
- Trophozoite: feeding, growth. Happens in all protozoa. Often motile via cilia, flagella, or pseudopodia (cytoplasm extension)
- Cyst: not in all protozoa. Environmentally resistant, not feeding, similar to endospores. Can survive GI tract then become a trophozoite in the gut.
Animal characteristics
Multicellular, complex organ systems w/variation among groups. Mostly sexual reproduction.
Domain Eukarya characteristics
- Membrane bound nucleus
- Sexual or asexual
- Can have cell wall
- insensitive to antibiotics
- 80s ribosomes
- fungi, protists, animals
Cestoda
Tapeworms (animals). Flat, segmented bodies, intestinal parasites that absorb nutrients from host gut. No digestive systems - nutrients are absorbed through the skin. Every segment has both M/F parts.
Scolex: at one end, has hooks and suckers for attachment to the host
Domain Bacteria characteristics
- No membrane-bound nucleus
- Asexual reproduction (mitosis)
- Have cell walls
- Sensitive to antibiotics
- 70s ribosomes
Domain Archea Characteristics
- No membrane-bound nucleus
- Asexual
- Have a cell wall w/no peptidoglycan
- Not sensitive to abx
- 70s ribosomes
- Adapted for extreme heat, low pH, high salinity. Not pathogens.
- Cell membrane is monolayer with isoprenoid subunits, not fatty acids (would melt)
- Methagenous - converts CO2 to methane
Halobacteria s.p.p.
Require high salt concentrations for growth (hot springs)
Methanogen
Converts CO2 to methane. Live in soil, H2O, landfills, mammalian digestive tracts
Virus
Mostly nonliving entities, not cells. Acellular infections agents that rely on enzymes/substrates of a host cell. Very small. Inert outside of a host. Naked or enveloped
Capsid
Protein coat that protects viral nucleic acid. Many shapes, all viruses have. Made of capsomeres.
Viral envelope
Acquired from a host cell’s internal or cell membranes. Can be a phospholipids bilayer or other proteins.
Glycoprotein spikes
In both naked/enveloped viruses. Function in attachment to a host cell, and to ensure that a virus infects the right cell, as viruses have very specific hosts.
Viral nucleic acids
Viruses can have DNA or RNA but not both. Can be circular, linear, or in segments (like chromosomes).
DNA: dsDNA, ssDNA
RNA: dsDNA, -ssRNA, +ssRNA
+ is the code, - is the template
+ssRNA acts like RNA
-ssRNA has the template for the code
Nucleocapsid
The capsid of a virus with the enclosed nucleic acid
Bacteriophage
Viruses that infect bacteria. Found everywhere.
Animal Virus Replication Step 1
Attachment. Glycoproteins/other molecules attach to host cell receptors. Chemical attraction between virus and cell receptors
Animal Virus Replication Step 2
Entry/Penetration. Enveloped: endocytosis or membrane fusion. Naked: endocytosis or injection into cell
Animal Virus Replication Step 3
Uncoating
Animal Virus Replication Step 4
Synthesis of nucleic acid.
RNA replicates in cytoplasm
DNA replicates in nucleus
Transcriptases
Virus enzymes that can read RNA to make copies.
Protein synthesis in RNA and DNA
RNA - Cytoplasm
DNA - Cytoplasm
Animal Virus Replication Step 5
Assembly of proteins.
RNA - Cytoplasm
DNA - Nucleus
Animal Virus Replication Step 6
Release. Naked viruses released via lysis, enveloped released via exocytosis (nuclear membrane) or budding (cell membrane)
Family of viruses
Viridae
Virus classification
Separate from organism classification and the tree of life.
Process by which dormant prophage comes out of DNA and switches to lytic replication
Induction
Lysogenic Conversion
The ability of phages to survive in a bacterium by integrating in to the DNA of the host. Once integrated they are a prophage.
C. diphtheriae
V. cholerae
Prions
Proteinaceous infections agents that are simpler than viruses, do not have nucleic acid. Native prions change to infections prions due to a change in the secondary structure.
Cellular PrP
Prion protein made by all mammals. Normal structure is alpha-helices. Functions in membrane transport.
Prion PrP
Infections! Folds of beta sheets instead of alpha-helices. Nonfunctional, indigestible, folds up in cell to disrupt cell function. Brain disease - spongiform encephalopathy (BSE, fatal, loss of brain matter). No treatment aside from prevention.
Kuru
Rare infectious disease, originally caused by cannibalism after death.
Enzymes
Biological catalysts, make reactions possible.
- Proteins (usually)
- reused
- lower activation energy
- ribosomes are enzymes
- may require cofactors/coenzymes
Cofactor
Inorganic. Metal ions common (MG)
Coenzyme
Organic non-protein, NAD+, FAD, coenzyme Q
NAD+
Reduced to NADH, needed for glycolysis, Krebs, Acetyl CoA synthesis. Oxidized to NAD+ at the ETC or during fermentation.
Enzyme acitvity regulation (3)
Competitive inhibition, allosteric inhibition, allosteric activation
Endoenzymes
Found within the cell, active inside the cell, produced/utilized inside the cell
Exoenzymes
Active outside the cell, secreted by the cell into the environment
Metabolism
Sum of all reactions inside a cell
Metabolic pathway
Series of chemical reactions mediated by enzymes. The product of one becomes the substrate of the next
Catabolism
The break down of large molecules into smaller ones, releasing energy (exergonic). Hydrolysis = process of making large molecules into smaller ones
Anabolism
Synthesis of large molecules from smaller ones using ATP (endergonic).
Metabolism regulation
Feedback inhibition (a type of allosteric inhibition). Synthesize molecules only pan. Tryptophan, which is expensive to make, has an allosteric inhibitor at many steps.
Catabolite repression
Presence of cheaper substrate prevents the use of an energetically unfavorable one.
Presence of cheaper substrate prevents the use of an energetically unfavorable one.
Catabolite repression
ATP energy (3)
Stored in the terminal phosphate groups with high energy covalent bonds.
- Substrate-level phosphorylation
- Oxidative phosphorylation
- Photophosphorylation
Photophosphorylation
Photosynthesis
Oxidative phosphorylation
ETC
Substrate-level phosphorylation
Krebs, glycolysis, fermentation
Cellular respiration
Aerobic - O2 is final electron acceptor. Via ETC/chemiosmosis. 34-36 ATP
Anaerobic - inorganic molecule (NO3-, SO42, CO2). Via ETC/ehcmiosmosis. 32 ATP. Example is methanization.
Fermentation
Organic molecule. Yields 1-2 ATP.
Glycolysis pathways of fermentation (2)
EMP: glucose is converted to 2 pyruvate + 2 ATP + 2 NADH
Entner-doudoroff: glucose is converted to 2 pyruvate + 1 ATP + 1 NADH + 1 NADPH
Two types of EMP fermentation
- Alcohol. Fermentation by yeast. Beer wine bread. Glucose + 2 ADP –> 2 ATP + CO2 + Ethanol
- Lactic acid, in human muscle cells.
Glucose + 2 ADP –> 2 ATP + lactate
Types of bacterial fermentation (6)
Homolactic Heterolactic Propionic acid Mixed acid 2, 3 butanediol ABE
Homolactic fermentation
End products: lactic acid. (yogurt, cheese)
Heterolactic fermentation
End products: lactic acid, ethanol, CO2 (saurkraut, kimchi)
Propionic acid
End products: propionic acid, acetic acid, CO2 (emmentaler)
Mixed acid
End products: lactate, succinate, acetate, formate, ethanol, co2, h2. (E. coli)
2, 3 butanediol
End products: 2,3 butanediolh, acetic acid, lactic acid, formic acid, co2
ABE
End products: acetone, butanol, ethanol. (potential biofuel)
Photosynthesis
Light dependent: Use light to produce ATP and reduce NADPH.
Light independent: autotrophs use ATP and NADPH to fix inorganic carbon
Hep C
Hepacivirus
Hep B
Orthohepadnavirus
HHV1, HHV2
Simplexvirus
HHV3
Varicellovirus
Influenza
Influenzavirus
HIV
Lentivirus
Noro
Norovirus
HPV, warts
Pappillomavirus
Measles
Morbillivirus
German measles
Rubivirus
Mumps
Rubulavirus
Binary fission
Each cell divides into 2 new cells.
Doubling time
(Generation time). The time required for a bacterial population to double in size, for a bacterial cell to grow/divide. Dependent on intrinsic, nutritional, and physical conditions.
Exponential growth
Nn = No x 2^n
bacteria generation = Original # of bacteria x growth factor
Can calculate expected increase in population if generation time and total growth is known.
Lag phase
No growth or death. Acclimating to new environment. Cells increase in size but do not divide.
Log phase
Exponential increase, intrinsic growth rate. Ideal time for study for many experience.
Stationary phase
Population size does not change, nutrients are decreasing, waste products are increasing. Sporulation begins. Growth rate = death rate
Death/decline phase
Number of live bacteria declines. Nutrients are depleted, waste products are abundant.
Indirect method of measuring bacterial growth
Turbidity. Don’t know the # of cells but know that there has been growth. Can track using spectophotometer.
Direct methods of measuring bacterial growth.
- Petroff - Hauser chamber slide. Slide with grid, count cells and multiply. Works for dead/non-motile bacteria
- Serial dilution and viable plate count: can estimate the number of live cells in an original sample (CFU/mL). Serial dilution reduces the # of cells to give a countable # of colonies on plates. (30-300). Decreased by a factor of 10 each dilution.
Nutrients
Chemicals that an organism needs to build biological molecules. (C,H,N,O,S)
Heterotrophs
Acquire carbon from existing organic molecules. “feeding off the other”
Autotrophs
Take in carbon at CO2 (inorganic carbon). “Feeding yourself”
Chemotrophs
Use chemical reactions as a source of energy.
- Organotrophs: use organic molecules as energy source
- Lithotrophs: use inorganic molecules as energy source. Found only in microbes.
Phototrophs
Use sunlight as a source of energy.
Uses inorganic molecules as an energy source.
Lithotrophs.
Bacteria: nirtosomonas, nitrobacter
Archea: methanogens. H2 is electron and energy source.
Oxygen toxicity
Use of O2 and O2 containing environments produce molecules that can cause damage to biological molecules. Organisms that tolerate the presence of O2 have to have mechanisms to dealt with reactive molecules like superoxide CO2- and Peroxides O2-2, H2O2). Bacteria have enzymes to detoxify these molecules.
Obligate aerobe
Requires O2 for metabolism. Uses aerobic respiration. Able to detoxify reactive O2 molecules using detoxification enzymes.
Obligate anaerobes
Do not use O2, use anaerobic respiration or fermentation. Cannot detoxify reactive O2 molecules, must live in anaerobic environment.
Facultative anaerobes
Can detoxify O2 molecules using detoxification enzymes. Will use aerobic respiration of O2 is present but use fermentation if in anaerobic conditions. (E. coli)
Aerotolerant anaerobes
Do not require O2, use aerobic respiration or fermentation. Can detoxify O2 radicals with enzymes. (lactobacillus)
Psychrophiles
-5 to -20 C
Mesophiles
15 - 45 C. All pathogens! Human body temperature.
Thermophiles
45-80C
Hypertheromphiles
65-105C
Acidophile
1-5.5 pH
Neutrophile
5.5-8.5 pH
Alkaliphile
7.5-11.5 pH
Water activity
Amount of free H2O molecules in a substance. All organisms need H2O to carry out metabolic pathways. Water activity (Aw) is a measure of the amount of water in products. Most organisms are inhibited at Aw
Osmolarity
Most organisms live in a nearly isotonic environment. The solute concentration in an environment affects the amount of H2O available to organisms. Some are well adapted to NaCl in the environment.
Halophiles
Require NaCl for growth. 3.5-35% g/mL
Halotolerante
Do not require NaCl, but can grow in increased salinity
Enzymes that protect against reactive oxygen (2)
Superoxide dimutase, Catalase
Streptomycetaceae
Antibiotic agent, especially agains tuberculosis and the plague
Corynebateriacea
Diptheria
Mycobacteriacea
Tuberculosis
Clostridiacea
Bolulism, perfringens (food poisoning), tetanus, difficile
Bacillaceae
Anthrax
Rickettsiaceae
Typhus, rocky mountain fever
Enterobacteriaceae
Salmonella, E. Coli, yersinia pestis, shigella
Alcaligenaceae
Bortadella pertussis
Helicobacteriaceae
H. pylori - ulcers, stomach cancer
Neisseriaceae
Gonorrhea, meningitis
Spirochetaceae
Syphilis, lyme
Campylobacteriaceae
Food poisoning