Lecture Midterm I Flashcards
Leeuwenhoek
First to observe microbes ( except viruses) in 1670’s through 300x simple microscopes.
Hooke
Invented microscope and discovered cells in cork.
Redi
Disproved spontaneous generation (proposed by Aristotle), with meat in sealed flask experiment. 1600’s
Needham
Boiled nutrients, sealed with cork, and “spontaneously” grew microbes. 1740’s
Spallanzani
Boiling solution for longer and heat sealing glass prevented growth. 1768
Pasteur
Swan-necked flasks. Pasteurization for wine. Rabies vaccine. 1800’s
Koch
Agar plates, isolation of bacteria. Causative agent of anthrax. Koch’s postulates. 1870’s
Gram
Staining method based on differential retention of dye. 1880’s
Semmelweis
Handwashing prevents childbed fever. 1840’s.
Lister
Aseptic surgery. 1880’s.
Nightingale
Clean bandages and environment.
Jenner
First vaccine (smallpox/cowpox). 1772.
Compare number of cells in you vs. number of microbes on you.
You cells: 10 trillion.
Microbes on you: 100 trillion.
Name 11 components of prokaryotic cells.
cell wall, plasma membrane, flagella, pilli, fimbriae, glycocalyx, cytoplasm, ribosomes, inclusions, nucleoid
Glycocalyces
Protect cells from drying. Slime layer is a water soluble, loose biofilm. Capsules allow bacteria to disguise itself and prevent bacteria from being recognized because chemicals in many bacterial capsules are similar to chemicals normally found in body.
Flagella structure
- Made of protein (flagellin)
- 3 parts: filament, hook, basal body
- hollow core
- lengthens at the tip
Flagella arrangements
- peritrichous (all around)
- lophotrichous (few at one end)
- amphitrichous (one at each end)
- monotrichouse (one at one end)
Fimbriae
- made of protein
- biofilm formation
- movement by pulling
- electrical signals for communication
Pili
- type of fimbria
- transfer of DNA through hollow tube
Cell wall
- Made of peptidoglycan, which is made of repeating disaccharides NAG and NAM. Cross-linked by amino acid side chains
Gram positive
- Stains purple due to thick peptidoglycan layer.
- Teichoic acid and lipoteichoic acid (anchors peptidoglycan to plasma membrane).
Gram negative
- Stains pink
- Outer bilayer membrane composed of inner phospholipid layer and outer lipopolysaccharide (LPS) layer
- LPS contains lipid A (endotoxin)
- Porins allow passage of mid sized molecules such as glucose
- Periplasmic space allows for compartmentalization and enzymatic activities.
Plasma membrane
- Phospholipid bilayer
- ETC
- Selectively permeable, establish concentration gradient and electrical gradient.
Group translocation
Chemical modification on the way through. Membrane impermeable to altered form. Phosphorylation of glucose as it passes through maintains glucose gradient.
Size of prokaryotic vs eukaryotic ribosome
Prokaryotic ribosomes are 70S, eukaryotic ribosomes are 80S. Many antibacterial drugs act on bacterial 70S ribosomes without deleterious effects on 80S ribosomes of eukaryotes
Describe genetic material of bacteria
Nucleoid, no membrane around DNA. Circular chromosome, usually only 1.
Two genera of bacteria capable of forming endospores
Bacillus and Clostridium, both gram positive
Characteristics of endospores
- v. low metabolism
- resistant to drying, heat, radiation, chemicals
- remain dormant until conditions are favorable
Structure of endospores
- Core: DNA, RNA, proteins, dipicolinic acid, Ca+2
- Cortex: 2 membranes, with peptidoglycan in between
- Spore coat: layers of keratin-like protein
Name the 6 basic cell shapes
- coccus
- coccobacillus
- bacillus
- vibrio
- spirillum (stiff)
- spirochete (flexible)
Define pleomorphic
vary in size and shape
What is the most common process of prokaryote reproduction, and what are the other processes?
Binary fission is the most common. Prokaryotic cells may also divide by snapping division and reproductive structure formation (budding).
Name the arrangements of prokaryotic cells
- diplo
- strepto
- tetrad
- sarcinae
- staphylo
Characteristics of viruses
- non-living
- infectious
- acellular (no ribosomes, cytosol, or cytoplasmic membrane)
- all have genetic material
What is the extracellular form of a virus called?
virion
Describe the structure of a virus
The nucleic acid is enclosed in a capsid (protein coat) composed of capsomeres. A viral nucleic acid surrounded by a capsid is called a nucleocapsid. Some virion have a phospholipid envelope, which comes from the host cell.
Shapes of virions
- helical
- polyhedral
- complex
Name the 2 main types of viral replication strategy
- Lytic: results in the death of host cell
- Lysogeny: infected host cells grow and reproduce for many generations before they lyse. Passed on to daughter host cells. Feature of bacteriophages. Called temperate phages or lysogenic phages.
Name the 5 stages of the lytic replication cycle
- Attachment
- Entry
- Synthesis
- Assembly
- Replication
Name the 5 stages of the lysogenic replication cycle
- Attachment
- Entry
- Prophage (inserts into DNA of host cell, not active)
- Replication (of host cell, including prophage)
- Induction: prophage is excised from host cell and continues with Synthesis, Assembly, and Release.
Describe the oncogene theory of induction of cancer
It usually take multiple hits to activate a protooncogene. In the first hit, virus inserts a promoter to activate protooncogene. In the second hit, virus inserts (disrupts) repressor gene.
How can viruses cause cancer?
- carry copies of oncogenes as part of their genome.
- promot oncogenes already present in host
- interfere with tumor suppression
What are prions?
Proteinaceous infective particles. Prions have no nucleic acids. Prion PrP influences folding of normal PrP molecules and converts them to prion PrP form
Name a disease caused by prions
bovine spongiform encephalopathy
Metabolism
Sum of the anabolic (synthesis) and catabolic (degradation) reactions
Oxidation
Loss of electrons (or hydrogen), releases energy.
Reduction
Gain of electrons (or hydrogen), stores energy.
Parts of an enzyme
Apoenzyme is the main protein component. Organic coenzymes, inorganic cofactors. Apoenzyme + Coenzyme + Cofactor = Holoenzyme. Site where substrate binds is called Active Site.
Factors that affect enzyme activity
Temperature, pH, and concentration.
Types of enzyme inhibition
- Competitive inhibition: Inhibitor competes with substrate for active site.
2a. Allosteric inhibition: Allosteric inhibitor distorts active site.
2b. Allosteric activation: Allosteric activator makes a distorted, nonfunctional site, active.
Describe feedback inhibition
A type of allosteric inhibition. The end product of a catalyzed reaction acts as and allosteric inhibitor on the apoenzyme, inhibiting further catalysis.
Name 3 important electron carrier molecules, and their reduced states.
- NAD+ to NADH (carries 1 of the 2 e- as part of H)
- NADP+ to NADPH (carries 1 of the 2 e- as part of H)
- FAD to FADH2 (carries both e- as part of H)
What are the 2 different pathways of glucose catabolism, and what are the end products?
- Aerobic respiration. End products are CO2 and H2O. Theoretically, 38 ATP are produced: 2 net from glycolysis, 2 from Krebs, 34 from ETC.
- Anaerobic fermentation: organic waste products (lactic acid, alcohol). 2 ATP produced.
What are the end products of glycolysis?
1 glucose –> 2 pyruvate + 2 ATP
Besides ATP, what is the key end product of fermentation, and why?
In fermentation, one of the key end products is NAD+, which is reused in glycolysis. 2 NADH –> 2 NAD+
What are the end products of glycolysis?
2 pyruvate + 2 net ATP + 2 NADH
What are the 2 alternatives to glycolysis used by certain bacteria, and what is the common glycolytic pathway called?
The common glycolysis is called Embden-Myerhoff. The alternatives are:
1. Enter-Doudoroff
2. Pentose phosphate shunt
Both can lead to Krebs or fermentation
What are the products of Enter-Doudoroff?
2 pyruvate + 1 net ATP + 1 NADH + 1 NADPH
What are the products of the pentose phosphate shunt?
G-6-P –> ribose + ribulose + 2 NADPH
How are organisms classified with respect to how they acquire energy?
Photo- vs. Chemo-
How are organisms classified with respect to how they acquire carbon?
Auto- vs. Hetero-
How are organisms classified with respect to how they acquire electrons?
Litho- vs. Organo-
Factors affecting bacterial growth
- Oxygen
- Temperature
- pH
- Nutrition
How are the different bacterial tolerances to oxygen described?
- Aerobes
- Obligate anaerobes
- Microaerophiles
- Facultative anaerobes (can tolerate lack of oxygen, but grow better with oxygen)
- Aerotolerant anaerobes (grow equally well in aerobic and anaerobic environments)
What are the 4 toxic forms of oxygen, and what are the mechanisms for dealing with them?
- Singlet oxygen - Carotenoids
- Superoxide radicals - Superoxide dismutase
- Peroxide anions - Catalase and peroxidase
- Hydroxyl radicals - Aerobes prevent formation with catalase and peroxidase
How are bacterial tolerances to temperature described?
- Psychrophile
- Mesophile
- Thermophile
- Extreme thermophile
How are bacterial tolerances to pH described?
- Alkalinophile
- Neutrophile
- Acidophile
How are bacterial tolerances to osmotic pressure described?
- Nonhalophile
- Moderate halophile
- Extreme halophile
Name 2 types of nutrient growth media
- Defined synthetic medium. All components are chemically defined.
- Complex medium. At lease one component is a complex biological material, and may have slight variation from batch to batch.
Name 2 types of diagnostic growth media
- Selective medium: A medium that encourages the growth of some organisms and inhibits the growth of others.
- Differential medium: Allows differentiation of organisms by the presence or absence of a particular chemical reaction. (e.g., in Manitol Salt Agar, the fermentation of manitol by certain bacterial changes the color of the medium.)
What are the phases of bacterial growth?
- Lag phase
- Log phase
- Stationary phase
- Decline, or Death phase
Define generation time
Time required for population to double.
What is the formula for calculating the population of bacteria after a certain time, with a known generation time?
P(t1) = P(t0) x 2^n n = number of generation
Describe the - structure, - number of chromosomes, - number of copies, and - location of prokaryotic chromosomes.
- circular
- 1
- haploid
- nucleoid
Compare and contrast prokaryotic chromosome with archaeal chromosome.
Archaeal DNA is also haploid, located in nucleoid, and circular. However, archaeal DNA is wrapped around histones (globular protein), similar to eukaryotes.
Each plasmid carries info required for its own replication. T/F
True
What are the function of plasmids?
Plasmids are not needed for normal metabolism, growth, or reproduction.
Plasmids can confer advantages to cells that carry them.
What are some examples of plasmid functions?
- Fertility plasmids: carry instructions for conjugation
- Virulence plasmids: become pathogenic
- Bacteriocin plasmids: kills other bacteria that lack the plasmid
- Resistance plasmids: resistance to antibiotics
Characteristics of prokaryotic DNA replication
- Bidirectional from a single point of origin. Helicase unzips DNA at origin.
- Topoisomerases: make DNA break so rings can separate.
- Methylation: parent strand (usually adenine) is methylated; daughter strand is not methylated.
What are the functions of methylation of the daughter strand of DNA?
- Control of genetic expression (turn genes on/off)
- Initiation of DNA replication
- Protection from viral infection by allowing cells to distinguish self DNA from viral DNA to selectively degrade viral DNA.
- Repair of DNA (distinguishes between new and old DNA)
Describe the mechanism and direction of DNA synthesis.
DNA synthesis always precedes in the 5’ to 3’ direction, with new DNA being added on the 3’ end. The leading strand is synthesized continuously. The lagging strand is synthesized discontinuously in units of Okazaki fragments. DNA ligase seals the gaps between Okazaki fragments.
Name 4 differences of eukaryotic vs. prokaryotic DNA replication
Eukaryotic DNA replication has:
- Four families of DNA polymerase (initiate replication, elongates leading strand, replicate lagging strand, replicates mitochondrial DNA)
- Thousands of replication origins
- Shorter Okazaki fragments
- Plant and animal cells methylate cytosine bases
DNA is ________ to RNA, which is ________ (by ribosomes) to form polypeptides.
transcribed, translated
Name the 3 steps of transcription
- Initiation. RNApol binds to promoters. Sigma factor attaches to RNApol and enhances promoter recognition.
- Elongation. Only one DNA strand is transcribed. Multiple copies of RNApol can transcribe at the same time.
- Termination. Self-termination G-C loop or Rho-dependent (termination protein that wedges between RNApol and DNA)
Where does transcription in Eukaryotes occur?
Nucleus (and mitochondria, chloroplasts)
Name the 3 stages of translation
- Initiation. Two ribosomal subunits (50S, 30S) mRNA, protein factors, and tRNA^fMet form an initiation complex. Initiation in prokaryotes may occur while the cell is still transcribing mRNA from DNA.
- Elongation. Can form polyribosomes, with multiple ribosome translating at the same time.
- Termination. Release factors recognize stop codons and activate ribozymes to sever polypeptide.
Translation in eukaryotes vs. prokaryotes
In eukaryotes:
- initiation with 5’ gunning cap (instead of AUG)
- first amino acid is methionine (instead of formyl-methionine)
Three types of horizontal gene transfer
- Transformation
- Transduction
- Bacterial conjugation
Describe transformation
Competent recipient cell takes up DNA from the environment.
What is transduction?
Transduction is a form of horizontal gene transfer involving the transfer of DNA from one cell to another via a replicating virus.
What are the two types of transduction?
- Generalized transduction
2. Specialized transduction
Define generalized transduction
Random DNA fragment from host bacterial cell packaged into newly formed phage. The transducing phage infects donor DNA into recipient host cell. Donor DNA is incorporated into recipient’s chromosome by recombination.
Describe specialized transduction
Occurs when lysogeny ends, at induction of the Lytic cycle.
Bacterial DNA on either side of viral DNA is excised along with the phage DNA.
Phage infects new cell.
Phage incorporates into new host DNA, along with DNA fragments from previous host.
Recombinant DNA is formed.
Describe bacterial conjugation
Donor attaches to a recipient cell with its pilus.
One strand of plasmid DNA transfers to the recipient.
The recipient synthesizes a complementary strand; the donor synthesizes a complementary strand, restoring its complete plasmid.
Describe high frequency bacterial conjugation
Similar to regular bacterial conjugation, but the F plasmid does not remain independent in the cytosol but instead integrates into the cellular chromosome.
What are transposons
Transposons are segments of DNA that transpose themselves from one location in a DNA molecule to another location in the same or a different molecule. Contain palindromic sequences at each end.
What are constitutive genes
Genes that are always on.
What are inducible operons, and what is an example
Inducers activate transcription. Eg: lac operon. Normally inactive, with repressor blocking RNApol on DNA. In the presence of lactose, an inducer (allolactose) inactivates the repressor and mRNA transcription proceeds.
What are repressible operons, and what is an example
Repressors deactivate transcription. Eg: tryptophan operon. If there is tryptophan, gene turns off because don’t need to synthesize more.
Anabolic pathways tend to be _______.
Catabolic pathways tend to be _______.
repressible (normally on)
inducible (normally off)
What is decimal reduction time?
Time required for 90% of population to die.
What are the two main mechanisms of action of antimicrobial agents?
- Disruption of cell membranes or cell walls
2. Damage to proteins and nucleic acids
