Microbiology Quiz 2 Study Guide PDF

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Summary of bacterial pathogens for lecture quiz 2 / Professor: Jen Fisher...

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M200 Quiz 2 Study Guide Review Quiz 1 study guide and Quiz 1 for the general topics covered. Modified versions of questions from Q1 will also be on this quiz. Make sure you understand the concept; don’t just memorize the answer to the question. Chapters 1-5 any material covered is fair game! But I will focus on Ch 2, 3, & 5

From Quiz 1: I.

Disease terminology and concepts

- Genomics: the branch of molecular biology concerned with the structure, function, evolution, and mapping of genomes

- Endosymbiosis: organisms living inside a larger organisms in a helpful way, specifically living inside cells and becoming part of the cell’s function II. Parts of a Bacterial cell (compare to….)

- Function: holds DNA in the cytoplasm - Parts: cell envelope, cytoplasm, nucleoid, plasmids, inclusion bodies, flagella, pili/ fimbriae. III. Parts of a Eukaryotic cell

- Function:!larger than pro cells; has a nucleus.! - Parts:!a membrane-bound!nucleus;! numerous membrane-bound organelles such as the endoplasmic reticulum, Golgi apparatus, chloroplasts, mitochondria, and others; and 3) several, rod-shaped chromosomes. IV. Gram positive vs Gram negative

- Gram Positive: cell walls composed of peptidoglycan. Stain purple.!Contains NAG. Also have teichoic acid, mycolic acid, and mycobacterium (waxy layer).!

- Gram Negative: cell wall with a THIN layer of peptidoglycan and an outer membrane of lipopolysaccharide not found in Gram pos.!Stain red/ pink. Has periplasmic space, lipoproteins, plasma membrane V. Cell envelope composition: The!cell envelope!comprises the!cell!membrane, the!cell!wall and an outer membrane if present. Gram positive bacteria!cell envelope!consists of the cytoplasmic membrane,!cell!wall and capsule. Gram negative!envelope!consists of the cytoplasmic membrane,!cell!wall, periplasmic space, outer membrane and capsule

VI. Staining:

Application of:

Reagent:

Cell color (Gram +):

Cell color (Gram -)

Primary dye

crystal violet

purple

purple

Trapping agent

iodine

purple

purple

Decolorizer

alcohol/acetone

purple

colorless

Counter stain

safrain/carbol fuchsin purple

pink

VII. Start connecting some of the concepts in bacterial growth/genomics to diseases

Chapter 6 I.

What can we culture? Why (not)?

- Only 1% of bacterial species have been cultured and grown in lab.! - Some pathogens/ environmental organisms still cannot grow on a petri plate bc complex nutritional/ environmental needs AND dependent relationships w other organisms.!

- Some CAN because the higher the % of pathogens the more they divide leading to success. II. Limits on microbial growth

- Ecological niches outside the norm for humans are considered ‘extreme.’! - Extremophiles bacteria, archaea, and some euk that can grow in extreme conditions.!

- Every protein and macromolecular structure within a cell is affected by changes in the environment.!

- ADAPTATION TO RAPID CHANGE IS DIFFICULT!!! - THE ULTIMATE GOAL OF ANY SPECIES IS TO MAKE MORE OF ITS KIND!!!! III. Nutrients and growth factors needed to grow

- Limiting nutrients help control bacterial overgrowth. - Rickettsia spp. Have such complex nutrient requirements that we still do not know how to grow them using artificial media.!

- Exponential growth cannot go on forever. 1. Nutrients are used up; 2. Toxic byproducts build up; 3. Growth rate slows until it stops. IV. Classifications based on how carbon and energy are obtained

- Heterotrophs: rely on other organisms to make the organic compounds that they use as CARBON sources.

- Autotrophs: use the CO2 discarded by heterotrophs to make complex cell constituents made up of C, H, and O, such as carbs.!

- Synthetic Medium/ Minimal Medium water, salts, carbon, nitrogen, and energy sources added in precise amounts.!

- Phototrophs: extract energy from absorption of light. - Chemotrophs: extract energy from oxidation-reduction reactions.! V. What is a pure culture and how is it obtained?

- Pure culture: a single, genetically homogenous strain of a single species.! - Obtained: 1. Can be grown in liquid or solid media 2. Used to examine growth rates and microbial biochemistry 3. Agar useful for separating mixtures of different organisms. VI. Types of media – selective & differential vs enriched

- Selective Media: favor the growth of one organism over another / contains bile salts and crystal violet.!

- Differential Media: expose biochemical differences between 2 species that grow equally well.

- Enriched Media: for particularly fastidious organisms, blood or blood components added to a basic complex medium.! ** Extra info for ^^^: **

-

Synthetic Medium/ Minimal Medium: water, salts, carbon, nitrogen, and energy sources added in precise amounts.!

-

Complex Medium/ Rich Medium: Nutrient-rich but poorly defined. Yeast/ beef extract, peptides, vitamins whose exact concentration and composition is not known.!

VII. How bacteria divide – binary fission & exponential growth

-

Binary Fission: one parent cell splitting into 2 equal daughter cells.! Can be symmetrical and asymmetrical.! Exponential Growth: growth in which the population size doubles at a fixed rate.! It cannot go on forever; nutrients get used up, toxic by-products build up, and growth rate slow then stops.!

VIII.Growth curves – stages

IX. Environmental factors that limit bacterial growth X. Effect on proteins XI. Response to oxygen – which organisms need/tolerate/cannot handle XII. Biofilms XIII.Spores

Chapter 7 I.

Metabolism = catabolism + anabolism - define these terms

- Catabolism: breaks the bonds of larger molecules to release energy - Anabolism: builds complex molecules from small ones ** Biosynthesis ——> of cell molecules and structures** II. What determines what bacteria can eat? III. What are the central metabolic pathways and what do they (generally) make? IV. What are 3 ways to make ATP? 1.

Fermentation

2. Aerobic Respiration 3. Anaerobic Respiration V. Why does fermentation make less ATP than respiration? VI. What are the key differences between these processes? VII. How is fermentation used in clinical diagnoses? VIII.What is the terminal electron acceptor in aerobic respiration? IX. What is PMF?

- PMF (Proton Motive Force): X. What happens during photosynthesis?

Chapter 8 I.

Genomes vs chromosomes

- Genomes: the complete/all genetic content of an organism; the sequence of all the nucleotides in a haploid set of chromosomes

- ** genome = chromosome(s) + plasmid (s) ** - Chromosomes: consists of double-stranded DNA, part or all of an organism’s genome; it is packaged into a highly compacted form II. Central dogma of biology

- Process of DNA is used to make mRNA then protein III. Differences in DNA and RNA

- DNA (Deoxyribonucleic Acid): holds all of the cellular potential / Genome replication necessary for cell division / double stranded / thymine

- RNA (Ribonucleic Acid): single stranded / uracil IV. Complementation – AT/GC or AU/GC base pairing

-

A ——> T (U) T (U) ——> A G ——> C C ——> G

V. Importance of plasmids

- Plasmids transfer genes from one species to another completely unrelated species

- Contain small number of genes (useful in a given environment / virulence genes / antibiotic resistance)

- Closest to “sexual” exchange bacteria VI. Key parts of DNA replication

- DNA Replication (semiconservative): each daughter cell receives one original strand (parental strand) and one newly synthesized strand

- Makes copy of genome / bidirectional / pairing one strand with complementary base 1. Initiation: unwinding of helix, priming, and loading of DNA polymerase enzyme complex 2. Elongation: the sequential extension of DNA by adding DNA nucleotide triphosphate (dNTPs) with release of pyrophosphate, followed by proofreading 3. Termination: DNA helix is completely duplicated and replication stops VII. Key parts of transcription 4. Find promotor 5. DNA “unzips” to reveal bases 6. Polymerase catalyzes addition of bases to mRNA VIII. Key parts of translation

- As soon as mRNA gets made, a ribosome can start translating

IX. Types of mutations and how they occur ** Mutation = any permanent, heritable change in a DNA sequence, whether harmful, beneficial, or neutral ** What causes mutation… A “mistake” by DNA polymerase that fails to be repaired (1/1000) / Physical agents (ionizing radiation - nuclear, X-rays, UV radiation - cause pyrimidine dimers) / Chemical agents (reactive oxygen molecule (H2O2), superoxide radicals (O2-), dyes (intercalating agents - sticks between strands), certain biological processes (mutator strains)

- Point mutation/base substitution: a single nucleotide is changed in a DNA sequence

- Silent mutation - Missense mutation - Nonsense mutation - Insertion/Deletion: involves the addition of subtraction of one or more nucleotides

- Frameshift mutation - Inversion: fragment of DNA is flipped in orientation in relation to the DNA on the other side X. What is tRNA & what does tRNA do?

- tRNA: transfer RNA - Brings amino acids to ribosome XI. Gene regulation – repressible vs inducible

- Repressible: the down-regulation of gene transcription (turning off/keeping off) - Inducible: increased transcription of target genes due to an inducer binding a repressor, which prevents repressor-operator binding (turning on) XII. Why do bacteria regulate gene expression (especially pathogens)?

- Pathogens in particular regulate expression of virulence genes XIII.Role of quorum sensing

- Communication between cells (a lot of cells must be present) XIV.How bacteria sense changes in the external environment?

- By binding of substrate to certain proteins/enzymes/repressors Chapter 9

I.

How do microbial genomes differ (e.g., bacteria vs virus vs human/Eukaryote in general)

- Efficient. We assume that the structure does something. Densely packed and then eukaryotes has more fillers II. How do bacteria acquire new genes?

- Through horizontal gene transfer III. What is horizontal gene transfer? How does it differ from vertical?

- Horizontal Gene Transfer: large scale gene traffic between species, process that accelerates natural selection ( coming from outside the source)

- Vertical Gene Transfer: passing of genes from parent to offspring (cell division) IV. Conjugation: Horizontal gene transmission involving cell-to-cell contact.

- In bacteria, pili draw together the donor and recipient cell envelopes, and a protein complex transmits DNA across

- In ciliated eukaryotes, a conjugation bridge forms between two cells, connecting their cytoplasm and allowing the exchange of micronuclei V. Transformation: 1. The internalization of free DNA from the environment into bacterial cells 2. The viral conversion of a normal cell to a cancer cell VI. Transposition: the process of moving a transposable element from one DNA region to another; often encoded by the transposable element VII. Transduction (general, specific)

- General Transduction: picks up random parts - Specific Transduction: pick up specific parts VIII.How do genomes evolve?

- Random mutation - Natural selection - Reductive evolution (degenerative evolution) IX. What defines the process of evolution

- All life originated from microbes, and species continue to evolve through change to genomes

- Genomes change via random mutation and natural selection X. Homologs, paralogs, orthologs

- Homolog: group of genes or proteins with shared ancestry and whose DNA sequences and amino acid sequences are similar

- Paralog: a gene that arises by gene duplication within a species and evolves to carry out a different function from that of the original gene; the protein expressed by that gene

- Ortholog: gene (or protein) present in more than one species that derived from a common ancestral gene and encodes the same function in each of the species XI. How do new pathogens arise?

- New pathogens emerge to cause new disease by adapting to changing environments XII. Natural selection: the mechanism by which a change occurs in the frequency of genes in a population under environmental conditions that favor some genes over the other XIII.Genomic islands: a region of DNA sequence whose properties indicate that is has been transferred from another genome. Usually compromises a set of genes with shared function, such as pathogenicity or symbiosis support XIV.Human pathogens = mesophiles

EXAMPLE QUESTIONS – you can find the answer to these in your notes or book 1. Which of the pathways below is the FIRST step in producing ATP from glucose? A. electron transport chain B. fermentation C. glycolysis D. TCA Cycle 2. A random error that results in a single base change to DNA is called a ________. A. deletion mutation B. selective insertion C. point mutation D. frameshift mutation 3. “Central dogma of biology” states that _____________________. A. any mutation will lead to evolution of the species B. proteins are made from mRNA, which is made from DNA

C. daughter cells receive a single strand of DNA from the mother cell D. cells must make ATP to survive 4. A series of three mRNA bases that encode for a specific amino acid is called ______. A. a codon B. an operon C. an anticodon D. a tRNA 5. Pseudomonas aeruginosa forms biofilms that cause chronic infections in A. the colons of IBS patients. B. the lungs of cystic fibrosis patients. C. the arteries of patients with heart disease. D. the tissues of the toes and fingers of people with diabetes. 6. A series of connected, enzyme-catalyzed reactions in a cell is called _______. A. a virulence factor B. a metabolic precursor C. an endergonic reaction D. a biochemical pathway 7. Bacteria reproduce through a process called __________. A. binary fission B. sporulation C. exponential division D. mitosis 8. True or False: Respiration has a higher energy yield than fermentation. A. True; respiration makes many ATP by using the electron transport system. B. True; fermentation does not yield much energy because no electrons are transferred. C. False; fermentation yields more energy than respiration because it does not require electrons to be transported across the cell membrane.

D. False; fermentation and respiration yield the same amount of energy. 9. Because of semiconservative replication, if one daughter cell receives the following strand of DNA from the mother cell, what would the maternal DNA in the other daughter cell be? A. 3’-TACGCGA-5’ B. 3’-ATGCGCT-5’ C. 5’-ATGCGCT-3’ D. 5’-TACGCGA-3’ 10. What is happening during the lag phase of growth? A. cells are metabolizing, but have not started dividing yet. B. cells are growing rapidly. C. cells are dying rapidly. D. cells are growing and dying at an equal rate...