chat gbt generated flashcards for microbiol exam 2

Microorganisms + history/economy

Disease can reshape society, migration, warfare + history; Public health: infection waves, mortality, healthcare overload; Economy: supply-chain collapse, job loss, market crashes; Social/political: closures, travel bans, policy change, unrest, cooperation/division

Disease occurrence patterns

Outbreak/epidemic = more disease than expected in a time/place

Pandemic = epidemic spread across countries/continents

Endemic = continually present, often at stable level

Types of disease/infection

Infectious = invasion + multiplication of microorganisms

Acute = sudden + short; e.g. smallpox, measles, influenza

Chronic = extended duration; e.g. HIV/AIDS, TB

Latent viral = dormant/inactive period → possible reactivation

Vector-borne = transmitted by infected arthropods

Zoonotic spillover

Pathogen starts in animal host

Jumps to susceptible human through close contact

May then spread human → human

Plague of Athens

430–426 BCE

Pathogen uncertain

Crowding + poor sanitation favored spread

Killed up to ~2/3 of Athens

Contributed to Athens’ defeat by Sparta

Plague of Justinian

Pathogen = Yersinia pestis

Gram-negative bacterium

Reservoir = rodents/other mammals

Vector = fleas

Major historical plague outbreak

Black Death / plague

Caused by Yersinia pestis

Flea/rodent transmission important

Spread widely through Europe and beyond

Massive mortality reshaped European society/economy

Spanish conquest of Mexico + smallpox

Smallpox = Variola virus; Devastated Aztecs during Spanish conquest

Native population had little/no prior immunity

Weakened resistance + contributed to drastic population decline

Typhus + history

Caused by Rickettsia prowazekii

Gram-negative bacterium

Transmitted by human body louse

Thrives in crowded/unsanitary conditions

Historically affected soldiers

Irish potato famine

Pathogen = Phytophthora infestans

Fungus-like organism, more closely related to algae than fungi

Potato disease → crop failure/famine + major social effects

role of the USDA

Monitor foreign diseases and shut down exports/imports to prevent a pandemic

Yellow fever + Panama Canal

Yellow fever = viral disease

Mosquito control/disease control was important for canal construction

Example of microbiology affecting infrastructure/history

Microbial cell factories

Chaim Weizmann developed bacterial acetone synthesis

Organism = Clostridium acetobutylicum

Example of microbes driving industrial/economic innovation

Ages of microbiology

Ancient microbiology: ~3000 BCE–1665

Early microbiology: 1666–1857

Golden Age: ~1858–1914

Modern microbiology: 1914–present

Redi + Hooke

Redi: meat/maggot experiment argued against spontaneous generation

Hooke: microscopy + foundations of cell theory

Cell theory: living things are composed of one or more cells

Anton van Leeuwenhoek

First to describe microorganisms

Used early microscopes

Documented “animalcules” in detailed drawings

Louis Pasteur

Father of modern microbiology in lecture framing

Strong use of scientific method

Work helped reject spontaneous generation

Major work on microbes/fermentation + rabies vaccine

Discovered vaccination, pasteurization, germ theory, and microbiology tools

Disproved spontaneous generation with S-shaped flask experiment

Scientific method

Ask question → background research → hypothesis

Design/run experiment → collect data

Analyze → conclusion → communicate; Revise + repeat

Important because microbial claims are tested experimentally

Koch + Koch’s postulates

Linked specific microorganisms with specific diseases

1: microbe in diseased, not healthy hosts

2: isolate + grow in pure culture

3: culture causes disease in susceptible host

4: re-isolate same microbe

Semmelweis

Associated childbed fever with transmission by physicians

Handwashing/cleanliness reduced disease

Important early evidence for infection control

Ancient Microbiology

3000 BCE to 1665

Early Microbiology

1666 - 1857

Golden Age microbiology

~1858–1914

Rapid development of germ theory + disease-microbe links

• Ignaz Semmelweis - handwashing tech against childbed fever

• Florence Nightingale - modern nursing

• Louis Pasteur - rabies vaccine and pasteurization

• Joseph Lister - wounds and bandages with phenol

• Robert Koch - postulates, linking microbes to diseases for anthrax and tuberculosis

• Weil-Felix testing - found antibodies present to detect typhus

Modern Microbiology

1914-present

DNA

Information molecule in living cells

Determines which proteins a cell can produce

Made of nucleotides with A, T, G, C

Organized into genes

DNA structure

Nucleotide = 5-C deoxyribose + phosphate + N-base

Phosphate on C5; base on C1

Free phosphate side = 5′ end

unlinked C3 = 3′ end

Purines A/G = double ring

pyrimidines T/C = single ring

Double-stranded + antiparallel

Complementary base pairing

A pairs with T = 2 H bonds

G pairs with C = 3 H bonds

Specific pairing lets either strand serve as template

Opposing strands run antiparallel

Genes

DNA nucleotide sequence containing information for a protein

Base sequence specifies amino-acid sequence

Gene expression determines which proteins are produced

Genome

All genetic information of an organism

Includes genes coding for proteins/functional RNAs

Includes regulatory DNA, noncoding DNA + repetitive sequences

Chromosomes

DNA organized into discrete chromosome units

Chromosome = DNA + associated proteins

Packaging condenses DNA + helps organize it by wrapping/looping around the proteins

Bacterial vs eukaryotic DNA organization

location: chromosome in the cytoplasm vs the nucelus

dna shape: circular vs linear

chromosome count: one vs 23 pairs

gene copies: one vs two

Why DNA replicates ?

DNA copied before cell division; Each daughter cell must receive genetic information; Complementary base pairing allows accurate template copying

Prokaryotic DNA replication

Circular DNA

starts at single origin and forks move in opposite direction

complementary daughter stand created with opposite base pairing

Forks meet when complete

Produces 2 identical circular DNA molecules

DNA Polymerase

Enzyme that moves along each strand to read the nucleotide sequence and adding the complimentary daughter strand

One strand is serial and another strand is chunked

Makes very few errors and can detect & correct them

Mutations arise however during this part of replication

Eukaryotic DNA Replication

Linear

Multiple origins and happens simultaneously at opposite directions

Replication enzymes

DNA encodes proteins → proteins can act as enzymes → therefore dna can catalyze biological rxns

Initiator proteins help open origin; Helicase = separates/unwinds strands; Primase = RNA primer; DNA polymerase = adds complementary DNA nucleotides; Ligase = joins DNA fragments

Leading vs lagging strand

DNA strands are antiparallel; New DNA synthesis proceeds 5′→3′; Leading = continuous synthesis; Lagging = discontinuous fragments joined later

Central dogma

DNA → RNA → protein

Replication = DNA → DNA

Transcription = DNA → RNA

Translation = RNA → protein

Transcription

DNA → RNA thru complementary base pairing

1. RNA polymerase is an enzyme that finds start of gene, binds, unwinds dna sequence

2. RNA polymerase assembles nucelotide strands into mRNA with Uracil instead of Thymine

3. reaches termination site, detatches and release mRNA

T/T concurrent in bacteria/prokaryotic but not in eukaryotic bc mRNA has to leave nucleus first

• Only on the non coding is transcribed bc it has the promoter region

• The coding strand has the complementary version of the promoter

Transcription across kingdoms

• “Christmas trees” rep genes being transcribed by multiple RNA polymerase with varying lengths of mRNA bc of varying start times

• DNase digest DNA

• RNase digest RNA

• Bacteria has RNA polymerase bind to promotor and start transcribing

• Eukaryotes have transcription factors bind to promoter and the RNA polymersae binds to them

• Archae use transcription factors too

Introns & Extrons

• Introns - noncoding regions, not in mRNA 0-100 in eukaryotic cells

  • the nonsense letters

• Exons - coding regions translated into proteins

Types of RNA

mRNA = carries protein-coding message, 1-10%

tRNA = carries amino acids to ribosome, 10-25%
rRNA = structural/functional part of ribosome & catalyst for protein synthesis - 50-90%

Translation

RNA → protein

1. Initiation - ribosome reads mRNA to look & start codon

2. Elongation - complimentary amino acids brought sequentially by tRNA

   1. trna is basically holding another set of 3 N-bases that are also holding onto an amino acid

   2. peptide bond is formed between the amino acids and chains together above the nucleotide while the trna releases

3. Termination - stop codon triggers release of protein synthesized

aug most common start codon, or gug and uug

stop codons are only for ribosome to stop translation not for the amino acids

ts is actually like coding where lines are super specifc to make specific rules

recoding

• removes specific codons

• reassigns different meanings for codons

• making essential genes depend on synthetic components not found in nature

  • i assume its for like if u naturally dont have the capability

Prokar & Eukar differences in protein synthesis and gene regulation

• t/t happens simultaneous vs sequential

• smaller vs complex

• operons common vs individual regulated

gene regulation

• regulated genes - turned on/off based on cellular need

• constitutive genes - always on, for producing essential proteins like strx

• eukaryotic: inactive genes tightly bound, active genes loose

• microRNAs - small rna molecules that regulate genes

Genotype vs phenotype

Genotype = genetic makeup/information

Phenotype = observable characteristics; DNA → gene expression/proteins → phenotype

Prokaryotic (bacterial) DNA Replication

1. Circular single origin with replication forks at opposite ends and meet at the end

Bacteria reproduce by binary fission

Genetic variation comes from mutation + DNA exchange

Variation can alter phenotype, adaptation + drug resistance

asexual reproduction

bacteria

single parent cells divided into two identical daughter cells

sexual reproduction

multicellular organisms

new genetic combo by using two halves from parents

male and female gametes

Alleles

different forms of genes for heredity

when m/f gametes unite, their scrambled alleles combine and no two offspring r the same

Horizontal gene transfer

• Transformation = naked DNA, no contact between donor and recipient

• Transduction = bacteriophage-mediated DNA transfer

• Conjugation = direct cell-to-cell DNA transfer

  • Plasmid is like a needle to inject it, F+ (fertility)

• Can rapidly spread traits such as antibiotic resistance

Transposons in bacteria

Short DNA sequences that can move from one location to another

In prokaryotes, can involve plasmids and chromosomes

Encode for transposase, enzyme that cuts/reseals DNA

Large transposons carry drug/toxic resistance/production

Mutation types

Changes in DNA from errors in replication

• Neutral/Silent - DNA change, same amino acid

• Missense = change in amino acid sequence, ±

• Nonsense = premature stop codon

• Frameshift = insertion/deletion of a base → changes all subsequent codons

• Spontaneous = naturally due to errors in DNA replication from polymerase

Mutagens

agents that increase frequency of mutations

• nitrous acid - remove amino group from n-bases → base pairing errors

• intercalating agents - mold molecules insert into DNA causing frameshift mutations

Why mutations matter

Can arise spontaneously or from DNA damage; DNA repair can correct damage/errors; Unrepaired changes create genetic variation; Variation can support adaptation + antibiotic resistance

Mutation repair techniques

• Enzymes - p/e cells have enzymes that correct mutations

• Proofreading - DNA polymerase checks itself as it adds the nucleotides during replication

• Mismatch repair - enzymes cut out the dmgd dna section and replace it with correct ones, back up to proofreading

radiation

gamma radiation and x rays can cause DNA dmg by creating free radicals

• uv radiation = thymine make covalent bonds with each other → thymine dimers → distort dna, block replication → skin dmg

• uv light for microbial control = kill microorganisms but doesnt penetrate human skin

• vancomycin resistance = bacterium developed resistance to vancomycin from mutagens

genetic variability

some individuals better to survive in their environments

caused from mutations

if no mutations present, all species would be identical → preventing evolution & adaptation

Operons

Cluster of genes functioning together

Related genes can be turned on/off together

Common in prokaryotes

i.g. lac operon regulates genes responsible for lactose digestion and makes all enzymes produced

Lac operon

Inducible system for lactose digestion

No lactose: repressor binds operator → RNA polymerase blocked → transcription blocked

Lactose present: lactose binds to repressor→ releases operator → transcription
Low glucose: CAP-cAMP helps RNA polymerase → high transcription

Trp operon

Repressible system controlling tryptophan synthesis

High tryptophan: activates repressor → operator blocked → OFF

Low tryptophan: repressor inactive/detached → transcription ON

Constitutive vs induced vs repressible genes

Constitutive = expressed continually/housekeeping

Induced = expression increases when inducer/condition is present

Repressible = expression can be shut off when product/condition activates repression

Regulation changes protein concentration in cell

Antibiotic targets

Different antibiotics target essential bacterial functions

Major targets in course: cell wall, DNA/RNA processes, protein synthesis

Blocking essential function prevents normal growth/reproduction

Metabolism

Sum total of reactions in a cell for energy

Extracts energy from molecules

Uses energy for vital processes + synthesis of new material

Closely tied to microbial growth

Other materials for metabolism

Uses sugar, fats, proteins, for enegy like glucose

Fats → broken into glycerol & fatty acid by lipases

Proteins → amino acids by protease

Exergonic / endergonic / coupled

Exergonic = releases energy from bond breaking; products lower energy, heat/light

Endergonic = requires energy; products higher energy, intakes

Coupled = exergonic reaction supplies energy for endergonic reaction

ATP + ADP

ATP = cell main energy source; captures energy from exothermic rxns for fueling endothermic rxns

• ribose, adenine, three phosphate groups

ATP hydrolysis can drive energy-requiring reactions

ADP + Pi can be phosphorylated to regenerate ATP

ATP/ADP cycle couples energy release to energy use

redox rxn

energy tranferrence

electrons held loosely have more energy and energy is released when transferred to another more tightly bound atoms

molecule losing electrons is oxidized and loose hydrogen

one gaining electrons is reduced and gain hydrogen

Electron carriers

NAD+ accepts electrons/H → NADH

Can later be oxidized and donate the electrons to another molecule

Facilitates transfer of electrons, and the energy released is for ATP

Cellular respiration overview

break down of biological molecules to produce ATP for cells

glucose is the main energy as polysaccharides

1. Glycolosis - glucose broken down into chunks with some energy captured as NADH

2. Krebs Cycle - further oxidized, forming more NADH and some ATP

3. Electron transport - all energy carriers oxidized, oxygen is reduced, and ATP final stage

Glycolysis balance

Glucose → 2 pyruvate → 2 NADH produced and lite ATP from exothermic rxn

Partial oxidation of glucose

Krebs cycle

Oxidation of pyruvate

1. pyruvate (3C) → acetyl-CoA (2C) + 1 CO2

2. Enters the cycle → forms citrate with 4 Cs → more CO2 released and captured as NADH, FADH2, and lite ATP

Electron transport chain

NADH/FADH2 are oxidized & Electrons move through membrane carrier

Released energy pumps H+ across membrane

Creates proton gradient

H+ flows through an enzyme complex → ATP sythesized

Electrons + oxygen = water, generating most of the ATP

Aerobic respiration

O2 as the final electron acceptor

O2 accepts electrons + forms H2O

ETC makes most ATP

Course slide total = 38 ATP/glucose; 32 from ETC

Anaerobic respiration

Does not use O2 as final electron acceptor

Can use acceptors such as nitrate or sulfate; Usually lower ATP yield than aerobic respiration

May produce wastes such as H2S or methane

Anerobes are the microorganisms that do this

Fermentation

For cells that only use glycolysis for ATP production bc of no oxygen

• pryvuate is reused to generate NAD+ for continuation

• produces waste products like lactate

NAD+ regeneration lets glycolysis continue → Low ATP yield = glycolysis only

Saccharomyces cerevisiae → yeast → ethanol + CO₂ fermentation.

Heterotrophs vs autotrophs

Heterotrophs eat/absorb organic biological molecules, fungi/animal

Autotrophs make their own biological molecules from raw materials such as CO2, thru light (photo) or chem (chemo)

Trophic modes

Photo- = energy from light

Chemo- = energy from chemical reactions

autotroph = carbon from CO2/inorganic carbon

heterotroph = carbon from organic compounds

Phototrophic Metabolism

1. Sunlight used to gen atp & reduce NADP+ to NADPH to be electron and hydrogen carrier

2. Calvin Cycle - ATP & NADPH convert CO2 into glucose

   1. carbon fixation - CO2 incoperated into organic materials

   2. nadph provided electrons for carbon reduction and atp is energy

3. happy plants

cytoplasm for pro, chloroplast for euk

Chemoautotrophs

Use reduced chemical compounds as energy sources: ammonia, methane, hydrogen sulfide

ATP generated from oxidation of compounds

For nutrient cycling of anaerobic prokaryotic waste

Photosynthesis (?)

Endergonic synthesis of glucose/biological molecules; Light reactions use sunlight → ATP + reduced NADP+; CO2 supplies carbon; In plants/cyanobacteria, water supplies H and O2 is released

Binary fission + population calculation

1 parental cell → 2 daughter cells

Population doubles each generation → rapid population increases

N = N0 × 2^n; n = elapsed time ÷ generation time

Fastidious vs Nonfastidious organism

For ideal lab growth

Fastidious - demanding nutritional requirements like media with vitamins to grow

Nonfastidious - not demanding, not picky

Microbial growth curve

Lag = adaptation; little population increase

Log/exponential = rapid division

Stationary = new cells ≈ dying cells; nutrients limited/waste accumulates

Death/decline = deaths exceed new cells

Oxygen classes

Obligate aerobe = requires O2, catalase neutralizes harmful O compounds

Obligate anaerobe = O2 harmful/not tolerated bc they don’t have catalase

Facultative anaerobe = uses O when available (aerobic), but is anaerobic if needed

Aerotolerant anaerobe = tolerates O2 but does not use it

Microaerophile = needs lower-than-atmospheric O2

Temperature classes

Psychrophile = cold-loving

Mesophile = moderate temperature

Thermophile = high temperature

Hyperthermophile = extremely high temperature

pH classes

Acidophile = low pH/acidic <5

Neutrophile = near-neutral pH 6-8

Alkaliphile = high pH/basic 8.5

Halophiles

Microorganisms that thrive in high salt envio

Salt prevented microbial growth by dehydrating cells

Salt concentration affects water movement/osmotic stress; Different microbes have different salinity optima

Historical Microorganisms

• Variola virus = smallpox → Spanish conquest/New World

• Y. pestis = plague → Justinian + Black Death; rodents → fleas → humans

• R. prowazekii = typhus → body louse

• P. infestans = potato disease → Irish Potato Famine

• Yellow fever virus → Panama Canal

• C. acetobutylicum = acetone production → Weizmann

• M. tuberculosis = TB → Koch

• Plague of Athens = pathogen uncertain

Fermentation Microorganisms

• Lactobacillus → lactic acid

• Yeast / S. cerevisiae → ethanol + CO₂

• Propionibacterium → propionic acid

• Escherichia / Salmonella / Shigella → mixed acids