Microbiology Exam 1 Review

What is the Origin of Microbes?

Unit 1: Impact of Microbes

Origin of Microbes

1. 4 Bya - origin of cellular life

2. Anoxic phototrophic prokaryotes came first

3. Cyanobacteria began to oxygenate Earth

4. 2 Bya - first signs of eukaryotes

Koch’s Postulates

1. Bacteria must be present in diseased organisms, and not in healthy organisms 2. Bacteria must be isolated

3. Bacteria must cause disease when introduced to healthy organism 4. Bacteria must be reisolated and identified as identical to the original bacteria

Unit 2: Microbial Cell Structure and Function

Microscopy

● Magnification - enhances size uses ocular and objective lens

● Resolution - ability to recognize two seperate objects as distinct

● Resolving power - closest distance between two objects

● Limit of resolution has an inverse relationship with numerical aperture (light collected) Cell Size

What are the 4 criteria known as koch's postulates?

● Smaller size = greater surface area to volume ratio

● Better for diffusion and transfer of nutrients

Cytoplasmic Membrane

● Transfer of nutrients and molecules, control in and out flow, cell signaling, protection Gram Negative

● Thin layer of peptidoglycan between two membranes

● Stains pink because the membrane does not retain the purple stain Gram Positive

● Thick layer peptidoglycan outside of one membrane

● Stains purple because the crystal violet crosslinks with the peptidoglycan Peptidoglycan: Alternating NAM and NAG If you want to learn more check out plsc100

● Beta glycosidic bond - rigidity in one direction

○ It’s the O bond between rings

● Unique to bacteria

○ Provides target for antibiotic therapies

● Lysozyme - enzyme produced by animals that cleaves the beta glycosidic bond Other Cell Structures

What is Microscopy?

● Fimbria - short protein filaments present on cell surface

○ Adhere to cells and surfaces, Used to create biofilms and pathogenesis, Not involved with motility

● Pili - long protein filaments present on cell surface

○ Twitching motility, Move pathogens to proper colonization sites, Conjugation - genetic exchange, Spread antibiotic resistance

● Flagella - long thin protein filaments that are inserted within the cytoplasmic membrane ○ Moving - CCW rotation = run ; CW rotation = tumble

Unit 3: Microbial Metabolism

Fitness - the capacity of an organism to survive and reproduce as compared to competing organisms

1. For microbes, fitness is related to growth (increase in cell number)

2. ATP is generated by substrate level phosphorylation or oxidative/photophosphorylation Laboratory Culturing

1. Cell chemistry - microbial growth depends on altering molecular composition, but not elemental composition

2. Micronutrients - nutrients that are needed but in trace amounts e.g. iron 3. Culture Medium - a nutrient solution used to grow microbes

4. Laboratory techniques

a. Aseptic technique - taking steps to transfer specific biological samples between vessel

Energy Classes of Microorganisms

Chemotrophs - chemical (serves as electron donor) Don't forget about the age old question of ecu referencing

1. Phototrophs - light (excites electron with light sensitive molecules to a higher state) 2. Heterotroph - carbon obtained from organic compounds, like glucose 3. Autotrophs, carbon obtained from carbon dioxide

○ Carbon fixation

Bioenergetics

1. Free energy is either released (exergonic) or required (endergonic)

2. Microbes have evolved mechanisms to increase rates of reaction

a. Enzymes reduce activation energy

Electron Donors and Acceptors

1. Redox allows cells to harvest energy from environment

2. Oxidation state : effective charge of an atom in a compound

Redox and Metabolism

● Electron donors/acceptors (focus on structure)

● Electron carriers (focus on function)

● Microbes use electron carriers to facilitate redox intracellularly

Fermentation - growth strategy that occurs when terminal electron acceptor is absent Respiration - growth strategy that occurs when terminal electron acceptor is present Don't forget about the age old question of vyhu

Fermentation​ (anaerobic catabolism)

Input

Output

glucose

Glycolysis → pyruvate  → ATP

→

fermentation

ATP

Respiration

glucose

Glycolysis → pyruvate →  → ATP

Citric acid cycle Terminal

electron

acceptor

CO2

ATP

Glycolysis

● nearly universal, biochemical pathway that cells use to generate three type of fueling products from glucose

○ ATP, NADH, precursor metabolite (pyruvate, fructose-6-phosphate, etc) ● Stage 1 - convert glucose to 2 G3P

● Stage 2 - generates fueling products, ATP, NADH, and pyruvate

ATP Production

● Two options - fermentation or respiration

● Fermentative Diversity - ATP is needed more than NADH and pyruvate Respiration: Electron Carriers

● Reducing power is used to generate ATP via oxidative phosphorylation ○ Electrons dumped to a terminal electron acceptor

● Electrons are transferred among multiple carriers

○ Complex 1 (NAD+ to NADH and H+)→ Complex 2 (FAD+ to FADH2) → Complex 3 → Cytochrome C → Reduces Complex 4, H2O is produced

○ Pumps protons (H+) across membrane If you want to learn more check out cove management v. aflac inc

○ Rush of H+ back across membrane powers ATP synthase (ATPase)

Respiration: Citric Acid Cycle

NADH = reducing power

○ NAD+ becomes NADH so it can be oxidized in the ETC

1. Pyruvate is oxidized by enzyme CoA

○ Becomes Acetyl-CoA

○ Loses one carbon, becomes CO2 

2. Biosynthesis - generate precursor metabolites

○ E.g. oxaloacetate, succinate

3. Output - NADPH, FADH2, ATP/GTP

○ Waste: CO2 

Bioenergetics

1. Polysaccharides are present within cell walls

2. Gluconeogenesis - process to generate glucose

3. Pentose Phosphate Pathway - metabolizes glucose to generate:

a. Ribulose-5-P (precursor metabolite for nucleotides) Don't forget about the age old question of econ 1 study guides

b. NADPH

c. CO2 

4. Pentoses can enter PP for alternative purposes

a. Biosynthesis

b. Catabolism in the absence of hexoses

5. Why is gluconeogenesis important for a gram-positive bacterium growing on a C3 carbon source? We also discuss several other topics like What is a chemical change?

a. LPS is not used in gram positive bacteria

Unit 4: Central Dogma

Central Dogma of Molecular Biology - DNA → RNA → Protein

DNA Structure

1. Genome - all the genetic information that defines an organism

2. DNA = deoxyribonucleic acid

a. Negative charge at neutral pH (because of phosphate)

3. Structure - deoxyribose sugar + phosphate + base

a. Bases are connected to the 1’C (one prime carbon)

i. Base positioned away from backbone

b. Phosphodiester bonds link the nucleotides

c. Repetitive structure enables storage of information

d. DNA Nucleotide structure

i. Bases: A with T, C with G

e. Chromosome - single DNA molecule that contains a significant proportion of an organism’s genetic information

i. E. coli has 4.6 Mbp

DNA Replication

● Semiconservative replication - one original strand, one replicated strand ● Overview of replication

○ Initiation

i. Placement - DnaA binds to multiple sites in oriC (AT-rich region)

ii. DnaA uses ATP to melt strands - defines replication fork

iii. Helicase unwinds DNA

iv. Replisome uses helicase as scaffold, binds helicase to the end of

replication fork

○ Elongation

i. DNA polymerase synthesises DNA in 5’ to 3’

ii. Requires template and primer (specifies region elongated)

iii. 3’ to 5’ prime replication uses Okazaki fragments

○ Termination

DNA Transcription

1. Function

a. mRNA - template for protein synthesis

b. tRNA - keys for translating protein

c. rRNA - enzymatic RNAs involved in protein synthesis

2. Elongation

a. RNAP synthesizes 5’ to 3’

b. No primer necessary

c. Initiation - promoter

d. Sigma factor - interacts with RNAp and promoter (enables RNAP to recognize promoter)

3. Termination

a. Terminator - RNA structure that signals for transcription termination i. Stem-loop structure: RNA specific structure (pauses transcription) ii. Run of uracils : weak U-A interactions) promotes dissociate of RNA-DNA DNA Translation

1. tRNA binds anticodon with corresponding amino acid on other end 2. Occurs in ribosome

3. Start and stop codons dictate length