Exam 2 Micro

Convergent evolution

occurs when organisms that are not closely related evolve similar features or behaviors

selective pressure

similar environmental challenges that influence survival and reproduction.

phylogenetics

Understanding relatedness through analysis of genes

Phylogenetic tree

Analyzing the genetic

relatedness among (all)

organisms via their rRNA

sequences allows us to

visualize how they are related

Alphaproteobacteria example

Rickettsia rickettsii

↳ Causes Rocky Mountain spotted fever

↳ Spread by ticks

Deltaproteobacteria example

Myxococcus xanthus

− The bacterial equivalent of a wolf pack

− These social hunters move in tight huddles, secreting

digestive enzymes that break down cells in their path

Gammaproteobacteria example

Sulfur lithotrophs

− Acidithiobacillus

↳ Oxidize iron or sulfur

Bacteria convert _____ gas into _____ via _____. Sensitive to _____.

N2, ammonium, nitrogen fixation. oxygen damage

Deep-branching thermophiles

Includes extremophiles growing at high

temperatures (50-80ºC)

Cyanobacteria

Fundamental part of our biosphere

because of photosynthesis

gram-positive bacteria

firmicutes, mycoplasma (no cell wall), actinobacteria

Deep-branching Gram-negative bacteria

Spirochetes and Bacteroidetes

Chlamydiae

intracellular parasites that lose most of their cell envelope during intracellular growth

Verrucomicrobia

wart like protruding structures

planctomycetes

Aquatic bacteria with stalked cells that reproduce via budding; present a

“nuclear membrane”

Traits Distinct to Archaea

• ether links in phospholipid bilayer

• pseudopeptidoglycan in cell wall (no penicillin)

TACK (archaeal superphyla)

widest range of temps

Euryarchaeota

methanogens: remove excess H2, but releases greenhouse gas methane

halophiles: only life to grow in conc. brine

Methanogenesis

the biological production of methane mediated by anaerobic microorganisms

from the Archaea domain commonly called methanogens

Asgard

hyperthermophiles

DPANN

reduced genomes and metabolic capabilities

protist

single-cell and eukaryotes other than fungi

protozoa

protists that are single-celled heterotrophs

choanoflagellates

− Group of free-living unicellular and colonial flagellate eukaryotes

− Thought to be the ‘missing link’ between animals and microbial eukaryotes

mycorrhizae

extend root systems of plants

saprotrophic

fungi recycle biomass of wood and leaves

fungal hyphae

threadlike nonmotile filament of cells that forms the mycelium of a fungus.

yeasts

unicellular fungi (reproduce via budding)

primary algae

chloroplast evolved by endosymbiosis

between an ancient protist and a cyanobacterium

secondary algae

evolved through a secondary

endosymbiosis with a second protist host

amoebas

unicellular amorphous microscopic life aggregates to slime mold.

Why do bacteria regulate gene expression? At what levels?

not waste energy making uneeded proteins. At various levels, DNA, transcription, mRNA stability, and translation.

molecular regulation

Molecular regulation controls biological functions through networks of DNA, RNA, and proteins.

Can bacteria sense internal and external environments (changes in temp, salinity, pH, nutrient conc.)

Yes duh lmao

promoter definition and binds to _____

region of DNA just upstream of a gene. Needed for transcription initiation

(binding of RNA polymerase)

operons

Group of genes arranged in tandem that are transcribed into a single mRNA

(polycistronic), under control of a single promoter

regulatory proteins

help a cell sense internal changes and alter its gene expression to

match

- Under control of a separate promoter than the genes they regulate

- Can be repressors or activators

operator (regulatory sequence)

region of DNA sequence where repressor proteins can bind

activator (regulatory sequence)

region of DNA where activator proteins can bind

4 Levels of Control of Gene Expression

1. DNA Alteration

2. Transcriptional Regulation

3. Control of mRNA stability

4. Translational Control

DNA Alteration definition with examples

DNA rearrangements that alter gene expression

• Drastic form of molecular regulation

Examples:

phase variation - microbes use gene regulation to periodically change their appearance

Gene inversions

Slipped-strand mispairing - random slips (can turn on in subsequent generation)

phase variation is a ______, _______ _______ for gene expression

spontaneous, reversible switch

ligand

low-molecular-weight

compounds that alter the ability

of regulatory proteins to bind to

DNA

Regulatory proteins come in two forms

1. Repressors

2. Activators

Repressors

Bind to regulatory sequences

(operators) in the DNA and prevent

transcription of target genes

Activators

Bind to regulatory sequences (activators) in

the DNA and stimulate transcription of

target genes

catabolism

the part of metabolism that breaks down

large, complex molecules into smaller unit

lactose

disaccharide (galactose and glucose) that

needs to be broken down into monosaccharides to be

used for energy and carbon acquisition

glucose vs. lactose consumption

glucose = has enzymes always present to metabolize (constitutive expression)

lactose = enzymes that metabolizes lactose is produced only in the presence of lactose

The Lac Operon (lacZYA operon)

controls lactose uptake and catabolism and was the first

gene regulatory system described

LacY | Lactose permease

Membrane transporter that acquires lactose from the extracellular

environment

LacZ | Beta-galactosidase

cleaves lactose into glucose and galactose

LacA | Thiogalactoside transacetylase

unknown function, but believed to detoxify a harmful

by-product of lactose metabolism

In the ABSENCE of lactose

LacI repressor binds to the operator regions lacO and lacOI (as a tetramer)

In the PRESENCE of lactose: ____ = lactose uptake, ____ hydrolyzes lactose into glucose, galactose, and allolactose

LacY, LacZ

Allolactose

inducer gland, binds to lacI, reduces affinity to operator regions, allows induction of Lac operon

Cyclic AMP (cAMP) definition, combines with _____

ACTIVATOR: a second messenger molecule that accumulates

inside cells during carbon starvation. cAMP receptor protein (CRP)

presence of glucose ____ the Lac operon - catabolite repression

represses

Disadvantages of using proteins for regulation

• highly specific to single gene

• energetically costly (synthesis)

• large proteins = slow to diffuse

_________ molecules expand the reach of protein regulators

Small RNA (sRNA)

sRNA bind to ribosome binding site (RBS) result

inhibits translation

sRNA bind to mRNA and expose RBS result

allows translation to occur

RNase III cleaves ______ RNA, RNase cleaves _______ RNA

double stranded, single stranded

sRNAs have different ways to regulate gene

expression at the ______

posttranscriptional level

When iron is abundant

Fur protein (repressor) induces production of iron-storing proteins, represses expression of iron scavenging genes

When iron is scarce

RhyB: sRNA helps conserve iron by promoting the cleavage

of mRNAs of several iron containing proteins via RNAses

translational control uses the _____

stringent response

the stringent response

lower transcription of genes required for

rapid growth, and fewer ribosomes, thus,

less translation of mRNA into proteins. ppGpp

how do bacteria sense the extracellular environment?

two-component sign transduction systems

sensor kinase in the ________, binds to ________, activates itself via ________

cell membrane, environmental signal, phophorylation

• environmental “antenna” + phosphate donor

response regulator in the _______, activated via _____, binds ______

cytoplasm, phosphorylation, DNA

• intracellular “switch” that changes gene expression or behavior

The name tells you what it does! TWO COMPONENT SIGNAL TRANSDUCTION SYSTEM

Two Component - 1. Sensor Kinase, 2. Response Regulator

Signal - information from environment (nutrient, pH, temp.)

Transduction - (trans = across), cell carrying signal from outside the cell to inside

System - not one protein, coordinated set of parts working together to sense and respond

quorum

minimum number of members of a society that must be present to make the

proceedings of that meeting valid

quorum sensing, discovered in _____

process where bacterial cells recognize the abundance of their own species so they can coordinate and work together at high

density. vibrio fischeri (bacterium in hawaiian bobtailed squid

quorum sensing advantages

coordinates the behavior of single-celled organisms (e.g.,

bacteria) at the population level, allowing them to exhibit multicellular

behavior (e.g., biofilm formation)

Chemoorganotrophy

electrons from organic compound

Chemolithotrophy

electrons from inorganic compounds

Photoautotrophy

light absorption with CO2 fixation

Photoheterotrophy

light absorption without CO2 fixation

The actual amount of energy released by a

reaction can be determined by a _________

calorimeter

ATP always forms a complex with ____

Mg²+

Phosphorylation of ADP to ATP requires ______ (delta G?)

energy input, positive delta G

ATP can transfer energy to cell processes in

three different ways:

1. Hydrolysis-releasing phosphate (Pi)

2. Hydrolysis-releasing pyrophosphate (PPi)

3. Phosphorylation of an organic molecule

Hydrolysis-releasing phosphate (Pi)

biosynthesis

Hydrolysis-releasing pyrophosphate (PPi)

Pyrophosphate release and subsequent hydrolysis yields lots of energy. Used in reactions that must avoid reversal

Phosphorylation of an organic molecule

− ATP transfers its phosphate group to another molecule

− Energy is not released, but it can activate the molecule for a subsequent

rapid reaction

NADH carries ______ times as much energy as ATP

two or three (generates 2-3 ATP)

Overall ______ of _____ consumes 2 hydrogen atoms to make NADH

reduction, NAD+

_____ undergoes a similar _____ reaction as NAD+, but ____ protons are incorporated (instead of only one in NADH)

FAD, reduction, 2

_____ enter catabolic pathways

hydrolyzed products

glycerol

(three-carbon triol) enters catabolism as an intermediate of

glycolysis

carboxylic acid formed through

amino acid degradation is

degraded through the ______

TCA cycle

glucose breakdown three pathways to pyruvate

EMP (2 ATP 2NADH), ED (ATP, NADH, NADPH), PPP (NADPH) (biosynthesis)

EMP pathway stages

1. GLUCOSE ACTIVATION -

2. ENERGY YIELDING

EMP yields

2 ATP 2 NADH

(ED) pathway yields

1 ATP, 1 NADH, and 1 NADPH

PPP yields

2 NADPH

Substrate-level phosphorylation

movement of phosphates that

DOES NOT involve electron transport systems

− Example: generation of ATP during glycolysis

Oxidative phosphorylation

The process by which energy in NADH is converted to ATP via an

electron transport system

fermentation yield

2 ATP per glucose