CEE 582 Exam 1 Prep

What is part of the cell envelope

cytoplasmic membrane, cell wall, outer membrane, and S-layers

Function of cytoplasmic membrane and what its made of

selective permeability (nutrients transported in and waste products out) with proteins facilitating this reaction. Made of phospholipid bilayer containing embedded proteins

hydrophilic component of cytoplasmic membrane

glycerol + phosphate and other functional group

hydrophobic component of cytoplasmic membrane

fatty acid tail

Prokaryotic cell

Bacteria and Archaea with no organelles(membrane-enclosed structure) and no nucleus

Eukaryotic cell

Plants, animals, fungi, algae, protozoa containing organelles and DNA enclosed in membrane-bound nucleus.

What do coccus shaped cells look like?

spherical or ovoid

What do rod/bacillus shaped cells look like?

cylindrical

What do spirillum shaped cells look like?

flexible spiral

Bacteria structure type

Prokaryote, 80+ phylogenetic lineages

Archaea structure type

prokaryotes, associated with extreme environmentas

Eukarya

plants, animals, fungi, Protista

Three major functions of the cytoplasmic membrane

permeability layer, protein anchor, energy conservation

Simple transport in the cytoplasmic membrane

driven by the energy in the proton motive force

ABC transporter in the cytoplasmic membrane

binding proteins are involved and energy comes from ATP

Group translocation in the cytoplasmic membrane

Chemical modification of the transported substance by group pf proteins working together

Components of gram-positive cell envelope

cytoplasmic membrane and thick peptidoglycan cell wall

components of gram-negative cell envelope

cytoplasmic membrane, thin cell wall, outer membrane(containing lipopolysaccharide-LPS), and periplasm

What is Periplasm?

a compartment between cytoplasmic and outer membranes

What is peptidoglycan?

rigid polysaccharide layer that provides strength in all bacteria with a cell wall.

What does lysozyme do?

destroys peptidoglycan by breaking down the bond between sugars (found in saliva)

Function of outer membrane in gram-negative cell

facilitate surface recognition, has virulence factors, and adds mechanical strength

Porins

found in the outer membrane of gram-negative cells and acts as transmembrane transport channels for entrance and exit of solutes

What is the difference in the cell wall of Archaea?

lacks peptidoglycan, lacks outer membrane, S-layer instead of polysaccharide wall

What is the s-layer?

always outermost layer of cell envelope, made of proteins/glycoproteins, provides strength, protection from lysis, facilitates cell surface interactions, promotes adhesion

Pili

thin filamentous protein structures enabling organisms to stick to surfaces

gas vesicle

screens that can be used to get nutrients towards the outside of the cells

endospore

for enduring unfavorable growth conditions (vegetative > endospore > vegetative): activation, germination, outgrowth

Flagella structure and activity

main filament part composed of flagellin protein, hook, and basal body as motor powered by proton motive force

Archaella structure and activity

closer related to type IV pili, moved by rotation driven by ATP hydrolysis

Chemotaxis

directed movement in response to chemicals, run & tumble behavior

Phototaxis

directed movement in response to light

Exergonic

reactions that release free energy (negative net free energy)

Endergonic

reactions that require energy (positive net free energy)

Catabolic pathways

exergonic processes that generate free energy produced by making ATP

Anabolic pathways

endergonic processes where cellular synthesis requires energy from hydrolysis of ATP

What is ATP used for?

Storing energy and fuel processes

Phototroph

obtains energy from light

chemotrophs

obtains energy from chemical reactions (either organic or inorganic)

chemoorganotrophs

obtain energy and reducing power from organics

chemolithotrophs

obtain energy and reducing power from inorganics

Heterotrophs

obtain carbon from organics

Autotrophs

obtain carbon from CO2

Catalyst

speeds up reaction rate by lowering the activation energy

What is function of glycolysis and what does it produce?

pathway for glucose catabolism, by oxidizing glucose to pyruvate (2 pyruvate molecules formed), NAD+ reduced to NADH, Uses 2 ATP in stage 1 and produces 4 ATP in stage II. TOTAL: Net 2 ATP, 2 NADH, 2 pyruvate per glucose

Citric Acid Cycle

pyruvate is oxidized to CO2

What does fermentation do?

anaerobic conditions, doesn’t require an external electron acceptor, generates ATP using substrate level phosphorylation

What does respiration do?

aerobic, anoxic, and anaerobic conditions, requires an external electron acceptor, generates ATP using oxidative phosphorylation

ATP synthase (ATPase)

uses energy from proton motive force to form ATP

Anabolism

cells require carbon and nitrogen to perform biosynthesis, requires ATP and reducing power

Overall Process of Calvin Cycle

Glucose formed by reversal of glycolysis

Binary Fission

cell division following enlargement of a cell to twice original size

Generation time

time required for microbial cells to double in number

Phases of Microbial growth cycle

Lag, Exponential, stationary, death

extremophile

organisms that can grow under very hot or very cold conditions

psychrophile

optimal growth temperature: <15 C, maximum < 20 C, minimum < 0 C

psychrotolerant

can grow at 0 C, but have optima of 20-40 C

Thermophile

optima growth temperature between 45 C and 80 C

Hyperthermophile

optima greater than 80 C

neutrophile

grow optimally at pH close to 7

Acidophile

grow best at low pH (<5.5)

Alkaliphile

grow best at high pH (> 8)

osmosis

water diffuses from higher water concentration to lower water concentration

halophile

grow best at seawater

halotolerant

toleration some dissolved solutes, but generally grow best in absence of added solute

extreme halophiles

require very high levels of salt

osmophile

live in environments high in sugar

xerophiles

able to grow in very dry environments

Capsid

protein shell that surrounds the genome of a virus

naked virus

have no other layers (just nucleocapsid)

enveloped virus

have an outer layer consisting of a phospholipid bilayer and viral proteins

nucleocapsid

nucleic acid + protein in enveloped viruses

Virulent (lytic) infection

replicates and destroys the host

Lysogenic infection

host cell is genetically altered (not destroyed) because viral genome becomes part of the host genome

capsomere

individual protein molecules arranged in a highly repetitive pattern around the nucleic making up the capsid

Helical virus symmetry

rod shaped, length determined by length of nucleic acid and width determined by size and packaging of capsomeres

Icosahedral symmetry

spherical, efficient arrangement of subunits in a closed shell

Prokaryotic viruses

nucleic acid enters host cell

Eukaryotic viruses

virion enters host cell

5 steps of viral replication

attachment, penetration, synthesis, assembly and packaging, cell lysis and release of virions

Virus replication growth curve

eclipse: genome replicated and proteins translated

maturation: packaging of nucleic acids in capsids

latent period: eclipse + maturation

release: cell lysis, budding, or excretion

Latent infection

host cell is unharmed unless/until virulent pathway is triggered

persistent infections

slow release of virions from host cell by budding does result in cell lysis but infected cell remains alive and continues to produce lysis

Nucleotide

nucleic acid monomer consisting of: pentose sugar, nitrogenous base, phosphate

Nucleoside

has pentose sugar and nitrogenous base, no phosphate

Nitrogenous bases

(A+T/U) and (GC)

A - purine in DNA + RNA

G - purine in DNA + RNA

C - pyrimidine in DNA + RNA

T - pyrimidine in DNA

U - pyrimidine in RNA

Phosphodiester bonds

bonds in a double helix that connect 3’-carbon of one sugar to 5’-carbon of the adjacent sugar

Structure of DNA

double stranded, held together by hydrogen bonding between bases, two strands are antiparallel (5’-3’ and 3’-5’)

How is DNA Replicated?

DNA is duplicated by DNA polymerase (always from 5’ to 3’)

How is DNA Transcripted?

information from DNA is transferred to RNA by RNA polymerase

How is DNA translated?

information in mRNA is used to build polypeptides on ribosome

what is mRNA

messenger RNA, carry genetic information to ribosome

what is tRNA

transfer RNA, convert mRNA information to amino acid sequence

what is rRNA

ribosomal RNA, catalytic and structural ribosome components

DNA synthesis process

Double helix unwound at replication form by DNA helicase, primase and DNA polymerase enzymes loaded, DNA polymerase removes RNA primer and replaces it with DNA, DNA ligase seals nicks in DNA

Replisome

large replication complex of multiple proteins

Transcription in Bacteria Process

Process catalyzed by RNA polymerase, uses DNA as template only one strand transcribed, no priming needed. Transcription terminators mark end of transcription and promoters mark the start.

What is a Bacteria Transcriptional Unit?

DNA segments transcribed into one RNA molecule bounded by initiation and termination sites

operon

cluster of genes that encode several enzymes of a pathway and transcribed into a single mRNA