Microbiology Exam 2

chemical work

synthesis and break down of complex molecules

transport work

take up of nutrients, elimination of wastes, and maintenance of ion balances

mechanical work

cell motility and movement of structures within cells

first law of thermodynamic

that energy can be neither created nor destroyed

second law of thermodynamics

physical and chemical processes proceed in such a way that the randomness or disorder of the universe (the system and its surroundings) increases. However, even though the entropy of the universe increases, the entropy of any given system within the universe can increase, decrease, or remain unchanged

catabolism

breakdown moleculesa

anabolism

biosynthesize molecule

energy source for catabolism

organic compound reactions (chemotrophs)

energy producing processes

respiration and fermentation

where does respiration happen in prokyrotes

cell membrane, enzymes deposit on the cell membrane

where do autotrophs get their energy

glucose from photosynthesis

where do heterotrophs get theier energy

glucose from food, catabolism

final electron acceptor in aerobic respiration

o2

electron acceptors in anaerobic respiration

nonoxygen electron acceptors

final electron acceptor in fermentation

an organic molecule such as pyruvate or acetaldehyde

are eukaryotes or prokaryotes more efficient in producing ATP

eukaryotes, they produce more ATP than prokyraotes

what does aerobic respiration do to an organic substance

it completely catabolizes the organic substrate into CO2

what are the three steps of aerobic respiration

glycolysis, TCA cycle (or the Kreb’s cycle), and ETC

what step of aerobic respiration generates the most ATP

ETC

net products of glycolysis

2 pyruvic acid (pyruvates)

2 ATP

2 NADH

central metabolite

pyruvic acid

what enters during TCA

Acetyle-CoA

for each acetyl-CoA molecule oxidized, the TCA cycle generates what?

2 molecules of CO2

3 molecules of NADH

1 FADH2

1 GTP/ATP

at the end of the TCA, how many ATP are produced so far

4 (2 from glycolysis and 2 from the TCA cycle)

ATP production occurs through____?

oxidative phosphorylation

what does oxidative phosphorylation involve?

PMF and ETC

pyruvate to acetyl-CoA produces…?

2 NADH

net product of the Kreb’s cycle

6 NAD

2 ATP

2 FADH2

total net products for aerobic respiration

4 ATP

10 NADH (2.5 ATP per NADH in ETC) → 25 ATP

2 FADH2 (1.5 ATP per FADH2 in ETC → 3 ATP

total ATP= 32

proton motive force is required for bacterial cellular processes such as….?

flagella rotation and generates oxidative level of phosphorylation of ATP

with the same organic substrates, anaerobic respiration generates ____ ATP than aerobic respiration

less

fermentation is respiration

false, it has no ETC, no oxidative phosphorylation, only SLP

fermentation

oxidation of NADH produced by glycolysis

pyruvate or derivative used as endogenous electron acceptor

substrate only partially oxidized

products: organic acids, ethanol

3 types of phosphorylation

glycolysis

oxidative phosphorylation

photophosphorylation

light harvesting pigments

chlorophyll-based (oxygenic and anoxygenic)

rhodopsin based

use light energy to make ATP

chlorophyll-based phototrophy

light into chlorophyll → electron transport chain → PMF → photophosphorylation produces ATP

rhodopsin-based phototrophy

light into bacteriorhodopsin → PMF (directly generates it) → photophosphorylation produces ATP

do respiration and fermentation produce the same amount of ATP during glycolysis?

yes, 2 each

does anaerobic respiration produce the same amount of ATP as fermentation

no, anaerobic produces more

electron donor in photosynthesis

H2O, oxidized into O2

chemolithotrophy

electron source/donor: organic (glucose)

vs inorganic

ATP synthesized by oxidative phosphorylation (ETC)i

inorganic (litho) energy source

glucose + oxygen

less ATPs

principles governing biosynthesis

limited number of monomers (building blocks)

some double duty enzymes: catabolism and anabolism (pathway never identical, physically separated allowing to separate simultaneously but independently)

consume energy

different cofactors from catabolism (NADH vs NADPH)

carbon synthesis

uses ATP and NADPH

CO2 fixation (autotrophs)- Calvin-Benson cycle

gluconeogenesis- from non-carbohydrate sources

Calvin Cycle

3 ATPs and 2 NADPHs are used during the incorporation of one CO2

most important intermediate in gluconeogenesis

acetyl coenzyme A

chemolithoautotrophs are unique to what?

microbes

reverse electron flow chemolithoautotrophs

need both NADH and ATP for anabolism at the cost of energy

gene

a DNA fragment or sequence that codes for a polypeptide/protein, rRNA or tRNA

linear sequence of nucleotides with a fixed start point and end point codons are found in mRNA and code for single amino acids (3 nucleotides long)

genome

all DNA present in a cell or virus

bacteria and archaea generally have one set (haploid- 1N)

eukaryotes have two sets (diploid- 2N)

genotype

specific set of genes an organism possesses

phenotype

collection of observable characteristics

DNA

double stranded helix

basic pairing: A-T 2 hydrogen bonds

G-C pair 3 hydrogen bonds

major and minor grooves

RNA

single stranded

protein

complex, determines the cellular function

start codon

start site for translation

sense codons

the 61 codons that specify amino acids

stop codons

translation termination signals (UGA, UAG, UAA)

code degeneracy

up to six different codons can code for a single amino acid

reading frame

organization of codons in a way that they can be read to give rise to a gene product

how many reading frames are possible for a piece of DNA

6

reading frame and overlapping

most reading frames (genes) do not overlap

exception is some viruses which have overlapping reading frames

in bacterial and archaeal genome, coding information in genes is normally what?

continuous

exons

contains information coding

introns

region inside a gene that is not expressed

what kind of cells have exons and introns

eukaryotic cells

lead/regulate the mRNA transcription

transcribed but not translated

recognition/binding site for RNA polymerase

not transcribed or translated

direction of bacterial gene reading frame

3’-5’

right after stop codon

prepare releasing of RNA polymerase

transcribed but not translated

stop transcription

not transcribed or translated

operon

promoter + operator/ activator-binding sites + functionally related structural gene

operon structure in archaea and bacteria

grouped together in the DNA of prokaryote cells

regulatory proteins control gene expression

not common for eukaryotes

transcription

RNA synthesis under the direction of DNA

mRNA, tRNA, rRNA

translation

synthesis of polypeptide directed by sequence of nucleotides in mRNA

ribosome

protein synthesis initiation complex

30s (16s rRNA) + 50s → 70s

relationship between translation and transcription in prokaryotes

they are coupled

is translation and transcription coupled in eukaryotes

no

why regulation?

some need to always be on (like respiration)

constitutive geneS

housekeeping genes that are expressed continuously by the cell

no need to regulate

examples: respiration and dna transcription

regulatory genes

inducible genes and repressible genes

inducible genes

genes that code for inducible enzymes needed only in certain environments

many catabolic enzymes

produced only when their inducer is available

repressible genes

product will inhibit biosynthesis of the same compound (most biosynthetic enzymes)

regulation of gene expression

transcription initiation

transcription elongation

translation

alter activity of enzymes and proteins

posttransitional

how to regulate cellular processes

regulation of gene expression

alter activity of enzymes and proteins

different among organisms of three domains

regulation of gene expression at ____ step is the most energy efficient?

transcription initiation

most biosynthetic enzymes are coded by repressible genes

true

negative control of transcription initiation by regulatory proteins

repressor protein’s action, inhibit gene transcription

positive control of transcription initiation by regulatory proteins

activator protein’s action, promote gene transcription

how do repressor proteins act by binding DNA at regulatory sites in bacteria

repressor proteins bind to operator (overlaps or downstream of promoter), prevents polymerase functioning

how do activator proteins act by binding DNA at regulatory sites in bacteria

activator protein binds to activating site (upstream of the promoter, promotes polymerase binding)

global regulatory systems

regulatory systems that affect many genes and pathways simultaneously

important for bacteria since they must respond rapidly to wide variety of changing conditions

mechanisms of global regulatory systems

two component signal transduction systems

phosphorelay systems

regulatory proteins

alternative sigma factors

two component regulatory systems

not regulated by metabolites of the pathways

but by environmental conditions (T, pH, etc.)

links external events to regulation of gene expression

found in all three domains of life

two components it he 2-component regulatory system

sensor kinase

response-regulator proteins

sensor kinase

extracellular receptor for metabolite

intracellular communication pathway

response-regulator protein

activated by sensor kinase

dna binding protein

activator

enhances transcription needed

repressor

inhibits transcription unless needed

2 kinds of dna binding proteins

activator and repressor