BI323 Final Exam Material from Exam 3 Flashcards by Abbey Baksa

sum of ALL chemical reactions occuring in a cell

metabolism

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breakdown of complex molecules into smaller, simpler molecules releasing energy

catabolism

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biosynthesis of complex molecules requiring energy input

anabolism

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use of sunlight as an energy source

phototrophy

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obtain energy by oxidation of electron donors and organic molecules in their environment

chemoorganotrophy

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obtain energy by oxidation of inorganic molecules in their environment

chemolithotrophy

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release of electrons during oxidation, requiring an electron acceptor

chemotrophic metabolism

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does not use an electron transport chain but an acceptor that is endogenous to degrade and oxidize an organic energy source under anaerobic conditions with limited energy

fermentation

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electrons pass through the electron transport chain to an O2 terminal electron acceptor generating a potential energy source

aerobic respiration

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electrons pass through the electron transport chain to a non-O2 terminal acceptor yielding less energy

anaerobic respiration

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substances and processes origination within an organism, tissue, or cell

endogenous

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caused by factors or agents outside the organism or system

exogenous

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pathway for glucose degradation to pyruvate into cytoplasmic matrix
-AKA: Embden-Meyerhof pathway

glycolysis

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functions for NADPH serving as a source for biosynthesis, produce erythrose-4-P for amino acid synthesis, produce ribose-5-P for nucleic acid synthesis, and intermediate ATP production

Pentose Phosphate Pathway

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for every 1 glucose molecule, it yields 1 ATP, NADPH, and NADH

Entner-Doudoroff Pathway

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competes oxidation and degradation of glucose and other molecules as well as providing carbon skeletons for biosynthesis
-common in aerobic bacteria, free-living protozoa, most algae, and fungi

Tricarboxylic Acid Cycle

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process by which 1 STP is synthesized using energy from electron transport driven by oxidation of a chemical energy source

oxidative phosphorylation

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process of moving ions to the other side of the biological membranes generating a charge difference
-mechanism of ATP synthesis: proton motive force

chemiosmosis

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series of electron carriers flowing from a negative charge to a more positive charge by electrons from NADH and FADH2 transferring to the terminal electron acceptor

electron transport chain

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stationary phase, low aeration, high O2 affinity, and no H+ pump
-cyt b558d and cyt b595d

cyt bd branch

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log phase, high aeration, moderate O2 affinity, presence of H+ pump
-cyt b562o

cyt bo branch

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inhibit flow of electrons such as antibiotics - piericidin and antimycin

blockers

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disconnect electron flow from oxidative phosphorylation causing electrons to become lost by allowing ion movement without ATP synthase activity or directly inhibiting ATP synthase

uncouplers

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What is ATP production dependent on?

growth conditions and nature of the electron transport chain

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What are some principles governing biosynthesis?

1.) macromolecules synthesized from limited number of monomers 2.) many enzymes for catabolism and anabolism save material and energy 3.) catabolic and anabolic pathways are not identical 4.) ATP hydrolysis coupled with reactions in biosynthetic pathways 5.) anabolic and catabolic reactions have separate compartments allowing them to operate simultaneously or independently 6.) different cofactors for catabolic and anabolic pathways 7.) require precursor metabolites

C skeletons are a starting point for monomer synthesis needed to make macromolecules -lack a functional group including NH2 and -SH

precursor metabolites

synthesis of glucose-6-P from noncarbonhydrate precursors with 3 reactions catalyzed by enzymes specific for the process -synthesis of monosaccharides

gluconeogenesis

"carrier of glucose into the cell" -synthesis of monosaccharides

nucleoside diphosphate sugars

adjacent polysaccharides chains are cross-linked by bonds formed between stem peptides -cell wall biosynthesis with a backbone of alternating sugars of NAG and NAM

peptidoglycan synthesis

What does NAG stand for?

N-acetylglucosamine

What does NAM stand for?

N-acetylmuramic acid

What are the general steps of peptidoglycan synthesis?

1.) formation of peptidoglycan subunits 2.) formation of repeat unit 3.) transport of repeat unit via bactoprenol 4.) repeat unit attached to growing peptidoglycan chain 5.) chains are crosslinked via transpeptidation

carbon skeleton is remodeled and an amino acid group, sometimes sulfur, is added

amino acid synthesis

nitrogen is incorporated with ammonia, nitrate, and some nitrogen gas

nitrogen assimilation

replenish TCA intermediates allowing the cycle to function during periods of active biosynthesis through 2 ways

amplerotic reaction

only supplies TCA cycle with oxaloacetate - pyruvate carboxylase and phosphoenolpyruvate carboxylase

anaplerotic CO2 fixation

closed circular, supercoiled and associated with basic proteins

bacteria

linear molecules coiled with repeating units/nucleosomes and is associated with histones

eukaryotes

circular molecules coiled with nucleosomes and is associated with histones

archaea

bidirectional with a single origin of replication and replicon

prokaryote replication

single point of chromosomal replication

origin of replication

portion of genome that contains an origin and is replicated as a unit

replicon

circular template of DNA is replicated as a long single stranded DNA that is used by viruses and plasmids as its rapid and many copies can come from 1 initation

rolling circle mechanism

denatures doubling-stranded DNA

DnaA proteins

part of the replisome that requires a RNA primer

DNA pol III

synthesizes a short 10-base RNA molecule complementary to the template

primase

disrupts hydrogen bonds holding parental DNA strands together unwinds

helicase

coat single stranded DNA to protect it from damage

single-stranded DNA binding proteins

relieve the twist generated by rapid unwinding of double helix

topoisomerase

linear sequence of nucleotides with a fixed start and end point encoding polypeptide. tRNA, and rRNA

gene

gene encoding a polypeptide

cistron

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

reading frame

template strand directing mRNA synthesis

coding gene

RNA polymerase binding with consensus sequences being -35/-10

promoter

transcribed into mRNA but no translated into amino acid

leader

ribosome binding site at 16S

Shine-Dalgarno

encodes more than 1 polypeptide with gene products often functioning together

polycistronic

synthesis of RNA from a DNA template

transcription

What are the general steps of transcription?

1.) initiation 2.) elongation 3.) termination

What are some key points that happen during transcription's elongation step?

-RNA polymerase slides along DNA creating an open complex -DNA template strand is used to make a complementary copy of RNA -RNA is synthesized in a 5' to 3' direction -complementary rule

mRNA hairpin and 6 uridines release RNA polymerase during termination

Rho-independent

requires a rho factor during termination

Rho-dependent

What are the differences in archaeal transcription?

-single RNA polymerase -eukaryotic-like promoters -mRNA is polycistronic and has introns

decoding mRNA and using it to build a protein

translation

bacteria causing initation

fMet

prevents 30S from binding to 50S

IF-3

bings GTP and fMet-RNA and guides them to P site of 30S

IF-2

binds to 30S causing IF-3 to leave and create 30S initiation complex

IF-1

binds incoming aminoacyl-tRNA

aminoacyl/A site

binds initiator tRNA or peptidyl-tRNA

peptidyl/P site

briefly binds empty tRNA before it leaves ribosome

exit/E site

What are the 3 stop condons in translation termination?

UAA, UAG, and UGA

removal of part of the polypeptide before folding

protein splicing

removed portion of the polypeptide

inteins

portions of polypeptide that remain in the protein

exteins

aid in folding of nascent polypeptides and protect cells from thermal damage

molecular chaperones

What are the protein translocation pathways that are found in Gm- and Gm+?

1.) sec-dependent 2.) twin-arginine translocation pathways 3.) type I protein secretion pathway 4.) type IV secretion pathway

What are the protein translocation pathways that are only found in Gm- bacteria?

1.) type II pathway 2.) type III protein secretion pathway

BI323 Final Exam Material from Exam 3 Flashcards

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