BI323 Final Exam Material from Exam 3 Flashcards
sum of ALL chemical reactions occuring in a cell
metabolism
breakdown of complex molecules into smaller, simpler molecules releasing energy
catabolism
biosynthesis of complex molecules requiring energy input
anabolism
use of sunlight as an energy source
phototrophy
obtain energy by oxidation of electron donors and organic molecules in their environment
chemoorganotrophy
obtain energy by oxidation of inorganic molecules in their environment
chemolithotrophy
release of electrons during oxidation, requiring an electron acceptor
chemotrophic metabolism
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
electrons pass through the electron transport chain to an O2 terminal electron acceptor generating a potential energy source
aerobic respiration
electrons pass through the electron transport chain to a non-O2 terminal acceptor yielding less energy
anaerobic respiration
substances and processes origination within an organism, tissue, or cell
endogenous
caused by factors or agents outside the organism or system
exogenous
pathway for glucose degradation to pyruvate into cytoplasmic matrix
-AKA: Embden-Meyerhof pathway
glycolysis
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
for every 1 glucose molecule, it yields 1 ATP, NADPH, and NADH
Entner-Doudoroff Pathway
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
process by which 1 STP is synthesized using energy from electron transport driven by oxidation of a chemical energy source
oxidative phosphorylation
process of moving ions to the other side of the biological membranes generating a charge difference
-mechanism of ATP synthesis: proton motive force
chemiosmosis
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
stationary phase, low aeration, high O2 affinity, and no H+ pump
-cyt b558d and cyt b595d
cyt bd branch
log phase, high aeration, moderate O2 affinity, presence of H+ pump
-cyt b562o
cyt bo branch
inhibit flow of electrons such as antibiotics - piericidin and antimycin
blockers
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
What is ATP production dependent on?
growth conditions and nature of the electron transport chain
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
