-
chemotrophs
chemical substanes as source of energy
-
phototrophs
light as a source of energy
-
autotrophs
CO2 as a source of carbon
-
heterotrophs
organic compounds as source of carbon
-
organotrophs
organic compounds as soruce of electrons
-
lithotrophs
inorganic compounds as source of electrons
-
nitrogen cycle
bacteria play critical role, such as nitrogen fixation
-
nitrogen fixation
conversion of N2 from the air into NH3
-
ATP
storage molecule for chemical enegry in all cells
-
-
-
what produces the energy needed for anabolism?
catabolism
-
reversible reaction
ATP is hydrolyzed to ADP + Pi + energy
-
ATP hydrolysis
where endergonic reactions that would not occur in living cells can be effectively promoted by coupling them into ATP hydrolysis
-
oxidation
loss of electrons
-
reduction
gain of electrons
-
redox
oxidation-reduction / electrons are transferred from one substace that becomes oxidized to another substance that becomes reduced.
-
what happens in a redox reaction?
two electrons and two hydrogen ions are transferred simultaneously
-
electron transport chains
proteins that are imbedded in membranes that transfer electrons and hydrogen ions in such a way that a pH gradient is generated accross the membrane
-
chemiosmosis
proton motive force - it drives the synthesis of ATP catalyzed by the enzyme ATP synthase when hydrogen ions pass through the enzyme.
-
enzyme
biological catalysts; most are proteins but some are catalytic RNAs (ribozymes)
-
active site
enzyme's site where the substrate binds
-
competitive inhibitors
compounds that compete for the binding of substrate to the enzyme
-
allostetric site
(distinct from the active site) where a noncompetitive inhibitor (or activator) can bind thereby affecting the activity of the enzyme
-
feedback inhibition
the final product of the pathway acts as a noncompetitive inhibitor of the first enzyme in the pathway.
-
example of feedback inhibition
some anabolic pathways (byosynthetic)
-
what do enzymes do?
lower activation energy needed for catalysis
-
the activity of an enzyme is influenced by...
pH, temperature, and the concentration of substrate
-
what is glycolysis?
the cleavage of glucose into two 3-carbon compounds
-
what does the kreb's (TCA) cycle do?
it converts acetyl-CoA into 2 CO2
-
what does substrate level phosphorylation result in glycolysis?
2ATP / glucose
-
what does substrate level phosphorylation result in the Kreb's cycle?
2GTP = 2 ATP
-
what does oxidative phosphorylation convert by chemiosmosis?
it converts NADH and FADH2 into ATP
-
aerobic respiration's maximum possible energy yield for one molecule of glucose is
38 ATP/ glucose; actual yield = 30-32 ATP/ glucose
-
respiration
serios of redox reactions in which an inorganic substance is the final electron acceptor. example: oxygen is this substance in aerobic respiration
-
fermentation
series of redox reactions in which an organic substance is the final electron acceptor. example: a small organic acid or alcohol.
-
fermentative microbes commercially important are...
bakers' and bewers' yeast (S. cerevisiae)
-
fermentation's ATP yield:
2ATP/glucose
-
what can be catabolized to yield energy (ATP)
lipids and proteins
-
why is metabolism extensively integrated?
so that the same or similar pathways can be used for production of energy or production of carbon chains for biosynthesis
-
photosynthesis
carbon fixation (CO2 added to carbohydrate) powered by ATP produced form the absorption of light by chlorophylls organized into photosystems.
-
photosystem 1
cyclic electron flow and does not produce oxygen
-
photosystem 2
noncyclic electron flow and produces oxygen
-
where do photosystems occur?
in chloroplasts in eukaryotes and in the plasma membranes of prokaryotes
-
what happens in the anabolism of macromolecules?
monomers are polymerized into polymers. for example: amino acids into proteins. nucleotides into nucleic acids. monosaccharides into polysaccharides.
-
DNA
genetic material in all cells and many viruses
-
who provided evidence that DNA is the genetic material?
Griffith's transformation experiment
-
where does vertical transmission DNA occur?
cell division
-
where does horizontal transmission of DNA occur?
within a generation
-
why is DNA a duplex molecule?
it is a molecule consisting of two strands - polymers of nucleotides attached by phophodiested bonds. each strand has 5' to 3' polarity
-
duplex DNA
it is antiparallel wit respect to the polarity of the two strands
-
DNA structure
4 bases (ACGT); form base pairs (AT and GC); two strands are complementary with respect to base pairing
-
what doest he major groove of the double helix of duplex DNA do?
it is where sequence-specific DNA binding proteins bind
-
DNA replication
separation of the two strands of parental DNA and copying as templates resulting in the synthesis of two new strands of daugter DNA
-
what is the main enzyme in DNA replication?
DNA polymerase; other important enzymes: primase and DNA ligase
-
where do most of the ATP used by cells go?
in the synthesis of proteins
-
lagging strand of DNA
DNA synthesis is discontinuous
-
leading strand of DNA
DNA synthesis is continuous
-
circular DNA
it has only one origin of DNA replication
-
large linear chromosomal DNA
many origins of DNA replications
-
nucleid acid synthesis
(both DNA and RNA) proceed in the 5' to 3' direction
-
telomeres
repeated DNAs on both ends of eukaryotic chromosomes
-
how are telomeres generated?
by the action of telomerase (enzyme that copies RNA in making DNA)
-
transcription
synthesis of RNA complementary to the template strand of DNA in the gene
-
RNA polymerase
enzyme that catalyzes the polymerization of ribonucleotides into RNA
-
where does the RNA polymerase bind to?
a sequence of DNA called the promoter
-
who has a RNA polymerases?
E.Coli has one that syntesizes mRNA, rRNA and tRNA; eukaryotes have separate RNA polymerases for each of them
-
what happens to bacteria related genes?
they are clustered together and transcribed into plycistronic mRNAs that are translated into several proteins
-
what happens in eukaryote's genes?
they are transcirbed individually into monocistronic RNAs that are translated into one protein
-
exons
eukaryotic genes coding sequences
-
introns
eukaryotic genes noncoding sequences that separate exons
-
what is the first product of transcription in eukaryotes?
heterogeneous nuclar RNA (jmRNA) - must be spliced (by sliceosomes) to remove introns
-
sliceosomes
complex of small nuclear RNAs and proteins; they perform splicing
-
what is the triplet code that is universal in biology?
genetic code
-
protein product of the gene
3 nucleotides in mRNA encode one amino acid i nthe protein product of the gene
-
how many common amino acids are in proteins?
20
-
how many codons are in proteins?
61
-
why is the genetic code said to be degenerated?
more than one codon per amino acid
-
what is the start codon?
AUG
-
what are the stop codons?
UAA, UAG, UGA
-
what does tranfer RNAs have?
an anticodon that matches the sequence in the codon.
-
how are amino acids attached to tRNAs?
by aminoacyl-tRNA synthetases (requires ATP)
-
what is the peptidyl transferase activity in protein synthesis in bacteria?
23S rRNA
-
what is the peptidyl transferase activity in protein synthesis in eukaryotes?
28S rRNA
-
catalytic RNAs
they catalyze the formation of peptide bonds between amino acids
-
where does protein synthesis occur on the ribosome in bacteria?
70S bacteria
-
wher does protein synthesis occur on the ribosome in eukaryotes?
80S eukaryotes
-
what is requried for protein synthesis?
protein initiation factors (IFs), elongation factors (EFs) and GTP
-
what do protein release factors (RFs) bind to?
stop codons and mediate termination of protein synthesis
-
chaperones
specific proteins that some proteins require to fold. (protein folding may occur spontaneously)
-
how is gene expressino regulated?
at the level of transcription by proteins biding to specific sequences of DNA
-
where does regulation occur?
at the level of translation, especially in eukaryotes. mRNA splicing can also be regulated
-
constitutive genes
always expressed
-
inducible genes
function in catabolism; not expressed but can be turned on
-
repressible genes
function in anabolism; expressed but can be turned off
-
how is the lac operon regulated?
by a repressor that binds to an operator. (like the trp operon)
-
what happens when the repressor is bound?
transcription is blocked
-
how does transcription occur?
when lactose (inducer) is present and binds to the repressor and causes it to change shape so that it can't bind to DNA
-
how is the trp operon regulated?
by a repressor that binds to an operator. (like the lac operon)
-
what happens when tryptophan (corepressor) is present?
it binds to the repressor and activates itso that it bind to the operator sequence of DNA
-
negative regulation
inhibition of transcription
-
positive regulation
stimulation of transcription
-
what type of regulation does the lac operon exhibit?
both: negative by the repressor and positive by the CAP- cAMP
-
what happens when glucose levels are low?
adenlyl cyclase converts ATP into cyclic AMP (cAMP) + PPi. then, cAMPbiind to the catabolite activator protein (CAP) to form a functional complex that binds to DNA and stimulates the binding of RNA polymerase to its promoter
-
what eliminates the mRNAs from being translated into proteins?
small nuclar RNAs (siRNAs) bind to m RNAs and cause them to be degraded by a nuclease (dicer)
-
how can novel sequences be yied?
DNA sequence recombination
-
mutation
change in the sequence of nucleotides in DNA.
-
why are mutations caused?
by chemicals (mutagens) or electromagnetic radiation (UV or x-rays)
-
point mutations
changes in one base pair in the DNA
-
missense mutations
change a codon into a codon for another amino acid
-
nonsense mutations
change a codon for an amino acid into a stop codon
-
silent muations
chagne a codon for an amino acid into another codon for the same amino acid
-
when do thymine-thymine dimers occur?
when DNA absorbs UV light?
-
what enzymes correct damage to DNA?
repair enzymes: excision repair and mismatch repair
-
who does an excision repair serve?
any DNA sequence
-
who does mismatch repair serve?
newly replicated DNA only
-
how do repair enzymes work?
they remove damaged DNA segments, polymerization of nucleotides to fill in the gap, and DNA ligation
-
carcinogens
chemicals that cause cancer; mutagens in the Ames test that measures the frequency of reversion of a his- mutation to the wild type, his+.
-
auxotroph
nutritional mutant
-
where does homologous recombination occur?
between related DNA sequeces
-
where does site-specific recombination occur?
at specific sites
-
plasmids
small circular DNAs with their own origin of DNA replication. they replicate independently of baterial chromosomal DNA
-
F factor
plasmid that is requried for conjugation; the F factor itself is transferred; it can integrate into the bacterial chromosomal resulting in a Hfr (high frequency of recombination) cell.
-
what kind of F factor is donor E. Coli?
F+
-
what kind of F factor is recipient E. Coli?
F-
-
what can an Hfr corss with?
an F- cell; chromosomal genes are transferred
-
transposon
mobile sequence of DNA; they harbor genes for drug resistance
-
transformation
uptake and integration of DNA. (occurs in high frequencies in bacteria)
-
transduction
uptake and incorporation of DNA mediated by a virus
-
generalized transduction
encapsidation of a piece of bacterial DNA into a virus particle
-
recombinant DNA
DNA from two sources that is spliced together
-
restriction enzymes
cut DNA at specific sequences (palindromes); many have been isolated from different microbes.
-
vector
sequence of DNA that can be used for the formation of recombinant DNA
-
cloning vector
production of DNA inserts
-
expression vectors
prodcution of the proein product of that gene
-
complimentary DNA (cDNA) produced from mRNA by reverse transcriptase
-
selectable marker
gene for resistance to an antibiotic; used to ensure that transformed bacteria contain the recombiant DNA desired
-
libraries
series of cloned DNAs (genomic, cDNA)
-
DNA fragments
separated by size by agarose gel electrophoresis
-
The Southern blot
comibnes the separation of DNA by size with the detection of specific DNA sequences by hybridization (allowing mixed duplexes to form between a test DNA or probe and the DNA being studied)
-
polymerase chain reaction (PCR)
way to aplify DNA
-
how does polymerase chain reaction works?
it uses oligonucleotide primers and Taq DNA polymerase (thermostable) in a thermocycler to produce many copies of DNA in a test tube
-
DNA sequencing by Sanger method
it uses dideoxynucleotides as chain terminators
-
how are results analyzed in the Sanger method?
by polycrylamide gel electrophoresis
-
GenBank
public database where tens of billions of nucleotides of DNA sequences are available
-
genome
consist of all genes in an organism
-
microarrays
many genes can be analyzed simultaneously
-
what represents all proteins in an organism?
the proteome
-
how can proteome be analyzed?
by a two-dimensional gel electrophoresis
|
|