exam 2 Flashcards
RNA Polymerase I
Found in the nucleolus
Responsible for synthesizing most of ribosomal rRNA and rRNA genes
RNA polymerase II
Located in the nucleus (associated with the chromatin)
Catalyzes synthesis of mRNA which serves as the template strand for protein synthesis coding for non coding and coding genes
RNA Polymerase III
Located in the nucleus
Responsible for coding tRNA and snRNA and other small RNA
initiation of transcription
- recognition step, finding promoter region
- stage complete when DNA strands separate near the promoter to form an open complex
promoters in bacteria
sigma first binds to the DNA, but then sigma and RNA polymerase together form a holoenzyme
10 box upstream of RNA polymerase (opposite direction) TATAAT
35 box is 35 bases upstream TTGACA
promoters in eukaryotes
bind to the TATA box, 30 base pairs upstream from the start of the transcription start site
holoenzyme
made up of sigma and RNA
sigma open DNA double helix and the template strand is threaded through the RNA polymerase active site
NTP pairs with the complementary base on the DNA template strand and the RNA starts to be created
sigma then disconnects after the initiation stage is over
elongation (transcription)
RNA polymerase walks along one strand of DNA known as the template strand in the 3 to 5 direction (the other strand is in the 5 to 3 direction)
RNA polymerase adds matching RNA nucleotide to the 3 ends of the new RNA strand
termination (transcription)
process of ending transcription happens once the polymerase transcribes a sequence of DNA known as the terminator
transcription
DNA to pre-mRNA to mRNA
happens in the nucleus
RNA processing
only happens in eukaryotes
the removal of noncoding stretches of nucleotides that lie between coding regions
RNA splicing process
SNURPS bind to the 3 and 5 ends of the pre-mRNA
more SNURPS bind bringing the two ends together (in a loop)
introns cut out and exons are moved together
spliceosome
made of up SNURPS
assist in RNA splicing
introns
the intervening noncoding sequences, transcribed not transmitted
exons
the coding regions of eukaryotic genes that are found in mature mRNA
capping
a cap (modified guanine is added to the 5 end of the mRNA once it is done being transcribed
poly-A tail
100-200 adenine nucleotides added to the 3 end
transfer RNAs
connect mRNA codons to the amino acids they encode; had anticodons that bind to mRNA and the other end carries the amino acids specified by codon
ribosomes
where polypeptides are built; ribosomes are made up of rRNA
small subunit- holds mRNA in place during translation
large subunit- where peptide bonds form
aminoacyl-tRNA synthetase
catalyzes the attachment of amino acids to tRNA reactions result in tRNA and amino acids attached
initiation (translation)
mRNA binds to ribosomal subunit; ribosomal subunit in bacteria, guanosine @ 5 end for eukaryotes
aminoacyl tRNA with f-met binds to the start codon
large ribosomal subunit binds, completing complex
tRNA is on the p-site
In eukaryotes it binds to the 5 guanine cap first and then finds the start codon
elongation (translation)
aminoacyl tRNA brings a new amino acid to the A site, binding occurs (anticodon/codon), peptidyl tRNA is on the P site, aminoacyl tRNA is on the A site
peptidyl transfer reaction occurs
translocation of ribosomes towards 3 end of mRNA by one codon; shifts tRNA @ the P and A set to E and Psite, next codon @ A spot and uncharged tRNA exits from E spot
peptidyl transfer reaction
peptide bonds are formed between amino acid @ A site and the growing peptide chain, polypeptide removed from tRNA in the P site and transferred to amino acid @ the A site
termination (translation)
when the stop codon is found on A site, translocation ends
recognized by the release factors
substrate level phosphorylation
ATP is formed when an enzyme transfers a phosphate group from a substrate to ADP
chemiosmosis
energy stored in an electrochemical gradient is used to make ATP from a phosphate and ADP
catabolism
break down of large molecules into smaller molecules, releases ATP
anabolism
synthesis of small to big molecules, need energy to make it happen
oxidation reaction
gives up an electron and becomes oxidizes
reduction reaction
an atom or a molecule gains an electron and it becomes reduced in energy
glycolysis
in the cytosol
glucose + 2 pyruvate—>2 NADH+ 4 ATP+ 2 pyruvate
energy investment: glucose and 2 ATP are hydrolyzed to create fructose-1, 6 bisphosphate (that’s one molecule)
cleavage: 6 carbon molecules (that molecule) are broken down into 2 3 carbon molecules of glyceraldehyde-3-phosphate
energy liberation: 2 glyceraldehyde-3-phosphate molecules are broken down into two pyruvate molecules, producing 2 NADH, and 4 ATP (2 net)
pyruvate oxidation
in the mitochondria matrix
2 pyruvate—-> 2 CO2+ 2 NADH+ 2 acetyl CoA
-pyruvates are broken down by pyruvate dehydrogenase
-molecules of CO2 (removalof the carboxyl group) removed from each pyruvate
-remaining acetyl group attached to CoA to make acetyl CoA
citric acid cycle
in the mitochondrial matrix
2 acetyl CoA—-> 2 ATP+ 6 NADH+ 2 FADH+ 4 CO2
citrate
isecitrate
alpaha ketoglutatate
succinyl CoA
succinate
fumarate
malate
oxialoate
***Come in and shit some fucking milk out
electron transport chain
inner mitochondrial membrane
oxidative phosphorylation: high energy electrons removed from NADH and FADH2 to make ATP
- the movement of electrons through embedded proteins creates an electrochemical gradient providing energy to make ATP
NADH+ FADH2+ O2—–> 30-34 ATP+ H2O
proteins in the ETC and their roles
- NADH dehydrogenase: oxidative reaction of NADH to NAD+ and H+ which is pumped across the membrane
- succinate reductase: oxidative reaction FADH to FAD+ +2H and then pumps the H+ across the membrane
- cytochrome oxidase: reduction reaction takes the electrons and creates water as a by-product
- ATP synthase: pumps the protons back across the membrane, creating ATP in the process
Fermentation
The breakdown of organic molecules without net oxidation under anaerobic conditions (no oxygen)
Eukaryotes : lactic acid fermentation, reduces pyruvate into lactate by oxidizing NADH To NAD+ and then lactate is converted to glucose when O2 is available, done by the liver
Bacteria (yeast primarily): alchol fermentation makes ethanol by converting the pyruvate to CO2 and acetaldehyde and then with NADH oxidation converts to ethanol
