exam 2 Flashcards by Paige Jackson

RNA Polymerase I

Found in the nucleolus

Responsible for synthesizing most of ribosomal rRNA and rRNA genes

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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

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RNA Polymerase III

Located in the nucleus

Responsible for coding tRNA and snRNA and other small RNA

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initiation of transcription

recognition step, finding promoter region
stage complete when DNA strands separate near the promoter to form an open complex

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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

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promoters in eukaryotes

bind to the TATA box, 30 base pairs upstream from the start of the transcription start site

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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

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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

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termination (transcription)

process of ending transcription happens once the polymerase transcribes a sequence of DNA known as the terminator

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transcription

DNA to pre-mRNA to mRNA

happens in the nucleus

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RNA processing

only happens in eukaryotes

the removal of noncoding stretches of nucleotides that lie between coding regions

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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

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spliceosome

made of up SNURPS

assist in RNA splicing

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introns

the intervening noncoding sequences, transcribed not transmitted

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exons

the coding regions of eukaryotic genes that are found in mature mRNA

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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