Bio 107 Exam 3 Ch 14, 15 & 7

What enters the citric acid cycle?

Acetyl CoA from pyruvate oxidation

What’s the products from the citric acid cycle for each glucose?

4 ATP, 6 CO2, 2 FADH, 10 NADH

What does the citric acid cycle do?

Oxidizes the acetyl group from pyruvate to make NADH and FADH for the ETC

What happens during the electron transport chain?

The ETC is a series of membrane-bound electron carriers, and electrons from NADH and FADH are transferred to different complexes which build a proton gradient, and go to the ATP synthase.

How much ATP is produced per glucose molecule in bacteria?

32

How much ATP is created per glucose molecule in eukaryotes?

30

The final electron acceptor in the ETC is..

Oxygen, and it makes water

Step 1 of the Citric Acid Cycle

condensation, acetyl-CoA combines with oxaloacetate to make citrate

Steps 4,5,7 and 9 of the Citric Acid Cycle

oxidation of sugar

Steps 4 and 5 of the Citric Acid cycle

release of CO2

Step 6 of the Citric Acid Cycle

Substrate level phosphorylation — ATP produced!

Substrate level phosphorylation

transfer phosphate group from organic molecule directly to ADP

In the Frederick Griffith Experiment, why did the mixture of heat-killed virulent and live non virulent strains of pathogen kill the mouse?

The heat-killed virulent and live non-virulent strains of S. pneumoniae killed the mouse since the heat-killed virulent exchanged DNA with the non-virulent strain. This transfer of virulence is called transformation

In the Hershey and chase experiment, how was it concluded that DNA is the genetic material?

Bacteriophage DNA was label with radioactive phosphorus (32P), and bacteriophage protein was labelled with radioactive sulfur. (Bacteriophages are only made of DNA and protein). Phages are grow to be radioactive, they infected bacteria, and then the phage coat was separated via blending centrifugation. The radioactivity was tracked, and the radioactivity was in the pellet of DNA which shows that the bacteriophage DNA entered the bacteria and was able to produce more bacteriophages.

Overall structure of DNA

a 5-carbon sugar, a phosphate group (5’), a nitrogenous base (A,T,G,C), and a free hydroxyl group —OH (3’).

What’s on the on the 5’ C in DNA?

A phosphate group

What’s on the 3’ C in DNA?

Free hydroxyl group

What’s on the 2’ C in DNA?

H in DNA, and OH in RNA

What is a phosphodiester bond?

A bond between adjacent nucleotides, they’re formed by the phosphate group of one nucleotide and the 3’ OH of the next nucleotide. These chains have a 5’ to 3’ orientation

What are Chargaff’s rules?

He determined that there’s always an equal proportion of 2-ringed purines (A and G) and single-ringed pyrimidines (C and T). Amount of A = amount of G, and amount of C = amount of G.

Structure of a single strand of DNA

Phosphodiester BB, made of repeating sugar and phosphate units joined by phosphodiester bonds. A single strand extends in a 5’ to 3’ direction. Each phosphodiester strand has inherent polarity based on orientation of sugar-phosphate BB. One end terminates in 3’OH, and one end terminates in 5’ PO4.

What is the difference between major and minor groove?

In a double helix there are two grooves, major and minor. The major groove occurs when bbs are far apart, and minor is when they’re close.

What are the models of DNA Replication?

Conservative model, semiconservative, and dispersive model

Conservative model

Both strands of parental DNA remain intact; new DNA copies consist of all new molecules

Semiconservative model

Daughter strands each consist of one parental strand and one new strand

Dispersive model

New DNA is dispersed throughout each strand of both daughter molecules after replication

How did Meselson stahl conclude replication is semi conservative? What does it mean for replication to be semi conservative?

This was determined by combining two stands of DNA, one was lighter and one was heavier. The heavy DNA was replicated with the light DNA, so if it was conservative and both bands were made, we’d see a prominent heavy band (bottom) and light band (top). If it was semiconservative, then there’d be a band in the middle, and a light band. Lastly, if it was dispersive then there’d be multiple bands. In the second round there were two bands, with one of them being in the middle, which shows that it wasn’t just heavy DNA or light DNA being made, and that light DNA is still present since it is the template for the heavy DNA’s replication.

What does DNA polymerase do?

DNA polymerase is used to synthesize new strands of DNA. They can add nucleotides to growing DNA strands, can cut DNA internally (endonucleases), or remove nucleotides from end of DNA (exonucleases)

What are the three polymerases in E. coli?

Pol 1, Pol 2, and Pol 3

What does DNA polymerase 1 do?

Acts on lagging strand to remove primers and replace them with DNA?

What does DNA polymerase 2 do?

Involved in DNA repair processes

What does DNA polymerase 3 do?

Helps with most gene/chromosomal replication. Extends leading-strand, it lets the polymerase stay attached with a beta subunit (sliding clamp).

Why does E. coli have 3 DNA polymerases?

All 3 have 3’ to 5’ exonuclease activity (proofreading), and DNA Pol 1 has 5’ to 3’ exonuclease activity (removes RNA primers)

Endonuclease

Cut DNA internally

Exonuclease

Remove nucleotides from end of DNA

Telomeres

Specialized structures found on the ends of eukaryotic chromosomes. They’re composed of specific repeat sequences, they protect ends of chromosomes from nucleases and maintain the integrity of linear chromosomes. 

What is the purpose of topoisomerase?

It’s an enzyme that prevents supercoiling. Supercoiling happens when torsional strain caused by the unwinding of DNA leads to the twisting of helix. 

Replication fork

The partial opening of the helix formed where double stranded DNA is being unwound.

DNA gyrase

Same thing as topoisomerase, prevents supercoiling. DNA gyrase can unlink two copies.

What does Pol 1 do in a replication fork?

It gets rid of primers used to replicate the lagging strand

DNA ligase

Joins Okazaki fragments to form complete strands

DNA primase

Makes RNA primer for Okazaki fragments

Why is one strand of DNA replicated continuously, and the other is discontinuous?

DNA is translated from 5’ to 3’, and when a strand is split, the added strand must be antiparallel. If there’s a 3’ to 5’ strand, then the complementary strand must be 5’ to 3’, but it can only translate to the extent where the strand is open, so a primer must be added to act as a starting point for translation to occur. 

Mismatch repair (MMR)

Removes incorrect bases incorporated during DNA replication. Replaces with the correct base by copying the template strand. To distinguish between the newly synthesized strand the strand is unmethylated for a brief window to get MMR identify the strands.

Photorepair

Specific repair mechanism, thymine dimers caused by UV light where adjacent thymines become covalently linked together. A photolyase absorbs light in visible range, and this energy is used to cleave those thymine dimers.

Excision repair

Non specific repair. Damaged regions are removed and replaced by DNA synthesis. First there’s recognition of damage, removal of the damaged region, resynthesized using the information on the undamaged strand as a template. In E. coli these proteins are encoded by uvr-A, -B and -C to carry out this repair. 

What is the relationship between coding strand, template strand, and RNA?

Coding & template: complementary

RNA & coding: same

RNA & template: complementary

How is RNA read?

In groups of 3 (codons)

What determines which nucleotides starts protein synthesis?

There’s a starting sequence AUG, from there it codes in 3 starting after that

What is the start codon?

AUG (Met)

Stop codons

UAA, UGA, UAG

What is the protein responsible for protein synthesis?

rRNA, ribosomal RNA

All RNA is synthesized from a ___ template by ____.

DNA, transcription

What are the different kinds of RNA?

mRNA, rRNA, and tRNA

Messenger RNA (mRNA)

Intermediate form of information from nucleus to cytoplasm for processing

Ribosomal RNA (rRNA)

Class of RNA found in ribosomes, is essential for their function in protein production

Transfer RNA (tRNA)

intermediary adapter molecule between mRNA and amino acids during protein synthesis

Transcription requirements

Promoters, start sites, and terminator

Promoter

forms recognition and binding site for RNA polymerase

Start site

actual site where RNA synthesis begins

Terminator

Signal to end transcription

Transcription unit

Region from promoter to the terminator

What allows the polymerase to recognize the promoter?

The sigma subunit, it recognizes the promoter, brings the polymerase and then leaves it once the DNA is opened.

What allows the terminator to stop transcription?

An RNA-DNA hybrid in the transcription bubble is dissociated, this lets the RNA polymerase release the DNA so the DNA can rewind. The simplest terminator is a hairin, which cuases RNA polymerase to pause at uracil (the U-A bonds are the weakest which results in the dissociation of RNA from DNA).

What is the purpose of transcription factors?

Transcription factors get the RNA Pol 2 enzyme to a promoter to initiate gene expression. They interact with RNA polymerases to form initiation complexes at the promoters. 

What is 5’ capping?

In eukaryotes, the primary transcription must be modified to become mature mRNA. GTP is added to the 5’ end, with a methyl group is called methyl-G cap. It’s involved in translation initiation, RNA stability and further processing

What is 3’ Adenylation?

It’s an addition of a 3’ poly-A tail created by poly-A polymerase. Other termination mechanisms exist using other factors

What is removed during splicing?

Introns

Splicing process

A number of modifications are made while the mRNA is in the nucleus: introns are removed and exons are spliced together, a 5’ cap is added; a poly-A tail is added

Introns

They’re invening sequences, non-coding sequences

Exons

Expressed sequences, sequences that will be translated

Which does the spliceosome consist of?

Small ribonucleoprotein particles (snRNPs), they cluster with other proteins to make the spliceosome. They’re responsible for removing introns via splicing

______________ _______________ refers to genes being spliced together in different patterns. The number of proteins and pre spliced mRNA is not the same. Why do you think this is?

he same mRNA transcript can be spliced in different ways. Different proteins can be yielded from the same gene, it just depends on what you decide to cut out. There’s different pol-A sites on the different 3’ Poly-A tails for different proteins

What does tRNA do?

Interact with mRNA and amino acids, carry amino acids to the riibosome for incorportaion into a polypeptide

What is the purpose of the ribosome?

A key machine used for translation, needs mRNA, and tRNA.

tRNA binding sites

A (aminoacyl) site, P (peptidyl) site, E (exit) site

A (aminoacyl) site

binds the tRNA carrying the next amino acid

P (peptidyl) site

binds the tRNA attached to the growing peptide chain

E (exit) site

binds the tRNA that carried the previous amino acid added