Biology

Question 1

What does exonuclease mean?

Answer 1

“cutting a nucleic acid chain at the end.

Question 2

What will an endonuclease do?

Answer 2

Cut a polynucleotide acid chain in the middle of the chain, usually at a particular sequence.
Two types:
1. Repair enzymes, which remove chemically damaged DNA from the chain.
2. Restriction Enzymes, which are endonucleases found in bacteria that destroy DNA of infecting viruses, thus “restricting” the host range of the virus.

Question 3

How many polymerases are there in prokaryotes?

Answer 3

There are DNA pol III, II, I.
DNA pol III 5’ to 3’ polymerase, 3’ to 5’ exonuclease. (fastest)
DNA pol II unkown
DNA pol I 5’ to 3’ polymerase (same as III), however a 5’ to 3’ exonuclease (to remove RNA primers)

Question 4

Can thier ever be 3’ to 5’ polymarease activity?

Answer 4

No, no matter what no exceptions. Polymerase is always 5’ to 3’!

Question 5

Name all the ways RNA is different than DNA.

Answer 5

• Single stranded
• Uracil instead of Thymine
• 2’ carbon on pentose ring actually contains its OH “hydroxyl” group, hence “ribose” rather than deoxyribose.

Question 6

What is the stability of RNA compared to DNA and why?

Answer 6

RNA polymer is less stable, because the 2’ hydroxyl group can nucleophilically attack the backbone phosphate group of an RNA chain, causing hydrolysis when the remainder of the chain acts as a leaving group. This does not occur in DNA, since there is no 2’ hydroxyl group.

Question 7

Anticancer drugs often seek to block growth of rapidly dividing cells by inhibiting production of thymine. Why is than an attractive target for cancer therapy? All cells require RNA

Answer 7

All cells require RNA production, even if they are not growing, in order to continually replenish degraded RNA. Thus, if thymine production is blocked, only DNA replication will be inhibited and only rapidly dividing cells such as cancer cells will be affected. Cells that divide a lot in the body will also be affected such as hair follicles and cells lining the gut - hence why patients undergoing chemo therapy vomit and loose their hair.

Question 8

how many polypeptides can one eukaryotic mRNA encode?

Answer 8

One and only one polypeptide.

Each mRNA is “monocistronic” and obeys the “one gene, one protein” principle.

Question 9

Hoy many polypeptides can prokaryotic mRNA code for?

Answer 9

Polycistronic - more than one. Usually the different genes on the same polycistronic mRNA are generally related in function.

For instance, if five enzymes are necessary for the synthesis of a particular molecule, then all five enzymes might be encoded on a single piece of mRNA.

Question 10

How many types of tRNA are there?

Answer 10

20 different amino acids, so 20 different tRNAs’, since their job is to deliver the proteins called for by the mRNA genetic code for a specific protein.

Question 11

Do the polymerase enzymes in both replication and transcription require a primer?

Answer 11

No, RNA polymerase does not require a primer. Remember, the primer in replication is a pice of RNA, made by an RNA polymerase.

Question 12

A virus possessing an RNA genome relies on RNA polymerase rather than DNA polymerase to replicate its genome. Will this virus have a higher or lower rate of spontaneous mutation that organisms with ds-DNA genomes?

Answer 12

Since 1) RNA itself is less stable than DNA, and 2) RNA polymerase has not been shown to possess the ability to remove mismatched nucleotides (lacks exonuclease activity); the virus will have a very high rate of mutation. It is a general law that most mutations are harmful. Hence, individual viruses will be far less likely to survive than organisms with DNA genomes. However, the high mutation rate will allow the entire species of virus to evolve very rapidly, making it very successful as a parasite (since it will evade host defense systems).

Question 13

What is the name of the site where Transcription first occurs?
What is the name of the site where Replication first occurs?

Answer 13

Transcription: Start Site
Replication: Origin of Replication

Question 14

What is required for DNA polymerase to begin DNA Replication?
What is required for RNA polymerase to begin the process of Transcription?

Answer 14

DNA polymerase requires a special RNA polymerase called an “RNA primer”, which adds a small RNA primer that DNA polymerase can elongate by adding deoxyribonucleotides to the existing ribonucleotide primer, which is later replaced by DNA.

RNA polymerase requires a promoter, which is a sequence of nucleotides on a chromosome that activates RNA polymerase to begin the process of transcription.

Question 15

What is the part of DNA that is actually transcribed into an mRNA? What is the unused strand called?

Answer 15

The strand which is actually transcribed is called the “template”, “non-coding”, or “anti-sense strand”

The other DNA strand is called the “coding” or “sense strand”, and does not get transcribed.
-This unused DNA strand will also have the same sequence as the transcript, except it will have T instead of the U in the RNA transcript.

Question 16

What is an operon?

Answer 16

An operon has two components.

1) coding sequence for enzymes
2) upstream regulatory sequences (control sites)

Operons may also include genes for regulatory proteins, such as repressors or activators, but don’t have to.

Question 17

How many phosphate bonds are hydrolyzed per amino acid to make aminoacyl-tRNAs during prokaryotic tranlsation?

Answer 17

two phosphate bonds are hydrolyzed per amino acid to make the aminoacyl-tRNAs.

Question 18

How many phosphate bonds are required for each elongation step in prokaryotic translation?

Answer 18

Two phosphate bonds; one for entrance of each new aminoacyl-tRNA into A site, and the other for translocation.

Question 19

How many phosphate bonds are hydrolyzed during inititiation step of prokaryotic translation?

Answer 19

One GTP is hydrolyzed to position the first tRNA and mRNA on the ribosome.

Question 20

Approximately how many high energy bonds to make a peptide chain during prokaryotic translation?

Answer 20

4n high energy bonds

“n” is the number of amino acids in the chain.

Question 21

Why doesn’t peptide bond formation require GTP hydrolysis, like the other steps in prokaryotic translation?

Answer 21

Because the bond between each amino acid and its tRNA is a high energy bond whose hydrolysis drives peptide bond formation. Remember that the aminoacyl-tRNA bond was formed using the energy of two phosphate bonds from ATP.

Question 22

Prokaryotes or Eukaryotes use Shine-Darlgarno sequence to initaiate translation?

Answer 22

Prokaryotes use Shine-Dalgarno sequence to initiate translation.

Eukaryotes can use Kozak sequence, a consensus sequence typically located a few nucleotides before the start codon.

Question 23

How must Eukaryotic mRNA be processed before it can be translatied?

Answer 23

Spliced, capped, tailed and transported from nucleus to cytoplasm.

Question 24

What is the N-terminal amino acid during translation of both Prokaryotes and Eukaryotes?

Answer 24

Prokaryotes use fMet

Eukaryotes use Met

Question 25

Are the nascent polypeptide chains emerging from a polyribosome in eukaryote all the same?

Answer 25

Yes, only in eukaryotic mRNA since it is monocistronic.

-in prokaryotes different polypeptides may be translated from 	a single piece of mRNA, since prokaryotic mRNA is 			polycistronic.

Question 26

What is the function of the nucleus?

Answer 26

Contain and protect DNA, transcription, partial assembly of ribosomes.

Question 27

What is the purpose of the smooth endoplasmic reticulum?

Answer 27

Detoxification and glycogen breakdown in the liver; steroid synthesis in gonads.

Question 28

What is the purpose of a telomere?

Answer 28

In a Eukaryotic cell, Telomeres are large numbers of repeats of a specific DNA sequence. With the help of a special DNA plymerase, “telomerase”, telomeres maintain the ends of the linear chromosome during DNA replication. -without telomeres and telomerase, the chromosome will become shorter and shorter until lost gene sequence affects critical cell function, resulting in cell death. In most cells telomerase is turned off and its inactivity is implicated in cell aging and death.

Question 29

Describe heterochromatin?

Answer 29

A region of a chromosome folded into densely packed chromatin, within which genes tend to be inaccessible and turned off.

Question 30

Describe euchromatin?

Answer 30

A loosely packed region of the chromosome which genes are often expressed (activated).

Question 31

If a retrovirus inserts its genome into regions of heterchromatin and nowhere else, how is this likely to affect the infections process?

Answer 31

The retroviral gene will not be expressed very frequently, and the virus will tend to remain as provirus unless a change in the surrounding heterochromatin allows viral genes to be expressed.

Question 32

What will be left of a nucleus if treated with DNase w/ detergent?

Answer 32

An insoluble mesh of protein; nuclear matrix or nuclear scaffold is left behind.

Question 33

What is the nucleolus made of?

Answer 33

With no membrane separating the nucleolus from the rest of the nucleus, it consists of loops of DNA, RNA polymerases, rRNA, and the protein components of the ribosome.

Question 34

The nucleolus possesses loops of DNA in its structure, what purpose do these loops serve?

Answer 34

The DNA will serve as a template for ribosomal RNA production.

Question 35

What is the site of rRNA transcription?

Answer 35

The nucleolus is the site of transcription of rRNA by RNA pol I.

Question 36

T/F: Bacteria have only a single kind of RNA pol which is responsible for all transcription?

Answer 36

True.

Question 37

Are the protein components of the ribosome produced in the nucleolus?

Answer 37

No, they are transported into the nucleus from the cytoplasm.

Question 38

What part of the cell does translation take place?

Answer 38

In the cytoplasm.

Question 39

What are the requirements for a protein to pass from the cytoplasm to the nucleus?

Answer 39

Molecules smaller than 60 kd, and proteins containing a “nuclear localization sequence” may pass through the nuclear pores.

Question 40

If the inner mitochondrial membrane is impermeable, how does pyruvate get into the matrix where pyruvate dehydrogenase is located?

Answer 40

Pyruvate is transported through the inner mitochondrial membrane by a specific protein in the membrane.

Question 41

Where would a bacterial electron transport occur that resembles the inner membrane of the mitochondrion?

Answer 41

In a gram-negative bacterium, this membrane would correspond to the mitochondria inner membrane.

Question 42

Where are proteins synthesized that are destined for the secretory pathway?

Answer 42

The rough endoplasmic reticulum.

Question 43

What cellular organelle will assist in the breakdown of toxins in the liver?

Answer 43

The smooth endoplasmic reticulum.

Question 44

What cellular organelle is involved in steroid hormone sythesis in the gonads?

Answer 44

The smooth endoplasmic reticulum.

Question 45

T/F: The membrane of the endoplasmic reticulum is joined with the outer nuclear memebrane in places?

Answer 45

True, the space within nuclear membranes is continuous with the interior of the ER lumen, which plays a key role in directing protein traffic to different parts of the cell.

Question 46

Where might pros synthesized on the rough ER end up?

Answer 46

Secreted into the extracellular environment, integral plasma membrane proteins, in the membrane or interior of the ER, Golgi, or lysosomes.

Question 47

A water tank, with a lid, has some gaseous liquid molecules above the surface of the liquid. If the pressure at 40m = 520 kPa, and the pressure at 50m = 600 kPa, what is the pressur of the gas above the surface of the liquid?

Answer 47

Ptotal = Pgas + Pliquid
520 kPa = Pgas + pg(40)
600 kPa = Pgas + pg(50)
	since there are two unknowns, subtract the equations from each other:  (50 = 600) - (40 = 520) we get pg(10) = 80 kPa:  therefore pg = 8 kPa/m.  Plug that in to any of the equations to get your answer, keep consistent with lines of data. (pay mind to units and you will know what to do):  
Ptotal = Pgas + Pliquid
520 kPa = Pgas + (8 kPa/m)(?)
	-obviously it must be meters to get pressure by itself:
520 kPa = Pgas + (8 kPa/m)(40)
Pgas = 520 kPa - 320 kPa 
Pgas = 200 kPa

Question 48

Define Archimedes’ Principle?

Answer 48

The magnitude of the buoyant force is equal to the weight of the fluid displaced by the object.

Force (buoyant) = p (fluid) x V (submerged) x g
F=pVg
F = (kg/m^3)(m^3)(m/s^2) = Kgm/s^2

Question 49

What are all of the expressions of Force in relation to pressure?

Answer 49

The units for Force are Kgm/s^2 (“Newton”), Force over Area will come out to Kg/ms^2 (“Pascal”). Converting between P and F, is simply a matter of either multiplying or dividing Area.

simplified version:
P = w/A = mg/A = pVg/A = pADg/A = pDg
F = w = mg = pVg = pADg

Pressure = (wieght of fluid / A)
Pressure = (mass of fluid x g / A) 
Pressure = (density of fluid x volume of fluid x g / A) 
Pressure = (density of fluid x Area x Depth x g / A)
Pressure = (density of fluid x Depth x g)