BIO 209 Lecture Notes - Lecture 9: Transcription Bubble, Guanosine, Pyrophosphate

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amethystlouse762

9 Nov 2016

School

Drexel University

Department

Bioscience & Biotechnology

Course

BIO 209

Professor

Loudon Robert P.

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Document Summary

Central dogma of biology- the process by which dna yields protein. In eukaryotes, these processes occur in different parts of the cell. In prokaryotes, these processes occur simultaneously and are said to be coupled. Transcription: dna is transcribed into single stranded rna. Either strand of dna can serve as the template strand. The rna sequence is identical to the non-template strand, except that. Uracil replaces thymine: direction of synthesis is determined by promoters, orientation determines the direction. Causes it to be more short-lived than dna: rna produced is: Identical to the dna non-template strand: rna can come in: Transfer rna (trna)- transfers amino acids to ribosomes. Can unwind and rewind dna without any help elimination of the pyrophosphate. Includes a short dna/rna heteroduplex: transcriptional unit- segment of dna transcribed to produce one rna molecule. Can have one or more genes per rna: multigenic- synthesis of the same rna that has different genes.

Related Questions

Biochem:

1. Indicate whether the following describes DNA polymerase, RNApolymerase, both, or none:

a. Binds to single stranded DNA

b. Uses an RNA primer

c. Has proof-reading ability

d. Reads from 3' to 5'

e. Phosphodiester bonds are formed using rNTPs

f. Requires a DNA primer

g. Multiple types are present in eukaryotes

h. Mutiple types are present in prokaryotes

i. Is synthesized bi-directionally

j. Requires there to be a terminal sequence on DNA

k. Is part of a larger complex made up of several proteins

2. Post-translational damage causes the loss of the 2' hydoxylgroup on several adenosine nucleotides within the intron sequenceof a primary RNA transcript. What could possible happen to theresulting mature RNA sequence and consequent protein?

3. Where on the below strand of RNA would you most likely findthe following:

a. Start of transcription

b. Start of translation

c. TATA box

d. Enhancers

e. Initiator

f. Activators

g. Repressors

4. How would the following mutation in the template strand ofDNA affect the translated protein? (x=any base, / = exon/intronjunction)

5-XXXXC/CTGAAGAGGAAGXXXXGTTAGXXXXACTCAC/CTCGC-3 to5-CCTGAAGAGGAAXXXXXXXXGTTAGXXXXACTCACCTCGC-3

5. When will there be a 5'-5' linkage in RNA? When is this bondformed? Which base is commonly involved in this process? What wouldhappen if there was an inability in this enzyme to make the 5'-5'likage?

6. Consider the following strand of mRNA. What protein would beproduced if this strand was translated?

5'- CGUAUGCCCUUUACUAGUAUGUGAUACUAGUAAACC-3'

7. What would be the new protein if the following mutations weremade to the strand in 6? Label/classify each type of mutation.

a. 5'-CGUAUGCCCUUUAACUAGUAUGUGAUACUAGUUAACC-3'

b. 5'-CGUAUGCCCUUCACUAGUAUGUGAUACUAGUUAACC-3'

c. 5'- CGUAUGCCCUUUACUAGUAUUGAUACUAGUUAACC-3'

d. 5'- CGUAUGCCCUUGACUAGUAUGUGAUACUAGUAAACC-3'

e. 5'-CGUAUGCCCUUCACUAGUAUGAGUAACUAGUAACC-3'

f. 5'-CGUAUGCCCUAAACUAGUAUGUGAUACUAGUAAACC-3'

8. What are examples of two different types of point mutationsin sequences coding for hemoglobin production?

pearbeaver961

1. Which of the following is the correct sequence of events (from start to finish) in cellular fatty acid oxidation?

A. Fatty acid activationÃ carnitine shuttleÃ beta-oxidation

B. Beta-oxidationÃ carnitine shuttleÃ Fatty acid activation

C. Fatty acid activationÃ carnitine shuttleÃ beta-oxidation

D. Carnitine shuttleÃ Fatty acid activationÃ beta-oxidation

2. What reaction is catalyzed by lipoprotein lipase, or lipase?

A. Hydrolysis of TAGs into fatty acids and glycerol

B. Hydrolysis of TAGs into amino acids and glycerol

C. Hydrolysis of cholesterol in to fatty acid and water

D. Hydrolysis of cholesterol into acetyl-CoA

3. How do fatty acids of different carbon lengths cross into the mitochondrial matrix for oxidation?

A. Small FAs of 10 carbons or fewer can freely diffuse through the membrane

B. Large FAs are cleaved into two smaller units that are actively transported across the membrane

C. A membrane-bound transferase catalyzes the conversion of long-chain FAs and FA-carnitine esters, which are transported across the membrane via a specific carrier

D. The breakdown of large FAs starts outside the matrix, allowing for the smaller particles to pass easily through the membrane

4. How can any RNA nucleotide be easily distinguished from a DNA nucleotide?

A. RNA nucleotides have a unique phosphodiester bond linkage

B. RNA nucleotides have uracil nitrogenous bases

C. RNA nucleotides have an -OH on the 2â carbon of the ribose

D. RNA nucleotides cannot be easily distinguished from DNA nucleotides

5. Which of the following statement is true concerning the sequence pTACGTAACGTA?

A. This is an RNA sequence

B. In order to have a more rigid structure in a double-stranded molecule, the sequence given would need more adenosine

C. If the complementary strand were present, the number of purines would be equal to the number of pyrimidines

D. The amount of purines is equal to the amount to pyrimidines

6. Complementary base pairing is considered which level of structure?

A. Secondary

B. Tertiary

C. Quaternary

D. Primary

7. Which of the following is/are required for the polymerization reaction catalyzed by DNA polymerase III?

I. RNA primer

II. DNA primer

III. RNA template

IV. DNA template

V. NTPs

VI. dNTPs

VII. Magnesium

VIII. Calcium

A. II, IV, V, and VII

B. II, IV, VI, and VII

C. I, IV, V, and VIII

D. I, IV, VI, and VII

8. DNA polymerase I, from E. coli, has three different catalytic sites. Which of the following is NOT one of them?

A. RNA-dependent RNA polymerase

B. RNA-dependent DNA polymerase

C. DNA-dependent RNA polymerase

D. DNA-dependent DNA polymerase

9. Eukaryotes solve the problem of replicating the ends of their linear chromosomes by:

A. Using a protein as primer

B. Enzyme activity that uses an RNA template and reverse transcription in a series of repeat cycles

C. All of the listed solution

D. Terminal redundancy whereby each end of the chromosome is duplicated allowing recombination

1. (a) What is the structural differencebetween all deoxyribonucleotides and all ribonucleotides and whydoes this make DNA more appropriate to act as the genetic materialthan RNA. (4 points)

(b) Why is uracil replaced by thymine in DNA? (4 points)

(d) The two strands in DNA are antiparallel. What does thismean? (4 points)

(e) Why are they antiparallel? (4 points)

2. A single stranded DNA molecule has thefollowing sequence: 5'-GGTTAGGTTAGGTTAGGTTA-3'

(a) To fully replicate this molecule, what is the sequence ofthe primer that must be synthesized by the primase enzyme (assume aprimer length of 5 bp). (Here and below write how you wouldconventionally write a single stranded DNA sequence, i.e. withoutthe template.) (4 points)

(b) When fully replicated, what is the sequence of the newlysynthesized DNA strand? (4 points)

(d) What is the sequence of what would be synthesized in theabsence of DNA ligase? (4 points)

(e) What is the total number of H-bonds that are formed duringthe synthesis of the DNA strand (from the very beginning)? (4points)

3. Different temperature sensitive mutants ofE. coli in genes encoding proteins involved in replication weregrown at the permissive temperature for several generations andwhile still actively growing the temperature was raised to therestrictive temperature. After raising temperature, the synthesisof new DNA was assessed using radioactively labeled nucleotides.Assume the mutations completely inactivate the proteins at therestrictive temperature and that function of the mutant protein wasabolished instantly temperature was raised. Would any new DNA bedetected in the following mutants after raising thetemperature?

(4 points each) (a) DnaA

(b) DNA helicase

(d) DNA pol I

(e) DNA pol III

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BIO 209 Lecture Notes - Lecture 9: Transcription Bubble, Guanosine, Pyrophosphate

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