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BIO120H1 Lecture Notes - Membrane Potential, Antiporter, Amphiphile

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lemongnu935
2 Feb 2013
School
UTSG
Department
Biology
Course
BIO120H1
Professor
Jennifer Harris

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BIO120H1 Full Course Notes
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BIO120H1 Full Course Notes
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Document Summary

We have 1 midterm, 1 final exam and 6 labs. Labs are 27% with 8% from quizzes, best 2 out of 3 (4% each). 65% is from exams: the midterm is 25% and covers section 1 of lectures and labs 1 to 2. The final exam is worth 40% and covers all lectures and labs 1-6. Midterm is different from course manual: it is actually on friday february. If you have any questions, asked the professor after lecture, come to tutorials or ask on the course website on blackboard. This is a picture of a cell and the central dogma of biology is that dna encodes mrna which gets translated into proteins. You go from dna to proteins and proteins are functional components of living cells. Then the mrna needs to be transported out of the nucleus and into the cytosol. In the cytosol is where ribosomes bind to mrna and starts the translation into proteins.

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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?

1. In addition to identifying the genetic material, the experiments of Avery, MacLeod, and McCarty with different strains of Streptococcus pneumoniae demonstrated that
DNA is a double helix.
DNA may be taken up by bacterial cells and be active.
DNA is present in bacteriophage T2.
eukaryotic cells may be genetically transformed.
DNA binds to the cell wall of the bacterium.
2. In order to show that DNA in cell extracts is responsible for genetic transformation in Streptococcus pneumoniae, important corroborating evidence should indicate that _______ also destroy transforming activity.
temperatures high enough to kill cells
enzymes that hydrolyze proteins
enzymes that hydrolyze DNA
enzymes that hydrolyze polysaccharides
enzymes that hydrolyze RNA
3. Based on what you have learned about the experiments conducted by Griffith and Avery and colleagues with bacteria, which of the following would result in transformation of living R cells?
Pure RNA from S cells
Cell-membrane extracts from S cells
A mixture of pure RNA and protein from S cells
Cell-free extracts from S cells
Pure protein from S cells
4. A-T base pairs in a DNA double helix
form three hydrogen bonds with each other.
are more heat-stable than G-C base pairs.
are of a substantially different length than G-C base pairs.
are not accessible to DNA binding proteins.
are chemically distinct from G-C base pairs.
5. If 23 percent of the bases in a sample of double-stranded DNA are adenine, what percentage of the bases are uracil?
27
50
0
73
23
6. The uniform diameter of the DNA structure provides evidence for
antiparallel DNA strands.
a right-handed helix.
a double-stranded helix.
3′ end phosphorylation.
purine–pyrimidine pairing.
7. If a sequence of one strand of DNA is 5′-TGACTATC-3′, what is the complementary strand?
5′-ACTGATAG-3′
3′-TGACTATC-5′
3′-ACTGATAG-5′
3′-ACTGATAG-3′
5′-TGACTATC-3′
8. What structural aspect of the DNA facilitates dissociation of the two DNA strands for replication?
3′ end phosphorylation
Purine–pyrimidine pairing
Antiparallel DNA strands
Covalent bonds between sugars and phosphate groups
Hydrogen bonding between paired bases
9. If the Meselson–Stahl density gradient experiment had resulted in two bands of DNA molecules after only one round of replication, one containing only 15N and the second only 14N, this result would have indicated that replication was
unidirectional.
dispersive.
conservative.
bidirectional.

semiconservative.
10. The nucleoside analogue acyclovir, which is used to treat herpes simplex virus (HSV) infections, lacks a 3′ hydroxyl group (–OH). Predict what will happen if the host cell DNA polymerase incorporates a molecule of acyclovir into an elongating strand of HSV DNA.
The replication complex will no longer bind to origins of replication.
The DNA polymerase will only incorporate acyclovir molecules.
Acyclovir will bind single-strand binding proteins.
DNA polymerase will not be able to link a successive nucleotide.
Acyclovir will block the activity of the DNA helicase.
11. Which of the following does not demonstrate the stability of the DNA double helix?
Single-strand binding proteins are required to keep the strands apart.
Paired bases form hydrogen bonds.
High temperatures are required to denature it.
DNA synthesis requires energy.
DNA helicases require ATP.
12. What effect would a primase inhibitor have on DNA replication?
DNA polymerase would not be able to add bases to the DNA.
Primase would be blocked from joining the DNA replication complex.
Primase would not be able to provide primers for DNA polymerases.
DNA polymerase would not be able to use DNA as a template.
There would be no effect on DNA replication.
13. To replicate their DNA in a timely manner, most eukaryotic chromosomes
normally have uncoiled DNA.
have multiple origins of replication.
contain linear molecules of single-stranded DNA.
have two replication forks that move in the same direction.
are composed entirely of DNA.
14. Which statement about DNA replication is false?
Okazaki fragments are synthesized as parts of the leading strand.
Error rates for DNA replication are reduced by proofreading of the DNA polymerase.
The sliding clamp increases the rate of DNA synthesis.
Replication forks represent areas of active DNA synthesis on the chromosomes.
Ligases and polymerases function in the vicinity of replication forks.
15. In many eukaryotes, there are repetitive sequences called telomeres at the ends of chromosomes. After successive rounds of DNA replication, the _______ strand becomes shorter. In some cells, an enzyme called _______ repairs the shortened strand.
leading; telomerase
lagging; telomerase
lagging; DNA polymerase I
leading; DNA polymerase I
leading; replicase
16. A researcher studies normal human fibroblast cells. They can be maintained in culture but die off after about 30 cell generations. Unexpectedly, a colony of cells continues to survive and divide past 30 generations. Which scenario is most likely true for these cells?
DNA polymerase is constantly active.
Primase is able to extend the telomeres.
The mismatch repair system is extra efficient.
The telomerase gene is being expressed.
The cells do not need the ends of their chromosomes.
17. If DNA polymerase III introduces an incorrect nucleotide, what is the first corrective action made by the DNA repair system?
The replication complex excises the incorrect nucleotide.
The excision repair proteins remove the incorrect nucleotide.
The mismatch repair system scans for base-pairing mismatches.
There is no correction, because nucleotide errors by DNA polymerases are not repaired.
DNA ligase connects the correct nucleotide.
18. Choose the correct order of the following four events in the excision repair of DNA:
(1) Base-paired DNA is made complementary to the template.
(2) Damaged bases are recognized.
(3) DNA ligase seals the new strand to existing DNA.
(4) Part of a single strand is excised.
1, 2, 3, 4
2, 1, 3, 4
3, 4, 2, 1
2, 4, 1, 3
4, 2, 3, 1
19. Six complete cycles of PCR should result in a _______-fold increase in the amount of DNA.
64
32
12
128
6
20. When double-stranded DNA is heated to temperatures above 90°C, it denatures. Denaturation is a process that
breaks covalent bonds.
hydrolyzes DNA.
separates double-stranded DNA into two single strands.
causes new hydrogen bonds to form.
irreversibly destroys the double helical structure.

DNA EXTRACTION LAB

Objective

The purpose of this lab is to extract DNA from the nuclei of an onion, cup of strawberries or a banana.

Introduction

In every eukaryotic cell there are long strings of DNA. The DNA encodes for every protein needed by the organism. The DNA can be millions and millions of bases long. When the DNA is in the nucleus, it is tightly coiled around a set of proteins called the histones. When DNA is released from the nucleus by detergent, it can become long and stringy. In this lab we are going to be extracting the DNA from the nuclei of onions and wrapping the DNA around a glass rod.

Materials

Straw or Coffee Stirrer

2-plastic water bottles (single serving disposable)

Ice

Rubbing Alcohol

Liquid soap (laundry detergent) DawnR works best

Coffee filter

Water- distilled

Onion, Cup of Strawberries, or Banana

Table salt

Procedure

1. First place a bottle of rubbing alcohol on ice to chill.

2. Then make the following detergent/salt solution:

Mix together (1/8 cup) 20 mL of liquid soap, (2-tsp) 20 grams of salt, and (1 1/8 cup) 180 mL of distilled water. When you are finished making the solution, put it on ice to chill for at least 10 minutes.

3. Cut an onion in half and chop it up either in the blender, or with a knife. If using strawberries chop them up to small pieces. If using the banana smash it up in a cup.

4. Add (half) 100 mL of the detergent/salt solution to the chopped onion, strawberries, or banana. Continue crushing the onion, the onion needs to be pulverized.

5. Let the slurry sit for 5 minutes on ice.

6. Cut the top 1/3 from the water bottle and flip it over onto the lower cut portion. Use the top as a funnel and the lower portion to catch the solution as it filters through.

7. Place a coffee filter in the top funnel. Pour the slurry through and capture the filtered solution below.

8. Once all of the slurry is in the beaker slightly tilt the beaker and slowly pour down the side of the beaker an equal volume of ice cold rubbing alcohol. This will form two distinct layers. A white stringy material will form at the interface of the two layers.

* Do not mix the alcohol and the slurry.

8. Carefully insert a glass stir rod in the center of the beaker, being cautious not to touch the sides.

9. Now, twist the stir rod in a clockwise direction (like twirling spaghetti) and you should see a white stringy material collecting onto the rod.

This white stringy material is DNA. Keep twisting until you acquire the maximum amount of DNA.

* If you do not collect any DNA on the stir rod then use a piece of sandpaper to rough up the end of the stir rod and try again.

Questions

What did you observe?

Were you able to isolate DNA?

What did it look like?