BIOL 212 SI, Molly
Dr. Coffman and Dr. Peterson
EXAM 2 REVIEW 2/19/15
1.) What are four bases contained with DNA, and how can we classify them into groups? Which base pairing are you likely to find in a thermophilic bacterium? Why?
Adenine (A) and Guanine (G) = Purines
Thymine (T) and Cytosine (C) = Pyrimidines
C-T because they have three hydrogen bonds between them, making them more stable under harsh conditions.
2.) Using Chargaff’s Rules, how much Adenine is contained within the DNA of a turtle, knowing that Guanine makes up 22.0% of its nucleotide bases?
G = 22%
C = 22%
T = 28%
A = 28%
3.) Given the sequence 5’-ATGAGCGACCCC-3’, the reverse complement is…
3'-TACTCGCTGGGG-5' OR 5'-GGGGTCGCTCAT-3'
4.) What is the backbone of a DNA molecule composed of? The linkage exists between a hydroxide and a phosphate of the next deoxyribose (within the same strand). This gives rise to the 3’ and 5’ polarity on a strand. The two strands of the helix are antiparallel to each other.
5.) Explain the Hershey-Chase Experiment. What was the purpose? How did they conduct it? What were the results?
The Hershey-Chase experiment was designed to see if genes were made of protein or DNA. They injected radioactive dye into a virus. The dye was either sulfur (which denoted protein) or phosphorus (which denoted DNA). They allowed the virus to inject it’s genes into the E. Coli cell, then they centrifuged them so they could separate the phage from the cell. They received a supernatant in the top of the tube, and a pellet in the bottom of the flask. Results: They found the sulfur ended up in the supernatant and the phosphorus ended up in the pellet. This meant that the genes from the virus was made of DNA.
6.) DNA Replication— Using the word bank below, draw this process and explain the function of each enzyme along the way: [Double helix strand, single-strand binding proteins, DNA topoisomerase, Replication fork, DNA helicase, DNA ligase, DNA Polymerase, Okazaki fragments, Leading strand, Lagging strand, DNA Primase, RNA Primers]
Helicase – breaks H-bonds between DNA
Single-Strand Binding Proteins (SSBP) – bind to separated DNA so they don’t recoil
Topoisomerase – relieves tension from helicase
RNA Primase – synthesized RNA primers where DNA polymerase III starts
DNA Polymerase III – adds DNA to the RNA primers on both leading and lagging strands/proofreads strands
Sliding Clamp – ring-shaped molecule that holds DNA Polymerase III onto DNA template so replication can keep going
DNA Polymerase I – removes RNA primers and replaces them with DNA bases
DNA ligase – catalyzes phosphodiester bond formation between Okazaki fragments
7.) DNA folding and compaction is a field of biology still containing many unknowns. We do know that…(Buzzwords: nucleosome, histones)
DNA strands wrap around histone proteins to create nucleosomes. The nucleosomes condense and fold to form chromosomes.
8.) A chromosome is just a long molecule of DNA. Chromosomes are most compact during mitosis/meiosis.
9.) What purpose do telomeres serve during DNA replication?
They protect the ends of the chromosomes. They allow the DNA Primase to attach and put the primer down.
10.) What is the "central dogma" of molecular biology?
DNA ---transcription---> RNA ---translation---> Protein
11.) mRNA is the end product of transcription. We then begin translation, which takes place in the cytosol within the ribosomes.
12.) mRNA is read in groups of three bases, known as codons.
13.) Draw the general structure of an amino acid. If you had multiple amino acids bonded together, draw and name the type of bond that would exist between the two. Looking at the structure you have drawn, how can we label the C and N terminus?
Bonded through phosphodiester bonds. N terminus starts at the amino group end. C terminus ends at the carbonyl group end.
14.) RNA polymerase needs a primer, just like DNA polymerase needs a primer.
a. True
b. False
15.) Explain how transcription begins based upon your answer to question 14.
Since transcription does not require a primer, it begins at a section of genes on the DNA strand called the promoter. This is also called the “TATA box”. Transcription continues until the RNA polymerase reaches the terminator sequence.
16.) What are the three stages of transcription? What key enzyme facilitates this process?
I. Initiation
II. Elongation RNA Polymerase
III. Termination
17.) Now to summarize it all graphically draw a general step-wise outline of this “central dogma” in eukaryotes. (Think: DNA → pre-mRNA → mRNA → tRNA → amino acids)
DNA à transcription à pre-mRNA --> spliceosomes splice out introns --> tailing and capping of mRNA strand --> mature mRNA àtRNA anticodon binds to mRNA start codon àrRNA contains mRNA and tRNA, helping create the peptide bonds between amino acids à translation occurs until stop codon is reached à protein is released from rRNA and sent into the cytosol
18.) MicroRNAs are 21-22 NT RNAs that bind to specific target mRNAs. This mRNA is changed in one of two ways.
I. complete destruction of the mRNA strand
II. Translation of the mRNA strand is inhibited
19.) The Lac operon allows for transcriptional regulation; this is accomplished by regulating the initiation of transcription at the promoter site. When Lactose is present, lac operon is induced because…
the lactose acts as the inducer that changes the shape of the repressor and takes it off the strand of DNA to allow the RNA Polymerase to transcribe the genes.
20.) Due to alternative splicing in mRNA, different exons can be included. This means that…
multiple proteins may be synthesized from the same strand of RNA.
21.) Describe the difference between chromosome-level mutations and point mutations.
Point Mutation = single-base change
Chromosome-level Mutation = addition or deletion of chromosomes from the karyotype
22.) Chromosome-level mutations can be visualized via the karyotype of the cell.
23.) Define the following in your own words:
a.) Inducer: initiates removal of repressor
b.) Repressor: shuts down transcription
c.) Operator site: where repressor binds
d.) Promoter: where RNA polymerase binds
24.) Explain alternative splicing. What is a major benefit of it?
Alternative splicing leads to the production of different proteins by splicing out some exons. This allows different proteins to be made from the same strand of mRNA.
25.) Match the following words to their definitions:
Point Mutation A single nucleotide switch that does not change the amino acid
Silent Mutation A random nucleotide is added to the strand
Frameshift Mutation A stop codon is inserted where it isn't supposed to be
Missense Mutation One nucleotide is switched
Nonsense Mutation A single nucleotide switch that changes the amino acid
26.) Describe how prokaryotes and eukaryotes are different in protein synthesis.
Prokaryotes: everything happens in the cytoplasm; no splicing, just immediate translation
Eukaryotes: starts in nucleus and ends in the cytoplasm; splicing occurs with capping and tailing before translation occurs
27.) In what two ways can a gene be regulated after transcription has occurred? Briefly explain each.
1. Alternative Splicing: joins exons in various ways to produce multiple proteins from one gene
2. MicroRNAs (miRNAs): can bind to complementary mRNAs and prevent translation
28.) DNA sequencing is the process of determining the precise order of nucleotides in a strand of DNA.
29.) Transposable elements are also called "jumping genes". They are....
Segments of DNA that can move from one location in a genome to another
30.) They primary purpose of transposable elements is still unknown, but the two leading hypotheses are:
a. TEs are parasites of the genome
b. TEs help species adapt