Module 2 ER/SA

Present an overview of two classical experiments that demonstrated that DNA is the genetic material. Can RNA be the genetic material? Explain.

(1) transformation in bacteria (Griffith through Avery et al. ); see appropriate figures in the text. (2) the Hershey and Chase experiment in bacteriophage; see appropriate figures in the text. Yes, RNA can be the genetic material as described for the Tobacco Mosaic Virus (TMV), retroviruses, and many others.

Which three general characteristics must the genetic material possess?

1. must be able to encode complex informationthat encodes phenotype; 2. must be able to replicate (faithfully); 3. must be able to mutate to generate diversity.

Suppose that in the use of polynucleotide phosphorylase A and C are present in a ratio of 1A:5C. What is the probability that an AAA sequence will occur?

1/216

An organism has a G content of 30%. What is the percentage for A?

20%

In transcription, nucleotides are always added to the _____end of the elongating strand.

3'

The Meselson and Stahl experiment provided conclusive evidence that DNA replication in E. coli is semiconservative. Imagine that DNA replication were conservative, rather than semiconservative. What pattern of bands would occur in a CsCl gradient after the first generation of replication? What pattern of bands would occur after the second generation of replication?

?

Name the three major modifications of mRNA of eukaryotes before it is transported to the cytoplasm. In addition, tell why each of the modifications is necessary.

Add 5' cap (protect against degradation, acts as a binding site for the ribosome); Add poly-A tail (possibly protect against degradation, possibly helps in the transfer of the mRNA to the cytoplasm); Remove introns (forms a message that can be translated into a functional protein).

What is an intron, and what is the relationship between an intron and a heterogeneous nuclear RNA (hnRNA)?

An intron is a section of DNA, which, when transcribed as part of an RNA, is eventually spliced out of that RNA. The entire gene transcript, which may serve as an eventual mRNA (after intron removal and other forms of processing), is called heterogeneous nuclear RNA.

Are Okazaki fragments formed on the leading strand during DNA replication? Explain your answer.

Answer should mention lagging strand in explanation

A friend gave you the following molecule and told you that it was a fragment of his RNA. Do you believe him? Justify your answer. 5' TCC TGA CGA TGC TAC CGA 3'

Answer: No, the molecule has T's. If it were truly RNA, it would have U's rather than T's

Name the pyrimidines and the purines in DNA.

Ardenine cytosine guanine thymine

Briefly define the term "autoradiography". Identify and describe a classic experiment that used autoradiography to determine the replicative nature of DNA in eukaryotes.

Autoradiography is a technique that allows an isotope to be detected within a cell: The Taylor, Woods, and Hughes (1957) experiment used 3H-thymidine.

Describe two ways in which bacterial DNA differs from eukaryotic DNA

Bacterial DNA is circular and not complexed to histone proteins. Other answers are acceptable if true.

A major difference between eukaryotes and prokaryotes is that eukaryotes have a nucleus, whereas prokaryotes do not. Discuss the impact of having a nucleus on the creation of mature mRNA.

Because prokaryotes do not have a nucleus, the translational machinery is able to attach to the mRNA as it is being synthesized. Thus, there is no time to process the mRNA. In eukaryotes, the translational machinery is not present in the nucleus. Thus, there is time for the cell to process the mRNA before it is transported from the nucleus to the cytoplasm and translated into protein. Alternative: Why is processing necessary in eukaryotic cells?

Explain at least two reasons why the following definition of a gene is incomplete: "A gene consists of DNA sequences that encode a single polypeptide."

Definition does not include 1. regulatory sequences 2. not all genes are DNA sequences (see RNA virus) 3. not all genes transcribe a single RNA molecule 4. not all RNA molecules encode for a single polypeptide. Answer should have 2 of these elements (or others that make sense).

Why would a given dsDNA molecule that is very GC rich be harder to dissociate into single stranded DNA than another dsDNA molecule of the same length that is very AT rich?

GC base pairs have 3 hydrogen bonds, versus 2 hydrogen bonds in AT base pairs, making GC rich DNA molecules more tightly bonded together with hydrogen bonds, and therefore requiring more energy to dissociate into ssDNA.

What are histones? How many families of histones exist? Which families are considered linker histones, and which are considered core histones? What is the structural relationship between histones and the nucleosome?

Histones are represented by five main classes of relatively small basic proteins containing relatively large amounts of lysine and arginine. The classes are as follows: H1, H2A, H2B, H3, H4. Each nucleosome is made of 8 histones: 2 from each core family.

What is unusual about the amino acid composition of histones? How is the function of histones related to the amino acid composition? Of which histones are nucleosomes composed?

Histones contain large amounts of positively charged amino acids such as lysine and arginine. Thus, they can bind electrostatically to the negatively charged phosphate groups of nucleotides. Nucleosomes are composed of all histones except H1.

Below is a list of several phenomena relating to protein structure. Clearly describe each phenomenon, the conditions under which each occurs, and the probable influence each has on protein structure. - Hydrophobic interactions - Hydrogen bonds - Disulfide bridges

Hydrophobic interactions: Nonpolar side chains of amino acids tend to associate to form hydrophobic clusters usually away from the protein surface. - Hydrogen bonds: Such bonds may occur between the components of the peptide bond, the side chains, or a combination of the two. They are responsible for helical and pleated sheet structures of proteins. - Disulfide bridges: Such bonds are formed between two cysteine side chains and, because of their covalent nature, represent relatively strong attractive forces between different regions (sometimes distant) of proteins.

Briefly describe what is meant by the term exon shuffling.

In the 1970s, Walter Gilbert suggested that the functional regions of genes in eukaryotes consist of collections of exons originally present in ancestral genes that are brought together through various recombination events over time.

Q: Describe the role of the various types of nucleic acids in the storage and expression of information in living organisms.

Information contained in the base sequences of DNA is transcribed into a variety of RNAs. Certain RNAs (tRNA) carry amino acids to the site of translation where proteins are assembled. Other RNAs (mRNA and rRNA) provide a mechanism for ordering the sequence of amino acids in proteins.

Referring to the genetic code, what is meant by "wobble"?

Last nucleotide in a codon

Describe the function of N-formylmethionine in prokaryotes.

Modified starting amino acid

Why does DNA polymerase III exist as a dimer?

One for each strand of DNA

List two similarities between bacterial chromosomes and eukaryotic chromosomes.

Single molecule of DNA, semiconservative replication

What DNA sequence occurs at the end of the Tetrahymena chromosome? Give both the sequence and the name of the structure. How does this sequence affect the conclusion of chromosome replication?

Telomeres terminate in a 5'-TTGGGG-3' sequence, and telomerase is capable of adding repeats to the ends, thus allowing the completion of replication without leaving a gap and shortening the chromosome following each replication.

Which of the following are role(s) of the 5' cap?

The cap protects the RNA from degradation. The cap acts as a binding site for the ribosome. The cap helps the RNA polymerase find the promoter and initiate transcription.

Describe how the sigma subunit of E. coli RNA polymerase participates in transcription.

The sigma subunit may give specificity to the RNA polymerase and play a regulatory function. It may be involved in the recognition of initiation sites or promoters.

What is the spliceosome?

The spliceosome is the RNA-protein complex that is responsible for intron-exon splicing in eukaryotes. Following the GU-AG rule, introns are excised and removed from mRNA and the exons are joined to form a mature mRNA molecule ready for translation. The spliceosome is made of five small nuclear ribonucleoproteins (snRNPs) which consists of proteins and one of five snRNAs (U1, U2, U4, U5 and U6) which together with over 100 proteins form the large biological machine used for splicing.

Explain the experimental method of "differential labeling"

This is a method used to differently label 2 molecules of interest in an experiment so that investigators are able to distinguish between the two molecules in the results

Briefly define transformation and describe the relationship between the phenomenon of transformation and the discovery that DNA is the genetic material in bacteria.

Transformation is the process whereby one organism is genetically altered by exposure to DNA from another organism. Since DNA can carry heritable "traits" from one organism to another, it must be the genetic material.

Present two forms of post-translational modification of proteins.

Upidation, acetylation

Three forms of DNA are...

Z-DNA A-DNA B-DNA

Splicing of eukaryotic pre-mRNA involves ___ reactions and occurs in the ___ . a. methylation b. transesterification c. polyadenylation d. nucleus e. cytoplasm

b,d

The 3' untranslated region affects the ___ of mRNA and the ___ of the mRNA protein-coding sequence. a. translation b. splicing c. stability d. transcription

c,a

The concept that genetic information passes from DNA to RNA to protein is called

central dogma

Electrophoretic separation of HbA from HbS is based on a difference in their ________.

charges

Match the term with the best letter choice: a. supercoil removal b. RNA primer synthesis c. 3' → 5' exonuclease activity d. lagging strand e single-strand breaks f. unidirectional replication g. strand invasion h. leading strand i. phosphodiester bonds at DNA nicks j. translesion DNA synthesis k. bidirectional circular replication Enter only the letter of your choice. rolling-circle replication

f

Supercoiling caused by unwinding of the dsDNA molecule is relieved by what enzyme?

gyrase?

RNA differs from DNA in that it: (more than one answer may be correct)

has ribose sugars rather than deoxyribose sugars in its nucleotides. is usually single-stranded rather than double-stranded. has uracil rather than thymine.

In eukaryotic replication, there is another fundamental level of complexity because of what proteins?

histones

A(n) ________ is a section of an RNA that gets spliced out.

intron

Match the term with the best letter choice: a. supercoil removal b. RNA primer synthesis c. 3' → 5' exonuclease activity d. lagging strand e single-strand breaks f. unidirectional replication g. strand invasion h. leading strand i. phosphodiester bonds at DNA nicks j. translesion DNA synthesis k. bidirectional circular replication Enter only the letter of your choice. theta replication

k

This new strand of DNA has its 3' end oriented in the opposite direction as that in which the replication fork travels.

lagging strand

This new strand of DNA has its 3' end oriented in the same direction as the replication fork travels.

leading strand

This enzyme links two separate lengths of nucleic acid by creating a phosphodiester bond between them.

ligase

Assume that a base addition occurs early in the coding region of a gene. Is the protein product of this gene expected to have more or fewer (state which) altered amino acids compared with the original gene with a base deletion late in the coding region?

more

Sidney Brenner argued that the code was nonoverlapping because he considered that coding restrictions would occur if it were overlapping. A second major argument against an overlapping code involved the effect of a single nucleotide change. In an overlapping code ________ adjacent amino acids would be affected by a point mutation, while in a nonoverlapping code ________ amino acid(s) would be affected.

multiple,one

This organic subunit is the monomer from which nucleic acid is formed.

nucleotide

Short "bursts" of DNA synthesis on the lagging strand produce ___________.

okazaki fragments

Two "naked" (without histones or other proteins) double-stranded fragments of DNA are exactly the same length. At 89°C, fragment A has completely denatured, which means that the two strands have separated. At that temperature, fragment B is still double-stranded. How might these fragments differ, to result in different denaturation temperatures?

one has a higher g-c content which makes it harder or easier to denature bc of boil pts? look up which one

Given that the origin of replication is fixed in E. coli, what region signals the location of the origin? Give both the name of this region and a description of the sequences present.

oriC repeating 9mers and 13mers?

_____________ is seen primarily among prokaryotes where one mRNA carries coding information and internal punctuation for the translation of more than one protein.

polycistronic RNA?

In eukaryotes, what factors (either DNA sequences or proteins) appear to encourage the specific association of RNA polymerase(s) to a specific region of DNA?

promoters, enhancers, transcription factors?

Chromosomal regions that represent evolutionary vestiges of duplicated copies of genes that have underdone sufficient mutations to render them untranscribable are called ________.

pseudogenes

Uridine contains ________ as sugar.

ribose

The base content of a sample of DNA is as follows: A = 31%, G = 31%, T = 19%, and C = 19%. What conclusion can be drawn from this information?

single stranded or contains loops

What are the three classes of "functional" RNAs (not including mRNA)? Briefly describe the role of each class of functional RNA.

tRNA -- brings the correct amino acid to the mRNA during translation. rRNA -- major component of ribosomes. snRNA -- helps process RNA transcripts (especially, helps remove introns).