IB Biology HL - Unit 5: Nucleic Acids

Outline the process of how nucleosomes package DNA.

- Allow DNA to wrap around histone proteins in nucleosomes, and nucleosomes are held together by linker DNA - Structure of nucleosomes contributes to supercoiling and allows DNA to be compact - When a chromosome is formed, nucleosomes fold in on themselves repeatedly, which condenses DNA even more

Describe the role of noncoding regions of DNA.

- Control gene activity - Help guide tRNA and rRNA production - Ex: satellite DNA, telomeres, introns, etc.

Describe the basic structure and the role of nucleosomes.

- Created when histone proteins are used by a cell to package the DNA - Have central cores of eight histone proteins (octamer) with DNA coiled around them - Octamer has two copies of four different types of histones - Linker DNA connects nucleosomes - H protein binds the DNA to the core molecule - Histones allow DNA to supercoil, which allows DNA to be packed into a smaller space in the nucleus - Nuclueosomes facilitate the packing of large genomes

Describe the structure of DNA.

- Double helix made up of two antiparallel strands of nucleotides linked by hyrdogen bonding between complementary base pairs - One strand is 5'-->3', other is 3'-->5' - A = T, C = G

List the stages of the cell cycle and identify the stage in which DNA replication takes place.

- G1, S1, G2, cytokinesis, mitosis - DNA replication occurs in S phase, where each chromosome is duplicated

Describe the role of each replication enzyme. - Helicase - RNA Primase - DNA Polymerase I - DNA Polymerase III - DNA Ligase

- Helicase: separates DNA strands - RNA Primase: adds RNA primer - DNA Polymerase I: Replaces RNA primer - DNA Polymerase II: Synthesizes new strands - DNA Ligase: Joins fragments together

Identify and describe the role of telomeres.

- Repetitive sequences on the ends of eukaryotic chromosomes - Serve a protective function - Enzymes that replicate DNA cannot continue replication until the end of the chromosome during interphase - Cells would lose the genes at the end of chromosomes if they went through the cell cycle without telomeres

Explain the use of tandem repeats and their role in DNA profiling.

- Short nucleotide sequence - Shows variation between individuals in terms of the number of times the sequence is repeated - Each variety has the ability to be inherited as an allele

Describe Okazaki fragments and how they are joined together.

- Short sequences of DNA nucleotides that are synthesized discontinuously in the lagging strand

The diagram shows a ribosome and associated mRNA. (FLIP TO SEE PICTURE) Which of these events occurs first in translation? - Initiator tRNA enters E site. - Small ribosomal subunit binds to mRNA. - Initiator tRNA enters A site. - Large ribosomal subunit binds to mRNA.

- Small ribosomal subunit binds to mRNA

Explain the function of nucleosomes.

- To suppress transcription in order to facilitate the packing of large genomes - Form roadblocks in the way of RNA polymerase, which can impact transcription elongation

Describe semi-conservative DNA replication and how it depends on complementary base pairing.

- When a new double-stranded DNA molecule is formed, one strand is from the original template strand and the other is new - When DNA is replicated, each new strand is identical to the original strand extracted from the template, and the two molecules formed have an identical base sequence to the original molecule

Discuss when and why the need arises for a cell to replicate the DNA.

- When cells are dividing, DNA must be relicated - Daughter cell has a copy of the genome and therefore the same genetic traits

Which feature is common to both mRNA and DNA? A) Covalent bonds between adjacent nucleotides B) Hydrogen bonds between guanine and cytosine C) Ribose sugar attached to phosphate D) Antiparallel arrangement of polynucleotide strands

A) Covalent bonds between adjacent nucleotides

What usually distinguishes DNA from RNA? (FLIP TO SEE PICTURE) A) B) C) D)

D)

Outline the steps to DNA replication. Describe the replication of DNA including the leading & lagging strands, role of various enzymes, addition of nucleotides to 3' end of primer.

1. Helicase unwinds DNA at the replication fork. Enzyme DNA gyrase (topoisomerase) relieves the strain in the molecule. Single-stranded binding proteins keep strands apart for a long enough time to allow the template strand to be copied. 2. DNA primase creates one RNA primer on the leading strand and many on the lagging strand. The RNA primer acts as an initiator for replication. 3. RNA primer allows DNA polymerase III to bind and start replication. 4. DNA polymerase III adds deoxyribonucleotide monophosphate to the 3' end of the growing strand. It reads the strand 3' to 5 and adds nucleotides in the 5' to 3' direction. Different organisms have different kinds of DNA polymerase, which have different functions such as proof reading, polymerization, and removal of RNA primers once they are no longer needed. 5. One DNA strand is replicated in a continuous manner in the same direction as the replication fork (leading strand). 6. Second strand is replicated in Okazaki fragments in opposite direction (lagging strand). 7. As molecules are added, DNA polymerase I removes the RNA primers and replaces them with DNA 8. DNA ligase joins Okazaki fragments together to form a continuous strand. 9. In the end there are two strands of DNA, each with an original strand and a new strand.

Analysis of the DNA of an organism reveals that it is composed of 20% T (thymine). Based on this information, what would you predict the % C (cytosine) to be? - 20% - 60% - 30% - 20%

30%

Transcription occurs in a ____ direction.

5' to 3'

Translation occurs in a ____ direction.

5' to 3'

This image is taken from a visualization of a eukaryotic ribosome. The arrows show the direction of movement of mRNA. Which letter represents a tRNA exiting from the E site?

A

This question refers to the following DNA diagram. (FLIP TO SEE PICTURE) What type of bond does Z represent? A) Covalent bond B) Hydrogen bond C) Peptide bond D) Semi-conservative bond

A) Covalent bond

The diagram below shows part of a DNA molecule that is being replicated. Where would DNA polymerase link the next nucleotide during replication? (FLIP TO SEE PICTURE) A) I B) II C) III D) IV

A) I

Which types of interactions are found in a part of a protein with secondary but not tertiary structure? I. Hydrogen bonds II. Disulfide bridges III. Ionic bonds A) I only B) I and II only C) II and III only D) I, II and III

A) I only

Which molecules form the nucleotide marked in the diagram? (FLIP TO SEE PICTURE) A) Phosphate, deoxyribose and nitrogenous base B) Phosphorus, ribose and nitrogenous base C) Phosphorus, deoxyribose and guanosine D) Phosphate, ribose and guanine

A) Phosphate, deoxyribose and nitrogenous base

The diagram shows a dinucleotide. (FLIP TO SEE PICTURE) Which type of bond is identified by the arrow? A) Phosphodiester/Covalent B) Hydrogen C) Covalent D) Peptide

A) Phosphodiester/Covalent

What is formed during transcription? A) RNA strand complementary to DNA strand, formed by RNA polymerase B) DNA strand complementary to DNA strand, formed by DNA polymerase C) RNA strand complementary to RNA strand, formed by DNA polymerase D) DNA strand complementary to RNA strand, formed by RNA polymerase

A) RNA strand complementary to DNA strand, formed by RNA polymerase

When does DNA replication occur? A) S phase of interphase B) Early prophase C) G phase of interphase D) Late prophase

A) S phase of interphase

Which statement applies to tRNA? A) There is at least one type of tRNA that combines with each known amino acid. B) One type of tRNA can combine with all of the known amino acids. C) tRNA carries out its main role within the nucleus. D) tRNA is produced by the process of translation.

A) There is at least one type of tRNA that combines with each known amino acid.

RNA polymerase adds an RNA nucleotide to a growing mRNA molecule during transcription. (FLIP TO SEE PICTURE) The diagram shows that the direction of transcription is 5' to 3'. Which of the following statements best describes what this means? A. RNA polymerase adds the 5' end of a nucleotide to the 3' end of the mRNA molecule. B. RNA polymerase moves from the 5' to the 3' end of the template strand. C. RNA polymerase adds the 3' end of a nucleotide to the 5' end of the mRNA molecule. D. RNA polymerase adds the 5' end of the mRNA molecule to the 3' end of the nucleotide.

A. RNA polymerase adds the 5' end of a nucleotide to the 3' end of the mRNA molecule.

Which of the following is one of the roles of nucleosomes in eukaryotes? A. Regulation of transcription. B. Protection of mRNA C. Initiation of translation. D. DNA replication

A. Regulation of transcription.

Which of the following could be described as 'non-coding DNA' A. The promoter region B. The pyrimidine bases C. DNA bases transcribed into mRNA D. Adenine nucleotides

A. The promoter region

Which sequence represents the order of events in protein synthesis? (FLIP TO SEE PICTURE) A) B) C) D)

B)

A strand of mRNA consists of the following nucleotides: AUUCUGGCUA Which of the following represents the non-transcribed (sense) strand of the DNA? - ATTCTGGCTA - UAAGACCAU - AUUCUGGCUA - TAAGACCGAT

ATTCTGGCTA

The diagram shows the three-dimensional structure of tRNA. (FLIP TO SEE PICTURE) What can attach to the region marked X? - An anticodon - mRNA - An amino acid - The P site of the ribosome

An amino acid

The diagram represents transcription and translation. (FLIP TO SEE PICTURE) What structures do the letters X and Y represent? - C - B - D - A

B

Which letter (A-D) indicates where a new nucleotide would attach? (FLIP TO SEE PICTURE)

B)

What is a codon? A) A sequence of nucleotides on rRNA that corresponds to an amino acid B) A sequence of nucleotides on mRNA that corresponds to an amino acid C) A sequence of nucleotides on tRNA that corresponds to an amino acid D) A sequence of nucleotides on DNA that corresponds to an amino acid

B) A sequence of nucleotides on mRNA that corresponds to an amino acid

What occurs during DNA replication? A) DNA polymerase separates the two DNA strands B) DNA molecules containing nucleotides from the original molecule are produced C) Adenine forms a base pair with either thymine or uracil D) New bases attach to the original sugar-phosphate backbone

B) DNA molecules containing nucleotides from the original molecule are produced

What is required to replicate DNA? A) Temperature of 37 °C B) Free nucleotides carrying A, C, G and T bases C) Plasmids D) Endonuclease

B) Free nucleotides carrying A, C, G and T bases

What is common to RNA and DNA? A) Thymine B) Nitrogenous bases C) Histones D) Deoxyribose

B) Nitrogenous bases

What are Okazaki fragments? A) Short lengths of RNA primase attached to the DNA during replication. B) Short sections of DNA formed during DNA replication. C) Nucleotides added by DNA polymerase I in the same direction as the replication fork. D) Sections of RNA removed by DNA polymerase III and replaced with DNA.

B) Short sections of DNA formed during DNA replication.

How does DNA replicate? A) The deoxyribose of a free nucleotide is linked to the phosphate of the last nucleotide in the chain. B) The phosphate of a free nucleotide is linked to the deoxyribose of the last nucleotide in the chain. C) Nucleotides are linked in a 3' to 5' direction and the new strands are anti-parallel to the template strands. D) Nucleotides are linked in a 5' to 3' direction and the new strands are parallel to the template strands.

B) The phosphate of a free nucleotide is linked to the deoxyribose of the last nucleotide in the chain.

This question refers to the following diagram of DNA. (FLIP TO SEE PICTURE) What does the structure labelled Y represent? A) Ribose B) Thymine C) Guanine D) Deoxyribose

B) Thymine

The following diagram shows a short stretch of DNA. (FLIP TO SEE PICTURE) What bases are indicated by labels Y and Z? A) Y: Thymine, Z: Adenine B) Y: Thymine, Z: Guanine C) Y: Uracil, Z: Guanine D) Y: Uracil, Z: Adenine

B) Y: Thymine, Z: Guanine

On which molecule is a codon found? A) DNA B) mRNa C) tRNA D) rRNA

B) mRNA

In some research geneticists were able to compare methylation in several genes thought to be linked with breast cancer. What can be concluded from this data about the connection between methylation patterns and gene expression? A. Some gene loci are methylated. B. Higher methylation seems to have less gene expression. C. Higher methylation seems to promote gene expression. D. Methylation seems to have no effect on gene expression.

B. Higher methylation seems to have less gene expression.

After transcription, which of the following could happen to mRNA in eukaryotic cells? A. It unzips and uncoils. B. It is modified. C. It is coiled into a helix. D. It is transported to the golgi apparatus.

B. It is modified.

RNA processing occurs in eukaryotic cells but not prokaryotic cells. Which of the points below describe how this processing can produce more than one protein from just one gene? A. Polyribosomes are formed on a mRNA molecule B. mRNA is spliced in different ways. C. mRNA is copied forwards and backwards. D. Different tRNA molecules attach to ribosomes when they are bound to mRNA.

B. mRNA is spliced in different ways.

Where does a tRNA-activating enzyme attach the appropriate amino acid to the tRNA molecule? (FLIP TO SEE PICTURE)

C

Which one of the following proportions is true for DNA? - C = G - C > T - C > G - C = T

C = G

Which enzyme catalyzes the elongation of the leading strand? (FLIP TO SEE PICTURE) A) RNA polymerase B) Helicase C) DNA polymerase D) Ligase

C) DNA polymerase

Which regions of DNA code for production of specific proteins? A) Telomeres B) Genes for ribosomal RNA C) Exons D) Regulators of gene expression

C) Exons

The image shows a DNA molecule. (FLIP TO SEE PICTURE) Which correctly identifies the parts labelled I and II? A) I: base, II: phosphate B) I: ribose, II: uracil C) I: deoxyribose, II: base D) I: ribose, II: adenine

C) I: deoxyribose, II: base

In which process(es) do nucleosomes play a role in eukaryotes? I. tRNA activation II. Transcription regulation III. DNA supercoiling A) I only B) II only C) II and III only D) I, II and III

C) II and III only

The hydrolysis of a pure sample of an organic molecule produces a pentose sugar, thymine, guanine, and cytosine. What other substances could be expected to be present in the hydrolysed sample? A) RNA B) Uracil C) Phosphate D) ATP

C) Phosphate

Some regions of DNA do not code for the production of proteins. What are these regions of DNA used as? A) They have no known function and are recycled to provide nucleotides B) Gene regulation and coding for production of enzymes used in translation C) Telomeres and coding for production of tRNA D) Introns and coding for production of structural proteins

C) Telomeres and coding for production of tRNA

The percentage of thymine in the DNA of an organism is approximately 30%. What is the percentage of guanine? A) 70% B) 30% C) 40% D) 20%

D) 20%

In nucleic acids, which type of bond links the 5-carbon sugars with an organic base? - Covalent - Peptide - Phosphate - Hydrogen

Covalent

Explain Watson, Crick and Franklin's contributions to the understanding of the structure of DNA.

Crick and Watson: - Built models - First model had triple helix with bases on the outside and magnesium holding the strands together - Second model was correct Franklin: - X-ray diffraction showed double helix

The base sequences of a short section of DNA are shown, together with mRNA that has been transcribed from it and one of the tRNA anticodons that could be used to translate the mRNA. (FLIP TO SEE PICTURE) Which strand of DNA is transcribed and to which codon in the mRNA would the tRNA anticodon bind during translation? - A - B - C - D

D

What is correct for the DNA double helix? (FLIP TO SEE PICTURE)

D

The diagram shows how pre-mRNA is processed into mature mRNA. Which structures are indicated by the letters W and X? (FLIP TO SEE PICTURE) A) B) C) D)

D)

What sequence of processes is carried out by the structure labelled X during translation? (FLIP TO SEE PICTURE) A) Combining with an amino acid and then binding to an anticodon B) Binding to an anticodon and then combining with an amino acid C) Binding to a codon and then combining with an amino acid D) Combining with an amino acid and then binding to a codon

D) Combining with an amino acid and then binding to a codon

What is replicated by a semi-conservative process? A) Messenger RNA (mRNA) only B) Messenger RNA (mRNA) and transfer RNA (tRNA) only C) Messenger RNA (mRNA), transfer RNA (tRNA) and DNA only D) DNA only

D) DNA only

What type of bond is labelled X? (FLIP TO SEE PICTURE) A) Ionic B) Peptide C) Covalent D) Hydrogen

D) Hydrogen

In the model of the DNA molecule shown below, which arrows point to covalent bonds? (FLIP TO SEE PICTURE) A) I, II and III only B) II, III and IV only C) I, III and IV only D) I, II and IV only

D) I, II and IV only

This is a sequence of nucleotides from a section of mRNA. AUGAAACGCACGCAG From which DNA sequence has it been transcribed? A) ATGAAACGCACGCAG B) UACUUUGCGUGCGAC C) TACUUUGCGTGCGTC D) TACTTTGCGTGCGTC

D) TACTTTGCGTGCGTC

Very soon after fertilization, parental epigenetic methylation is reversed in the DNA. Later, tissue-specific epigenetic modifications are made to the embryonic DNA. The graph follows the degree of methylation from different sources during embryonic development. (FLIP TO SEE PICTURE) According to the graph, what are the changes in DNA methylation during embryonic development? A) Only the paternal DNA becomes demethylated B) The maternal DNA becomes demethylated first C) The methylation patterns of the parents' DNA are erased before fertilization D) The methylation patterns of both parents are erased after fertilization

D) The methylation patterns of both parents are erased after fertilization

For which discovery about DNA do Watson and Crick receive credit? A) DNA is the molecule that genes are made of B) The amount of adenine equals the amount of thymine in an organism C) Phosphate-pentose bonding along the nucleotide backbone is covalent D) The shape of DNA is a double helix

D) The shape of DNA is a double helix

What is the relationship between enzymes and DNA? A) Enzymes contain the code for DNA B) Enzymes act on DNA during translation C) Both enzymes and DNA have similar shapes D) The structure of enzymes is determined by DNA

D) The structure of enzymes is determined by DNA

How is the information in the genetic code used? A) To predict the genotype of gametes B) To distinguish prokaryotic genomes from eukaryotic genomes C) To deduce phenotypes in pedigree charts D) To translate mRNA into polypeptides

D) To translate mRNA into polypeptides

What will be the sequence on the mRNA molecule that is produced when the DNA base sequence ACTGATGCC is transcribed? A) ACTGATGCC B) ACUGAUGCC C) TGACTACGG D) UGACUACGG

D) UGACUACGG

The base sequence of a fragment of DNA is: ACC GTG CAG GAT What is the base sequence on the messenger RNA (mRNA) molecule transcribed from it? A) TGG CAC GTC CTA B) TGG CUC GTC CTU C) UGG CTC GUC CUT D) UGG CAC GUC CUA

D) UGG CAC GUC CUA

Which of the following is a method of regulating gene expression? A. RNA molecules bind to the DNA at specific places. B. Enzymes break the DNA into fragments. C. Lipids bind to specific bases in the DNA. D. Proteins bind to specific base sequences.

D. Proteins bind to specific base sequences.

The color of fur in Himalayan rabbits is affected by a gene which is only active at cooler temperatures (15°C to 25°C). If a Himalayan rabbit is reared at 20°C it has dark coloured fur on it's ears, nose, and feet. At 30°C the gene is not expressed and so a Himalayan rabbit living in warmer climates has white fur on these parts. Which of the following points best explain this situation? A. The fur pigmentation is controlled by two genes. B. The expression of the gene is affected by a promoter. C. The fur pigment is affected by the environment. D. The expression of the gene is affected by the environment.

D. The expression of the gene is affected by the environment.

Which of the statements correctly compares the functions of DNA Gyrase and Helicase? - DNA gyrase relieves twists in DNA helix and helicase separates the two strands of DNA - DNA gyrase and helicase both separate the DNA strands. - DNA gyrase and helicase both relieve twists in the DNA helix. - DNA gyrase separates the two strands of DNA and helicase relieves tension in the twists.

DNA gyrase relieves twists in DNA helix and helicase separates the two strands of DNA

Which of the following is not found in all nucleotide molecules? - adenine - nitrogenous bases - pentose (a 5-carbon sugar) - phosphate group

adenine

Compare and contrast the structure of DNA and RNA.

DNA: - Deoxyribose - 2 antiparallel strands - A, T, G, C - Base pairs - Double helix RNA: - Pentose - 1 strand - A, U, G, C - Lone bases - Helix

What does post-transcriptional modification of eukaryotic mRNA include? I. Introns are removed from mRNA. II. Exons are joined together to form mature mRNA. III. A 5' cap and 3' poly-A tail are added to mRNA. - II and III only - I and III only - I only - I, II and III

I, II and III

Which are necessary to make DNA replication semi-conservative? I. Separation of the strands by RNA polymerase II. Complementary base pairing III. Use of a pre-existing strand as a template - I and II only - II and III only - I and III only - I, II and III

II and III only

What contribution did the X-ray diffraction conducted by Rosalind Franklin make to our understanding of DNA? - It identified DNA as the genetic material. - It indicated the helical shape of the molecule. - It showed that replication was a semi-conservative process. - It showed that the DNA of eukaryotes was associated with histone proteins.

It indicated the helical shape of the molecule.

Promoters are non-coding regions in DNA. What is the role of a promoter? - It starts translation. - It is a binding site for RNA polymerase during transcription. - It is a binding site for DNA polymerase during DNA replication. - It starts mRNA splicing.

It is a binding site for RNA polymerase during transcription.

Which of the following best describes how DNA replication changes the chromosomes in a cell? - It makes a non-sister chromatid for each chromosome - It makes a sister chromatid for each chromosome. - It increases the length of the DNA in each chromosome - It increases the number of chromosomes.

It makes a sister chromatid for each chromosome.

Compare and contrast the difference between leading and lagging strands.

Leading Strand: - Continuous DNA replication - Follows replication fork - Made in one strand - Opens up in the 3' to 5' direction - Grows in the 5' to 3' direction - Needs one primer - Starts growing at beginning of replication - Does not require DNA ligase Lagging Strand: - Discontinuous DNA replication (5' --> 3') - Moves away from replication fork - Made in Okazaki fragments - Opens up in the 5' to 3' direction - Grows in the 3' to 5' direction - Needs new primer for each fragment - Starts growing later in replication process - Requires DNA ligase

During modification in eukaryotes, mRNA is spliced. What is splicing of mRNA? - Separation of mRNA from DNA during transcription - Replacement of primers with RNA bases - The removal of non-coding RNA sections in prokaryotic cells - Linking together exons

Linking together exons

In transcription, which enzyme has a role similar to that of helicase in replication? - DNA polymerase I - Gyrase - RNA polymerase - DNA polymerase III

RNA polymerase

What is a function of DNA polymerase I? - Adds nucleotides in a 5' to 3' direction to elongate the chain - Removes RNA primer and replaces it with DNA - Produces sugar-phosphate bonds to link Okazaki fragments - Uncoils the DNA double helix and splits it into two template strands

Removes RNA primer and replaces it with DNA

This diagram shows a simplified diagram of DNA replication. (FLIP TO SEE PICTURE) Which statement correctly describes a detail of DNA replication shown in the diagram? - Replication happens using the same enzymes on both leading and lagging strands. - Replication is in a 5' to 3' direction on the leading strand but in 3' to 5' on the lagging strand. - Replication is continuous on the leading strand and discontinuous on the lagging strand. - Replication is faster on the lagging strand than the leading strand.

Replication is continuous on the leading strand and discontinuous on the lagging strand.

Which are two proteins that assist in the unwinding and separation of DNA strands during replication? - DNA gyrase and DNA polymerase I - Single-strand binding protein and DNA gyrase - Helicase and DNA polymerase III - Helicase and DNA primase

Single-strand binding protein and DNA gyrase

The diagram illustrates some of the processes involved in DNA replication. (FLIP TO SEE PICTURE) What is shown in the diagram? - Single-stranded DNA-binding proteins on the old strands - Gyrase reforming the double helix - DNA ligase joining Okazaki fragments in the leading strand - DNA polymerase bonding nucleotides in a 3' to 5' direction

Single-stranded DNA-binding proteins on the old strands

In the RNA molecule: - cytosine pairs with thymine - adenine pairs with uracil - guanine pairs with thymine - adenine pairs with thymine

adenine pairs with uracil

Which of the following is a role of nucleosomes in eukaryotes? - Used in the unwinding of DNA for translation. - They are involved in the regulation of the transcription of DNA. - They carry out DNA replication - Used in the unwinding of DNA for translation.

They are involved in the regulation of the transcription of DNA.

Which of the following nitrogenous bases is found in DNA, but is not found in RNA? - Uracil - Adenine - Thymine - Guanine

Thymine

A DNA triplet on the strand that is transcribed has the bases TAG. Which anticodon on tRNA is used in translation? - TAG - UAG - ATC - AUC

UAG

DNA is made up of a phosphate group, a nitrogenous base, and __________. - a protein - a glycerol - a molecule of ATP - a pentose sugar

a pentose sugar

The two strands of a DNA double helix are held together by: - peptide bonds - hydrogen bonds - ionic bonds - covalent bonds

hydrogen bonds

In DNA, adenine always pairs with: - guanine - uracil - cytosine - thymine

thymine

In RNA, adenine always pairs with: - thymine - guanine - cytosine - uracil

uracil