IB Biology HL: DNA and Biotechnology Objectives

Describe the three post-transcriptional modifications of pre-MRNA in eukaryotes.

-Addition of a 5' cap -Addition of a 3' poly-adenylation tail -Splicing (introns are removed and extrons are joined together)

Identify the four bases of DNA based on the number of rings (purines or pyrimidines) and the number of hydrogen bonds it can form.

-Adenine: 2-Hydrogen bonds; purine -Thymine: 2-Hydrogen bonds; pyrimidine -Guanine: 3-Hydrogen bonds; purine -Cytosine: 3-Hydrogen bonds; pyrimidine

Outline the role of Chargaff, Watson, Crick, Franklin, and Wilkins in the discovery of DNA structure

-Chargaff: determined that there are equal numbers of A/T and G/C bases -Watson: determined how nitrogenous base pairs fit within a helix while maintaining a constant diameter -Crick: determined that the helix backbone is antiparellel -Franklin: took clear photos of the DNA structure that aided every other scientist mentioned -Wilkins: studied DNA through X-Ray Diffraction

Define "coding sequences" and "repetitive sequences" of DNA.

-Coding: codes for polypeptides creating during translation -Repetitive: majority of DNA; exists for gene expression, telomeres, etc.

Define codon, redundant, and degenerate as related to the genetic code.

-Codon: a sequence of 3 nucleotides that form a unit to specify a particular amino acid -Redundant/Degenerate: a single amino acid may be coded for by more than one codon

Outline the process of DNA sequencing, including the role of chain terminator nucleotides, fluorescence, and electrophoresis.

-Copies of DNA sequences are placed with polymerase, nucleotides, and primers -Polymerase replicates the sequences and stops when adding dideoxynuceotide -Strands of new replications of various lengths end with fluorescent nucleotides -DNA is separated by size in electrophoresis

Compare the structure of DNA and RNA.

-DNA: Double helix, composed of deoxyribose sugars contains thymine -RNA: Single-stranded, composed of ribose sugars, contains uracil -Both are made of nucleotides and have phosphate groups.

Compare dispersive, conservative, and semi-conservative replication.

-Dispersive: original DNA strands are broke into segments that replicate and reassemble (interpreted with new copies) -Conservative: original strand remains intact and the new copy contains 2 new strands -Semi-Conservative: Replication produces 2 copies, each of which contain one of the original and one new strand

Outline the process of translation elongation, including codon recognition, bond formation, and translocation.

-Elongation: new amino acids are brought to the ribosome according to codon sequences -Recognition: tRNA matches codons with appropriate amino acids -Formation: amino group of the A site and carboxyl group attach to the P-Site of tRNA -Translocation: amino acids are translocation to a growing polypeptide chain

Outline the role of enhancers, silencers and promoter-proximal elements in regulation of gene expression.

-Enhancer: short region of DNA that can be bound by proteins to increase the likelihood of a gene's transcription -Silencer: region of DNA that represses gene transcription -Promoter-Proximal Elements: binds proteins that assist RNA polymerase bindings

Define epigenetic and epigenome.

-Epigenetic: relating to non genetic influences on gene expression -Epigenome: a multitude of chemical compounds that can instruct the genome on what to do

State the differences between free and bound ribosomes.

-Free: produces proteins to be used within the cell; found in the cytoplasm -Bound: produces proteins to be shipped out of the cell; found in the ER

List destinations of proteins synthesized on bound ribosomes.

-Golgi complex -Lysosome

Outline the role of the following proteins in DNA replication: helicase, topoismerase, single-stranded binding proteins, & primase.

-Helicase: unwinds double helix, breaks hydrogen bonds between base pairs -Topoisomerase: relieves tension on DNA while it unwinds -Single-Stranded Binding Proteins: binds to single-stranded DNA to prevent parent strands from reconnecting -Primase: synthesizes RNA primers needed to start replication

Compare replication on the leading strand and the lagging strand.

-Leading: DNA polymerase III moves in the same direction as helicase to add complementary base pairs to the daughter strand -Lagging: Polymerase has to move in the opposite direction, and it is synthesized in short pieces called Okazaki fragments

Use a genetic code table to deduce the mRNA codons given the name of an amino acid.

-Left: Codes for the first base -Top: Codes for the second base -Right: Codes for the third base

List types of models used in science.

-Photographs -Computer Models -Physical Models -Mathematical Models

Outline the role of the following proteins in DNA replication: DNA polymerase III, DNA polymerase I, & DNA ligase.

-Polymerase III: main enzyme that builds a complementary base strand by adding nucleotides -Polymerase I: removes RNA primer and replaces it with DNA nucleotides -Ligase: covalently bonds sugar-phosphate backbone between adjacent Okazaki fragments to join them togethero

Compare the timing and location of transcription and translation between prokaryotes and eukaryotes.

-Prokaryotic: continuous process, translation can occur immediately after transcription (no nuclear membrane) -Eukaryotic: needs the removal of introns to form mature mRNA (splicing), genes may contain non-coding sequences

List types of epigenetic tags.

-Psychological state -Diet -Social interactions -Disease exposure

Identify nitrogenous bases as either a pyrimidine or purine.

-Purine (2-Ring Structure): Adenine & Guanine -Pyrimidine (3-Ring Structure): Cytosine, Thymine, & Uracil

List ways in which models are different from the structure or process it represents.

-Variations in size/dimensions -Simplify complexity (but lack smaller details)

Outline the deductions about DNA structure made from the X-ray diffraction pattern.

-X-shape follows pattern of double helix -Regular spacing indicates helix's consistent diameter -Distance from middle/top is the same distance between 2 stacked base pairs

State the two types of nucleic acid.

1) DNA 2) RNA

Outline two examples of environmental influence on gene expression.

1) Diet 2) Exposure to chemicals

State two reasons why gene expression must be regulated.

1) Different sets of genes in cells 2) Repressed genes can be harmful if activated again

List 2 major differences in gene expression between prokaryotic cells and eukaryotic cells.

1) RNA transcription in eukaryotic cells occurs prior to protein formation in the nucleus, while translation occurs in the cytoplasm. In prokaryotes, transcription and protein formation occur simultaneously. 2) Prokaryotic gene expression is regulated at the transcription level. Eukaryotic gene expression is regulated at different levels.

Outline 5 functions of non-coding DNA sequences found in genomes, one of which must be the telomere.

1) Telomere: Regions at the end of a chromosome that protect against deterioration 2) Introns: non-coding sequences removed by RNA splicing before translation 3) Gene Regulation: processes transcription 4) Satellite DNA: repetitive sequences used for profiling 5) Non-coding Genes: RNA codes that are not translated

Outline 2 functions of helicase.

1) Unwinds the double helix 2) Separates the strands by breaking hydrogen bonds

State the number of nitrogenous bases per complete turn of the DNA double helix.

10 (20 nucleotides).

State the direction of movement of the ribosome along the mRNA molecule.

5' to 3'.

State the names of the nitrogenous bases found in DNA and RNA.

Adenine —> Thymine/Uracil Guanine —> Cytosine

Describe the meaning of semi-conservative in relation to DNA replication.

After the helix separates into 2 strands, one serves as a "template" to form a complementary strand, both of which complete the molecule. Therefore, half of the original code is conserved.

Outline the benefits of using gene transfer in the production of pharmaceutical insulin.

All bind to the human insulin receptor, so using insulin from plants reduces the risks for those with allergies. The universality also allows for gene transfer between several species.

Describe the use of twin studies to measure the impact of environment on gene expression.

Although twins are similar, environmental factors can impact the development of a trait or disorder. Identical and fraternal twins are experimented on to evaluate specific traits and their correlation with outside elements.

Outline the process of X-ray diffraction.

An X-ray beam is directed onto a DNA sample, causing its atoms to diffract. The pattern is captured on a photographic plate.

Discuss the role of reprogramming and imprinting on epigenetic factors.

An organism's genotype interacts with the environment to produce its phenotype, providing a framework that explains individual variations despite genetic similarity.

Outline the process of translation termination, including the role of the stop codon.

At certain stop codons, the translation process ends and the polypeptide is released.

Explain the procedure of the Hershey and Chase experiment.

Bacteria were infected with genetic material while proteins were labeled with radioactive sulfur, so separated particles within the bacteria were then distinguished according to their relationship with the radioactive phosphorus.

Use a genetic code table to determine the amino acid sequence coded for by a given antisense DNA sequence or mRNA sequence.

Begin with the "start" codon (AUG), then use the left, top, and right columns respectively to translate the codons to amino acids.

Outline the features of DNA structure that suggested a mechanism for replication.

Complementary base pairing conserves the genetic code when each strand replicates. The covalent bonds between the phosphate backbones keep their connections strong and correctly sequenced, while the hydrogen bonds allows the strands to easily separate for replication.

Outline the formation of a DNA double helix by hydrogen bonding between nitrogenous bases.

Complementary nucleotides form hydrogen bonds between the nitrogenous bases, creating the 2 strands of the double helix.

Define antiparellel in relation to DNA structure.

Complementary strands run in opposite directions alongside one another - one is oriented in the 5' to 3' direction, while the other runs from 3' to 5'.

State the location of translation in the cell.

Cytoplasm

State the complementary base pairing rules.

DNA from any cell should have a 1:1 ratio of purine and pyrimidine bases, so the pairings are Adenine/Thymine, and Cytosine/Guanine.

Explain the levels of supercoiling.

DNA —> nucleosome —> beads on a string —> 30 nm fiber —> unreplicated interphase chromosome —> replicated metaphase chromosome

Outline the process of Polymerase Chain Reaction (continued).

During PCR, thermal cycling is critical to amplifying the sequence. 4) Denaturing: mixture is heated to denature double-stranded template into a single strand. 5) Annealing: mixture is cooled to allow oligonucleotide primers anneal to (base pair with) the template. 6) Extension: mixture is heated up again to allow Taq polymerase to perform synthesis, after recognizing oligonucleotide primer as the starting point.

Describe the procedure of the Meselson and Stahl experiment.

E. Coil divided in nitrogen solutions to incorporate "heavy" nitrogen into the nucleotides. When spun in a centrifuge, DNA sunk to the bottom because it was now heavier, and this allowed for the scientists to divide it with a new band in the center to show semi-conservatism.

Explain why VNTR are used in DNA profiling.

Each person has a different VNTR, which can be differentiated by the size of the fragments after they are cut by restriction enzymes.

State the role of tRNA activating enzymes.

Each tRNA molecules binds with a specific amino acid in the cytoplasm in a reaction catalyze by a tRNA-activating enzyme.

Deduce the antisense DNA base sequence that was transcribed to produce a given mRNA sequence.

Find the complementary base pairs or use the codon chart if provided with the amino acids.

Describe the movement of DNA polymerase along the DNA template strand.

Following helicase, DNA polymerase moves along the template strand in a 3' to 5' direction, adding new nucleotides to form a complementary strand.

Contrast the number of origins in prokaryotic cells to the number in eukaryotic cells.

For prokaryotic cells, a single origin is sufficient whereas eukaryotes need many origins (replication is initiated on all) to increase efficiency of replication process.

Outline the effect of acetylation of nucleosome tails on rates of gene expression.

Histone acetylation allows a less-condensed DNA to undergo higher levels of transcription, neutralizing charges on the histone proteins to prevent attraction. This allows polymerase to begin the transcription process.

Outline the mechanism of histone-DNA association.

Histones are proteins that have many positively-charged amino acids, allowing them to associate with negatively-charged DNA.

State why DNA strands must be separated prior to replication.

If the strands are separated, both can be used as a template to produce a complementary strand that then combines with the template to find a new double helix (doubles the efficiency).

Outline the process of translation initiation.

Initiation begins when an mRNA molecules binds to the sub-unit of the ribosome. It then moves to the start codon to assemble the ribosomal complex.

State the experimental question being tested in the Hershey and Chase experiment.

Is the genetic material passed from one generation to the next composed of proteins or nucleic acids?

Identify nucleosome structures using molecular visualization software.

Look for the octomere core of the histones and the two wraps of DNA surrounding the core.

Outline the role of messenger RNA in translation.

Messenger RNA carries the genetic information copied from DNA in the form of codons that specify a certain amino acid.

State the effect of DNA methylation on gene expression.

Methylation is a signaling tool that indicates the genes should be locked in the "off" position.

Compare methylation patterns in twins using superimposed images of dyed chromosomes.

Metlation patterns may change over the course of a lifetime, so the influence of heritability is not predetermined. Different cell types have different methylation patterns, and these can be influenced by environmental factors; this means no two are the same.

State a common feature of models in science.

Models serve as a visual representation of certain phenomena, so they present conceptions that are not able to be easily observed. This means they all simplify abstract ideas to be more easily studied.

Outline the formation of Okazaki fragments on the lagging strand.

Okazaki fragments are sections of replicated DNA on the lagging strand. RNA polymerase adds nucleotides in a 5' to 3' direction and builds until the next primate, so sections between the primers are called Okazaki fragments.

Explain the role of complementary base pairing in DNA replication.

Only complementary bases pair together, so this conserves the base sequence of the DNA.

Outline the process of Polymerase Chain Reaction.

PCR is used to amplify (create) millions of identical copies of a particular DNA sequence. 1) DNA template is isolated. 2) Enzyme Taq DNA Polymerase adds complementary nucleotides during synthesis. 3) Oligonucleotide primers, short segments of single-stranded DNA that match up to sequences flanking the region, are responsible for ensuring that only the region of interest is copied.

Outline the source and use of pharmaceutical insulin prior to the use of gene transfer technology.

Porcine and bovine insulin were extracted from the pancreas of pigs and cattle as an alternative source for human insulin use.

Outline the role of promoter DNA.

Promoter DNA is the region that initiates transcription of a particular gene, located near the transcription start sites (towards the 3' region of the anti-sense strand).

Describe the initiation of transcription, including the role of the promoter, transcription facotrs, the TATA box, and RNA polymerase.

RNA polymerase binds to the promoter region in order to signal the DNA to unwind so the enzyme can read the bases of the DNA strand. A transcription factor is a protein that controls the rate of transcription by binding to the DNA sequence. The TATA box is a sequence of DNA found in the core promoter region that is considered to be "non-coding".

Explain the need for RNA primers in DNA replication.

RNA primers act as a starting point for replication, and are needed because polymerase can only add nucleotides in a 5' to 3' direction on an existing strand.

Describe the process of alternative RNA splicing.

RNA splicing is a regulated process during gene expression that results in a single gene coding for multiple proteins. The final processed mRNA produced from that gene varies depending on which exon is included or excluded.

Explain how the results of the Hershey and Chase experiment supported the notion of nucleic acids as genetic material.

Radioactive DNA ended up in bacteria, demonstrating that phage DNA codes for the formation of next generations phages. Phage proteins were only used to deliver DNA to the bacterial cell.

Describe Rosalind Franklin's role in the elucidation of the structure of DNA.

Rosalind Franklin applied X-ray diffraction techniques to present images of DNA in the shape of an x, revealing that it was oriented as a double helix.

Predict experimental results in the Meselson Stahl experiment if DNA replication was dispersive, conservative, or semi-conservative.

Semi-conservative replication was demonstrated with different band colors, so if it was dispersive or conservative, then the bands would have stayed consistent throughout because they would have remained identical.

Outline an example of alternative splicing that results in different protein products.

Splicing increases the number of different proteins an organism can produce. Alternative splicing is a process in which multiple exons code for multiple proteins. Particular exons may be included in the final mRNA strand, resulting in a variety of separate translations.

Describe termination of transcription, including the role of the terminator.

Termination is the end of transcription, occurring when the RNA polymerase codes a "stop" sequence into the gene, called a terminator.

Explain how using a 4-letter nucleic acid "language" can code for a "language" of 20 amino acid letters in proteins.

The 4 nucleic acid bases can be divided into 3-letter codons that define different amino acids.

Outline the environmental regulation of the breakdown of lactose in E. Coli.

The bacteria must express the "lac" gene, which can code for key enzymes in lactose uptake and metabolism. E. Coli expresses this gene when lactose is available but glucose is not.

Describe the action of DNA polymerase III in pairing nucleotides during DNA replication.

The enzyme adds individual nucleotides to the 3' hydroxyl group of a DNA strand, using a complementary single strand as a template.

Explain the use of Taq DNA polymerase in TCR.

The enzyme recognizes an oligonucleotide primer as the starting point for synthesis and places free-floating nucleotides into the correct positions on the DNA template. This allows a new complementary strand to extend from the primer.

Explain how Meselson and Stahl demonstrated semiconservative DNA replication.

The experiment displayed the densities of differing DNA fragments, and after 2 replication cycles, one two bands of DNA were seen. One was intermediate, and one was light, showing semi-conservative replication.

Explain why replication is different on the leading and lagging strands.

The leading strand can be ranslated in the 5' to 3' direction, while the lagging strand goes from 3' to 5' so the polymerase moves in the opposite direction and splits the process into fragments.

State the role of the origin of replication in DNA replication.

The origin is a sequence of DNA where replication is initiated on a chromosome, plasmid, or virus, allowing for replication to begin.

Explain how nucleotides can connect to form a nucleic acid polymer.

The phosphate of one nucleotide attaches to the 3-Carbon of next nucleotide's phosphate, forming the sugar-phosphate backbone.

Identify and label the 5' to 3' ends on a DNA or RNA diagram.

The primary strand runs from 5'—>3', while the complementary strand goes antiparellel from 3'—> 5'. The 5' end is indicated by the presence of a phosphate group, while the 3' end is indicated by a pentose sugar.

Define gene expression.

The process by which information from a gene is used in the synthesis of a functional gene product. Products are often proteins, but can be functional DNA.

Outline how a ribosome becomes bound to the endoplasmic reticulum.

The protein must first be targeted fro secretion and then becomes bound after having first been attached, then collected in the cisternal space.

Identify the sense and antisense strands of DNA given a diagram of translation.

The sense strand runs in a 5' to 3' direction while the antisense strandruns from 3' to 5'.

Define transcription.

The synthesis of mRNA copied from the DNA base sequences by RNA polymerase.

Define translation.

The synthesis of polypeptides on ribosomes.

Outline the effect of methylation of nucleosome tails on rates of gene expression.

They turn off genes to regulate gene expression. Methylation "switches off" genes by causing the DNA to be condensed and "silent" to prevent transcription.

Define VNTR.

Variable Number Tandem Repeat (sequences of repeating nucleotides)

Outline the process of transcription, including the role of RNA polymerase and complementary base pairing.

When the DNA double helix separates into 2 strands, free RNA nucleotides are assembled by RNA polymerase using one DNA strand as the template. The nucleotides then link to form an RNA strand.

Outline the role of complementary base pairing between mRNA and tRNA in translation.

tRNA has an anticodon that binds to the complementary codon on mRNA, and also binds to a specific amino acid that corresponds with the anticodon. Uracil and Adenine pair together, while Cytosine and Guanine pair together.