DNA
Assume that a 100-base pair DNA double helix contains 65 adenines. How many cytosines are there?
35
What are the four levels of structure for proteins? Provide a brief description of each.
Primary structure is the amino acid sequence
○Secondary structure is the folding of the amino acid sequences due to the hydrogen bonds being formed
Tertiary structure is further folding of more complex proteins into complex 3D shapes
Quaternary structure occurs in proteins that are made up of more than one polypeptide
chains to create complex 3D shapes
Define receptor proteins.
Receptor proteins have a specific
shape. They bind to one specific
messenger molecule with
complementary shape.
They allow cells to communicate with
other cells.
How do the following factors affect enzyme activity?
1. As concentration of reactants increases so does rate of reaction, however once all of the reactants have bound with the available enzymes then reaction rate plateaus.
2. As concentration of the enzyme increases so does rate of reaction, however once all of the enzymes have bound with the available reactants then reaction rate plateaus.
Discuss the ethical and economic issues related to the collection of genetic information.
Disadvantages: discrimination (e.g. susceptibility to disease), economic cost of collection, convicting wrong people, refuse to insure people with disease susceptibility
DNA has direction. Describe the importance of this characteristic of DNA in relation to the structure of the molecule, and the process of transcription.
Structure: the 2 strands of DNA are opposite, one strand is 5’ to 3’ and the other is 3’ to 5’ which allows for complementary base pairing.
Transcription: DNA and RNA can only be read from the 5’ to 3’ direction
Describe the difference between DNA codons, RNA codons, anticodons, and amino acids.
DNA codons - sections of 3 nucleotides that form the DNA sequence
RNA codons - sections of 3 nucleotide bases that form the RNA strand
Anticodons - groups of 3 nucleotide bases attached to the tRNA molecules. These match with the complementary codons to deliver the amino acid
Amino acids - delivered by the tRNA, are the building blocks of protein
What is DNA methylation and what affect does it have on transcription?
DNA methylation is when methyl groups (CH3) are attached to cytosine bases in a gene. Increased methylation means that the gene cannot be ‘read’, and is therefore switched off.
Describe how enzymes affect the activation energy required for reactions to take place.
A small amount of energy is required to start off a chemical reaction, this energy is called activation energy.
Activation energy breaks the bonds in the reactant molecules before a reaction between them will proceed.
Enzymes lower the activation energy required by:
● Placing stress on the substrates bonds, which means that less energy is needed to break the bonds in the substrate.
● Holding the substrate molecules in the correct orientation at the active site, which increases the chance of a reaction between them taking place.
Describe how CRISPR is able to edit any gene of interest.
Uses a bacterial protein called Cas9 which is
able to cut DNA at a specific site.
Scientists are able to program Cas9 to cut
DNA at ANY predetermined location by altering the guide RNA inside the protein.
This technique can also be used in live cells
to edit genes, and to switch them on and off by cutting the gene and damaging it.
What are three structural differences between DNA and RNA?
-deoxyribose sugar vs ribose sugar
-thymine vs uracil
-double stranded vs single stranded
-DNA is stable; RNA is unstable
What are the 4 types of RNA and what is their function?
1. mRNA - messenger RNA, is a copy of the genetic code and takes the
2. rRNA - ribosomal RNA, structural components of the ribosomes, assists in protein synthesis
3. tRNA - Delivers amino acids to the ribosome
4. miRNA - help regulate gene expression
Describe the promoter region of DNA, and the difference between an activator and repressor.
The promoter region is a section of DNA that is upstream of a specific gene. This is where transcription factors (activators and repressors) attach to. This determines whether a gene is ‘read’ or not. Activators allow the gene to be read, repressors silence the gene.
Activator: Promotes the expression of one or more
genes by facilitating the binding of RNA
polymerase.
Repressor: Inhibits the expression of one or more
genes by preventing the binding of RNA
polymerase.
Describe the difference between germline and somatic mutations, and how these affect offspring.
Germline = occur in gametes. Can be transmitted to offspring and every cell in the offspring will have the mutation
Somatic = occur in other cells of the body. May have little effect on the organism because they are confined to just one cell and its daughter cells. Somatic mutations cannot be passed onto offspring
Germline mutations are inheritable, somatic mutations are not.
Describe how particular genes can be selected using probes and removed using restriction enzymes.
The probes have a specific RNA code that is able to locate the gene of interest. It then binds with the gene to become hybridized. This marker is radioactive or fluorescent, which can then be observed.
The gene of interest can then be removed by restriction enzymes which cut the DNA at specific sites, and is therefore able to remove the gene of interest.
Describe the structural properties of the DNA molecule (backbone, nucleotides, bonds etc.)
Two strands made of sugar phosphate backbone, double helix structure, strands connected by base pairs of nitrogenous bases (these are connected by weak hydrogen bonds), the nitrogenous base connects to the backbone via the sugar molecule.
Describe the process of transcription and translation.
Transcription - A section of DNA (gene) is unzipped and ‘read’. Free bases in the cytoplasm attach one at a time to the DNA to form mRNA.
Translation - The mRNA attaches to the ribosome. tRNA molecules attach to the mRNA 3 bases at a time (one codon). The tRNA molecules bring an amino acid, which attach together to form a polypeptide chain.
Define exons and introns. Describe how one gene can code for multiple different proteins.
Exons = coding DNA that is both transcribed and translated, to turn into a protein. Introns are NON-CODING segments of DNA and are removed (spliced) out after transcription and before translation.
It can change how the pre mrna is spliced, it can change the order, and also remove exons.
Describe insertion and deletion mutations. Why do these mutations always result in a significant change in DNA?
Insertion = singular nitrogenous base is added. Deletion - singular nitrogenous base in deleted. Causes frame shift mutation – can change every amino acid that is produced, protein will not function
Describe the 3 stages of polymerase chain reaction.
Denaturation - PCR mixture first heated to 95°C to separate the strands of DNA
Annealing - cooled to 65°C to allow the primers to stick to the ends of the DNA
Extension - heated again to 72°C to allow heat-stable DNA polymerase to add nucleotides to the strands
DNA replication needs to occur before cell division can take place.
State two structural differences in a eukaryotic chromosome in comparison to a prokaryotic chromosome.
Name the part of a eukaryotic cell in which DNA replication occurs.
State two structural properties of the eukaryotic DNA molecule and explain how it aids in the replication process.
Describe how DNA is replicated in eukaryotes with reference to the original DNA strands and the newly synthesized DNA strands
Prokaryotic cells have circular chromosomes whereas eukaryotes have linear. Eukaryotic DNA is coiled around histones whereas prokaryotic have no histones. Eukaryotic cells have introns whereas prokaryotes have no introns.
Nucleus
Nucleotide composition and pairing. The composition of nucleotide bases allows for two hydrogen bonds to form between A-T and 3 between C-G bringing about the specific base pairing rule. During replication, this allows free floating nucleotides to form complementary strands with the exposed bases of the template strand of DNA.
Weak hydrogen Bonds between strands.
During DNA replication the weak hydrogen bonds allow the DNA molecule to be unzipped, exposing bases for the formation of two new strands complementary to the template strand. The collective forces created by hydrogen Bonds provide the two newly formed double helices with stability and allows for the formation of the double helix structure.
DNA replication in eukaryotes is semi-conservative. Each strand acts as a template for the other strand, so that each new molecule of DNA contains one old and one new strand of DNA.
Titin is the largest protein in the human body, functioning as a molecular spring to enable normal contraction in muscle tissues, such as those found in the heart. Titin is encoded by the TTN gene. One form of Titin in humans is composed of 34,350 amino acids.
Altered forms of Titin have been implicated in numerous human diseases, including dilated cardiomyopathy (DCM), in which the heart is enlarged and weakened, leading to heart malfunction.
Scientists have identified many forms of Titin that result from differences in the processing of the MRNA molecule produced from the TTN gene.
Determine the minimum number of bases in the TTN gene required to produce the form of Titin composed of 34,350 amino acids.
Describe how such an mRNA molecule is processed immediately following its production, and explain how the presence of one or more additional exons in the final mRNA may alter the titin protein produced and lead to heart disease.
a)103,050
b) Introns are removed to produce an mRNA molecule composed only of exons. If there are additional exons, there would be more codons and this would lead to additional amino acids in the polypeptide. With a longer polypeptide, this will likely change the folding or change the shape of the polypeptide. As the function of a protein is determined by its shape, this new form of Titin may not function normally or as effectively.
Colorectal cancer is a common disease worldwide. Studies have shown that changes to DNA methylation patterns in a range of tumor suppressor genes (TSG’S) can trigger the development of colorectal cancer.
DNA methyltransferases (DNMTs) are enzymes that catalyze the addition of methyl groups to DNA. DNMTs are required to maintain methylation patterns from parent cells to daughter cells in the process of cell division.
Explain why the semi conservative replication of DNA prior to cell division does not maintain a cell's DNA methylation pattern in the absence of DNMTs.
Semi-conservative DNA replication produces two identical DNA molecules, each molecule will contain one original Strand and one newly synthesized strand. When DNMTs are not present, the newly synthesized strands will not be methylated
Beckwith-Wiedemann syndrome (BWS) is a rare disorder in which individuals have abnormal growth and an increased risk of childhood cancer. Cyclin-dependent kinase inhibitor 1C (CDKN1C) is a protein that inhibits cell division. In human beings, this protein is coded by the CDKN1C gene. In some patients with BWS, there is more DNA methylation of the CDKN1C gene then there is in individuals who do not have BWS.
State the name of the DNA nucleotide that is most often methylated
State the effect of increased DNA methylation of the CDKN1C gene on its expression
Explain how altering the expression of the CDKN1C gene could lead to cancer
a) cytosine
b) reduced expression/silenced/switched off/transcription prevented
c) the protein produced by the CDKN1C gene inhibits cell division. Reducing the expression of the CDKN1C gene leads to less protein. This could result in uncontrolled cell division, which is the cause of cancer.
Scientists have discovered that an enzyme called GaINAc-T6 is absent in healthy colon tissue, but present in colon cancer cells. The research team used CRISPR/Cas9 on colon cancer cells to inactivate the GaINAc-T6 gene and produce cells that could not synthesize GaINAc-T6. These cells showed more normal growth than cells with an active GaINAc-T6 gene.
Explain why it is necessary to know part of the base sequence of the GaINAc-T6 gene in order to use CRISPS/Cas9 to inactivate the gene
Describe one consequence of the guide RNA that is attached to the Cas9 protein being too short
State one function of the Cas9 protein that is used to edit the GaINAc-T6 gene
Because protein needs to be programmed with guide RNA to enable it to locate the GaINAc-T6 gene. The guide RNA must have a base sequence that is complementary to part of the GaINAc-T6 gene.
If the guide RNA is too short, then the Cas9 protein might bind to other sites and a consequence to other DNA, or could cause an effect not only at the intended site.
It cuts the DNA at a specific position