Cell Biology & Genetics

What is DNA ? Polymer composed of 2 Polynucleotide chains that coil around each other to form a double helix. What direction do the DNA strands run ? antiparallel, one runs 3' to 5' and the other 5' to 3'. What is the purpose of the sugar phos- To protect the bases inside it, and prephate backbone twisting around itself in vent them from being damaged by the a coil ? environment. What is a Chromosome ? Thread like structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes. - Made up of DNA tightly coiled many times around histones = proteins that support its structure. Chromatin Long linear DNA molecule associated with proteins, forming a compact complex of proteins and DNA. - Contains the vast majority of the DNA of an organism. Where can a small amount of DNA inherited maternally be found ? Mitochondria What are Histones responsible for ? First and most basic unit of chromosome organisation, the nucleosome. Why is DNA replication important? - To make new identical copies of chromosomes for cell division (growth) - To help maintain continuity of genetic information (reproduction) - Continuous surveillance of DNA and its repair What are the 3 main steps of DNA replication ? initiation, elongation, termination 1/9 - starts with a single molecule of DNA made up of two complementary strands - ds DNA must be unzipped into single strands - Helix structure is unwound by breakage Describe the fork formation in DNA repli- of the weak hydrogen bonds between cation ? bases that holds 2 strands together - DNA helicase disrupts the H-bonds between base pairs separating the 2 strands into a Y shape. - This area will now be the template for replication to begin. DNA replication direction ? - Only progresses in the 5' to 3' direction - Leading strand 5' to 3' - Lagging strand 3' to 5' 5' end = attached to a phosphate group 3' end = attached to a hydroxyl group What happens once the DNA strands have been separated ? - A primer (short piece of RNA) bind to the 3' end of the strand - Primers are generated by Primase. - DNA polymerase adds DNA nucleotides in a 5' to 3' direction (Elongation) - Complementary DNA nucleotides are added to the exposed bases on both strands - Complementary bases pair up e.g., A-T - the leading is synthesised continuously - lagging strand begins replication by binding with multiple primers, several bases apart = synthesised in fragment by Okazaki fragments (DNA polymerase) to the strand between primers - Ligase enzymes seals fragments together - Process of replication is discontinuous 2/9 - Exonuclease removes all RNA primers from the original strands - Primers are then replaced with approWhat happens once both strands of DNA priate bases are formed ? - Another exonuclease then proofreads the newly formed DNA to check, remove and replace any errors. What are Telomeres ? - repeated DNA sequence found at the end of the parental strands - acts as protective caps at the end of the chromosomes to prevent nearby chromosomes from fusing What does Telomerase do ? Catalyses the synthesis of telomere sequences at the end of the DNA. - unwind and separate double stranded DNA as it moves along the DNA. What is the role of the enzyme DNA He- It forms the replication fork by breaking licase in DNA replication ? the H-bonds between nucleotide pairs in DNA. Synthesises RNA primers that act as What is the role of the enzyme DNA Pritemplates for the starting point of DNA mase in DNA replication ? replication. Synthesises new DNA molecules by What is the role of the enzyme DNA Polyadding nucleotides to leading and lagmerase in DNA replication ? ging strands of DNA. Unwinds and rewinds DNA strands to What is the role of the enzyme Topoisoprevent the DNA from becoming supermerase in DNA replication ? coiled. Group of enzymes that remove nuWhat is the role of the enzyme Exonuclecleotide bases from the end of a DNA ase in DNA replication ? chain. What is the role of the enzyme DNA Lig- Facilitates joining of DNA strands by forase in DNA replication ? mation of Phosphodiester bonds. How does DNA polymerase correct errors in bases ? 3/9 - Excise bases that are 'mismatched' - Replace with the correct base - Then move forward to next base Genetic information flows from DNA to mRNA and then to protein What is the central dogma of molecular - Concept is the basic principle combiology ? mon to all organisms from prokaryotes to eukaryotes, including bacteria and humans. Where does Transcription occur in Eu- Nucleus = to produce a pre-mRNA molkaryotes ? ecule What are Genes ? Small sections of DNA that carry genetic information and instructions for making proteins, which help build and maintain the body. Describe Transcription ? - Genetic information for a protein contained in DNA is transcribed into mRNA - this is synthesised using DNA as a template - this takes place in the nucleus - TFIID binds to the TATA box via the TBP (TATA-binding protein) - Five more transcription factors and Describe the initiation of Transcription ? RNA polymerase combine around the TATA box in a series of stages to form a transcription-initiation complex. - RNA polymerase moves along the DNA template from the 3' to 5' end Describe the Elongation of Transcription - this builds the mRNA molecule us? ing complementary base pairing with nucleotides being added to the 3' end of the growing RNA molecule. In Bacteria: Describe the Termination of Transcrip- - the Polymerase stops transcription at tion in Prokaryotes ? the end of the terminator and mRNA can be translated without further modification 4/9 The termination of transcription is differDescribe the Termination of Transcrip- ent for the different RNA polymerases tion in Eukaryotes ? - mRNA needs to be modified before translation takes place. What happens during Translation ? A protein is synthesised from mRNA by ribosomes. In Eukaryotes: Occurs in the cytoplasm Describe Translation Initiation ? - codon AUG initiates the process of translation and one of three stop codons e.g., UAA, UAG, or UGA for chain termination - in Eukaryotes and archaea , the amino acid encoded by the start codon = Methionine GTP = energy source - codons of mRNA will be read in the 5' to 3' direction Describe Translation Elongation ? Amino acids are brought to the mRNA by tRNAs and are added, one by one to a growing polypeptide chain. Describe Translation Termination ? A stop codon in the mRNA is recognised by a protein release factor, and the translational apparatus comes apart, releasing a completed polypeptide. What is the lac operon ? An operon, or group of genes with a single promoter (transcribes as a single mRNA) . - genes in the operon = encode for proteins that allow the bacteria to use lactose as a energy source in lactose metabolism When is the lac operon expressed? When lactose is present and glucose is absent. What regulators turn the Lac operon 'on' and 'off' in response to lactose and glucose levels ? - The lac repressor - Catabolite activator protein (CAP) 5/9 What is the role of the promoter in the Lac operon ? - It is the binding site for RNA polymerase - enzyme that performs transcription. What is the role of the Operator in the Lac operon ? - A Negative regulatory site bound by the lac repressor protein. - it overlaps with the promoter, when the lac repressor is bound, RNA polymerase cannot bind to the promoter and start transcription. Positive regulatory site that is bound by catabolite activator protein (CAP). What is the role of the CAP biding site in When CAP is bound to this site, it prothe Lac operon ? motes transcription by helping RNA polymerase bind to the promoter. Acts as a lactose sensor - normally blocks transcription of the operon What is the role of the lac repressor ? - stops acting as a repressor when lactose is present - senses lactose indirectly through its isomer allolactose Acts as a glucose sensor - Activates transcription of the operon = What is the role of the Catabolite activaonly when glucose levels are low tor protein (CAP) ? - Senses glucose indirectly, through the hunger signal molecule cAMP. What are Mutations ? Permanent alterations/changes in a DNA sequence that are propagated through cellular generations. Somatic Mutations Occur in somatic cells - only affect the individual in which the mutation arises Germ-line mutation Alter gametes and passed to the next generation. Missense mutation A change in one DNA base pair resulting in the substitution of one amino acid for another in the protein. 6/9 Nonsense mutation A point mutation in a sequence of DNA that results in a premature stop codon, nonsense codon in the transcribed mRNA, and in a truncated, incomplete and usually non-functional protein product. What does the functional effect of the Nonsense mutation depend on ? The location of the stop codon within the coding DNA. Insertion Mutation Insertion changes the number of DNA bases in a gene by adding a piece of DNA = the protein made by the gene may not function properly. Deletion mutation Changes the number of DNA bases by removing a piece of DNA. - Small deletions = may remove one or a few base pairs within a gene - Large deletions = can remove an entire gene or several neighbouring genes. Deleted DNA may alter the function of the resulting proteins. Duplication mutation Consists of a piece of DNA that is abnormally copied one or more times = May alter the function of the resulting protein What is a Frameshift mutation ? - Occurs when addition or loss of DNA bases changes a gene's reading frame. - it shifts the grouping of these bases and changes the code for amino acids - resulting protein = non-functional Insertions, deletions, and duplications can all be frameshift mutations. Name some Agents that damage DNA ? Radiations Chemical in the environment Radiation - Damage to DNA - Highly reactive O2 radicals produced during normal cellular respiration and other biochemical pathways 7/9 - Ionising radiation = Gamma & X-rays - Ultraviolet rays (UV-C and -B) Chemicals in the environment - Damage Aromatic hydrocarbons, plant and microto DNA bial products, chemotherapy agents. Compartmentalisation = formation of Describe one way cells can become spespecific compartments with distinct funccialised ? tions within the Eukaryotic cells. What is the specialised feature of the Gut cells ? They have increased Golgi What is the specialised feature of the White blood cells ? They have increased lysosomes What is the specialised feature of the Muscle cells ? They have increased mitochondria - Hydrogen bonds forms between the carbonyl oxygen of one residue and the ±amino nitrogen four residues away. - H-bonds between atoms in the backDescribe Hydrogen bonding in the ±helix bone are approximately parallel to the of proteins ? helix axis of the ±- Amino acid side chains that point away from the backbone do not participate in hydrogen bonding within the ±helix. - The sugar phosphate backbone is not involved in hydrogen bonding Describe Hydrogen bonding in the dou- - 2 or 3 hydrogen bonds that are approxble helix of DNA ? imately perpendicular to the double helix axis are formed between complementary bases in opposite DNA strands. - Individual H-bonds in the ±helix are weak - the combined force of those bonds staWhat is the role of hydrogen bonding in bilise the ±helix structure stabilising ±helix of proteins ? - mainly in the hydrophobic core of the protein where water is excluded and cannot compete for H-bond. 8/9 - Main function of hydrogen bonding is to allow each DNA strand to act as a template for the other - hydrogen bonds between complemenWhat is the role of hydrogen bonding in tary base pairs help stabilise the double stabilising DNA ? helix However , stacking interactions between the base pairs in the hydrophobic interior contribute greater to helix stability. Explain the role of Helicases in DNA replication ? Catalyse the unwinding of DNA during replication. Explain the role of topoisomerase II (DNA gyrase) in DNA replication ? - Introduces negative coils into DNA ahead of the replication fork. - Negative supercoils compensate for the torsional strain caused by the unwinding of the helix - they cause for the separation of the parental strands at the replication fork. What happens during Semi-conserva- Each strand is a template for the synthetive replication ? sis of a complementary strand. What happens during Conservative replication ? Double stranded DNA is a template. What happens during Dispersive replica- Parental and daughter strands are comtion ? bined during replication. 9/9