Concept Check Exam 4 PDF

Property of the University of Cincinnati and Dr. LaSharon Mosley (you may not post this to online resources) BIOL1081 Authors: Dr. LaSharon Mosley, Martin Ogbebor, & Chloe Bower Concept Check Exam 4 Sex chromosomes - XX/XY - Found in most mammals and so...

Property of the University of Cincinnati and Dr. LaSharon Mosley (you may not post this to online resources) BIOL1081 Authors: Dr. LaSharon Mosley, Martin Ogbebor, & Chloe Bower Concept Check Exam 4 Sex chromosomes - XX/XY - Found in most mammals and some insects - XX individuals possess a female phenotype - XY individuals possess a male phenotype - Males only possess one X chromosome, they are referred to as hemizygous (hemi = half) - The sex-determining region of the Y chromosome (SRY region) is what causes sex differentiation into a male phenotype - ZZ/ZW - Found in birds and some fish - ZZ individuals possess a male phenotype - ZW individuals possess A female phenotype - Females only possess one Z chromosome, they are referred to as hemizygous o - XX/X0 - Found in almost all arachnids and many insects - XX individuals possess a female phenotype - X0 individuals possess a male phenotype - The “0” in X0 refers to that males possess only one X chromosome, and no other sex chromosomes - Haplodiploidy - Found in all bees, ants, and wasps as well as some other insects - Diploid individuals (arising from fertilized eggs) possess a female phenotype - Haploid individuals (arising from unfertilized eggs) possess a male phenotype  - Almost all individuals in these species are female, with males only transiently existing during reproductive seasons Sex linkage - Sex-linked traits are typically traits that are coded for by genes on the X chromosome - Different inheritance patterns to autosomal traits - Males possess a single X chromosome, and will express any traits found on it regardless of if it is dominant or recessive - Males are more vulnerable to conditions caused by sex linked genes - Example: color blindness - Most forms of colorblindness are linked to genes found on the X chromosome - Colorblindness is a recessive trait - Many colorblind individuals are male because males possess only one X chromosome - Females can be colorblind, but it is uncommon - Males can only pass their chromosome their female offspring and their Y chromosome to their male offspring - Females pass on either of their X chromosomes to their male and female offspring Gene Linkage & Mapping - Using the recombination frequency of linked genes to determine the distance of their loci from each other on a chromosome DNA Structure - Structure: - Phosphodiester bonds link nucleotides (monomer) together to form nucleic acids (DNA & RNA) - 3’ hydroxyl group - 5’ phosphate group - Nucleotides: - 5 Carbon Sugar (hexose): - DNA: Deoxyribose - RNA: Ribose  - Phosphate group - Nitrogenous Base: - Purines: A & G - Pyrimidines: T, U & C - DNA: - A forms 2 hydrogen bonds with T - C forms 3 hydrogen bonds with G - RNA: - Uracil is ONLY in RNA DNA Replication - Location: - Nucleus - When: - S Phase of the cell cycle - Proteins & Enzymes: - Helicase: - Unwinds DNA double helix at the replication fork - Single Stranded Binding Proteins: - Prevents separated strands of DNA from coming back together again - *NOT ENZYME* - Topoisomerase/ DNA Gyrase: - Relaxes DNA double helix from the tension & supercoiling - Primase: - Places RNA primers at the origin of replication, initiating DNA replication - DNA Polymerase III: - Builds new DNA strand by adding nucleotides in 5’ → 3’ direction - Proofreading /error correcting 3’ → 5’ - DNA Polymerase I: - 5’ → 3’ - Removes RNA primer laid by primase & adds complementary DNA nucleotide - DNA Ligase: - Re-anneals semi-conservative strands & joins Okazaki fragments on the lagging strand - Telomerase: - Synthesizes telomeres - Ensures the chromosome does not shorten - Telomeres have their own RNA primers Gene Expression, Transcription, & mRNA Processing - Gene Expression: - Gene: segment of DNA that contains the code for a specific protein - Central Dogma of Biology: - DNA → RNA → Protein - DNA → DNA: DNA Replication - DNA → RNA: Transcription - RNA → Protein: Translation - Transcription: - Location: - Prokaryotes: cytoplasm - Eukaryotes: nucleus - End-product: - Produces mRNA which is a copy of the non-template strand of DNA & replaces the thymines with uracil - Three steps: - Initiation: - RNA Polymerase binds to the promoter region (A-T-A-T rich) on the DNA strand - Elongation: - RNA Polymerase elongates the new strand of DNA - Synthesizes the new mRNA strand in the 3’ → 5’ direction & reads the template in the 5’ → 3’ direction - Termination: - When the RNA Polymerase reaches the terminator region (A rich) of the DNA, it falls off the strand - mRNA Processing: - Mainly occurs in Eukaryotes due to Prokaryotes not having introns - Introns: - Non-coding regions of mRNA that are spliced out during mRNA processing - They do not contribute to the coding sequence of the protein but are involved in the regulation of gene expression and can contain regulatory elements  - Exons: - Contains the coding regions of mRNA - These sequences will ultimately determine the sequence of amino acids in the protein during translation - Splicing: - Splicing removes introns from the mRNA transcript and joins the exons together - This ensures that the mature mRNA contains only the coding regions (exons) that will be used to synthesize a protein - Alternative Splicing: - Alternative splicing is a process where different combinations of exons are included in the mature mRNA transcript - This increases the diversity of proteins that can be generated from a single gene - Stabilizing Modifications: - 5’ cap: - Helps protect the mRNA from degradation and assists in ribosome binding for translation - 3’ poly-A tail: - Helps stabilize the mRNA and facilitates its export from the nucleus to the cytoplasm tRNA Charging & Translation - tRNA Charging: - The enzyme aminoacyl-tRNA synthetase binds tRNAs to their corresponding amino acid - This process uses energy: ATP - When the tRNA has been matched to its corresponding amino acid, it is referred to as charged - Translation: - Location: - Prokaryotes: cytoplasm - Eukaryotes: cytoplasm & rough ER - End-product: - Polypeptide which usually has to be folded into a functional protein (folding of the protein is usually facilitated by chaperone proteins) - Ribosomes:  - Carry out the process of translation and can also be referred to as ribozymes - Three Steps: - Initiation: - Does not require energy - Ribosome starts at the start codon (AUG) which is located at the 5’ end of the mRNA strand - The start codon, AUG, codes for the amino acid methionine (Met) - The tRNA that contains the anticodon for the start codon will enter the ribosome at the P site - Elongation: - Requires energy: GTP - The tRNA’s have complimentary anticodons to the codons - The tRNA’s then bring in the amino acids that are specified by the codons in the mRNA transcript - Termination: - Requires energy: GTP - When the ribosomes detect the stop codon (located towards the 3’ end), the ribosomes fall off the mRNA transcript - Stop codons: - 3 possible stop codons: - UAA - UGA - UAG - There are 64 possible codons, but only 61 of them code for amino acids since three of them are stop codons which do not code for any amino acid Mutations & DNA Repair - Mutations - What are mutations? ○ - How do they occur? - They can occur spontaneously (during or after DNA replication) or due to environmental factors. - The effects of mutations vary - Mutations in introns have little effects. - Types of mutations:  - Point Mutations - Silent - Mutation does not change the amino acid coded for by the codon. - Missense - Mutations code for a different amino acid than the original sequence. - Nonsense - Mutation converts codon to a stop codon. - Prematurely terminates translation. - Leads to severe polypeptide truncation (shortening). - Protein no longer can accomplish its job. - Frameshift - Deletion or addition of a base pair. - Causes a shift in the reading frame of a sequence - Chromosomal mutations - Deletion - Inversion - Translocation - Duplication DNA repair - Mutagen - An agent that causes mutations - What are some examples of mutagens? - DNA Polymerase III - Has regular 5’ to 3’ ability. - Also has proofreading ability and can act and a 3’ to 5’ exonuclease. - Considered an exonuclease since it can only cause repairs at the ends of DNA strands. - DNA Polymerase III acts to ensure that the recently attached nucleotide was added correctly. - If DNA polymerase does not notice its mistake, it is incapable of fixing it later on. - DNA Polymerase II - Repairs errors within strands of DNA.  - Can fix the mistakes that DNA Polymerase III did not notice, or mutations that occurred due to spontaneous mutations that happened after DNA mutations. - Is said to have endonuclease since it can enter strands of previously existing DNA and start repairs. - Excision Repair - Cuts out Damaged DNA and synthesizes new DNA in it’s place Regulation of Gene Expression - Regulation in Prokaryotes - Negative regulation: when a repressor binds, gene expression is inhibited - Positive regulation: when an activator binds, gene expression is promoted ○ Example: CAP - Inducible system: normally off, but can be turned on in the presence of an inducer ○ Example: Allolactose is an inducer of the lac operon - Repressible system: normally on, but can be turned off in the presence of a repressor/co- repressor ○ Example: tryptophan is a co-repressor of the trp repressor - Lac operon - Negatively and positively regulated - Inducible system - The lac operon contains genes associated with lactose degradation (used for energy) - The lac repressor is normally bound to the operator - When lactose is introduced to the cell, it can be converted to allolactose - Allolactose inactivates the lac repressor and acts as an inducer by allowing transcription of the lac genes to occur - However, this only accomplishes a basal level of transcription - CAP is required to be bound to the CAP binding site in order for transcription of the lac genes to occur at its maximal rate, meaning that CAP functions as an activator - CAP requires cAMP in order to be active - cAMP levels are high in the cell when glucose levels are low  - Conversely, cAMP levels are low when glucose levels are high - Therefore, CAP will not be active in the presence of glucose - CAP will only be active if there are low levels of glucose - Thus, the lac operon will only operate at its maximal rate if lactose is present and glucose levels are low - Trp operon - Negatively regulated - Repressible system - The trp operon contains genes associated with tryptophan synthesis - The trp repressor is NOT usually bound to the operator - the trp operon is normally on - Which means RNA polymerase can bind to the promoter and pass through the operator freely - For the trp repressor to be active, it must bind to its corepressor - The corepressor is tryptophan! - Thus, as the trp operon produces more tryptophan, more of the repressor molecules will begin to activate - Once the trp repressor binds to tryptophan, it will bind to the operator and prevent RNA polymerase from passing through and preventing the genes just beyond the operator from being transcribed - Regulation in Eukaryotes - Primarily controlled by transcription factors - Eukaryotes require the assembly of a transcription pre-initiation complex - General / basal transcription factors facilitate the binding of RNA polymerase at the promoter of a gene - Eukaryotic promoters often have a TATA box - What is the TATA Box? - An activator is transcription factor that binds to enhancer regions of DNA in order to increase the rate of transcription - Certain repressors bind to silencing regions of DNA to decrease transcription - Transcription factors are DNA-binding proteins, though not all DNA-binding proteins are transcription factors - DNA-binding proteins utilize a variety of structural motifs in order to interact with DNA - Helix-turn-helix - Often associated with repressors - Helix-loop-helix - Often associated with activators