DNA
State two reasons why gene expression must be regulated
(often proteins) they use the information of the gene to make a product. - To produce the right amount of protein/the proper proteins for the correct cell function in different areas (since every cell has the same DNA). - So that excess or unused proteins do not build up in the cell. - All cells have the same DNA, so gene expression must be regulated to allow for cell differentiation to perform different functions in different parts of the body in eukaryotic organisms.
Common Misconceptions about Alleles
- Recessive alleles are less frequent in the population. - Only recessive alleles cause disease. These statements are NOT true. They are misconceptions because people think that they are true.
Examples of Alleles
- gene for chloride ion channel protein - gene for Huntington Disease - gene for sickle cell disease - gene for blood type protein
Outline five functions of noncoding DNA sequences found in genomes, one of which must be the telomere
1) The telomere is at the end of the chromosomes that helps protect it, such as against chromosomal deterioration during replication. 2) Regulates where, when, and how many proteins are made. .3) Provides the code to make RNA, but NOT protein. .4) Might be left-over DNA from viral infections. 5) "Junk DNA" that we don't know the function of yet. Regions of DNA that do not code for protein include areas that act as regulators of gene expression, introns, telomeres, and genes that code for transfer ribonucleic acids (tRNAs). Another possible 5: 1. The promoter in the transcription process is a prime example of non-coding section of DNA with a function. 2. Prokaryotic mRNA does not requires processing because no introns are present. 3. Methylation may regulate the expression of either the maternal or paternal form (allele) of a gene the methyl group appears to cause a section of DNA to wrap more tightly around histone, thus preventing transcription of that allele. 4. Temoere is a region of repetitive DNA sequences at the end of a chromosome that protects the ends of chromosomes. 5. Environmental factors can stimulate release of certain hormones that can cause methylation.
Levels of Regulation of Eukaryotic Gene Expression
1. Chromosome Regulation 2. Transcriptional Regulation 3. Post-transcriptional Regulation 4. Translational Regulation 5. Post-translational Regulation
List five example species for which the entire genome has been sequenced.
1. Rice - Oryza sativa 2. Yeast - Saccharomyces cerevisiae 3. Fruit fly - Drosophila melanogaster 4. Human - Homo sapiens 5. Virus - T2 Phage 6. Bacteria - Escherichia coli 7. Japanese Alpine mountain flower - Paris japonica
List two examples of genes with multiple alleles.
1. The ABO blood type is controlled by a single "Isoagglutinogen" that has three versions/alleles: IA - codes for antigen type A IB - codes for antigen type B i - codes for no antigen; the i allele is missing a single G nucleotide in the gene sequence, which results in a stop codon early in the translation code. 2. The pea color trait studied by Mendel is controlled "by a single gene SGR, stay green gene" that has two versions/alleles: Y "yellow" - codes for a protein whose job is to turn on a set of chlorophyll destroying genes, turning peas from green to yellow y "green" - codes for a defective SGR protein which can't activate the chlorophyll destroying genes, so peas stay green
Gene to Product Overview Steps
1. Uncoiling or coiling of DNA from the nucleosome; chromosome regulation. 2. Proteins binding specific sequences in DNA; transcriptional regulation.
Frameshift
A frameshift mutation shifts the grouping of the 3 bases that code for 1 amino acid. The resulting protein is usually nonfunctional. The reading frame has moved after the insertion or deletion of a base so all amino acids after the base can be wrong.
Spontaneous Mutations
A mutation that arises naturally and not as a result of exposure to mutagens. Occur due to errors in DNA replication.
Regulation of Gene Expression by Proteins
A promoter is a sequence of base pairs located near a gene that onto which RNA polymerase binds. It does not code for a protein but plays a role in protein synthesis by initiating transcription. Proteins can attach to the DNA near the promoter to make the DNA more or less accessible for DNA polymerase.
Use a computer software tool ti create an alignment of the gene sequences between different species.
A sequence is a way of arranging DNA sequences so that similarities and differences between the sequences can be identified. Example: Human - ATCCGATTGCAT Mouse - TTCCCA-TGGAT Rat - TTCCCA-TGGAA Any of the same base pairs in the same spots are homologous sequences. The dashes are indels. Any dissimilar base pairs are SNPs (Single Nucleotide Polymorphisms).
Gene
A sequence of DNA nucleotides that codes for an RNA or protein that in turn influences a trait/characteristic. A heritable factor that consists of a length of DNA and influences a specific characteristic. Sequence of DNA nucleotides that codes for a functional RNA or protein product. Also referred to as a trait. The basic functional unit of inheritance. Vary in size from a few hundred to a couple million base pairs
Allele
A version/variation of a gene. One of the variety of different forms of a single gene. The various specific forms of a gene. Alleles are alternative versions of the same gene and therefore occupy the same locus on the chromosome. Only one allele can occupy the locus of the gene on a chromosome.
Insertion
Adding a nucleotide (or more) of DNA.
Genome
All of the DNA found in within the organism.
State the difference between alleles of the same gene.
Alleles are different from each other in the sequence of nucleotides. They can vary by just one base (ex: A->T), called a single nucleotide polymorphism OR by an insertion or deletion. Alleles differ from each other by one or only a few bases. Differ by one to a few base pairs. A difference in a base between two genes is called a single nucleotide polymorphism (SNP)- pronounced "snip". Several SNP's can be present in one gene.
State a similarity between alleles of the same gene
Alleles of the same gene: - found at the same locus on a chromosome - have mostly the same nucleotide sequence; slight differences in sequences due to mutations are what causes alleles - code for the same type of protein, although, may have different functionality - Because they are the same gene, they code for the same type of protein with the same role in the cell - They occupy the same locus on homologous (similar) chromosomes. - The majority of the sequence remains the same between alleles.
Determine a DNA sequence from an electropherogram.
An electropherogram is the result of automated DNA sequencing. Well-defined, colored peaks are read from left to right to determine base order.
Nonsense
Base substitution that results in a shortened polypeptide that may function improperly or not at all. Protein production ends early due to a stop codon.
Silent
Base substitution that results in no change of the amino acid when the altered messenger RNA (mRNA) is translated. While the DNA or mRNA has changed, the amino acid sequence has not.
Missense
Base substitution that results in the replacement of one amino acid for another in the protein made by the gene. The resulting protein will have altered structure and function. One amino acid in the protein is changed to another.
Define bioinformatics
Bioinformatics is the use of computer technology in the gathering, storage, and analysis of biological information.
Define "coding sequences" of DNA
Coding Sequences are the sequences that code for a certain protein that is expressed in the organism. Single copy genes that have coding functions base sequences essential to produce proteins at the cell ribosomes coding fragments make up exons, and white non-coding fragments make up introns.
Exons
Coding regions of DNA. Usually shorter. Makes up about 2% of DNA.
Outline why computers are necessary for genome analysis.
Computers allow for data storage, rapid analysis and more accurate comparison of genome data. Developments in scientific research follow improvements in computing...the use of computers has enabled scientists to make advances in bioinformatics applications such as locating genes within genomes and identifying conserved sequences.
Gene for Chloride Ion Channel Protein
Cystic fibrosis is controlled by a single gene (the CFTR gene). The gene is located on the 7th chromosome (locus 7q31.2). The CFTR gene codes for a chloride ion channel. F allele: Dominant, Codes for functioning channel f allele(s): Recessive, Any mutant allele* that gives rise to a defective CFTR protein. *Well over a hundred different mutations of five major types have been found in the population. Any one of these mutations results in the synthesis of a defective CFTR protein.
Explain why cytochrome oxidase 1 is often used to assess the differences in the base sequences of a gene between two species.
Cytochrome oxidase 1 (cox1) is used to compare gene sequences between species because: - the gene is present in the majority of eukaryotic species - the gene has been sequenced for many species and is therefore accessible from genome databases
Protein Synthesis
DNA (Genotype) →(Transcription) RNA → (Translation) Polypeptide (Chain of Amino Acids) → (Folding) Protein (3D functional molecule) → Metabolism (Chemical Reactions of Cell) → Trait (Phenotype)
Gene Expression Process
DNA (genotype) -> Transcription -> mRNA -> Translation -> Polypeptide (Chain of amino acids) -> Protein folding -> Protein (3D functional molecule) -> Metabolism (chemical reactions of cell) -> trait (phenotype). In the nucleus DNA goes through transcription to create pre-mRNA. This is exported out of the nucleus and matures to become mRNA. It then goes through translation to form a polypeptide, which is a chain of amino acids. Ribosomes are also attatched to the polypeptide. The polypeptide folds into a specific shape to become a protein.
Where is DNA found outside the nucleus? Describe this DNA and what it proves.
DNA is found in the mitochondria. This DNA is circular and naked, which is evidence of the Theory of Endosymbiosis.
Why does replication stop with dideoxynucleotides?
DNA polymerase III can perform the condensation reaction between -OH of deoxyribose and the phosphate group. Without the -OH on the dideoxynucleotide, DNA polymerase III can not connect the next nucleotide.
Repressor Proteins
Decrease gene expression. Normally produced and will bind to the operator preventing transcription.
Method of the Human Genome Project
Dr. Fred Sanger developed the most commonly used sequencing technique, called chain termination sequencing, in 1977. The main ingredients in a sequencing reaction and their uses include: - DNA template strand, initial strand to be copied backwards - primer, hydroxyl groups for detection - deoxynucleotides, to build the other strand - DNA polymerase, to add the deoxynucleotides - Dideoxynucleotides, to terminate synthesis The strands must be initially heated to break hydrogen bonds and separate the strands. Once the temperature is lowered, the primers anneal. When a dideoxynucleotide is added to the strand, the strand ends because it can't continue 5'-3' building because no hydroxyl group, chain terminating nucleotides. DNA fragments are separated via polycrylamide gel electrophoresis. The DNA sequence is read smallest fragment to longest fragment, bottom to top. This is the COMPLEMENTARY strand; it must be converted using base pair rules to get the original.
Methylation and Acetylation Processes
During supercoiling, while the DNA is still double stranded, a methyl group binds only to cytosine. Then, whilst nucleosomes are in groups, because of the methyl group, the methyl group (an epigenetic factor) causes DNA to be inaccessible and the gene is inactive. Then, the nucleosomes are not grouped and appear as beads on a string. The DNA becomes accessible because it is demethylized and the gene is active. Acetylation (an epigenetic factor) allows for it to be less winded and it binds to a histone tail. Supercoiling continues and histones coil into chromatin that coils into chromosomes.
Outline the role of enhancer, silencers, and promoter-proximal elements in regulation of gene expression.
Enhancers: are DNA codes that increases gene expression. Silencers: are DNA codes that decreases gene expression. Promoter-proximal elements: are any regulatory sequence in the DNA (enhancers, silencers etc).
Alleles in Eukaryotes
Eukaryotes have at least two copies of each chromosome, therefore individuals have two alleles that can be the same or different.
Supercoiling (Nucleosomes)
Eukaryotic DNA is associated with proteins called histones. The DNA is wrapped around a core of 8 histone molecules which is known as a nucleosome. Nucleosomes are then compacted in chromatin form. Chemical modifications of histone tails through acetyl/methyl groups.
Identical Twins
Have the same exact DNA sequence (except mutations). Different genes are expressed because different environmental conditions over their lifespan impacts epigenetics.
Outline the effect of acetylation of nucleosome tails on rates of gene expression.
Histone acetylation results in loose packing of nucelosome. Transcription factors can bind the DNA and genes are expressed. Interferes with the positive charge of nucleosomes and turns on genes. Before transcription in eukaryotes, the DNA has to uncoil from the nucleosome. When the DNA uncoils, the gene can be turned "on".
Outline two examples of environmental influence on gene expression.
Histone modifications can accumulate and change over the lifespan based on environmental conditions. These include: nutrition, stress, toxicants, pathogens, etc. These conditions cause environmental cues, which cause the actions of the epigenome which then affects gene expression of the genes in the genome. This leads to regulation of genes differing, and the phenotype changes. In some rare cases, it can be inherited by offspring. For example: a woman who smokes while pregnant induces epigenetic changes in three generations at once: in herself, her unborn daughter, and her daughter's reproductive cells. They are usually removed during DNA reprogramming during embryonic development. Another example is the idea that licking of the pup by the mother causes a release of adrenaline and noradrenaline in the pup. Thyroid hormones released then enter the brain and cause specific neurochemical signals to turn on, one of which being seratonin. Rat pups that had been licked a lot as kids had more proteins that activate maternal behavior. Certain genes code for proteins through transcription (DNA to RNA) and translation (RNA to polypeptide, then folded into a protein). Seratonin is released onto the brain cells in the hippocampus. Another example is that a boy's (of age 9-12) starvation would cause his children and grandchildren to have less incidence of heart disease, with the grandchildren have ¼ less incidence of it. They also saw that the grandchildren were less prone to diabetes, lived longer lives (roughly 30 years longer). It is believed that the starving children released a chemical that reached the DNA in their sperm, that performed a methylation process.
Describe the relationship between the number of genes in a species and the complexity in structure, physiology, and behavior.
In general, eukaryotes have more genes than prokaryotes. However, within plants and animals there is little correlation between complexity and the number of genes.
Outline the effect of methylation of nucleosome tails on rates of gene expression.
Methylation of DNA and histones cause nucleosomes to pack tightly together. Transcription factors cannot bind the DNA, and genes are not expressed. Before transcription in eukaryotes, the DNA has to uncoil from the nucleosome. By remaining coiled in a nucleosome, the gene is turned "off".
State the effect of DNA methylation on gene expression.
Methylation of histone results in inhibition of transcription. It covers sections of DNA and keeps the DNA tightly coiled and inaccessible; gene inactive.
Epigenetics
Modifications to the DNA, or histone protein, via acetylation and methylation that affects gene expression without changing the DNA nucleotide sequence.
Search NCBI or OMIM for a given gene.
NCBI, National Center for Biotechnology Information) and IMIM (Online Mendelian Inheritance in Man) are comprehensive databases of human gene sequences and information. A user can type in a sequence of DNA nucleotides and search for known genes with matching sequences. Use of databases to identify the focus of a human gene and its polypeptide product.
Formation of Alleles
New alleles are formed by mutations, which are changes to the base pair sequence of the organism's genetic code. Ex: Insertion, Substitution, Deletion
Formation of new alleles through mutation
New alleles form through MUTATION:Because so many diseases are associated with mutations, it is common for mutations to have a negative connotation. However, while many mutations are indeed deleterious, others are "silenf', that is, they have no discernible effect on the phenotype of an individual. In addition, some mutations are actually beneficial. For example, the very same mutation that causes sickle-cell anemia in affected individuals (i.e., those people who have inherited two mutant copies of the beta globin gene) can confer a survival advantage to unaffected carriers (i.e., those people who have inherited one mutant copy and one normal copy of the gene, and who generally do not show symptoms of the disease) when these people are challenged with the malaria pathogen. As a result, the sickle-cell mutation persists in populations where malaria is endemic.Beyond the individual level, perhaps the most dramatic effect of mutation relates to its role in evolution; indeed, without mutation, evolution would not be possible. This is because mutations provide the "raw material" upon which the mechanisms of natural selection can act. By way of this process, those mutations that fumish individual organisms with characteristics better adapted to changing environmental conditions are passed on to offspring at an increased rate, thereby influencing the future of the species.
State the source of new alleles of a gene.
New alleles, or versions, of a gene are formed through mutation, or changes, in the DNA sequence of the gene.
Introns
Noncoding segments of DNA. Usually longer. Makes up about 98% of DNA. Switches that turn on and off the exons, tell mRNA how to splice, etc.
Substitution
One base is replaced by a different base.
Epigenome
Overall pattern of chromatin modifications possessed by each individual organism. The study of all the epigenetic modifications (chemical tags) that is involved in telling the genome what to do (epigenome). Epigenome is a layer on top of the genes/a second channel of heredity. Epigenetics is modifications to the DNA, or histone protein, via acetylation and methylation that affects gene expression without changing the DNA nucleotide sequence. The epigenome is able to change based upon your experiences, unlike the genome which a only changes due to mutations.
Gene Expression in Prokaryotes
Prokaryotes have naked DNA, no histones and no nucleosomes, so they are unable to control gene expression in this way.
Transcription Factors (activators)
Protein binds to the enhancer sequence to increase rate of transcription. Increases gene expression.
Uncoiling or Coiling of DNA from the nucleosome
Remember, prokaryotes have naked DNA (no histones, no nucleosomes), so they are unable to control gene expression in this way. Before transcription begins in eukaryotes, the DNA has to uncoil from the nucleosome. If the DNA is not uncoiled from the histone proteins, the enzyme required for transcription cannot get close enough to the DNA to attach. In other words, by remaining coiled in a nucleosome the gene is turned "off". When the DNA uncoils, the gene can be turned "on".
Deletion
Removing a nucleotide (or more) of DNA.
Define "repetitive sequences" of DNA
Repetitive Sequences (non-protein coding) are the sequences which does not code for a protein but is repeated over and over in the genome, they're also known as "tandem repeats." DNA sequences composed of 5-300 base pairs per repetitive sequence. Sometimes referred to as satellite DNA when clustered discretely. Generally, they are dispersed regions of DNA that do not have any coding functions. They are transposable elements, meaning they can move from one genome location to another.
Define sequence in relation to genes and/or genomes.
Sequence (noun) - the order of the nitrogenous bases in a gene or genome. Ex: The sequence of the gene is ATCCGTA. Sequence (verb) - the process of determining the order of the nitrogenous bases in a gene or genome. Ex: To sequence the gene, use dideoxynucleotides.
Outline the information that can be determined given gene sequence alignment data.
Sequence alignment data can be used to measure evolutionary relationships between species. The more similar two sequences, the more closely related two species.
Silencer Sequence
Sequence on the DNA that decreases the rate of transcription when proteins bind to them. Decreases gene expression.
Enhancer Sequences
Sequence on the DNA that increases the rate of transcription when proteins bind to them.
Components of Transcriptional Regulation
Sequences of DNA regulating expression of a nearby gene include enhancer sequences and silencer sequences. Proteins attach to DNA near a gene to make the DNA more or less accessible for transcription include transcription factors (activators) and repressor proteins.
Gene for Sickle Cell Disease
Sickle cell disease is caused by a mutation in the hemoglobin-Beta gene (the HbBgene) The gene is located on the 11th chromosome (locus 11p15.5). The Hb gene provides instructions for making a protein called hemoglobin. The function of this hemoglobin is to transport oxygen in the blood. Hb^N allele: Codes for functioning hemoglobin. Hb^S allele: Gives rise to a defective hemoglobin protein can lead to sickle cell disease.
Causes of a Mutation
Spontaneous, Physical, Chemical, Biological
Mutation Type(s) : Affect on the Gene Expression
Substitution : nonsense, silent, missense Insertion or Deletion : Frameshift
Describe a base substitution mutation.
Substitution mutations replace one base with another. The new allele that results from the mutation might: - missense: cause a small change in the protein produced by the gene - silent: have no effect on the protein produced by the gene - nonsense: cause an incomplete, non-functioning protein to form
Chromosome
Supercoiled DNA and associated structural proteins. Molecules of DNA wrapped around protein where genes are located. There are relatively few of these in each cell, but thousands of genes... therefore we can deduce that each chromosome carries many genes.
Gene for Blood Type Protein
The ABO blood type is controlled by a single gene (the isoagglutinogen gene, the "I" gene) The gene is located on the 9th chromosome (locus 9q34). The I gene has three alleles: - I^A (dominant - codes for type A cell surface proteins) - I^B (dominant - codes for type B cell surface proteins) - i (recessive - codes for no cell surface protein)
Locations of Mutations
The DNA in any cell can be altered through environmental exposure to certain chemicals, ultraviolet radiation, other genetic insults, or even errors that occur during the process of replication. If a mutation occurs in a germ-line cell (one that will give rise to gametes, i.e., egg or sperm cells), then this mutation can be passed to an organism's offspring. This means that every cell in the developing embryo will carry the mutation. As opposed to germ-line mutations, somatic mutations occur in cells found elsewhere in an organism's body. Such mutations are passed to daughter cells during the process of mitosis, but they are not passed to offspring conceived via sexual reproduction.
Outline the parts of the Genome
The Genome is all of the DNA. It splits into the coding regions, about 2% of DNA, and noncoding regions, about 98% of DNA. Coding regions show as genes to make a protein product. Noncoding regions include repetitive DNA consisting of interspersed and tandem repeats, as well as introns, regulators (silencers, enhancers, promoters), etc.
Gene for Huntington Disease
The HTT gene codes for a protein called Huntingtin. The function on the Huntingtin protein is unknown, however it appears to play an important role in brain neurons and is essential for normal development before birth. If it is mutated the person will develop Huntington Disease. Huntington disease is a progressive brain disorder that causes uncontrolled movements, emotional problems, and loss of thinking ability (cognition). Huntington disease usually appears in a person's thirties or forties. H allele: Dominant, Codes for mutated protein, Has 37+ repeats of CAG-CAG-CAG nucleotides. h allele: Recessive, Codes for functional protein, Has 10-26 repeats of CAG-CAG-CAG nucleotides.
Outline outcomes of the Human Genome Project.
The Human Genome Project met the stated goals of determining the sequence of base pairs and locations of genes and also identified approximately 3 million human genetic variations (SNPs...Single Nucleotide Polymorphisms), developed new technologies to study genomes and lead the genetic sequencing of model organism genomes, mice and rats.
Use NCBI to BLAST search for COX1 sequences for different species.
The National Center for Biotechnology Information allows use of the 'BLAST' tool; Basic Local Alignment Search Tool. The tool allows people to search for gene or protein sequences in the NCBI databases.
Genome
The complete set of genes and genetic material present in a cell or organism. The whole of the genetic information of an organism. This includes the entire base sequence of each DNA molecule (aka: chromosome). All of the DNA in the organism/cell. Nuclear DNA Spread across chromosomes (in human, 46 total; 23 pairs) Includes sequences of nucleotides that are: Genes Regulatory (turn on-off genes) Non-coding (introns) Repetitive (tandem repeats) Mitochondrial DNA Chloroplast DNA (in plants & algae)
Human Genome Base pairs #, chromosome #, and gene #
The human genome is about 3.2 billion base pairs long spread among 23 pairs of chromosomes, so there are 46 total chromosomes in each somatic cell. Roughly 23,000 genes.
State the size in base pairs of the human genome.
The human genome is composed of about 3.2 billion base pairs within the 23 chromosome pairs and mitochondrial DNA.
Outline the technological improvements that have sped the DNA sequencing process.
The largest technological advancement in gene sequencing was the automatization of the process with computer tools. What used to take humans hours or days can now be done by a computer in minutes. For example, in DNA sequencing a computer is able to deduce the base sequence by reading the fluorescent markers indicating the type of nitrogenous base. Developments in scientific research follow improvements in technology-gene sequencers are used for the sequencing of genes.
Gene Locus
The location of a gene on a chromosome. Each chromosome carries many genes. A gene occupies a specific position on a chromosome. EXAMPLE: 7.q.31.2 Chromosome 7 Q arm Region 3 Band 1 Subband 2 *bands ARE NOT genes p = shorter segment, above centromere q = longer segment, below centromere
State the aim of the Human Genome Project.
The main aims of the Human Genome Project were to determine the sequence of the approximately 3.2 billion base pairs and identify the location of the approximately 20,000 to 25,000 genes. The entire base sequence of human genes was sequenced in the Human Genome Project. - identify all the approximately 20,500 genes in human DNA - determine the sequence of the 3 billion base pairs in human cells - store this information in a database - improve the tools for data analysis - transfer related technologies to the private sector - address the ethical, legal, and societal issues that may arise from the project - spent $3 billion on this project
Decribe the use of twin studies to measure the impact of environment on gene expression.
The nature - nurture debate is centered on the extent to which a particular human behavior or phenotype should be attributed to the environment or to genetics/heredity. Much effort has gone into twin studies especially when twins have been raised apart, and thus in different environments. 3 year old twins will have more similar DNA bands than 50 year old twins. Specifically, a study was done on two identical twin rats. One rat, however, was yellow and obese while one was brown and thin. This is believed to be because of methylation of the Agouti gene in the brown rat, while the yellow rat did not experience this methylation This is believed to be because of the epigenome, which scientists believe that can be affected by the experiences of the rat that results in releases of different hormones which can cause methylation. Environmental conditions impact methylation and acetylation. Interacts with DNA in the epigenome. Impacts which proteins are made. Alters metabolism behavior and physical characteristics.
Gene Expression
The process through which information from a gene is used to synthesize a protein. The combination of interactions of proteins that lead to the phenotype.
State the number of genes in the human genome.
There are an estimated 20,000-25,000 genes in the human genome.
Levels of Regulation of Eukaryotic Gene Expression Type: Chromosome Regulation Molecule Being Regulated: Vocab: Location: Defining Characteristic:
Type: Chromosome Regulation Molecule Being Regulated: DNA Vocab: Histones, methylation, acetylation, epigenetics Location: nucleus Defining Characteristic: 1st line of regulation
Levels of Regulation of Eukaryotic Gene Expression Type: Post-transcriptional Regulation Molecule Being Regulated: Vocab: Location: Defining Characteristic:
Type: Post-transcriptional Regulation Molecule Being Regulated: mRNA Vocab: pre-mRNA, exons, introns, alternative splicing, spliceosome Location: nucleus Defining Characteristic: Reason why humans have 23,000 genes but millions of proteins.
Levels of Regulation of Eukaryotic Gene Expression Type: Post-translational Regulation Molecule Being Regulated: Vocab: Location: Defining Characteristic:
Type: Post-translational Regulation Molecule Being Regulated: Protein Vocab: Ubiquitin, Proteosome, Protease Location: Cytoplasm Defining Characteristic: Occurs so excess or unused proteins don't build up in the cell.
Levels of Regulation of Eukaryotic Gene Expression Type: Transcriptional Regulation Molecule Being Regulated: Vocab: Location: Defining Characteristic:
Type: Transcriptional Regulation Molecule Being Regulated: DNA Vocab: activators, repressors, TATA box, hairpin loops, transcription factors Location: nucleus Defining Characteristic: Most crucial and widely used of all controls.
Levels of Regulation of Eukaryotic Gene Expression Type: Translational Regulation Molecule Being Regulated: Vocab: Location: Defining Characteristic:
Type: Translational Regulation Molecule Being Regulated: mRNA Vocab: 5' Guanine cap, Poly A tail (3'), RNA Binding Proteins Location: Nucleus and cytoplasm Defining Characteristic: Lifespan of mRNA regulates the amount of protein produced.
Outline the process of DNA sequencing, including the role of chain terminator nucleotides, fluorescence, and electrophoresis.
Use of nucleotides containing dideoxynucleic acid to stop DNA replication in preparation of samples for base sequencing. 1. Copies of the DNA sequence to be sequenced are placed into test tubes with raw materials for DNA replication including: DNA polymerase, primers, DNA nucleotides, and dideoxyribonucleotides which are DNA nucleotides without an -OH on carbon 3 and with a fluorescent marker on the base. 2. DNA Polymerase III begins to replicate the DNA sequence, adding free floating nucleotides complementary to the parent DNA strand. Replication will stop when by chance the polymerase adds a dideoxynucleotide. This results in many strands of newly replicated DNA with various lengths, all ending in fluorescently marked nucleotides. 3. The replicated DNA is run through electrophoresis, separated by size. 4. A laser fluoreses the marked nucleotide and a computer records the strength of the signal as a peak on an electropherogram.
Discuss the role of reprogramming and imprinting on epigenetic factors.
Usually in cell division, the methylation pattern is inherited to the daughter cell. When a sperm and an egg meet, the epigenome gets erased and goes through "reprogramming".Up to 1% of the epigenome is not erased thus yielding a result called "imprinting". Sperm and Oocyte are fertilized into a zygote that then goes through DNA demethylation (over 7 days there's a reduction in methyl groups, turs all cells into stem cells) and becomes a Blastocyst that then goes through de novo methylation and an Embryo/fetus is created when cells differentiate by adding back methyl groups to turn off the genes, then DNA methylation pattern maintenance takes place and it grows into an infant then an adult. DNA reprogramming adds and removes methyl groups and acetyl groups.
Hiroshima What? When? Effects?
What: The Hiroshima Bombing killed an estimated 90,000 to 120,000 people. The bomb that leveled Nagasaki 3 days later claimed another 60,000 to 70,000 lives. When: August 6, 1945 Effects: Death either instantaneously or over the following weeks and months from injuries or acute radiation sickness, the result of damage to bone marrow and the intestinal tract; (childhood) anemia, ulcers, asthma, brain tumors, thyroid growths, radiation associated cancers.
Chernobyl What? When? Effects?
What: The disaster at the Chernobyl nuclear power plant released 80 petabecquerel of radioactive caesium, strontium, plutonium and other radioactive isotopes into the atmosphere, polluting 200,000 km2 of land in Europe. During a test of the ability of the Chernobyl nuclear power plant to generate power while undergoing an unplanned shutdown, safety systems were turned off, leading to an explosion and nuclear fire that burned for ten days. One of the four nuclear reactors of the Chernobyl nuclear power plant exploded as a consequence of human errors owing to a temporary shutdown of the cooling system. The explosion transported vast amounts of radioactive material into the atmosphere, much of which was subsequently deposited not only in the immediate vicinity of the power plant in Ukraine, Russia, and Belarus, but also over large parts of Europe and other continents. When: April 26, 1986 Effects: chronic exposure to low-level radioactive contaminants, acute radiation sickness including dizziness, vomiting and fatigue; long-term physiological effects of immediate and later exposure have also shown changes in levels of antioxidants, immunity and hormones.
Determine the gene locus, abbreviated gene name, and description of the gene.
When you search for a gene in an online database, the results will include: - gene locus: 11p15.5 - gene name: INS (insulin) - description: codes for _______
Wildtype
Wildtype refers to the standard "normal" allele. The non-mutated version of the gene that codes for a functional protein.
Chemical Mutations
exposure to chemicals (i.e. heavy metal ions) that damage the DNA
Physical Mutations
exposure to radiation that damages the DNA
Developments in scientific research follow...
improvements in computing. The use of computers has enabled scientists to make advances in bioinformatics applications such as locating genes within genomes and identifying conserved sequences.
List types of Epigenetic Tags
methylation and acetylation
How is the human genome spit up?
nuclear genome and mitochondrial genome
Gene Expression
the process by which a gene creates a product
Biological Mutations
viruses that insert themselves into host DNA
