Genetics Exam 4

Order the sequence of events in epigenetic down-regulation of gene expression

1. acetylate the histone proteins and hypo-methylate the CpG islands 2. DNA chromatin loosens 3. genes are transcribed 4. genes are translated

How many amino acids are in the mature protein after processing?

326

How many genes have been identified in poplar?

41335

Environmental agents cause what percent of cancers:

50%

How many introns does HFE have?

6

What is the location of HFE1? Write in the format "chromosome, arm, band.sub band" (for example, 2a11.1)

6p22.2

library (genomic)

A collection of clones that contains all the DNA sequences of an organism's genome.

restriction mapping

A compilation of number, order, and distance between restriction sites along a DNA.

proto-oncogenes

A gene that functions to initiate, facilitate, or maintain cell growth and division. Proto-oncogenes can be converted to oncogenes by mutation.

oncogenes

A gene whose activity promotes uncontrolled proliferation in eukaryotic cells. Usually a mutant gene derived from a proto-oncogene.

tumor suppressor genes

A gene whose product functions to suppress unrestricted cell division, particularly of tumorous growth.

cancer

A group of genetic diseases caused by mutation of genes in somatic cells. Cancers show abnormal cell proliferation and metastasis.

probe

A macromolecule such as DNA or RNA that has been labeled and can be detected by an assay such as autoradiography or fluorescence microscopy. Probes are used to identify target molecules, genes, or gene products.

PCR

A method for amplifying DNA segments that depends on repeated cycles of denaturation, primers, and DNA polymerase-directed DNA synthesis.

ORFs

A nucleotide sequence organized as triplets that encodes the amino acid sequence of a polypeptide, including one initiation codon and one termination codon.

nonacute virus

A retrovirus that can induce activity of cellular proto-oncogenes

acute transforming virus

A retrovirus that carries a viral oncogene (picked up from a previous infection) and that can cause cancer.

genomic instability

A state observed in some cancer cells where the genome in abnormal and displays translocations, aneuploidy, chromosome loss, DNA amplification etc..

southern blot

A technique in which DNA fragments produced by restriction enzyme digestion are separated by electrophoresis and transferred by capillary action to a nylon or nitrocellulose membrane. Specific DNA fragments can be identified by hybridization to a complementary radioactively labeled nucleic acid probe using the technique of autoradiography. the technique was invented by Southern.

Evidence that cancer is clonal in origin includes:

A. all cancer cells in one patient have the same markers B. the original cancer and metastatic cancers in one patient have the same markers C. within a patient with a cancer caused by a translocation, all cancer cells will have the same translocation CorrectD. all of the above

Which of the following is a problem with gene therapy?

A. delivery of the gene B. avoiding changes to non-target genes C. appropriate expression of the gene CorrectD. All of the above.

which of the following about driver mutations is TRUE?

A. They allow the cancer cells to grow faster. B. They do not include passenger genes. C. They include mutations in tumor suppressor genes and oncogenes. CorrectD. All of the answers are true.

What else is known about the protein encoded by HFE?

A. Transmembrane protein CorrectB. All of these C. Regulates iron levels in the blood D. Glycoprotein

Which of the following are associated with cancers

A. genomic instability B. defects in DNA repair C. mutations in cell cycle control and cell cycle adhesion CorrectD. A, B and C

Products useful to humans can be put into and harvested from which of the following:

A. milk B. crops C. animals D. fruits CorrectE. all of the above

DNA microarray analysis

Also called DNA chips or Biochips; an ordered arrangement of DNA sequences or oligonucleotides on a substrate (often glass). Microarrays are used in quantitative assays of DNA-DNA or DNA-RNA binding to measure profiles of gene expression (for example, during development or to compare the differences in gene expression between normal and cancer cells).

domains

Amino acid sequences with specific shape and function that are structurally and functionally distinct from other regions on the same protein.

northern blot

An analytic technique in which RNA molecules are separated by electrophoresis and transferred by capillary action to a nylon or nitrocellulose membrane. Specific RNA molecules can then be identified by molecular hybridization to a labeled nucleic acid probe.

dna sequencing

An analytic technique in which the nucleotide sequence of a DNA molecule is determined.

Two dimensional gel electrophoresis (2DGE)

An analytical method for separating proteins; used in proteomics.

introns

An intervening sequence of DNA that lies between coding regions in a gene. Introns are transcribed but are spliced out of the RNA product and are not represented in the polypeptide encoded by the gene.

annotations

Analysis of genomic nucleotide sequence data to identify the protein-coding genes, the nonprotein-coding genes, and the regulatory sequences and function(s) of each gene.

whole genome sequencing

Can be done by whole genome shotgun sequencing or or map-based cloning to determine the DNA sequence of the entire genome; used in genomics.

transformation (cancerous)

Conversion to a condition of unregulated cell growth.

Please put the steps of RNA-seq in order.

CorrectA. Extract RNA and make cDNA from it. CorrectB. Shear ds cDNA and add adapters to the ends. CorrectC. Next generation sequencing (NGS) of the fragments. CorrectD. Map reads against the DNA sequence. CorrectE. Analyze amount of expression and splicing patterns

Know for the processes of replication, transcription and translation: enzyme, template, product, where it occurs in prokaryotes, where it occurs in eukaryotes; know genetic code is unambiguous, degenerate, non-overlapping, universal and what each of these mean;

DNA Replication: DNA synthesis; The process copies a double stranded DNA molecule to produce two identical DNA molecules. Template: DNA Product: DNA Enzyme: DNA polymerase(III) Prokaryotes: cytoplasm Eukaryotes: nucleus Transcription: RNA synthesis; information in a DNA strand is copied into a new RNA molecule. Template: DNA Product: mRNA, tRNA, rRNA Enzyme: RNA polymerase (makes RNA in the 5' PO4 to the 3' OH) Prokaryotes: cytoplasm Eukaryotes: nucleus Translation: Protein synthesis; process where a cell makes proteins using genetic information carried in mRNA. Template: mRNA Product: protein Enzyme: peptidyl transferase which is located within the ribosome. It works to bind amino acids together to make polypeptides. This occurs in elongation. Aminoacyl transferases are enzymes used to attach one amino acid to 3' end of tRNA. It is an accurate process that requires ATP. Prokaryotes: cytoplasm Eukaryotes: cytoplasm The genetic code includes 64 RNA triplets that display 20 amino acids. They also include start and stops for translation. The code is unambiguous which means each indicates each triplet only specifies one amino acid. The genetic code is also degenerate. This means more than one triplet can specify an amino acid. It is also non-overlapping which indicates a nucleotide will only identify one amino acid. The genetic code is universal as the code is applied to all living organisms.

vectors

DNA sequences into which genes of interest are cloned.

what actions can patients with hemochromatosis take in daily life to control iron levels?

Eat less food containing iron.

Eukaryote Genomes: know genome structure (linear chromosomes in nucleus, circular mt DNA and cp DNA) and origin (know origin from a common ancestor and endosymbiosis concept) and why we think the origins are what they are.Gene Expression in Eukaryotes: give evidence for regulation of gene expression in eukaryotes; what is the major point of control (regulation of transcription); know the five steps in regulation of gene expression (definitions); know definitions of: promotor, enhancer, silencer, transcription factors, alternative splicing, RNA silencing. Know the effect of methylation on gene expression (repression); know promoters, silencers, enhancers and operators are cis-acting; know repressors and transcription factors are trans-acting.

Eukaryote Genomes:In Eukaryote Genomes there are three specific genomes. They are Animal genomes, Plant genomes, and Fungal genomes. Eukaryotic genomes are confined within the nucleus. In animals genomes, they contain 39 chromsomes. They contain a cell membrane, a nucleus containing multiple linear chromsomes, and a mitchondria containing single double-standed circular chromosomes. In Plant genomes they contain a cell membrane and a cell wall with cellulose. Mitochondria containing single double-stranded circular chromosome. In addition plant genomes contains chloroplasts containing single double-stranded circular chromsomes. Plant genomes can be very large and flowering plants appear to have evolved by whole genome duplications. In fungal genomes they have a cell membrane and a cell wall with a chitin, and they contain a nucleus with multiple linear chromsomes. Like animal and plant genomes, fungal also has mitochondria containing single double-stranded circular chromosomes. The linear arrangement of the eukaryotic chromosome allows more DNA to be packed by tightly winding it around histones. More genetic material means that the organism can encode more information into a single cell. As we look into origins from a commmon ancestor, we can find that there are many similarities between genomes of nearly all species. Endosymbiosis involves one cell merge with another to produce, over time, a coevolved relationship in which neither cell could survive alone. All genomes is believed to have come from ancestral organism and share a common genetic code. Eukaryotes arose from prokaryotes by "invading" and endosymbosis. As a result cpDNA and mtDNA all have the same size and genomes as the bacterial chromosomes. The origin of genomes occured after an endosymbioti event and as a result mtDNA appeared and all mtDNA are the same. Endosymotic events also gave rise to different algaes. Such as for photosynthesis there are different pigments that include green, red, golden, and more. We can conclude that animals and fungi are closer than animals and plants. Meaning that they all share more homology. -Gene expression: In gene expression each cell of a multicellular eukaryote expresses a low percentage of it's genes. Gene expression control takes place during any number of steps. In gene expression of eukaryotes there are five steps in regulation of gene expression. The first step in gene expression is chromatin remodeling, which increases expressions signals and decrease transcription signaled. These expression signals modify the nucleosome structure and opens up DNA so promoters are available, by using transcription activators The second step is to regulate transcription. This is controlled by cis-acting DNA sequences and is used to save energy. The second step of gene expression is the most important step in gene expression in eukaryotes. Regulation of transcription uses a promoter, which is a recognition site for RNA polymerase and allows transcription to happen. During the second stage there are enhancers which binds to transcription factors. This helps increase the production of transcription. Located 5',3', or internal to the gene itself. There are also silencer in the second step. The silencers are cis-acting region binding factors and this decreases transcription. Silencers are located around promoters and act in tissues at a particular time. In addition, regulation of transcript is controlled by trans-acting transcription factors that bind DNA and activate or repress transcription. There are two protein domains in transcription factors that are DNA binding domains and trans-activating domains that and other transcription factors or RNA polymerase. Zinc fingers make proteins that bind major groove and basic leucine zipper holds the DNA together. These are all part of the second step of gene expression. The third step is RNA processing. RNA processing helps remove introns using post-transcriptional modification which controls the gene expression. In RNA processing there are splicing's called alternative splicing. This yields different products for different cells using 1 gene and produces several transcript. It has 5' cap, 3' poly tail added to protect transcript half life. The final steps of gene expression is translation(posttranslational region) regulation. Translational control is usually at initiation. Proteins can bind to 5' mRNA to block binding. Posttranslational regulation processes protein and degradation. RNA silencing is in the fourth and fifth step in gene expression. It is a newly discovered way of controlling gene expression and it is gene specific. It is a natural way that cells recognize and destroy ds RNA. It can be used to turn off gene expression. DNA methylation in eukaryotes often occur at position 5 of cytosine which causes the methyl group to extend into the major grooves of the DNA helix. DNA methylation represses gene expression. Methylation can repress transcription by inhibiting the binding of transcription factors to DNA which are classified as trans-acting elements. The elements such as promoters, silencers, enhancers, and operons which aid in eukaryote gene expression are classified as cis-acting elements. Cis-acting factors are mechanisms that affect gene expression only on the same chromosomal allele, while trans-factors act equally on both alleles. Transcription factors and long noncoding RNAs are examples of trans-acting factors.

Define: evolution, natural selection, microevolution, know that only natural selection leads to adaptations; explain why evolution can't make perfect organisms;

Evolution : Descent with modification; The emergence of new kinds of organisms deriving from preexisting ones. Natural Selection : Differential reproduction among members of a species owing to variable fitness conferred by genotypic differences; survival of the fittest Microevolution : A change in allele frequency of a given population seen between generations. 15b. Explain why only natural selection leads to adaptations The phenomenon of natural selection is based on the survival of the fittest theory. Genetic variations that thrive in a population are due to the success that they bring organisms in terms of surviving in their environment. With natural selection, only traits that are useful to a species will be favored, giving rise to adaptations to their environment. This makes organisms anatomically, physiologically, and behaviorally well suited for their habitat. 15c. Explain why evolution can't make perfect organisms; Evolution is defined as the rise of new organisms from preexisting species. Based on this accepted definition, evolution can only change characteristics of existing species, and not create new features. These existing species have also derived from the same ancestors and therefore seemingly different species all come from the same place. With evolution, chance also plays a factor into which traits are passed down and continue into new generations of species. 16. Mod 18 (Ch 20 in 10e) Know the definitions of quantitative traits, polygenic traits, Know how to interpret MZ vs DZ tables to determine if a trait is genetic or not (if MZ is high and DZ is significantly lower, the trait is genetic). 16a. quantitative traits: any genetic material that has a measurable phenotype that depends on the additive actions of two or more genes and environmental factors. polygenic traits: traits that are controlled by two or more genes and show a wide variety of phenotypes 16b. Know how to interpret MZ vs DZ tables to determine if a trait is genetic or not (if MZ is high and DZ is significantly lower, the trait is genetic). MZ and DZ tables is a method of genetic comparison between identical and fraternal twins. The tables represent how inheritance presents itself between the two; MZ meaning monozygotic identical twins and DZ being dizygotic fraternal twins. Using such information, twin studies are conducted to estimate the heritability of polygenic traits in human twin offspring. To understand the trends, we must know that if the rate of expression is higher for monozygotics twins over dizygotic twins, then there is genetic basis to that trait. If the rates are same, there are environmental factors that play a role.Traits are understood to be in concordance if both twins have the same outcome of the trait (both do not express or both express), and discordant if only one of the twins expresses it. Based on this, if there is concordance higher in MZ twins when compared to DZ twins, it is said to have genetic basis and environmental if the concordance is the same between both types.

environmental agents that cause cancer

Exposures from the environment that are thought to cause cancer or cause cells to progress to cancer, e.g. certain viruses, cigarette smoke, certain dietary exposures, radiation, asbestos and certain pesticides

Early death is NOT one of the symptoms of hemochromatosis

False

know 4 levels of protein structure and monomer for proteins (which is amino acids); know nucleosomes, chromatin packing, middle repetitive and highly repetitive and single copy DNA.

Four levels of protein structure Primary structure: the sequence of amino acids covalently bonded in a polypeptide chain. Secondary structure: the local folded structures that form within a polypeptide due to interactions between atoms of the backbone. The most common are the α helix and the β pleated sheet. Both structures are held in shape by hydrogen bonds. The α helix looks like a curled ribbon and the β pleated sheet looks like a pleated sheet. Tertiary Structure: the overall three-dimensional structure of a polypeptide. The tertiary structure is primarily due to interactions between the R groups of the amino acids that make up the protein. Quaternary structure: Some proteins are made up of multiple polypeptide chains, also known as subunits. When these subunits come together, they give the protein its quaternary structure. That being said, many proteins only have three levels of structure where they are made up of a single polypeptide chain. Nucleosomes: in eukaryotes, a nuclear complex consisting of four pairs of basic, positively-charged histone molecules wrapped by two turns of a negatively-charged DNA molecule. The major structure associated with the organization of chromatin in the nucleus. Nucleosomes are 11 nanometers wide. Chromatin packing: Nucleosomes that are 11 nm wide coil into 30 nm solenoids. The solenoids are looped into 300 nm wide chromatin. The chromatin is coiled into 700 nm wide chromatids. Eukaryotic DNA contracts 10,000 fold between mitosis, interphase and prophase. Highly repetitive DNA: It makes up 10% of total DNA. Occurs as variable length motifs (5-100 bp), in long tracts of up to 100 Mb. Most is located in heterochromatic regions around the centromere / telomere. Postulated functions include structural or organisational roles, role in chromosome pairing, involvement in cross-over or recombination, and junk. Middle repetitive DNA: It makes up 30% of total DNA. It is present at between 10 - 105 copies per genome. Found throughout the euchromatin, average 300bp in size, may be classes as microsatellites or dispersed-repetitive DNA. It is mainly transposable elements. Also includes 'redundant' genes for histones, and ribosomal RNA and proteins. Many moderately-repetitive sequences may be involved in regulation of gene expression. Single-copy DNA: unique sequence nucleotides in DNA that codes for protein that are sites of transcription. They are mainly found in the exons and are the sites for transcription to make mRNA. These are present in the euchromatin (lightly packed form of chromatin ) part. Single copy DNA makes up 60% of the total DNA. It is present in single or low copy numbers. Includes coding sequence for structural genes which account for 3% of the genome. Janis, great post! I like how you organized the information and your explanations were really informative. I was able to refresh my knowledge on repetitive DNA from reading your post!

screenable markers

Genes (or "markers") used to determine (by examination) which cells have the phenotype of interest; generally only a portion will , e.g., after selecting for transformants with the vector, scientists screen for the genes of interest on the vector .

selectable markers

Genes (or "markers") used to ensure that all of the cells have the vector ; e.g., an antibiotic-resistance gene on the vector is often used to select for transformants that have taken up the vector and to select against cells that have not.

Know definition of genetics; what is known about the human genome including SNP, CNV, indels; definition of negative eugenics.

Genetics is a branch of biology that studies genes and heredity. Genes are short sections of DNA which code for proteins, and heredity is how they are passed from generation to generation. Genome refers to the entire set DNA of an organism. The Human Genome Project sequenced the approximately 3 billion base pairs in a human cell, carried in a haploid set of 23 chromosomes plus the Y chromosome (24 chromosomes in all) 23 pairs of chromosomes, which give instructions for humans to be built and carry out the functions of living. We know that the majority of DNA is noncoding, only about 20,000 genes code for proteins. An SNP stands for single nucleotide polymorphism and is a type of genetic variation between people. It is a single nucleotide in the sequence of nucleotides which make up DNA, differing from person to person. In comparison, a CNV stands for copy number variant. This is also a type of genetic variation between people, but it is larger because it referrs to entire genes being duplicated or deleted. Indel is a general term that refers to INsertion or DELetion of nucleotides into the genome. If it is in a coding region, it will cause a frameshift mutation if it is not a multiple of three. Eugenics is a method of modifying the a population through selective breeding. Positive eugenics would mean encouraging the individuals with "desirable" genes to reproduce, while negative eugenics means preventing the "unfit or undesirable" genes from continuing on in the population, for example, sterilizing those with mental illness or preventing reproduction among members of a certain race. These types of ideas were common in the past, justifying events such as the Holocaust, but are no longer viewed as ethical.

clones

Identical molecules, cells, or organisms derived from a single ancestor by asexual methods.

Which of the following best describes the difference in silencing genes by epigenetic modifications versus imprinting?

Imprinted alleles stay off for life in every cell in the organism while epigenetic silencing may be lifted in some cells by environmental signals.

cyclins and CDKs

In eukaryotic cells, a class of proteins that are synthesized and degraded in synchrony with the cell cycle and regulate passage through stages of the cycle.

Know common modifications of inheritance patterns for monohybrid and dihybrid crosses (know your F1 and F2 ratios!)-Sana; know that chromosome movement in meiosis and fertilization accounts for rules of inheritance. Know definitions for epistasis, recessive lethal, complementation, etc-Khalil.

In monohybrid cross, the F1 ratio is 100% dominant phenotype, while the F2 ratio is 3:1 where 3 is for dominant and 1 signifies recessive phenotype. In Monohybrid incomplete dominance, there are 100% intermediate phenotypic ratio. In F2, the ratio is 1:2:1 where 1 is dominant phenotype, 2 is intermediate, a and 1 is recessive phenotype. Then, in monohybrid co-dominance, the F1 ratio is 100% both phenotypes. In F2, the ratio is 1:2:1. Lastly, in monohybrid recessive lethal, the F2 ratio is 1:2 since ¼ are dead. In Dihybrid cross, the F1 ratio is 100% double dominant. In F2, the ratio is 9:3:3:1. In dihybrid epistasis, the ratio is variations on 9:3:3:1, such as 9:7 or 9:4:3, with novel phenotype in F2 generation. In dihybrid complementation, the F2 ratio would show restoration of wildtype. In dihybrid sex-linked, the F2 phenotypic ratio shows more males are affected and there would be different ratio in cross and reciprocal cross.

what's the advantage of Next Generation Sequencing over Sanger Sequencing?

It's can generate a massive amount of sequence data, quickly.

Know Mendel's law of independent segregation and law of independent assortment; know common human genetic disorders (Tay Sachs, sickle cell, PKU, HD, Down Syndrome, Turner Syndrome, Kleinfelter Syndrome).

Law of segregation - this law states that if an individual contains two like units (ex. Tall and Tall) then all the gametes that individual produces will be that one unit. However if an individual has two unlike units (ex. Tall and Short) then there is a 50% chances for each unit to be placed into each gamete that is produced. Law of independent assortment - that all units are sorted independently of one another. Example: A pea plant can have two colors: green or yellow. It can also have two textures: smooth or wrinkly. The texture of the pea is sorted separately from the color of the pea as the color does not impact the texture and vise versa. PKU - is a genetic disorder that stands for Phenylketonuria. PKU causes phenylalanine to build up in the body and cause neurological problems including intellectual disability but can be easily treated with the proper diet. Sickle cell anemia - Causes a mutation in the hemoglobin-Beta gene. Individuals with this disorder have sickle shaped (cresent or moon shaped) red blood cells that can get stuck in small blood vessels causing periodic episodes of pain, swelling and fatigue and early death even with treatment. It also provides some immunity to Malaria as the virus is unable to attach to the cell and reproduce. This is different from Sickle cell trait, which is when only one copy of the gene is present. Tay-sachs is a disease that is commonly inherited among Ashkenazi Jews. Tay-sachs is caused by the loss of enzyme, hexosaminidase A (Hex-A), causing a deadly build up of gangliosides in the brain and spinal cord. It eventually causes the nervous system to deteriorate and leads to death. Huntington's - causes a breakdown of nerve cells in the brain. Individuals with this disorder suffer from uncontrolled movements, loss of cognition and eventually death. It is caused by the accumulation of 40 to 50 copies of the same trinucleotide repeat. Another major problem with this disorder is, genetic anticipation. This can cause the onset of symptoms to accrue earlier and earlier if the disorder is passed down in a family. Down syndrome - a trisomy at chromosome 21. Individuals with this syndrome have lower metal cognition and many suffer from heart problems. There are also physical differences that are seen in these individuals, such as round faces and shorter fingers. Turner syndrome - a monosomy at chromosome 23 (XO). People with this disorder usually do not possess strong secondary sex characteristics such as breast or wider hips and are unable to have children. Klinefelter syndrome - a trisomy at chromosome 23 (XXY). People with this syndrome have narrow shoulder, wider hips, and are unable to have children

restriction enzymes

Molecular "scissors" that cut double-stranded DNA at specific sequences.

DNA ligase

Molecular "tape" that sews together (ligates) DNA fragments that are linked by hydrogen bonds.

Gene Expression, prokaryotes: Define: operons, promotor, operator, repressor gene; know how the lac operon works; know the genomes of viruses, eubacteria, mt DNA and cp DNA.

Operon- cluster of genes with one regulatory region Promoter- RNA Polymerase binding site Operator- DNA adjacent to a gene set that binds the repressor protein Repressor gene- inhibits gene expression, made constitutively, allosteric regulator in that when it binds lactose it can't bind operator (and vice versa) How lac operon works- for the lac I operon, expression is inducible, if lactose present → binds RNA Polymerase and transcription on, if no lactose present → repressor binds operator, transcription off Virus genome- DNA or RNA that can be single or double stranded Eubacteria genome- double stranded DNA, usually one circle but can have additional linear or circular chromosomes, in nucleoid, associated with DNA-binding proteins, usually small Mitochondrial DNA genome- double stranded DNA circle lacking associated protein, rely on nuclear genes for some products needed for replication, transcription, and translation Chloroplast DNA genome- double stranded DNA circle lacking associated proteins, rely on nuclear genes for some products needed for replication, transcription, translation, and photosynthesis

Define penetrance, expressivity, onset, genetic anticipation, genomic imprinting, polygenic inheritance; define aneuploidy and explain what causes it: define: monosomy trisomy; know 4 common alterations in chromosome structure

Penetrance: proportion of individuals with a mutation that actually show the phenotype associated with a it Expressivity: degree to which a specific phenotype associated with a genotype/trait is expressed Onset: age when people with certain disease begin to express the disease phenotype Genetic anticipation: phenomenon in which the symptoms of genetic disorder become more severe and the onset becomes earlier in each subsequent generation Genomic imprinting: phenomenon in which expression of genes depends from which parent it was inherited (mother or father) Polygenic inheritance: when more than one gene play a role in determining the inheritance Aneuploidy and its cause: either having more or less chromosomes in a diploid set; chromosome number is not a multiple of the haploid; it is the result of errors in meiosis (nondisjunction) Monosomy: aneuploidy in which one chromosome is missing (chromosome number = 2n-1) Trisomy: each chromosome is present as two copies, but one is present as three copies (chromosome number = 2n +1) 4 common alterations in chromosome structure: Deletions, duplications, invertions, and translocations are all alterations in chromosome structure. These alterations often result in a mutant phenotype. Deletions: The lost portion of a chromosome as a result of mutation; may be responsible for mutant phenotypes. Duplication: Portion of a chromosome that is present more than once as a result of unequal crossing over or replication error; may be responsible for mutant phenotypes. Inversions: 180-degree flipped portion of a chromosome; may be responsible for mutant phenotypes; fertility may be decreased. Translocations: Change in the location of a particular portion of a chromosome; nonhomologous chromosomes may exchange genetic material between each other; fertility may be decreased.

checkpoints

Points in the cell cycle where there is monitoring for lack of DNA damage and correct attachment of chromosomes to the spindle; if the checkpoint is not traversed, the cell makes a decision either to repair damage or to undergo apoptosis. Previous Card

From the lab introduction, why is poplar so important in sustainability and why is rice so important in human ecology? Answer BOTH questions in 1-2 sentences.

Poplar is a very fast growing tree, and it can be used to make biofuel which is part of the fuel that we use in gasoline. Rice is important in human ecology as it requires little water to grow, retains soil nutrition, and is a primary food source for a major portion of the human population.

recombinant DNA technology

Procedures used to make new DNA sequences not found in nature.

apoptosis

Programmed cell death; involved in normal development and also involved in the killing of damaged cells

Which of the following is currently used by U.S. law enforcement for DNA profiling

STR DNA profiling

which of the following is usually used in police work to identify individuals

STRs

indels

Small insertions or deletions in one genome when compared with another.

exons

The DNA segments of a gene that contain the sequences that, through transcription and translation, are eventually represented in the final polypeptide product.

bioinformatics

The design and application of software and computational methods for the storage, analysis, and management of biological information such as nucleotide or amino acid sequences.

epigenetic changes

The modifications in an organism's gene function or phenotypic expression that are not caused by mutations in the nucleotide sequence. Epigenetic changes are thought to be controlled by other genes and the environment.

metastasis

The process by which cancer cells spread from the primary tumor to other parts of the body.

proteomics

The study of the expressed proteins present in a cell at a given time.

Why are miRNAs considered epigenetic gene expression?

They affect gene expression without changing the sequence of the DNA.

What role do cancer stem cells play in cancer?

They are the cells that divide in a tumor

homologous genes

Two or more genes with similar sequences and functions that have evolved from a common ancestral gene.

Metalloproteinase and TIMP Previous Card

Two types of genes that work together to determine invasively of cells; may be mutant in metastatic cancer cells.

Know inheritance patterns from review charts; define: genes, alleles, ploidy, haploid, diploid, chromatin, recessive, dominant, codominant etc;

a standard monohybrid cross involves only one pair or contrasting traits (for example: tall/dwarf).When we cross two true breeding traits (a monohybrid cross) is when we will see variation in the future generations. When we cross Tall with Dwarf we see the F1 phenotypes are all Tall, therefore Tall is dominant to Dwarf and the F2 generation gave a ratio of 3:1 Tall:Dwarf. We know from this ratio that Tall is Dominant and Dwarf is Recessive. IN SHORT: the monohybrid cross is a cross between two organisms involving 1 gene and will result in a F2 phenotypic ratio of 3:1 (3: A-, 1: aa) DIHYBRID CROSS: a standard dihybrid cross two pairs of contrasting traits (for example: yellow&round/green&wrinkled). The first generation (the F1) cross will all be the same, the dominant phenotypes will present. The F1 offspring would all be yellow&round, therefore yellow is dominant to green and round is dominant to wrinkled. In the F2 generation we have a phenotypic ratio of 9:3:3:1, that is 9/16 are yellow&round, 3/16 are yellow&wrinkled, 3/16 are green&round, and 1/16 are green&wrinkled. IN SHORT: the dihybrid cross is a cross between two organisms involving two genes and will result in a 9:3:3:1 phenotypic ratio in the F2 (9: A-B-, 3: A-bb, 3: aaB-, 1: aabb) RECIPROCAL CROSS: A pair of crosses where the genotype of the female in the first cross is the genotype of the male in the second cross and vise versa. This cross is made to determine if something is sex-dependent. (the results stay the same for autosomal traits and change for sex-linked genes) INCOMPLETE DOMINANCE: when a heterozygous organism shows a blended phenotype. In a monohybrid cross with incomplete dominance the F2 phenotypic ratio would be 1:2:1. For example: a flower color cross red x white, in the F2 you would get a phenotypic ratio of 1: red, 2: pink, 1: white (1:2:1) CODOMINANCE: when a heterozygous organism shows a phenotype fully and simultaneously expressing BOTH alleles. In a monohybrid cross with codominance the F2 phenotypic ratio is 1:2:1. For example: blood type alleles A and B are co-dominant when you cross IAIA x IBIB so in the F2 you get 1: A blood type, 2: AB blood type, 1 B blood type (1:2:1) MULTIPLE ALLELES: more than two alleles for a given gene (blood type ABO) LETHAL INHERITANCE: lethal inheritance causes lethality (death). A recessive lethal allele produces death when homozygous recessive (hh cause death, would survive if HH or Hh). A dominant lethal allele causes death when homozygous dominant OR heterozygous (HH or Hh cause death, would survive if hh). This produces a 2:1 phenotypic ratio (1/4 are dead) in the F2. SEX-LINKAGE: The dihybrid variation where an allele is on the X chromosome. "SEX LINKED IS X-LINKED" sex-linked traits effect more human males than human females because males are hemizygous (XY). If your cross and reciprocal cross give different results and/or more males than females are affected this is an indication of a sex-lined trait; variation on a standard dihybrid cross. EPISTASIS: one gene interferes with or prevents expression of another gene (in a dihybrid cross, expect a 3:1 ratio but get ratios that add to 16, expect a 9:3:3:1 ratio but get other ratios that add to 16 such as 9:4:3, or may get new phenotypes) means "stoppage"; variation on a standard dihybrid cross. COMPLEMENTATION: production of wildtype offspring when mating parents with recessive mutation with the same phenotypes (mutations are in 2 different genes); variation on a standard dihybrid cross. GENES: units of heredity, a DNA sequence coding for product located on a chromosome. ALLELES: alternative versions of one gene. HAPLOID: refers to the condition of having ONE set of chromosomes (A, Ab, ABc, are all examples of haploids, *gametes are haploid) DIPLOID: refers to the condition of having TWO sets of chromosomes (Aa, AbBb, AaBBcc, are all examples of diploids, *somatic cells are diploid) ***PLOIDY VS HYBRID*** PLOIDY is the number of chromosome sets in a eukaryotic cell where as a HYBRID is the number of different genesploidy = # of PAIRS of letters hybrid = # of DIFFERENT letters ploidy examples: Aa = diploid AaBb = diploid Aaa = triploid AaaBbb = triploid aaaA = tetraploid AaaaBbbb = tetraploid ABbCcDd = diploid with aneuploidy (note the singular A) hybrid examples: Aa = monohybrid Aaaa = monohybrid AaBb = dihybrid Aaa = monohybrid AaaBbb = dihybrid ABbCcDd = tetrahybrid CHROMATIN: consists of DNA, RNA, and proteins; it is the material of which eukaryotic chromosomes are composed. RECESSIVE: Allele that is hidden or masked in the phenotype if the dominant allele is present (example: a heterozygote: d in Dd) and is only present phenotypically if the dominant allele is absent (example: a recessive homozygote: dd) DOMINANT: Allele that is expressed in the phenotype of a heterozygote, that masks or hides the recessive allele (for example: D in Dd) and is also present phenotypically in homozygous dominant (for example: DD) CODOMINANT: Alleles that are both fully expressed in the phenotype of a heterozygote. (blood type AB)

In the glab rice data, what was the level of expression in each of the three tissues?

active in leaves, moderately active in pannicles, inactive in roots

What are symptoms of hemochromatosis?

all of the above

Which of the following about CRISPR-Cas9 is TRUE:

all of the above are true

transgenic means

an organism made by putting genes from one organism or species into another

dna ligase

enzyme that attaches one DNA molecule to another

Restriction enzyme

enzymes that cut DNA into fragments, molecular scissors that cut DNA at specific sequences

If there is a match in the 13 STRs in DNA profiling between the crime scene and a suspect, the suspect must be guilty.

false

Which of the following is defined as a therapy where the actual gene of a diseased individual is altered to cause a cure?

gene therapy

Which of the following is NOT a goal of personalized medicine?

help determine how one person is related to another

PCR

method for amplifying DNA

"Knock out" construction

method for engineering an organism missing all copies of a specific gene

"Knock in" construction

method for engineering an organism producing or overproducing a specific gene product

CRISPER Cas

method for genomic editing

cloning

method for making an exact copy of a gene, DNA, or even organism (in our book, it's copying a DNA sequence from one organism to another)

screen

method to check amongst a number of organisms for the one(s) with the desired phenotype

selection

method to get exactly those organisms with the phenotype that is desired

Recombinant DNA technology

methods used to make new sequences not seen before in nature

What is the medical term for medical treatment of hemochromatosis?

phlebotomy

Cellular genes which promote the cell cycle in normal cells are:

proto-oncogenes

How is HFE1 inherited?

recessive, autosomal

In question 6, we saw that proteins A, B and C are different. Which of the following is FALSE about why they are different?

the dna contained different exons

Why would you sequence different cDNA libraries from the same organism?

there are different genes on/off in different parts of the plant

Tumor-suppressor genes normally act:

to suppress cell division

The HFE protein normally interacts with transferrin receptor protein to control iron levels.

true

biotechnology is

use of a living organism to create a product or a process

DNA chip technology

uses DNA microarrays to genotype, stage cancers, analyze pathogens

vector

vehicle to transfer DNA