Genetics Exam 4

What is eugenics?

"well-born" the study of how to arrange reproduction within a human population to increase the occurrence of heritable characteristics regarded as desirable.

Describe missense mutations:

- in-frame mutation (insertion/deletion) - changing one codon to a different codon resulting in a change in the amino acid sequence of the protein

What are the three general types of mutations?

1) substitutions 2) insertions/ deletions 3) functional mutants

What are the two main types of non-point mutations?

1. Chromosomal mutations 2. Transposable elements

It was once thought that bacteria did not have immune systems. What do we now know?

Bacteria have a very rudimentary immune system... they have something that kind of acts like an immune system. 1987: Yoshizumi Ishino discovered and cloned repeated regions of bacterial DNA. These regions became known as short palindromic repeats (SPR of CRISPR) and the bacterial immune system became known as CRISPR.

Describe initiation as a step of translational regulation:

Most regulation exerted at this stage. Ribosomal subunit proteins and initiation factors form a complex that recognizes the 5'‐Cap of mRNA. Once bound, the complex scans down the mRNA until the initiation codon (AUG) is located. The initiation complex lines up the codon with the P site of the 60S ribosomal subunit and translation begins.

If CRISPR is there and a bacteria infects a cell but CRISPR does not recognize it, describe what would happen:

The bacteria would punch a hole in the cell wall and inject its DNA into the cell. If CRISPR was there, and it did not recognize the DNA (because it does not have a matching spacer), but the host still lives, cas 1 will make a spacer that matches it so that if it gets infected again, they can fight it through MEMORY!

Describe Alu elements as retrotransposons:

Thousands of our Alu elements occur in the introns of genes. These can then be spliced into the mature mRNA creating a new exon, which will be transcribed into a new protein product. Alternative splicing can provide not only the new mRNA (and thus protein) but also the old. In this way, nature can try out new proteins without the risk of abandoning the tried‐and‐true old one.

As identical twins age, they can begin to look a little different... how?

Well, identical twins have the same exact genome, but their epigenome is built based on the environmental factors that surround them as the develop. This means that their epigenomes could be completely different and give them slightly different features. Then, as embryo develops, cell specialization occurs. As each cells type specializes, epigenetic tags either activate or silence specific genes leading to further specialization. (It depends on where they are located as to how big of a change they make.)

Describe the mechanism by which Retrotransposons (Class 1) move throughout the genome:

"copy and paste" mechanism They function through the action of RNA intermediates and DO NOT encode for transposase. They produce RNA transcripts and rely on Reverse Transcriptase to reverse transcribe the RNA into DNA sequences prior to insertion into target DNA. It goes to the transposon, copies it, and pastes a copy of it into another place of the genome. The original is still in its position, but there is a displaced copy as well. Long Terminal Repeat Transposons are characterized by the presence of LTR on each end of the TE. They code for reverse transcriptase. NOT FOUND IN HUMANS. Non-Long Terminal Repeat Transposons have no LTR present. They are the only active class of transposons in humans. Come in autonomous and non-autonomous.

Describe the mechanism by which DNA transposons (class 2) move throughout the genome:

"cut and paste" mechanism All DNA transposons encode for the protein Transposase. Transposase comes in, cuts the transposon, and inserts it somewhere else in the genome. It is able to know where the transposon in because of its Terminal Inverted Repeats. These are inverted compliments of 9-40 base pairs located at both ends of the TE (PART OF THE TE) and are recognized by transposase. When the transposon is removed, Flanking Direct Repeats are left behind and signal places where the transposon could be reinserted. These repeats are NOT A DIRECT PART OF THE TE, but provide a marker for the excision site.

Describe nonsense mutations? Give examples:

- a type of missense because it changes what the codon codes for - frameshift mutation (insertion/deletion) - changing one codon to a "STOP" codon resulting in premature stoppage of translation Examples: - cystic fibrosis - duchenne muscular dystrophy

Describe how CRISPR can affect the epigenome:

- creates dCas9 protein (same thing as Cas9 but cannot cut) which is a dead Cas9 protein that cannot cleave DNA. - adds gRNA for areas around CpG islands. - rewrites epigenetic markers on both the DNA and the histone proteins

Describe silent mutations:

- in-frame mutation (Insertion/deletion) - changing one codon to a synonymous codon causing no change in the amino acid sequence of the protein - "degeneracy of the genetic code" - a change in the third nucleotide of a codon causes no change in the amino acid coded for; "a change in genotype causes no change in phenotype"

What is a transition mutant?

- one type of substitution mutation - exchange a purine for a purine or a pyrimidine for a pyrimidine - happens more often than transversion mutations because they fit better.

What is a transversion mutant?

- one type of substitution mutation - exchange nucleotides outside of nucleotide family; exchange a purine for a pyrimidine or vice versa

Describe the effects of epigenetics on behavior and the studies that have been done:

-decreased protein synthesis in depressed patients and decreased transcription is Alzheimer's patients are both regulated by methylation -anxiety -addiction -lots more methylation and lots less rRNA expressed in those who committed suicide -epigenetic markers increased 12-fold in abuse victims over non-abuse

What are the two mechanism of mutations? Define them:

1) Spontaneous mutations: any mutation where no artificial factor or external regulator causes the mutation 2) Induced mutations: any mutation that is caused by an artificial factor or external regulator

Genetic material must have what 4 things?

1) effective transfer between generations 2) ability to sore vast amounts of information 3) information can be changed/ mutable 4) effective replication/ high fidelity

Describe the two ways methylation can be used for transcription silencing:

1. Block Transcription Factor Binding: transcriptional activator binds to unmethylated DNA. Methyl groups block the binding of a transcriptional activator to an enhancer element. This would inhibit the initiation of transcription. 2. Induction of Heterochromatin (chromatin compacting): A methyl-CpG binding protein binds to the methylated CpG island. The methyl-CpG binding protein recruits other proteins such as histone deacetylases that convert the chromatin to a closed confirmation. It can prevent the PIC from forming or stop the other transcription factors from coming, but they can also recruit proteins like HDAC for themselves and put the DNA back into heterochromatic state to stop transcription.

What are the two types of chromosomal mutations? Describe them:

1. Chromosome duplication: duplication of a region of DNA that contains a gene resulting from ectopic recombination. Where this duplication occurs determines how detrimental it will be. can be homologous recombination and non-homologous recombination (results in insertion and deletion) 2. Chromosome deletions: can be small (less likely to be deleterious), medium (responsible for a number of genetic diseases), or large (often fatal). They can also be either in-frame or frame shift which has the most deleterious consequences.

What are the 2 types of transposons? Describe them:

1. Class 1 transposable element: requires reverse transcriptase (the transcription of RNA into DNA) in order to transpose. These are considered retrotransposons. 2. Class 2 transposable element: does not require reverse transcriptase in order to transpose. These are considered DNA transposons.

***Describe transposons in mutation as seen in grapes:

1. In black grapes, the VvmybA1 gene regulates the synthesis of anthocyanin pigments. 2. In white grapes, a retrotransposon has inserted near the VvmybA1 gene, disrupting the synthesis of anthocyanins. 3. In red grapes, a second mutation has removed most of the retrotransposon, but a piece is left behind. Anthocyanin production is partly restored.

Our immune system can be split into two categories. What are these categories and what are 3 examples of each?

1. Innate Immunity (first line of defense) - surface barriers (skin) - cellular barriers (cell walls, plasma membrane) - inflammation (when your injury gets really hot and swollen) 2. Acquired immunity (things that remember; they build antibodies; things that have IMMUNOLOGICAL MEMORY) - lymphocytes - T-cells - B-cells - vaccines can also be found in this category.

How does epigenetic control occur?

1. Post-translational modification 2. methylation of DNA

How does transposition occur (Class 2 transposons):

1. The TE is removed from the DNA sequence by Transposase. 2. Transposase carries TE to new target DNA. 3. Staggered cuts are made in the target DNA by Transposase. 4. The TE inserts itself into another location in the DNA. 5. Staggered cuts leave short, ssDNA pieces. 6.Replication of the ssDNA creates flanking DR

How does Retro-transposition occur (Class 1 transposon):

1. The retrotransposon sequence is transcribed to RNA 2. and undergoes reverse transcriptase to produce dsDNA 3. staggered cuts are made in target DNA 4. The retrotransposon integrates into the new site in the host DNA 5. Replication fills in the gaps at the site of insertion creating FDR

Describe the steps of miRNA regulation:

1. Transcription - formation of pre-miRNA 2. Exportin-5 exports the pre-miRNA from the nucleus 3. miRNA-protein complex forms and passenger RNA strand discarded 4. Dicer removes the hairpin loop region leaving dsRNA 5. miRNA-protein complex- - blocks translation by the ribosome - speeds up deadenylation (breakdown of Poly-A Tail)

Several things must happen for a gene to be expressed. Describe these steps of transcriptional regulation:

1. some kind of initiating signal 2. signaling pathway cascade: binding occurs at the membrane and triggers a cascade that almost always effects gene expression by turning it on or off (exp. phosphorylation cascade) 3. activation of a transcription factor 4. recruits other member of the transcription complex 5. transcriptional complex recruits RNA polymerase II 6. transcription is initiated at the promoter site

Describe chromatin remodeling as the first layer of eukaryotic organism regulation:

2 major protein classes regulate this process: 1. ATP-dependent chromatin remodeling complexes - protein complexes that regulate expression by moving, ejecting or restructuring nucleosomes. - uses ATP energy to associate/bind to heterochromatin and loosen it. - once protein complex binds to DNA around the nucleosome, chromatin structure is loosened allowing movement of the histone core octamer. 2. Histone Modifying Complexes -protein complexes that enzymatically modify N-terminal histone tails. (Include - methylation, phosphorylation, and acetylation) - histone acetylation = expression, de-acetylation = silencing - DNA methylation = silencing, de-methylation = expression *** recognize difference -histone code hypothesis

Describe chemical reactions as an induced mutation. Describe 5-Bromouracil as an example:

5-Bromouracil is a base analog of antimetabolite of uracil that can replace thymine in a strand of DNA. It can replace Thymine in a DNA strand and either pair with adenine or mis-pair with Guanines. Through DNA replication, this 5-Bromouracil will continue to show up in the new strand and will either pair or mis-pair. Doing this allows us to use 5-Bromouracil as a detection device to study cancer proliferation as it is neither radioactive nor toxic to the cell and other cell growths.

What is CRISPR? what does it stand for?

CRISPR is the bacteria immune system which is very unique. It stands for Clustered Regularly Interspaced Short Palindromic Repeats. The Short Palindromic Repeats are what Ishino discovered. They can be read forwards or backwards and say the same thing (palindrome). They are typically repeats of about 20-40 bases. The gaps between these repeats are the Clustered Regularly Interspaced part and are known as Spacer DNA. Each spacer is completely unique in sequence and each matches up perfectly with viral DNA.

Describe autonomous Non-Long Terminal Repeat Transposons:

Capable of moving on their own as they make their own reverse transcriptase required to move. LINEs (Long Interspersed Elements) DNA sequences that range in length from a few hundred to as many as 9,000 base pairs. Functional L1 elements are about 6,500 bp in length and encode proteins, including an endonuclease that cuts DNA and a reverse transcriptase that makes a DNA copy of an RNA transcript. Most L1 elements are not functional, they may play a role in regulating the efficiency of transcription of the gene in which they reside.

Describe the epigenetic effects of methylation:

Cytosine is the main base that is modified by DNA methyltransferase. DNA methyltransferase (or DNA methylase) converts Cytosine to 5-methylcytosine to change its properties. The more methylated, the stronger the effect. Unmethylated < hemi-methylated < fully methylated

Describe methylation of DNA and its effects:

DNA methylation usually inhibits transcription of eukaryotic genes especially in the region of the promoter. many eukaryotic genes contain CpG Islands near the promoter region and this is where methylation tends to occur because it is very GC rich = a lot of good cytosines = a good place for methylation. exps: -housekeeping genes: tend to be constitutively expressed in most cell types. CpG Islands usually unmethylated because they need to be ON. -tissue specific genes: gene expression is regulated by methylation at CpG Islands. Genes like these that are only needed at certain times can be turned OFF until they are needed.

describe elongation as a step of translational regulation:

Dependent on ribosomal elongation factors. 60S Ribosome reads down the mRNA strand resulting in synthesis of a polypeptide chain. Ribosomal Pausing - stacking of ribosomes on an mRNA molecule caused by changes in cellular environment. Can result in release of the ribosome and premature degradation of the incomplete polypeptide.

Describe the work that Barbara McClintock did with maize to discover "jumping genes":

Discovered that 4 genes come together to produce color in maize (epistasis). C' - dominant colorless C - color Bz - dominant purple bz - brown Ds - dissociater (TRANSPOSABLE ELEMENT) Ac - activator (allows dissociater to move) To show a color, you must be CC, no matter if you are Bz or bz. When she did a cross, she got a triploid that was C'CBzbz which SHOULD be colorless; however, it was colored. This led her to discover that color depends on what point in development the Ds got up and moved. All kernels started colorless, if the Ds moved early, lots of color would develop... if it moved later, some color may develop if there is time or they may stay colorless if the are almost fully developed.

What are epigenetic tags and imprinted genes?

During the first days post fertilization, epigenetic tags are erased from mom and dad's chromosomes. However, on some genes, the tags remain. These are known as imprinted genes. Imprinted genes transfer epigenic information rather than just DNA sequence information to offspring.

What do epigenetic tags do?

Epigenetic tags turn genes ON or OFF without changing the underlying genetic code. They interact with genetic information (DNA) to activate or suppress the expression of particular genes

describe how a gene codes for a functional protein in a eukaryotic cell:

Eukaryotic organisms have layers of regulation because of the organelles they possess. The layer of organization are: 1. Chromatin 2. Transcription 3. RNA Processing 4. Translation 5. Post-Translation

Whay are gene drives? explain how they work:

Gene drives are CRISPR genes and the proto-sequence within a "selfish gene". A gRNA shepherds the Cas9 cutting enzyme to a specific spot on the DNA. Cas9 cuts the DNA, creating a break in both strands, a piece of DNA carrying instructions for making cas9 and the gRNA matches up with the cut ends, and the cell heals the cut by inserting the DNA containing instructions for cas9 and gRNA. The genes are then self-replicating once they are in the genome. The genome begins to make Cas9 and gRNA. With normal inheritance of altered genes, the alteration is never really shown in the population... some will show it, some will be carriers, and some will be neither... but with gene drive inheritance, if you get the alteration from one parent, it inserts itself into the other parent strand so now you are homozygous and not heterozygous and have more than a 50 % chance of passing it on (altered gene is almost always inherited)

Describe the genetics of Calico cats:

In cats, one of several genes encoding coat color is located on the X chromosome. XB is orange and Xb is black because orange is dominant to black. But, XBXb does not give you orange, instead it gives you orange and black but almost only in females... why? Males are either orange or black because they (mostly) only have one X chromosome. Whatever is on that X is what they are, but females (mostly) have two X chromosomes so what happens? Lyonization: inactivation of one random X chromosome so as to not produce twice the gene product. Barr body: supercoiled X chromosome. With this, 1 of the 2 X chromosomes that a female cat has goes through lyonization and becomes a Barr body. So, when you think you are XBXB, you are actually only XB because the Barr body cannot be read... same goes with XbXb. When you are heterozygous, you are either XB or Xb because it is a 50/50 chance which X undergoes lyonization. Timing of methylation of the color gene located on the X chromsome can result in "Piebalding" where large patches of white indicate no color being produced at all. "Piebalding" happends wgen the barr body develops late in development white tortoishell color happens when it develops early. Depending on what time of development the Barr body forms, the cat could show all lots of black and orange, lots of one or the other, or lots of white.

What are the two types of post-TRANSLATIONAL regulation? Describe them:

Modification of amino acids in a protein resulting in structural changes or attachment of other biochemical functional groups Structural ‐ 1. Disulfide Bonds - between cysteine residues in close proximity as a result of a proteins tertiary structure. 2. Proteolytic Cleavage - cleavage of a pre‐protein resulting in a mature, functional protein. ‐ INSULIN ‐ Functional Groups ‐ 1. Myristoylation - attachment of lipid chains resulting in membrane localization of a protein. 2. Phosphorylation - attachment of phosphate groups to specific amino acids resulting in regulation of enzymatic activity.

Describe RNA processing as (post-transcriptional regulation):

Process where primary transcript RNA (nascent RNA) is converted to mature messenger RNA (mRNA). 1. 5' capping - when a growing RNA chain is 30 nucleotides long, a guanine group is added to the 5' end by capping enzymes. - the cap protects the growing RNA chain from degradation by nucleases. - this entire process occurs co-transcriptionally, or before transcription is finished. 2. 3' tail polyadenylation - nascent RNA is cleaved by ribonuclease downstream of the conserved AAUAAA site. - Poly(A) polymerase adds adenine ribonucleotides to the 3' end of the RNA molecule. Functions: enhance the stability of the RNA molecule and regulate transport to the cytoplasm. 3. RNA splicing - splicing: the mechanism by which introns are removed. -introns: intervening sequences of RNA not expressed in proteins. -exons: retained in mature mRNA and are the expressing sequences. -spliceosomes: protein/ RNA complex that directs and insures proper RNA splicing. responsible for both cleavage of the intron from the RNA and ligation of the remaining exons. 4. RNA transport -export of mature mRNA is controlled by a large number of Messenger Ribonucleoproteins (mRNPs) -mRNA export is through large multi-protein pore complexes. 5. miRNA -Nature microRNA (miRNA): a class of naturally occurring, small non-coding RNA molecule whose main function is to downregulate gene expression. -first identified around 2001 - approximately 20-25 nucleotides in length. -perturbed expression in tumors compared to healthy cells. -deregulated in different types of cancers making them highly useful as biomarkers in future diagnostics as well as attractive drug intervention targets.

Describe the controversy of CRISPR Technology:

Pros: - CRISPR Technology has proven to help animals with duchenne muscular dystrophy. - control disease - pest-specific pesticides - reduce rodent population - control invasive species - aid threatened species Cons: - How far is too far? Should we be able to genetically modify babies? - He Jiankui claimed to be the first person to edit humans. What he actually did was took the sperm and egg of a man with HIV and an unaffected woman and fertilized them. He edited the affected gene within the male sperm and went on with the birth waiting to see if the child would have HIV or not. This trial and error is not good. - literally anyone with $200 can buy a CRISPR kit and do whatever they want to their genome. This could include making their cells immune to antibiotics... imagine a doctor having to treat a virus that is immune to antibiotics. - gene drives can lead to major changes in populations... Bier and Gantz used gene drive to make fruit flies yellow. within 10 generations, ALL fruit flies were yellow. yellow fruit flies would not survive in the environment and this would mess with the entire food chain.

What are the two types of regulation of gene expression? Describe them:

Regulation of Gene Expression includes a wide range of mechanisms used by the cell to increase or decrease the production of specific genes. Up‐Regulation - process which results in INCREASED expression of one or more genes Down‐Regulation - process which results in DECREASED gene and corresponding protein expression.

describe termination as a step of translational regulation:

Ribosome reaches a STOP codon and Release Factor binds to the ribosome. Polypeptide chain is hydrolyzed from the ribosome and the protein is released from the ribosome.

How can we use CRISPR to "edit" genes?

Since we know the DNA sequence of eukaryotic organisms, if we want to do something to a specific gene we make a Proto-sequence (crRNA) which is a complimentary RNA sequence plus the palindromic repeats to make guideRNA (gRNA). This gRNA is produced by the plasmid (circular dsDNA that we have engineered) after it has been inserted into the cell and enters the nucleus. The gRNA is an exact match to some place with the eukaryotic genome. It knows where it needs to go by looking for the Protospacer Adjacent Motif (PAM) which is a sequence of 5' - NGG - 3' (one random base followed by two guanines). This site must be there for endonuclease activity (this is where the DNA will be cut.) Then, the DNA is put back together either by Non-Homologous End Joining or Homologous Recombination.

Where do most mutations occur?

Somatic Cells - non-sex cells; any mutations that occur here during the lifetime of the organism, depending on the stage of development, can have differential effects on phenotype ranging from silent to sever. However, any effect is only felt by that organism and the mutation is not passed on to the next generation. Germ Cells - sex cells/ gametes; mutations occurring affect the DNA which is carried in the sperm or the ova and thus is passed on to the offspring depending on the mode of transmission. Your offspring may not know it and may just be a carrier, but it WILL be passed on.

What is meant by the phrase "structure gives rise to function"? With this, what would happen if the structure was changed?

Structure or configuration of a peptide chain confers its function. Therefore, if you change the sequence pf the DNA or alter the structure of the polypeptide chain, you MAY alter the function of the resulting protein.

List and describe some of the cis-acting factors in transcriptional regulation:

TATA Box - DNA sequence found in the promoter region where Transcription Factor Complex proteins bind, specifically TATA Binding Protein. Promoter - region of DNA located upstream but near the transcription start site of a particular gene that initiates transcription. Enhancer - region of DNA that binds to Activator Proteins (trans-acting) to activate the transcription process. Silencer - region of DNA that binds to Repressor Proteins (trans-acting) to prevent binding of RNA Pol II to the promoter. Insulator - region of DNA that blocks the interaction of enhancers with promoters.

If CRISPR is there and a bacteria infects a cell, describe what would happen:

The bacteria would punch a hole in the cell wall and inject its DNA into the cell. If CRISPR was there, and it recognized the DNA (has a unique spacer that matches up with it), cas genes will begin to make proteins and a piece of RNA (crRNA). This crRNA is a perfect complementary match to one of the strands of viral DNA. When these get matched up, the cas genes will interact with the viral DNA, helicase will open it up, and the crRNA will complementary bind to the DNA. The endonuclease activity will eat up the DNA (no more viral DNA = no more viral proteins = no more virus.

If CRISPR was not there and a bacteria infects a cell, describe what would happen:

The bacteria would punch a hole in the cell wall and inject its DNA into the cell. If CRISPR were not there, the bacteriophages would continue to multiply, and the cell would eventually explode.

Describe how your diet can affect your epigenome and describe the example with the agouti mice:

The food we eat is turned into nutrients for our body. These nutrients can consist of folic acid and B complex vitamins which are methyl donating nutrients. Methyl donating nutrients regulate gene expression. These mice pictured are genetically the same agouti mice, but they have different diets. The one on the right has an agouti gene that made its brown color and then its promoter got methylated. Because of this methylation, it is now silenced for the rest of its life meaning that it will be a healthy brown mouse. The one on the left has an agouti gene that has never been methylated (it is constitutively active) meaning that it is an obese yellow mouse and it predisposed to cancer and diabetes. One unhealthy yellow mouse was bred to another unhealthy yellow mouse, with its normal diet and no supplements. Its offspring were mostly unhealthy yellow mice. However, another unhealthy yellow mouse was bred with another unhealthy yellow mouse, but during her pregnancy, she was supplemented with food rich in methyl groups. Most of her offspring were healthy brown mice! Two of these healthy brown mice were bred with a normal diet and no supplements and they had all healthy brown mice. Methylation protection extends beyond the F1 generation into the next. Epigenetic modification can be passed across many generations = epigenetic memory.

Describe Control CRISPR/ Cas9 Plasmid:

The red portion is the complimentary copy we want to affect, right next to it is the guide RNA, the promoters are involved in making Cas 9, the nuclear localization signal is used because Cas 9 must get to the nucleus, and the green portion is the only portion not needed, but is there to help us see which cells have been affected by cas 9 and gRNA... it allows us to track growth (fluorescent).

What did Dr. Doudna and Dr. Charpentier do?

They took Cas 9 and used it to make RNA for a specific protein and "edit it". They used Cas 9 because it has both the helicase and endonuclease functions. They won a Nobel Prize in chemistry.

Describe transcription factors as a part of transcriptional regulation:

Transcription Factors - control the rate of gene transcription either by helping or hindering RNA Polymerase binding to DNA. Interact with other proteins to build a Transcription Complex that may increase transcription as much as 100‐fold. Contain DNA Binding Domains in their tertiary structure that attach to specific DNA sequences. A single gene may have multiple binding sites for distinct transcription factors (ie. multiple Transcription Factors can affect expression of a single gene).

Describe homologous recombination (HR):

a DNA template is added to the mix with sequence matching the areas flanking the target site. Allows precise mutations to be inserted. We use this to KNOCK IN genes.

What is an in-frame mutation?

a mutation in which there is a gain or loss of a nucleotide or trinucleotide set that does not change the reading frame of the codon

What is a frameshift mutation? Give an example:

a mutation in which there is a gain or loss of a nucleotide that result in change in the reading frame of the codon. Example: - Crohn's Disease

What are transposable elements? Who were they discovered by?

a piece of DNA (transposons or "jumping DNA") that moves and sits somewhere else in the genome. "mobile DNA sequences that often generate some type of mutation when they move from one location to another on a chromosome in evolutionary terms, can increase the size of the genome." originally thought of as junk DNA, but they do have some sort of regulatory function and DO MAKE PROTEINS which allow them to move. They do code for proteins. They were discovered by Barbara McClintock with her work on maize. She called it the "mobile genetic element."

Can we change the epigenetic profiles of specific genes (can we cause the methylation of specific genes)?

cancer is uncontrolled cell growth. cancer cells have lower levels of methylation than healthy cells and activation of genes promoting cell growth. More methyl = cells OFF, so if we could target which cells to methylate, we could turn off cancerous cells.

What are cas genes? what are their functions?

cas genes are CRISPR Associated genes. Some of them function as helicases (unwind/ unzip DNA), some as endonucleases (cut out the backbone of DNA), and some as both. Each type of bacteria has its own unique cas genes.

What are chemical changes as a spontaneous mutation? What are the two types of chemical changes?

chemical changes: mutations caused by normal chemical reactions that occur in the cell. Depurination: a chemical reaction in which a beta N-glycosidic bond is cleaved by hydrolysis causing the release of an Adenine or Guanine from a DNA strand. (LOSING A PURINE) Deamination: the hydrolytic removal of an amine group from a nucleotide releasing ammonia and converting the nucleotide to another molecule. (LOSING AN AMINE GROUP) *the most common single nucleotide mutation in DNA!

Describe Non-Homologous End-Joining (NHEJ):

end of the DNA strands are directly ligated back together, often results in insertions or deletions... most likely disrupts the protein production, so we are KNOCKING OUT our genes with this process.

What are some factors that really affect your genome?

environmental factors diet physical activity or lack of physical activity toxins stress level ALL of this adds up to come together and make your epigenome

what are two types of insertions/ deletions?

frameshift mutants and in-frame mutants (within these we have silent, missense, and nonsense)

Describe environmental factors as an induced mutation. Describe free radicals as an example:

free radicals are very unstable and quick reacting molecules that steal electrons from nearby molecules such as our DNA. Many environmental factors can lead to the formation of free radicals such as UV light, smoking, metabolism, radiation, etc. We try to take in antioxidants (have LOTS of electrons) to combat these free radicals. UV light causes pyrimidine dimers (dimers of thymine mostly) by the formation covalent linkages localized on cysteine double bonds. These double bonds are not between strands, but between two pyrimidines on one strand and make a hump. DNA polymerase cannot read over this hump and this leads to replication errors (induced mutations) and even skin cancers.

Gene expression determines a cell's _______________.

function

What are two types of functional mutants?

gain/loss of function mutants and lethal mutants

What is the difference between the genome and the epigenome?

genome: the genetic material of an organism epigenome: record of the chemical changes to the DNA and histone proteins of an organism. Your genome is given to you at birth as a combination of both your parents genomes and epigenomes; however, your epigenome builds throughout your life due to environmental and chemical factors.

Describe hormone control of gene expression as a part of transcriptional regulation:

hormone: molecule that is produced in one cellular location but whose effects are seen in another (exp: glucocorticoid, testosterone, estrogen, etc.) hormones require the target cell to have receptors specific for that hormone. NO RECEPTOR = NO RESPONSE exp: estrogen controls expression of many different kinds of proteins such as cell cycle proteins and heat shock proteins. When estrogen levels are low, chances of osteoporosis increase, but when estrogen levels increase, chances of cancer increase. Signaling pathways can interest and be positive, negative, or both!

Describe the insulator as a promoter-proximal element:

insulators prevent transcription of non-target genes by binding to block the enhancer on one side or the other. They can prevent DNA from twisting and allowing specific enhancers to get close to specific promotors.

Describe slipped strand mispairings as a replication error (spontaneous mutation):

involves denaturation and displacement of DNA strands that results in mispairing of complimentary bases.

Describe the enhancer as a promoter-proximal element:

looping of DNA brings transcription factors and trans-activating factors together. Leads to higher efficiency transcription of gene of interest.

Describe non-autonomous Non-Long Terminal Repeat Transposons:

must "borrow" reverse transcriptase from autonomous Non-Long Terminal Repeat Transposons in order to move. SINEs (Short Interspersed Elements) Short DNA sequences (100-400 base pairs) that represent reverse‐transcribed RNA molecules originally transcribed by RNA polymerase II. Represent some 10% of our total DNA. The most abundant SINEs are the Alu elements consisting of a sequence that contains a site that is recognized by the restriction enzyme AluI.

What is a lethal mutation?

mutation that leads to the death of the organism carrying the mutation.

Describe "wobble" as a replication error (spontaneous mutation):

non-complimentary bases can pair due to the flexibility if DNA double helix which can accommodate slightly misshaped pairings

What is negative eugenics?

played on the worst fears of race and social degradation. -limited procreation -marriage restrictions segregation - forced sterilization - euthanasia - prenatal care for only a few

Can males pass down epigenetic memory as well?

probably... not much research has been done on it besides the study of the shortage of food for paternal granddads between the ages of 9 and 12 affecting the lifespan of grandchildren. food shortage = increased lifespan plentiful food = decreased lifespan due to an increased risk of heart disease and diabetes epigenetics???

describe how a gene codes for a functional protein in a prokaryotic cell:

prokaryotic organisms: single cell organisms lacking a defined nucleus. -free floating DNA in the cell because these cells do not have organelles (nucleus or mitochondria) -transcription, translation, and protein formation occur almost simultaneously. -when the protein is no longer needed, transcription stops. -regulation of transcription is the primary methos of controlling gene expression.

What is a gain-of-function mutation?

results in a gene product that has gained a new and abnormal function. (Neomorphic: a new or different function than normal). These mutations are typically dominant.

What is a loss-of-function mutation?

results in a gene product with little or no functionality (Amorphic: complete loss of gene function) Most of the time, these phenotypes are recessive.

What are the three types of insertions and deletions?

silent, missense, and nonsense mutations

What is the core promoter?

site of TATA-binding protein and basal factor binding; responsible for basal level of expression; binding by general transcriptional factors.

What is the promoter-proximal element?

site of additional activator protein binding; responsible for induced/ repressed level of expression; binding by tissue specific transcription factors. can lie far away (few hundred base pairs) from the gene of interest. retains its function even when element is reversed. DNA is flexible... promoter-proximal element can loop around to get close to it. It can also be on either strand or flip if needed... either strand can be template.

What is the histone code complex?

the hypothesis that transcription of DNA is regulated in part by specific chemical modifications to histone proteins. modifications to the histone proteins themselves recruit other proteins to the modified histone. The recruited proteins act to alter chromatin structure or affect transcription.

What are two types of substitution mutations?

transition mutant and transversion mutant

What is wrong with eugenics scientifically?

who decides which characteristics are desirable? there is no way to distinguish between traits that are good and bad.