Genetics Final

who broke the code

. In 1961, Marshal Nirenberg and Heinrich Matthaei deciphered the first codons, the beginning of "breaking the code."

What does the control help discern from the experimental group in this experiment?

....

What is the consequence of a tautomeric shift causing cytosine in in its amino acid form to pair with adenine?

....

How many Barr bodies would you expect to find in an XX cell in which the gene Xist had been inactivated (from both X chromosomes)?

1

Up to how many phosphates will we find bound to a sugar and nitrogenous base?

1

nitrogenous base attaches at the ____ C

1

MC1R1/MC1R2

1 "dose" of eumelanin

Homologous pair:

1. both are the same size and have the same centromere locations (except sex chromosomes) 2. early pairs or synapses in early states in meiosis 3. identical linear loci

Nucleosomal chromatin mods:

1. changing nucleosome composition 2. acetylation 3. chromatin remodeling by repositioning and opening spots on the chromosome to be transcribed

Assumptions for epistasis

1. discontinuous variation: distinct phenotypic classes are made that are clearly discernible for all others. 2. genes in a cross are not linked and assort independently 3. When we assume that there is complete dominance, with AA and Aa giving the same phenotype: A- or B- because either allele can be there without affecting the phenotype. 4. If all P1 crosses are homozygous (no matter the combo), all P2 will be AaBb 5. heterozygous parents are the main focus: 9 A-B- 3 A-bb 3 aaB- 1 aabb

initation

1. mRNA and IF1 bind to the small subunit 2. IF2 and IF3 binds to the complex and tRNA fmet binds to the mRNA codon in the P site 3. large subunit binds to the initiation complex, IF factors are released and EF-Tu binds to the tRNA, facilitating entry into the A stie. Once initiation is set, the reading frame is in place because the initial AUG start codon and the initial tRNA are in the P site of the ribosome. (We won't be focusing on all the additional factors that help with initiation.)

mendels rules

1. need a unit factors (exists for traits) 2. dominant and recessive traits 3. random segregation. 4. independent assortment

Chargaff's rules. What are these?

1. the amount of Adenine is proportional to T and G is proportional to C 2. A+ G = C + T 3. G + C dne A + T Refuted the tetranucleotide hypothesis and helped Watson and Crick make their model.

What is the leading hypothesis as to why there is a correlation with maternal age and Down Syndrome?

1/30 at age 45. Nondisjunction occurs more frequently over the age of 35. Meiosis is initiated in all of the eggs of a female when she is a fetus, and is arrested in development in meiosis I. Meiosis II continues in one age during each menstrual cycle. Older eggs are arrested in meiosis I longer.

What appears to be the function of the poly A tail for transcripts?

10-35 ribonucleotides from a highly conserved AAuAAA sequence. RNA transcripts degrade without it and cant travel.

BACs:

100-300 kb. Low copy number

Nucleosome core particle:

11 nm by 6nm 147 bp, linked together with H1 histone of 2 nm DNA. Coils around an octamer of histones. First level of packing. DNA helix is reduced to 1/3 of its original length.

Dominant epistasis:

12:3:1

A case of dominant epistasis gives a ______ratio.

12:3:1 a dominant allele at one genetic locus masks the expression of alleles at a second locus. AaBb x AaBb = 12/16 white, 3/16 yellow, 1/16 green.

Duplicate:

15:1

How long should the primer be? Sufficient GC content? Do primers have similar GC content so that they will anneal at same temperature?

18-22 base pairs so that it is specific but binds efficiently. 50% GC to anneal. in 3 to 5 direction. need the GC to make hydrogen bonds to hold on to the template DNA strongly. What is the consequence of a tautomeric shift causing cytosine in in its imino form to pair with adenine?

What is the phenotype of a heterozygote if there is incomplete dominance?

1:2:1 ratio for hetero cross. No dominance, so phenotypic ratio is the same as the genotypic ratio. Will be a cross/intermediate between the traits (ex pink)

MC1R1/MC1R1

2 "doses" of eumelanin

___RNAP polymerase is recruited to the promoter ___Pre-initiation complex recognizes and binds promoter ___RNA is synthesized ___DNA is unwound

2 1 4 3

If the non-disjunction occurs in meiosis II, how is this different?

2 normal (disomic), 1 trisomic, and 1 monosomic

During meiosis, if the non-disjunction event happens in meiosis I, what is the outcome?

2 trisomic gametes and 2 monosomic gametes (disomic is normal for gametes)

There are four bullet statements in the introduction.

2+ alleles for a locus in the population dominance may not be complete 2+ genes affect a single trait Expression is dependent on the interaction of 2+ genes, on interactions of genes with nongenetic factors, or both

How many alleles does one diploid organism have for a gene for the ABO blood type? How many alleles exist in the population?

2, 3

How many subunits make up a ribosome?

2. large and small.

Based on what scientists can accurately measure t this point, how many human conceptions lead to spontaneous abortion?

20% And how many of these are due to chromososomal imbalance? 30%

If you could build a protein with 10 amino acids, and any amino acid could be at each position, how many variations are possible?

20^10

YACs:

230-1900 kb

Plasmids can only accept

25 kb DNA max.

After calculated the chi square value, you find that p = 0.26, how do you interpret this?

26% probability value. Will exhibit 26% of this chance deviation in other experiments These deviations from the expected values (567, 189, 189, and 56) are: not due to chance

Trihybrid ratio:

27:9:9:9:3:3:3:1

When two yellow mice are crossed in Figure 4-3, what phenotypic ratio is found? What mendelian ratio is altered here?

2:3 to 1:3. AA AAy AyA AyAy (lethal) 2:1:1

calculating uniqueness

2^n gametes, then square that for random fertilization, then crossing over in prophase I

Number of possible gametes is

2^n, where n is the haploid number.

Why is monosomy so lethal?

2n-1. (turner syndrome). Develop more slowly, reduced body size, impaired viability. They have one copy of all genes, so if it is lethal and recessive, it is unmasked and results in death.

meiosis with 2n=4

2n=4 Anaphase I: dyad is pulled toward each pole of the dividing cell. Ends with a series of dyads that equal the haploid number in each pole. Telophase I: nuclear membrane forming around the dyads. Meiosis II: Prophase II: each dyad is composed of one pair of sister chromatids attached by a centromere Metaphase II: centromeres on metaphase plate Anaphase II: sister chromatids are pulled to opposite poles. Telophase II: one member of each pair of homologous chromosomes. Monad (one sister chromatid). 4 haploid gametes/meiotic event

elongation translation

2nd tRNA bonds to the A site and the amino acids are linked in peptide bonds amino acid moves from the P site to the A site, and the mRNA moves three nucleotides so that it is held in the P site, and the first tRNA moves into the E site.

direction of phosphodiester bond

3 to 5. covalent bonds between sugar and phosphate on the OH groups

During replication, because the RNA primers are removed, a gap is found on the

3' (lagging) strand. Normally the gap would be filled in with a new nucleotide, but the final gap has no fragments left to add it. Gap remains on the lagging strand, causing the double-stranded end to be shorter in each daughter cell. Could go beyond the telomere to delete gene-coding regions.

If DNA is going 5 to 3, RNA formed by adding to the

3' end, and T changes to U.

template strand is

3' to 5' The location of the promoter determines which one is the template.

human genome size and number of genes

3,200 Mb, 20,000 genes

Solenoid:

30 nm. Second level packing. 6x compacter. Seen in interphase of mitosis. Solenoids are folded into looped domains. 300 nm.

Each time it divides, an average cell loses _______base pairs from the ends of its telomeres.

30 to 200

________ of mutations that cause human diseases are single base-pair nonsense mutations

30%

Approximately what percent of genes in the human genome undergo alternative splicing?

30-60%

Hershey and Chase also conducted a very informative experiment that complemented the ones above. In their experiment, ____ labeled the DNA and _____ labeled the proteins of phages.

32 P, 35S

Together LINES and SINES make up what percent of the DNA of the human genome?

34%

Which phenotypic ratios are associated with crosses dealing with a single genetic locus? Select all that apply. 9:3:3:1 3:1 1:1:1:1 1:2:1 1:1 9:7 9:3:4

3:1 - monohybrid cross 1:2:1 - incomplete dominance/co-dominance monohybrid cross 1:1 - heterozygous test cross

phage vectors are also used:

45 kb max.

If you had an oligonucleotide that had 17 nucleotides, how many variations would be possible? Show your math:

4^17

chain elongation occurs in the

5' to 3' direction

The ribosome moves down the mRNA in the

5' to 3' direction and synthesizes protein in the direction of carboxyl terminus to amino terminus.

5' end: 3'end

5'Gp... everything is the same: pCpCpA-3'.

Phosphate group: attached to the _____________ of the pentose sugar. Possesses a _______________ charge at physiological pH.

5, negative

4. Human embryonic stem cells (hESCs) can be isolated from an embryo at what stage?

5-7 days after fertilization. 30 cells that form the inner cell mass witin the 100 celled blastocyst

How does the percent of human genome containing transposons compare to the amount coding for genes?

50% transposable vs 2% for genes LINES and SINES 30%

when the loci of two linked genes are far apart, the number of recombinant gametes approaches

50%, but does not exceed it

LINES (long interspersed elements):

6kb in length, repeated 850,000 times (retrotransposons) Ex. Li family 6,400 bp x 100,000

How many different skin tones would be possible with these three genes and one kind of pigment?

7

There are 3 exons in a gene. How many different proteins are possible?

7: 1, 2, 3 1, 2 1, 3 2, 3 1 2 3

SNP (G or C) is 8 m.u away from the β-hemoglobin gene Therefore, recombinant frequency (RF) =

8% This means that there is only an 8% chance of GB and Cb (recombinant) appearing in total phenotypic ratio of 100. Thus GB = 4% and Cb = 4% The remaining 92% will be the parental phenotypes: Gb and CB. Thus, 46% will be Gb and the remaining 46% will be CB

dihybrid cross

9/16 Both dominant 3/16 One dominant; one recessive 3/16 One recessive; one dominant 1/16 Both recessive

The crab-eating rat (Ichthyomys pittieri) has 92 chromosomes per diploid cell (2n=92). How many chromatids and how many chromosomes are there in a crab-eating rat cell that is in prophase of meiosis II?

92 chromatids and 46 chromosomes

Recessive epistasis:

9:3:4

Dominant:

9:6:1

Complementary interation:

9:7

Negative control

= expected outcome will have no response. griffin: heat killed IIIS with IIR cells

TRANSITION

= purine to purine

TRANSVERSION

= purine to pyrimidine or vice versa

3. Using Fig 7-1, explain what happens when two genes on two different chomosomes independently assort, how many combinations are possible?

A B A B a b a b 4: AB, Ab, aB, ab

H substance

A and B antigens are sugars that are bound to fatty acids that protrude from the membrane of the red blood cell. A and B antigen specificity is based on the terminal sugar on the H substance. If H is incompletely formed, the enzyme that adds the terminal sequence cannot bind: O, Bombay phenotype. Homozygotes cannot produce H substance. So, if they have I A and or Ib, they cannot be added to the cell surface. So its is O, even though parents are AB

They have a carrier test.

A couple is thinking about starting a family and is worried that they might both be carrying a recessive allele for sickle cell disease.

What is the difference between a gene and an allele?

A gene is a stretch of DNA that determines a certain trait. Genes mutate and can take two or more alternative forms; an allele is one of these forms of a gene. For the most part, we each get two copies of each gene (such as the leptin receptor gene). And thus, we get two alleles that may be the same or different. BUT, there are a pool of possible alleles in the population. We only get two alleles (forms of the gene) because we inherit one from mom and one from dad.

What was Nina Jablonski's hypothesis about the evolution of dark skin color?

A lack of folate causes birth defects and pregnancy. UV damages folate and leads to poor reproductive success. Skin has eumelanin to protect from UV damage of folate.

positive control for ames test

A mutagen (chemical) that is already known to cause mutations.

Kozak Sequence:

A or G three bases upstream from the AUG followed by a G. interacts with tRNA.

What does ubiquitin do?

A protein that tags other proteins for degradation by proteolytic enzymes.

What is haploinsufficiency?

A single copy of a recessive gene is insufficient for function

nucleosome

A structure composed of two coils of DNA wrapped around an octet of histone proteins. The nucleosome is the primary form of packagin of eukaryotic DNA. beads

Cytosine deaminates and becomes uracil which then pairs with adenine. Does deamination result in a transition or a transversion?

A) Transition

What if the two genes are linked on one chromosome and there is no crossing over between homologs (complete linkage). How many combinations are possible?

AB ab

Lastly, what if the two genes are linked on one chromosome and there is a crossover between two non-sister chromatids. How many combinations are possible? Which are the recombinants?

AB (non crossover) Ab (crossover) aB (crossover) ab (non)

Shine Falgarno sequence:

AGGAGG base pairs with 16S rRNA of the small ribosomal subunit that starts initiation.

5. Mutations in what gene were discovered that keep triglyceride levels low?

APOC3. The scientists found four mutations that destroyed the function of this gene

Degrading and stabilizing complexes:

ARE (adenosine-uracil rich element=stabilizer).

Real therapy based on stem cells is seen with bone marrow transplants, which contain what kind of stem cells?

ASCs.

What did Chargaff's data about nitrogenous bases reveal?

AT and GC in same proportions. Can calculate all the values if you have one

nuclein

Acid substance containing DNA

What is the relationship between degree of methylation of DNA and degree of gene expression?

Adding or removing DNA methylation from bases in DNA. Usually with cytosine. 2-7% methylated. Inverse relationship. Transcriptionally inert=large amounts of methylation. They inhibit the binding of transcription factors to DNA and can make chromatin remodel on the gene regulatory regions.

why use a centrifuge in the Hershey and Chase experiment?

After the phages had infected the bacteria, they were blended up to separate the phage particles from the bacteria and centrifuged. Blender to separate phages outside the bacteria from the cells and their contents. The bottom part is the cell, the top is the phage shells. radioactively labeled DNA on the bottom after centrifugation.

What is the purpose of these characteristics of cloning vectors? a) Several different kinds of restriction sites ("multiple cloning site")? b) Selectable marker gene? c) DNA primer sequencing site? d) Origin of replication?

Allow the insertion of DNA fragments to be cloned at many places To distinguish host cells that have taken up vectors from those that have not (usually antibiotic resistance gene or the gene for an enzyme that is absent from the host cell). So that polymerase can attach to replicate DNA So that a replication bubble can be formed and allow for the cloning of DNA

Why would a scientist do a complementation analysis? Give an example with fruit fly wings:

Allows us to find two mutations both of which produce a similar phenotype are isolated independently. Whether they are from the same gene or not. Find out by crossing two mutant strains and analyze the F1 generation. Ma or mb.

Why is a DNA not required for the cell-free system?

Amino acids are incorporated into a polypeptide chain.

holoenzyme

An enzyme made up of multiple subunits. They have subunits E and 0 that are core enzymes (3 to 5 activity), and a that is responsible for nucleotide polymerization on the template strands. 5 subunits form the gamma complex that loads the enzyme on the template.

What is telomerase and what cells express this protein?

An enzyme named telomerase adds bases to the ends of telomeres. In young cells, telomerase keeps telomeres from wearing down too much. But as cells divide repeatedly, there is not enough telomerase, so the telomeres grow shorter and the cells age. Telomerase remains active in sperm and eggs, which are passed from one generation to the next. If reproductive cells did not have telomerase to maintain the length of their telomeres, any organism with such cells would soon go extinct.

Where would a point mutation have the greatest chance of making the leptin receptor LEP-R non-functional?

An insertion or deletion near the N-terminus.

Down Syndrome most frequently happens as a result of non-disjunction in meiosis I or II?

Anaphase I or II. Normally errors in meiosis I. In the mother or the father during gamete formation? mother

True or false. Most human transposons appear to be inactive.

Appear to be: but mobility and mutagenic effects of transposable elements have far-reaching implications.

What is bioinformatics?

Applies math and science and computing technology to develop hardware and software for storing, sharing, comparing, and analyzing nucleic acid and protein sequence data. Gen-bank.

Gyrase (a type of topoisomerase)-

As the unwinding continues, tension is created ahead of the replication fork, resulting in supercoiling. DNA gyrase makes single or double stranded cuts to the DNA and catalyzes localized movents that undo the twists and knots. Powered by ATP hydrolysis.

Brainstorm three places that could be "valves" to turn up or turn down expression:

At DNA level: more or less transcription At RNA level: more or less translation At protein level: more or less stability of protein

sex linked phenotypes

Autosomal genes are responsible for the contrasting phenotypes displayed by both males and females. But the expression of genes is dependent on the hormonal constitution of the animal. Heterozygous would exhibit one phenotype in F and another in M.

Many forms of DNA exist, but _____ is the physiologically relevant form that Watson and Crick described.

B-DNA

What enzyme hydrolyses lactose? Gene name? If gene is mutated, we abbreviate this as:

B-gal. Lac Z. lac Z-

What kind of gametes can an individual with the genotype Bb;Dd make?

BD, Bd, bD, bd

What kind of gametes can an individual with the genotype Bb;DD make?

BD, bD

1) Why must we use reverse transcriptase on mRNA to obtain the template for a transgene of interest? Why can't we just copy genomic DNA if we know the sequence?

Bacteria lack the enzymes necessary for mRNA splicing, Bacteria are generally unable to accomplish such post-translational modifications, and eukaryotic genes expressed in bacteria may not function properly. The inability of bacteria to perform such modifications has driven scientists to use yeast (Saccharomyces cerevisiae) and eukaryotic cell culture to produce some recombinant products

Eukaryotic cells contain DNA in the mitochondria and chloroplasts (in addition to the nucleus). Is the organization of DNA in these organelles more similar to bacteria or eukaryotic chromosomes? Why?

Bacteria. mtDNA (mitochondrial DNA) is a double stranded circle free of chromosomal proteins that are characteristic of eukaryotic chromosomes. Introns are absent and there are hardly any gene repetitions. Chloroplast DNA (cpDNA): uniform in size. Circular and double stranded, and is free of proteins. Larger than mtDNA. Has introns and duplications.

expression vector

Bacterial RNA polymerase will not recognize a eukaryotic promoter.

What is the definition of dosage compensation?

Balances the dose of X chromosome gene expression in females and males.

Why would this mutation specifically be dominant?

"One bad apple spoils the bunch". The gain of function overrides the one wildtype allele.

predictive test

(family history)

Cell plate

(middle lamella) for plant cells across the metaphase plate. Layers of cell wall added between the middle lamella. For animal: cell furrow.

diagnostic test

(to detect the presence or absence of gene variants linked to a suspected genetic disorder in a symptomatic patient

Why is there a high level of genetic relatedness in the people of Iceland?

Because Iceland was founded 1000 years ago by a small population from Scandanavia. Genetic diversity was reduced by natural disasters and diseases. Not a lot of immigration.

Why are bacterial cells grown on agar plates that also contain ampicillin (amp)?

Because marker genes are resistant to the antibiotics like ampicillin.

If enhancers or silencers are far from the promoter, how do they interact with the complex of proteins that initiate transcription?

Bind to enhancers that interact with other proteins called co activators in an enhanceosome complex, making contact with TF in the PIC. By enhancing the rate of PIC assembly, transcription activators stimulate the rate of transcription initiation. They can also increase the rate of DNA unwinding within the gene and accelerate the release of RNA polymerase from the promoter into the transcribed region.

What is different about each restriction enzyme?

Binds to specific restriction site

A mutation in the -10 (Pribnow) consensus sequence would have what affect?

Both will severely diminish transcription

Scientists have hybridized (complementary base pairing) mature eukaryotic mRNA with the DNA containing the sequence from which the RNA was originally transcribed. What would be similar about them? Different? Draw what their hybridization would look like.

Both would have sequences for the exons No introns, has the tail and the cap. Introns would be extra loops that will be cleaved off. Look like hairpin loops.

PDG has been used for over a decade, what is being described as new in this article?

But some people who believe life begins with conception think P.G.D. is as unethical as abortion and perhaps more pernicious because it is psychologically less burdensome. Unused embryos may be frozen indefinitely, skirting one moral issue, but at a cost of several hundred dollars a year.

pyrimide

C and T. single ring

Deamination causes what kinds of mutations?

C or A becomes a keto group. C becomes U and A becomes hypoxanthine. The base-pairing specifities of those two bases during DNA replication is altered.

pyrimidines

C, T, U

Adding a phosphate group = nucleotide.

C-1/ links the carbon to the nitrogenous base. N-9 atom for purines, N-1 for pyrimidines. C-5' phosphate to sugar.

What does it mean that DNA is antiparallel?

C-5' to C-3' orient in the opposite direction.

A tautomeric shift occurred causing cytosine to pair with adenine. This leads to A) C/G T/A transversion B) C/G T/A transition C) A/T C/G transversion D) A/T C/G transition

C/G --> T/A transition

When glucose is NOT present and lactose is, as we've been talking about all along, where does CAP bind?

CAP exerts positive control by binding to the CAP site

Why would an anti-telomerase drug be useful in treating cancer?

Cancer cells do not senescence after cell divisions. 80% of human tumor cells have telomerase activity. Forces cancer cells to age and die.

O+ rescue?

Cannot rescue Oc because it is cis

What happens to mRNA before leaving the nucleus?

Caps and tails are added and introns are removes and exons are spliced together.

If all offspring develop normal wings, this means what? (Use genotypes from fig 4-9 to explain)

Case 1: All offspring develop normal wings: Two recessive alleles are in separate genes and are NOT alleles of one another. Complementation occurs.

. What is the main function of the rRNA molecules that make up the ribosome and how do scientists know this?

Catalyzes the functions of translation. Promotes the binding of various molecules involved in translation. Based on the observation that some of the catalytic functions in ribosomes even with ribosomal protein-depleted ribosomes.

In fact, CAP does not bind alone (cooperative binding), it is a complex with cyclic adenosine monophosphate (cAMP) and it is synthesized by an enzyme called adenyl cyclase, that catalyzses the conversion of ATP to cAMP.. When this enzyme is inhibited, what happens?

Causes the levels of cAMP in the cell to decline so that CAP cannot make the complex needed to positively control transcription inhibited by glucose

What does "in vitro" mean?

Cell-free

What are the main components of a cell-free system?

Cell-free protein synthesizing system and enzyme polynucleotide phosphorylase. Need ribosomes, tRNAs, amino acids and other translation molecules. mRNA, radioactive AA to trace protein synthesis.

Why do bacteria need a source of carbon?

Cellular respiration (energy) synthesizing new molecules (metabolism)

Recall from our studies of DNA replication that DNA polymerase adds to the 3 end of a growing polynucleotide (thus in the 5' to 3' direction). Is RNA the same or different?

Chain elongation in the 5' to 3' direction.

Chromatin assembly factors are specific to eukaryotic cells, why?

Chromatid consists of 200 bp of repeating DNA base pairs complexed with 8 histone protein molecules. These must be stripped away to allow the passage of replication proteins. As DNA synthesis proceeds, the histones and non-histone proteins reassociate. Assembly is carried out by chromatid assembly factors that move along the replication fork (CAFs).

nucleosomes

Chromatin has a repeating unit that is protected from enzymatic cleavage and is comprised of a linear array of spheres (beads on a string). each has one type of tetramer

Through drawings and words, what is the difference between metaphase of mitosis and metaphase I of meiosis? How is this linked to genetic variation?

Chromosomes are short and thick, tetrad moves to the metaphase plate. Random as to which homologous chromosome gets pulled to which end of the pole (genetic variation)

viral chromosomes

Circular, linear, made of DNA (single or double-stranded), made of RNA (single or double-stranded) Perfectly packed into the head. Genetic material is inert until released in the host cell.

Silencers do what?

Cis acting. Represses the level of transcription initiation.

Enhancers do what?

Cis. Located on either side of a gene, away from a gene, or in a gene. Needed to have max transcription. Responsible for time and tissue specific gene expression.

Why would you ligate a fragment of DNA into a cloning vector?

Cloning vectors: DNA molecules that accept DNA fragments and replicate inserted DNA fragments when placed into host cells. Vectors differ in host cells that they can enter and the size

What does MC1R gene do?

Codes for a protein that changes the type of melanin (eu to pheo) Negative selection in Africa: fixed in the population

What are a few of the important applications of bioinformatics once we have loads to genomic sequence data?

Compare DNA sequences, identify genes and find regulatory regions. Identify structural sequences. Predict amino acid sequences, analyze proteins, deduce evolutionary relationships.

What is cDNA?

Complementary dna copies of only expressed genes

How do the -10 and -35 consensus sequences in the bacteria promoter relate to our theme of evolution?

Consensus sequences: homologous sequences of DNA that are similar in different genes of the same organism or in one or more genes of related organisms. Critical to biological processes. TATAA (-10 region/Pribnow box) TTGACA (-35 regition)

Trans-acting molecules?

Control transcription of the gene cluster. When it binds to a cis-acting site, it can regulate the gene cluster negatively (turn off transcription) or positively.

What is the difference in function between core promoter elements (such as TATA and BRE) and a proximal promoter elements (such as a CAAT box)?

Core promoter: determines the accurate initation of transcription by RNA polymerase II. Can be focused (specify transcription iniation at a single nucleotide. Highly regulated) or dispersed (direct initiation from a number of start sides over a region. constitutive) Proximal promoter elements: modulate the efficiency of basal levels of transcription

How to determine the number of genes that are involved?

Cross all mutants with each other (all homozygous recessive) then cross each mutant with each other (complementation test) self cross will always be negative

What does a restriction enzyme do to DNA structure?

Cuts both strands of DNA by cleaving the phosphodiester backbone of DNA.

Scientists now think that transcriptionally active genes may be located where in a nucleus?

Cycled to the edge of chromosome territories at the border of interchromosomal domains. Brings the genes closer to the transcription factors

What are spindle fibers made of and what is their function in the cell during mitosis and meiosis?

Cytoplasmic microtubules. Run between poles in propase and crease an axis along which chromosomal separation occurs.

Levene:

DNA has 4 nucleotides, tetranucleotide hypothesis. Too little variation to hold all of the information, attn. shifts to proteins.

What are some difference about chromosome structure in eukaryotes that might make replication different compared to prokaryotes?

DNA has nucleosomes and is linear, not circular. Eukaryotic DNA polymerase is slower. Eukaryotic chromosomes have multiple replication origins (replication bubbles).

What is the problem with DNA that is bound to histones and compacted?

DNA is inaccessible to interaction with nonhistone proteins

the enzyme responsible for DNA replication in vivo.

DNA polymerase III

What is a transposon and how could it cause a mutation?

DNA sequences that can move or transpose within and between chromsomes. 50% of the human genome. Insertion sequences (IS elements) can move from one location to another and cause mutations if translocated in the gene coding system. IS produces the enzyme transposase that cuts the DNA to insert IS elements Ends of IS elements contain inverted terminal repeats that are short segments of DNA that have the same nucleotide sequence, but are organized in the opposite direction. 20-40 bp. Act as recognition sites for transposase.

central dogma

DNA to RNA to Protein

PCR

DNA: DNA polymerase, Mg 2+ (cofactor), and the four bases. Sequence information is used to make two oligonucleotide primers: short, single-stranded sequences that are complementary to the 5' end of the target DNA and one to the 3' end. The strand is denatured into two strands and primers bind to complementary nucleotides and flanking the sequence to be cloned. One cycle doubles the number of DNA molecules in the reaction.

What is a Barr body?

Darkly stained body seen in interphase in females but not in males. Highly condensed structure that is against the nuclear envelope. Sex-chromatin/barr body: inactivated X chromosome. Ohno hypothesized that it came from one of two X chromosomes.

dna polymerase direction

Daughter strand is the reference for 5' to 3' for the direction that DNA polymerase moves in.

What does Xist RNA do to the chromosome it is expressed from?

Deactivates the X chromosome. It spreads over the coat of the X chromosome and bears the gene that produced them. What happened when scientists deleted the XIST gene from an X chromosome? Lost its ability to become inactivated.

Molecular hybridization is important in many molecular methods used in the lab. What is meant by this?

Denaturation can be reversed. An RNA molecule will hybridize the segment of DNA from which it will be transcribed. Nucleic acid probes are used to identify complementary sequences.

three steps of a single PCR cycle

Denaturation: double stranded to single stranded DNA. Heated to 95 degrees celcius for about 1 minute. Hybridization/annealing: temperature of the reaction is lowered to 45 to 65 degrees to cause the primer binding to the target DNA. They serve as the starting point to synthesize new DNA. Extension: reaction temp is 65-75 degrees C, polymerase uses the primers as a starting point to synthesize new DNA strands by adding nucleotides to the ends of the primers. Cycles take several minutes, but can start again immediately after completion.

List the similarities and differences between a liver cell and a skin cell from the same person:

Development/differentiation.

Bacteria are haploid, but they used a method that allowed them to make merozygotes, which means what?

Diploid for specific genes. Allows I+ to be added to I- host cell

Diploid:

Diploid is a cell or organism that has paired chromosomes, one from each parent. 2n

helicase-

DnaA unwinds the helix, and its subunits attach to the 9mers (sequence of 9 repeating bases). DnaB and C further open and destabilize the helix. Helicases are proteins that need energy supplied by the hydrolysis of ATP break H bonds and denature the double helixes: helicases.

Which of these above is a test-cross?

Dominant phenotype (Ax) but unknown genotype with a homozygous recessive: so Aa with aa Or AA and aa

How are x-linked recessive disorders different from autosomal recessive disorders?

Dominant: More expressed in males because they only have one copy. Girls have two copies. Y lacks most X genes so they are hemizygous (cannot be homozygous or heterozygous for X-linked genes).

Telomeres are believed to protect the linear chromosomes of eukaryotes from what two outcomes?

Double-stranded breaks that can occur when a chromosome becomes fragmented internally. Double stranded loose ends can fuse to other end, but if they don't fuse, they can be degraded by nucleases. Protect from improper fusion or degradation.

What is the DSCR?

Down syndrome critical region. Genes that are dosage sensitive in the 21st chromosome and responsible for the phenotype. 3 copies of the genes present are necessary. Not sufficient for the cognitive deficiencies. Decreased risk of cancer and tumors. Vascular endothelial growth factor (VEGF) suppressed by a protein.

"I've been diagnosed with mosaic Turner's syndrome. I found out last week after a history of fertility problems. I'm 5ft 7, 27yrs, and show no other typical signs of Turner's, hence the not knowing until now has me shocked. They gave me the actual karyotyping results which show that I have 25% mosacisim (only 25% of cells are XO). where did nondisjunction occur?

During mitosis

What happens in prophase I of meiosis? How is this different from prophase of mitosis?

Each chromosome was duplicated to produce 2 identical sister chromatids. Homologous chromosomes have synapsed, called now, a bivalent (=n). as they condense and shorten, they are now called tetrads (2 pairs of sister chromatids. Crossing over. Nuclear envelope breaks down and centromeres of each tetrad attach to the spindle fibers.

telomeres

Each time a cell divides, telomeres get shorter because DNA cannot be replicated all the way to the end. As telomeres shorten, cells age and ultimately die. shorten at the 5' end

sex development

Embryo: potentially a male or a female, gonadal rediges become genetalia (bipotential gonads). XY: testes. No Y: ovarian tissue.

If the 5'cap or poly A tail were missing from a eukaryotic mRNA, what would be the consequence?

Ends of RNA would get chewed up by nucleases in the cytoplasm. Cap serves as a guiding pole, can't leave to the cytoplasm.

Why would you use an expression vector?

Ensures mRNA expression of a cloned gene with the purpose of producing many copies of the gene's encoded protein in a host cell. Ensures that it is pure

What is different about RNA polymerases in prokaryotes from eukaryotes?

Eukaryotes display three distinct forms of RNA polymerase, each with greater numbers of polypeptide subunits than in bacteria.

What are some of the ways prokaryotes and eukaryotes differ in gene regulation?

Eukaryotes: controlled to express genes at specific times, in specific cells, at specific levels, and in response to the environment. Regulation occurs at many levels (initiation of transcription, mRNA mods, synthesis, stability and mods of proteins Prokaryotes: occurs primarily at the level of transcription initiation

Predict the phenotypic consequence of a gain-of-function mutation in the receptor protein at the cell surface.

Excess cell division

What is pleiotrophy and how does Marfan syndrome illustrate its definition?

Expression of a single gene has multiple phenotypic effects. Marfan syndrome: autosomal dominant mutation in the gene that codes for fibrillin, a connective tissue. Lens dislocation, increased risk of aortic aneurysm, lengthened long bones in limbs.

How could you test to see whether an organic papaya is really transgene-free?

Extract DNA from an organic papaya and do PCR using primers that recognize sequences found only in the viral transgene. If the papaya is really organic, the PCR should not be able to amplify any DNA. You could check this with gel electrophoresis.

True/False? Three different mRNAs are made, one for each structural gene.

False: polycistronic mRNA so that the three genes have coordinated regulation.

mitochondrial inhertiance

Fathers cannot pass to any children; mothers pass to all children- mitochondrial

Xray diffraction was an important tool in the discovery of the structure of DNA. What information was learned about DNA from this methodology?

Fibers of a DNA molecule let the X rays scatter according to the molecules structure. Periodicity of 3.4 angstroms within the molecule. Bases are stacked.

, somatic stem cells are different in a few major ways.

First, they are difficult to find and isolate from adult tissues because they are often sparse within the tissue where they reside; they may be as infrequent as 1 in 10,000 cells. Second, whereas embryonic stem cells can grow and divide indefinitely in a dish with proper care, somatic stem cells do not divide often or easily; they may divide only a few times in a dish before dying. Third, somatic stem cells have less potential than embryonic stem cells. Scientists think they generally only give rise to one or a few cell types. For example, skin stem cells give rise to skin cells, and blood stem cells give rise to a few blood cell types.

1) What is the "mutagenic" method and how does it differ from GM technology?

For some 60 years scientists have been using "mutagenic" techniques to scramble the DNA of plants with radiation and chemicals, creating strains of wheat, rice, peanuts and pears that have become agricultural mainstays. The practice has inspired little objection from scientists or the public and has caused no known health problems. The difference is that selective breeding or mutagenic techniques tend to result in large swaths of genes being swapped or altered. GM technology, in contrast, enables scientists to insert into a plant's genome a single gene (or a few of them) from another species of plant or even from a bacterium, virus or animal.

Because there is no DNA template, polynucleotide phosphorylase will do what when incorporating ribonucleotides into a polynucleotide?

Forces high concentrations of ribonucleoside diphosphates reaction can be forced in the opposite direction to synthesize RNA. Random addition of ribonucleotides based on the relative concentration of the four ribonucleoside diphosphates.

How do you make cDNA?

From mRNA molecules of a cell population and represent the genes being expressed in the cells at the time the library was made. Mix mRNAs with oligo-dT primers, short, single-stranded sequences of T nucleotides that anneal to the poly-A tail. Reverse transcriptase extends the primer and makes complementary DNA copy of the mRNA sequence. mRNA and DNA hybrid, RNA is degraded, and the complementary DNA is synthesized by DNA pol. Can also be synthesized by primers that bind randomly to the mRNA and the first strand of cDNA to eventually create double-stranded cDNA from the original mRNA strand. Inserted into vectors (usually plasmids) but need a linker sequences to insert cDNA into a plasmid

mitosis

Function: Division for growth, maintenance, repair of somatic cells End result: Two identical cells Variation produced? No One equal division Somatic cells use. Consequences when awry: developmental problems, cancer (somatic cell issues)

meiosis

Function: Division to make gametes. End result: Four non-identical, haploid gametes. Variation produced? Yes Two divisions (not equal in oogenesis) Cells in gonads use. Consequences when awry: gametes that are not viable or ones with chromosomal imbalances.

Before we leave transcription, lets consider the different types of RNA that are transcribed. Which are functional RNAs and which are translated?

Functional: Xist, telomerase RNA, tRNA, rRNA, snRNA, microRNAs, siRNAs Translated: mRNA

You are a scientist engineering golden rice. What would you do to ensure that the gene for β-carotene is expressed in the seed endosperm?

Fuse the β-carotene gene to an endosperm-specific promoter.

purine

G and A. double ring

hydrogen bonds to bases

G and C have 3 and A and T have 2

2 consensus sequences in prokaryotes:

GC rich box: -35 and prisnow box: -10 (TATAAT) Eukaryotes: TATA box: -30

What kinds of things are done in testing ideas?

Gathering data (hypothesis, results/observations) interpreting data (supportive, opposing, inspiring, revising the hypothesis)

Genominc, parental imprinting.

Gene silencing occurs during early development. Silencing. Before gametic formation. Imprinting through the next generation depends on whether or not the gene passes through sperm-producing or egg-forming tissue. Imprinting applies to 50+ genes in mammals

What is the role of a cis-acting regulatory sequence in transcription initiation?

Genes do not just turn on and off, there are different levels of flow. Other cis elements beyond the core promoter. The maximal promoter elements, enhancers, and silencers that affect the efficiency or rate of transcription initiation.

Two ways to change expression of GR protein:

Genetic Mutations, take away genes, affect silencers/enhancers Epigenetic alter chromatin (methylation, acetylation)

What is GenBank?

Genomic database. Largest publically available. 100 biollion bases from over 100,000 species.

Anti codon and amino acid for mRNA 5' GAG

Glu. Anti codon is CUC

What molecule does IPTG mimic?

Gratuitous inducers: chemical analogs of lactose such as the sulfur analog isopropylthiogalactoside that behaves like natural inducers but do not serve as substrates for the enzymes that are subsequently synthesized.

What molecule does IPTG mimic?

Gratuitous inducers: chemical analogs of lactose such as the sulfur analog isopropylthiogalactoside that behaves like natural inducers but do not serve as substrates for the enzymes that are subsequently synthesized. Constitutive mutants: gene is produced continually.

DNA 3 big experiments

Griffith Avery MaCleod, McCarty Hershey & Chase

After selecting the right colony, how do you get HGH protein?

Grow each colony in individual culture. Isolate plasmid DNA. Cut with EcoRI. Run gel.

What happens when an individual is homozygous dominant for familial hypercholesterolemia?

Hetero: defect in low-density lipoproteins (LDL) receptors. Too little cholesterol is taken up by cells from the blood. Elevated plasma levels of LDLs. Heart attacks. Homo: way more heart attacks. 10 times normal LDL levels

What is the major difference between regions of DNA of a chromosome that are identified as either heterochromatin or euchromatin? Where would you find heterochomatin?

Heterochromatin: condensed. Inactive. Lacking or repressed genes. Replicates later in the S phase than euchromatin does. Uniquely eukaryotic. In the inactivated X chromosome in mammalian females, the Y chromosome, and the centromeric and telomeric regions of chromosomes.

How does an environmental condition such as temperature alter phenotype? Give an example.

Himilayan rabbit and Siamese cat: enzymes only active at lower temperatures (temp sensitive allele). Permissive condition: 25 C Restrictive condition: 42 C

Homologous chromosomes:

Homologous chromosomes are similiar but not identical. Each carries the same genes in the same order, but the alleles for each trait may not be the same.

Which alleles mask other alleles in blood

Homozygous presence of the mutant form of FUT1 masks the expression of Ia and Ib. They need at least one wildtype FUT1 to express A or B. those who lack it are O.

Although someone who is a carrier of Tay-Sachs disease is phenotypically normal, why might we see an intermediate at the gene product level?

Homozygous recessive individual are severly affected with a fatal lipid storage disorder. Almost no activity of the enzyme hexosaminidase in afflicted individuals. Heterozygotes extress 50% of the enzyme but are phenotypically normal. haplosufficient

Why are most affected individuals with an autosomal dominant disease usually heterozygotes (Aa) and not homozygotes (AA)?

Homozygous two affected copies = lethal. More common cross

Gene R (let's assume it is an enzyme in blood, causing blood clotting) To have wildtype function (that is, a person's blood clots normally) there must be 40 units of this protein. Each wildtype allele has 50 units. Each mutant allele produces 0 units. RR, Rr, rr?

How many units in R+R+ individual? 100 ; normal phenotype? yes How many units in R+r individual? 50 ; normal phenotype? yes How many units in rr individual? 0; normal phenotype? no

tRNAs and mRNA interact through what type of bond?

Hydrogen bonding of tRNAs to mRNA holds the amino acids in proximity so that a peptide bond can be formed.

Give an example of loss of function mutations that might occur in the lac operon:

I- (repressor cannot repress) Z- (B gal doesn't break down) Y- (permease doesn't let lactose into cell)

Is masks

I- and I+

FOUR WAYS TO CHARACTERIZE MUTATIONS:

I. Molecular changes (missense, nonsense, silent, transition, transversion, frameshift) II. Location (somatic/germline) III. Phenotype (Loss of function, null, gain of function, regulatory, lethal, neutral--altered/lower protein) IV. Spontaneous/Induced

How do the patterns of inheritance change if the gene is on the X chromosome and it is a recessive disorder?

If it is sex-linked, males are more affected but never pass from affected fathers

Do both the leading and lagging strands of the DNA get replicated at the same time? How?

If the leagging strand is spooled out to form a loop, nucleotide polymerization occurs on both template strands under the dimer enzyme. Looping inverts the orientation of the template but not the direction of the actual synthesis. The clamp maintains the processivity of the enzyme (the number of nucleotides that may be added during synthesis before the enzyme dissociates.

Why are DNA primers used for PCR rather than RNA primers?

If you used RNA primers, you would have to remove them after replication. This would lead to a shortening of the fragments (similar to what happens at the end of telomeres - but there's no telomerase equivalent in PCR to fix this!). Using DNA primers eliminates this problem since they don't have to be removed and instead stay as part of the duplicated fragments.

in a heterozygote, a phenotype is mutant if the mutant allele was inherited from a mother. If the mutant allele was inherited from the father, the phenotype was wildtype. Although both are heterozygotes, they have different phenotypes. This would be an example of parental imprinting and is caused by what at the DNA level?

Imprinting: thought

How are bacterial genes for the lactose metabolism organized on a bacterial chromosome?

In clusters and transcription of these genes is under the control of a transcription regulatory region.

complex eukaryotic genes

In complex eukaryotes, genes are farther apart with non-coding DNA in between genes. (Genes are larger and with more exons too.)

In eukaryotes, how is the 5' cap on the mRNA related to translation?

In eukaryotes, translation occurs on larger ribosomes whose rRNA and protein complexes are more complex. They share core sequences in rRNA, but are lengthened by expansion sequences in eukaryotes. In prokaryotes, translation and transcription are coupled, but are separated spatially and temporally in eukaryotic cells. Needed to transport to the cytoplasm.

here in the cell are miRNA and siRNA cleaved by DICER?

In the cytoplasm

Where would we be more likely to find a gene that is actively expressed in the cell?

In the lighter region of the chromosome. Dark: heterochromatin. Very compact with histone. Not active. To be active, it needs to make room for transcription, so it does not have histone proteins and is not compact enough to be visible.

What was the Lyon hypothesis?

Inactivation of X chromosomes occurs early on in somatic cells , randomly. All descendent cells have the same X chromosome inactivated. Observed turtle and calico cats, need two x chromosomes.

As human populations evolved to be more hairless, what happened to skin color?

Increased melanin production.

When histones are acetylated, does transcription increase or decrease? Why?

Increases: modifying the histones with histone acetyltransferase enzymes (HATs), lessening its attraction to DNA. Makes the promoter region available to binding to transcription factors.

translation

Initiation: two subunits, mRNA, and initiator tRNA binds to the start codon (AUG) Elongation: codon recognition, peptide bond formation (from P to A site), translocation Termination: stop codon, everything splits up

tRNA contains a modified nucleotide, inosinic acid or inosine that will sometimes be part of the anticodon. Looking at Figure 13-2, is the nitrogenous base of inosine a purine or pyrimidine?

Inosinic acid: purine Modified after transcription of tRNA (posttranscriptional modification).

Oc overrides

Is

gain of function mutation lac

Is: represses better

What would be predicted for a cell in which the repressor could not bind the inducer Is?

Is= super-repression because lactose binding region is altered. I+ doesn't affect it.

Summarize the components that we need in a human gene being expressed in bacteria:

Isolated GH gene with PCR and engineered in EcoR1 sites with primers Ligated GH fragments into plasmid that is cut with Eco R1 at multiple cloning sites Verifies that we had some transformant clones with out GH gene through Blue and white screen and digest or with PCR

What has the universality of the genetic code allowed scientists to do?

It arose early on (in terms of evolution). Possible to program one species to produce a protein from another species by transplanting DNA

What happens when DNA is subjected to heat?

It denatures and unwinds. Viscosity of DNA decreases and UV absorption increases (hyperchromic shift)

What happens to the sigma unit during the elongation phase?

It dissociates from the holoenzyme and elongation proceeds under the direction of the core enzyme.

Is the lacIs mutation dominant or recessive to the lacI+ mutation?

It is dominant. If the super-repressor is permanently bound, the presence of wild type repressors will not restore inducibility.

Who came up with the operon model?

Jacob and Monod. Negative control whereby a group of genes is regulated and expressed together as a unit.

How is codominance different from incomplete dominance?

Joint expression of both alleles in a heterozygote (MN blood group). DISTINT expression of BOTH, not a combination or intermediate.

epistasis in lac

Julie is incorrect in saying that lacOC is dominant to lacIS because they are alleles of two different genes. Dominance is used to describe the relationships that exist between alleles of the same gene, not of different genes. Rather, this is an example of multiple-gene interaction. The super-repressor can only repress transcription if it can bind to the operator. The lacOC mutation prevents this.

In 1944, Avery, MacLeod, and McCarty published a famous paper concluding what?

Large quantities of IIIS Virulent cells. They were heat killed and a soluble filtrate was left that could induce transformation of avirulent cells. Treated with a protein digesting enzyme (ribonuclease). Distroyes RNA too. Transforming activity still remained. Deoxyribonuclease destroyed the transforming activity, so it was DNA. Capsular polysaccharide is produced in successive generations. Transformation is heritable.

DNA ligase-

Later, RNA primer is clipped out and replaced with DNA under the direction of DNA polymerase I. Unites okazaki fragments into the lagging strand. Forms phosphodiester bonds that seals them together.

What does a phosphodiester bond link in DNA structure?

Links two mononucleotides. Phosphoric acid is joined to two alcohols (OH groups on the two sugars) by an ester linkage.

Mosaicism in female mammals:

Lyon hypothesis of female mammals: X-inactivation is random early in development and descendent cells keep the same X inactive (calico: some are orange, some are black

PCR requirements

MG2+, Taq polymerase, single stranded DNA primers. dNTPs, double stranded DNA

How does a bacteria RNA polymerase holoenzyme differ if it has one form of the sigma subunit verses another?

Major form is sigma 70. Differs in weight. Each recognizes different promoter sequences.

"reverse transcription"

Making DNA from an RNA template telomerase binds to 3' G-rich tail. telomeric dna is synthesized, translocated, and repeated. telomerase is released and primase and DNA polymerase fill the gap. primer is removed and the gap is sealed by DNA ligase.

forward primer

Matches the sequence of 5'-3' template strand at the start of the DNA sequence (complementary so binds to 3'-5' strand)

Law of equal segregation

Members of a gene pair (alleles) separate equally into each gamete.

How long does it take for an entire eukaryotic genome to be replicated?

Minutes to hours

VNTR

Moderate repetitive sequences (5% of hum genome) : 15 to 100 bp

Romano-Ward syndrome is an autosomal dominant disease that disrupts normal heart rhythms. The gene responsible for this syndrome is on chromosome 21. Mom has this syndrome and Dad does not. They have a son who has Down Syndrome but does not have Romano-Ward syndrome. Select any choices where non-disjunction could have occurred:

Mom, Meiosis II Dad, Meiosis I Dad, Meiosis II

What can you summarize about plants and monsomy or trisomy that is different from animals?

Monosomy is more sustained. Trisomy (2n+1). More viable in both animal and plants. In plants, viable but altered phenotype of the plant's capsule. Slower growth. Larger c=chromosomes cause greater genetic imbalance than smaller ones.

An mRNA that is more stable leads to more or less protein than an mRNA that degrades rapidly?

More stable in cells that have translation inhibitors.

How many different restriction enzymes are there?

More than 3500. 250 used commercially.

In prokaryotes, DNA is not packaged compactly around histones. How is this a challenge in eukaryotes?

Must be uncoiled and the DNA needs to be made accessible to the RNA polymerase and other regulatory proteins (chromatin remodeling).

2. Hereditary deafness is a heterogeneous trait, meaning what?

Mutant trait reflecting the many genes involved Other examples include high blood pressure and obesity.

lac operon cis and trans mutations

Mutation in trans-acting factors: repressor can't bind operator or lactose Mutation in cis elements: operator sequence won't bind with repressor. Promoter doesn't bind RNA polymerase.

What is a complementation group?

Mutations determined to be present in any single gene fall into the same complementation group and they will complement mutations in other groups.

There are many forms of the disease (such as ALS8, ALS9, etc.). This is a heterogeneous disorder.

Mutations in approximately how many different genes could give a similar phenotype About 20

UV light can penetrate living cells and cause what?

Mutations in skin cell DNA (melanin guards from damage with super-nuclear caps)

Label the N-terminus (amino end) and the C-Terminus (carboxyl end) of the dipeptide you made.

N terminus: left side always 5' C-terminus: right side always 3'

What is direct to consumer genetic testing and what are three companies that offer it?

Navigenics in Redwood Shores, California, deCODE Genetics of Reykjavik, Iceland, and 23andMe in Mountain View, California

Which component is radioactively labeled in the triplet binding assay performed by Nirenberg and Leder?

Needed to know which tRNA-amino acid was bound to the triplet RNA ribosome complex. Amino acids are radioactively labeled and charged tRNA are produced. They can narrow the range of amino acids should be tested for each triplet. The incubate it and put it through the nitrocellulose filter which retains the larger ribosomes. If radioactivity is not retained on the filter, then the incorrect amino acid has been tested. Leads to specific codon assignments

DNA replication

Needs RNA primer before the leading strand. Provided by RNA primase: has an available terminal nucleotide. DNA polymerase III elongates RNA primers with new DNA. DNA polymerase I removes the 5' RNA at the end of the neighboring fragment and fills the gap. DNA ligase joins the adjacent fragments. The strand that is closest to the 3' end of the parent DNA is the lagging strand

The three essential components of the building blocks are:

Nitrogenous base, pentose sugar, phosphate group and 9: purines (A and G) and 6 ringed pyrimidines (G,C, U). RNA has ribose while DNA has deoxyribose (sugars) DNA has a H atom rather than OH at C-2'.

. What will be the phenotype if Jak2 cannot bind?

No appetite suppression = obesity

1. What will be the phenotype if a mutation results in leptin not being able to bind?

No appetite suppression = obesity

A hypothetical bacterial strain has a mutated version of the sigma subunit. The mutated subunit can bind to the RNA polymerase core enzyme, but it cannot bind to the DNA. Would such a strain be able to transcribe RNA? Explain.

No because it needs to bind....

In prokaryotes, translation can occur while transcription is still completing. True in eukayotes? Explain.

No because it needs to move out of the nucleus into the cytoplasm

What does it mean if alleles are written as M1, M2, M3, M4 etc.?

No dominance between alleles. Use uppercase italic letters and superscripts to show alternative alleles.

What is meant by the idea that the code is commaless?

No internal commas used

DNA polymerase requires an RNA primer to initiate DNA replication. Does RNA polymerase require such a primer?

No primer needed

Promoter doesn't bind RNA polymerase

No transcription of Z,Y, A Cis

Do all promoters contain the same cis-elements?

No, different genes have different core promoter elements.

Are there 61 tRNAs?

No. Wobble

What is a tri-nucleotide repeat sequence and what consequence might it have if in the coding region of a gene, as is seen with Huntington's disease?

Normal individuals have about 30 repetitions, but some have 200+. When these appear in a coding region, (like CAG) they become long tracks of whatever aminoacid is coded for (in this case, glutamine). They can cause the proteins to aggregate abnormally. If these mutations occur outside of the coding regions, but within the mRNA, the mRNA will act as toxic RNA that binds to regulatory proteins, preventing normal function within the cell. Can also lead to silencing of gene transcription.

What makes a SNP different from what geneticists might call a single nucleotide change or point mutation?

Not all single-nucleotide changes are SNPs, though. To be classified as a SNP, two or more versions of a sequence must each be present in at least one percent of the general population. SNPs are not necessarily located within genes, and they do not always affect the way a protein functions.

What is significant about the bond between the 2nd and 3rd phosphate in ATP or GTP?

Nucleoside monophosphate (NMP) di (NDP) tri (NTP) Adenosine diphosphate (ATP) and guanosine triphosphate (GTP) : energy is released by removing the phosphate group

What is the phenotype of the Oc cell (operator doesn't bind repressor)?

Nucleotide sequence of the operator dna is altered so it cannot bind to a normal repressor molecule. Genes are transcribed.

Define wildtype allele in a population: occurs most frequently in the population.

Often, but not always, dominant.

How is the code non-overlapping? What would an overlapping code look like?

Once translation commences, each ribonucleotide at a specific location within the mRNA is part of only one triplet.

How transcription begins and ends:

One template strand of DNA. RNA polymerase links them. Initiation: promoter is located in the DNA at the beginning of a gene. RNA polymerase attaches here. Elongation: RNA grows longer and the DNA strands come back together in already transcribed regions Termination: RNA polymerase reaches a terminator. Polymerase detaches and DNA rejoins.

As is the case with a syndrome, not everyone with Down Syndrome exhibits the same phenotypic characteristics. What are some of these?

Only human autosomal trisomy that is not lethal past the first year of birth. Chromosome 21. Down syndrome has 12-14 characteristics, only 6-8 are expressed in each individual. Higher rates of leukemia. Death in down syndrome is usually due to alzheimers. Epicanthic fold in the eye, flat face, round head, mental retardation.

Why are there "leading strands" and "lagging strands" during replication?

Only one strand can serve as a template for continuous DNA synthesis. The newly synthesized dna is the leading strand. Many points of initiation are needed on the opposite DNA template. Therefore, the lagging strand is a discontinuous DNA synthesis. Okazaki fragments: newly formed DNA that is hydrogen bonded to the template strand in 1000-2000 nucleotides in length. RNA primers are part of these and are converted into longer strands.

What were some reasons for Mendel's success as an experimental biologist?

Organism that is easy to grow and hybridize artificially. Easy to cross bread, reproduces well, grows to maturity. Used controls, accurate quantitative records.

What is a palindrome?

Palindrome: nucleotide sequence reads the same on both strands of the DNA in the 5- to 3' direction. In restriction sites.

Besides Down Syndrome, do any other human aneuplodies survive to birth?

Patau (47, 13+) and Edwards syndrome (47, 18+). Lethal early.

Imagine a cell in which one X is maternal and one X is paternal. The paternal X is inactivated. This cell divides into two cells. Which X is inactivated in these two cells? And if these two cells divide again, which Xs are inactivated in these four cells?

Paternal (imprinting: affects one homolog but not the other).

During elongation, amino acids are brought close together because they are bound to tRNAs in the P and A sites. What kind of bond forms between the two amino acids and what catalyzes this reaction?

Peptide bonds catalyzed by peptidyl transferase/ribozymes (part of large subunit). Covalent bonds between the tRNA occupying the P site and its amino acid are hydrolyzed and the dipeptide remains attached to the end of the tRNA in the A site. P = peptidyl A = aminoacyl

Griffith's experiments

Polysaccharide capsules: virulent has it He used virulent strain of bacteria, the smooth or encapsulated bacteria. (not easily engulfed) He also used a non-virulent strain, the rough, or nonencapsulated bacteria (engulfed and destroyed by phagocytic cells)

. How is tryptophan a repressor?

Presence of a specific molecules inhabits gene expression. True for molecules that are end products of anabolic biosynthetic pathways. If enough tryptophan is present, then it is energetically insufficient of the organism to synthesize the enzymes needed for tryptophan production.

How is tryptophan a repressor?

Presence of a specific molecules inhabits gene expression. True for molecules that are end products of anabolic biosynthetic pathways. If enough tryptophan is present, then it is energetically insufficient of the organism to synthesize the enzymes needed for tryptophan production.

Incorporate restriction enzyme sites

Primers going from 3' to 5'. Design it so that ECOR1 hangs over and a part that can anneal to the 3' end of the DNA. Make exact copies via PCR. Anneal and extend oligos with 5' restriction sites.

prokaryotes and exons

Prokaryotes and single cell eukaryotes generally have one exon genes and no introns.

We know that not all the DNA in the genome and not even all the genes in the genome code for protein. When we have sequence data, we can find protein coding genes by looking for ORFs. What's an ORF?

Protein coding genes that contain sequences of triplet nucleotides that are translated into amino acid sequence of a protein after transcription and mRNA splicing. They typically begin with an initiation sequence (usually ATG) which transcribes into the AUG start codon of an mRNA molecule, and ends with a termination sequence (TAA, TAG, TGA).

nucleoside

Purine or pyrimidine and a sugar =

siRNA or miRONA associate with

RISC (RNA induced silencing complex). Short double-stranded RNA is denatured and the sense strand is degraded. RNA/RISC complex becomes functional and looks for complementary mRNA molecules to the antisense RNA and it either: cleaves the mRNA with RISC if it is a perfect match and then degrades it by ribonucleases. Not exactly complementary: RISC stays bound to the mRNA, interferes with the ability of the ribosome to translate mRNA.

initiation transcription -

RNA Polymerase (RNAP) finds gene, accesses the DNA template, makes a short RNA.

If the protein component were sufficient to catalyze the reaction, then what is the purpose of having RNA complexed?

RNA binds to the introns to recognize them Other RNA and protein complex: telomerase

in vitro system uses

RNA codons, ribosomes, amino acids and tRNAs to make codons

13. What was the rational of Nirenberg and Matthaei in creating homopolymers of ribonucleuotides?

RNA homopolymers with only one type of ribonucleotide. UUUU, AAAAA, CCCCC or GGGGG. Tested each mRNA each and determined which are incorporated into newly synthesized proteins by labeling 1/20 amino acids added to the in vitro system. Concluded that poly U directed incorporation of phenylalanine, so UUU = phen. Found that AAA = lysine, CCC = proline. GGG is not adequate

Lagging strand synthesis

RNA oligonucleotides (primer) copied from DNA. Polymerase III elongates RNA primers with new DNA. DNA polymerase I removes 5' RNA at end of neighboring fragment and fills gap. DNA ligase joins adjacent fragments.

probe:

RNA or DNA. Heat probe, cool to make it single stranded, added to solution with the membrane.

The book describes four cis-elements (sequences of DNA) involved in transcription initiation in eukaryotes.

RNA polymerase II: needs cis and trans TF CIS: core-promoter (determines where RNP II binds to the DNA and beings copying the DNA into RNA The core promoter functions in eukaryotes like the promoter in prokaryotes, which is where RNP II binds the DNA and begins copying DNA into RNA.

Primase-

RNA polymerase. Does not require a free 3' end to initiate synthesis. DNA polymerase III adds nucleotides to this.

RNA primer

RNA primer before the leading strand. Provided by RNA primase: has an available terminal nucleotide.

Retroviruses:

RNA serves as a template for the synthesis of the complementary DNA molecule.

repressor can't bind operator

RNAP not blocked. constitutive. TAF mutation I-

Operator sequence won't bind with repressor

RNAP not blocked...constitutive transcription of Z, Y, A Cis Oc

What kinds of information was learned from analyzing the genome of a single healthy 40 year old male?

Rapid single-molecule sequencing method. Found 2.6 million SNPs and 752 copy number variations. Sorted by which might effect phenotype by searching known SNPs in databases. Used PharmGKB to find variants within pharmacogenomically important genes. 63 relevant SNPs and 6 SNPs that can alter amino acid sequences in drug-response genes. Increased risk for type 2 diabetes, obesity, coronary artery disease.

X-linked dominant

Rare (and don't often see homozygous dominant individuals) Males and females affected (often more females affected) Doesn't skip (dominant) Never have father to son transmission (X-linked) An affected male passes to ALL his daughters.

autosomal dominant

Rare (and often unusual to see homozygous dominant individuals) Males and females equally affected Affected individuals have an affected parent (dominant) Doesn't skip generations (dominant)

X-linked recessive

Rare (assume females marrying in are not carriers) Males affected more frequently Skips generations (recessive) Unaffected individuals have affected children (recessive) Never have father to son transmission (X-linked)

autosomal recessive

Rare (assume people marrying in are not carriers) males and females equally affected unaffected individuals have affected children (recessive) skips generations (recessive) becomes more common with inbreeding

MC1R (receptor variant 2)

Receptor cannot stimulate eumelanin production. Melanocyte makes pheomelanin.

RNA polymerase from E.coli has been extensively studied and is called the holoenzyme. What is its role?

Regulates the initiation of RNA transcription.

What us the result of having mRNAs that exist longer in eukaryotes (not degraded) compared to prokaryotes that degrade within minutes?

Remain available longer to synthesize proteins.

What does the SWI/SNF complex do to DNA?

Remodels it by loosening the attachment between histones and DNA, allowing nucleosomes to slide along the DNA and expose regulatory regions. They can also loosen the DNA strand from the nucleosome core, or can reorganize the internal nucleosome components, all leaving DNA exposed to TFs and RNA polymerase.

repressor can't bind lactose

Repressor continually blocks RNAP. No transcription of Z,Y, A Trans acting mutation Is

What is the phenotype of bacteria in which the repressor is altered in its binding to the operator (I-)?

Repressor protein is absent or altered and cannot bind to the operator, genes are transcribed

The central question around the nature of the genetic code in the late 1950's was what?

Researchers thought that DNA directs protein synthesis directly. How does only four letters could specify 20 amino acids

How did frameshift mutations provide experimental evidence of a triplet code?

Results in the addition or subtraction of one nucleotides. Found that if three nucleotides were removed, frame of reading was not shifted

The difference in stability comes down to the chemistry of the pentose at the 2' carbon. Which statement is true about this carbon? Ribose carries an OH at the 2' carbon Deoxyribose carries an OH at the 2' carbon.

Ribose carries an OH at the 2' carbon

What makes RNA different from DNA?

Ribose sugar with an H on the C-2', not an OH like deoxyribose. Uracil instead of thymine. Single stranded. Sometimes RNA can fold back to make double stranded, complementary pairs. Some viruses use this as their genetic material.

What two macromolecules make up ribosomes?

Ribosomal proteins and rRNA to make a monosome.

What are "superweeds" and what do they do to crops? How did they become superweeds?

Roundup inhibits activity of an enzyme, EPSPS, needed to produce critical building blocks of plant pro teins plant's chromosomes replicate the gene that encodes the enzyme, which results in production of too much enzyme for the herbicide to do its job Resistance can also emerge when the plant develops some still undetermined means of protecting the meristem at its top. Rapidly dividing cells in the meristem remain healthy even as the leaves perish, allowing the plant to survive and regenerate.

Design an experiment to calculate the distance between two linked genes Starting materials: Purebreeding white, tall plants (rT/rT) Purebreeding red, short plants (Rt/Rt) Purebreeding white, short plants (rt/rt)

Rt/Rt x rT/rT all Rt/rT dihybrids THEN, a testcross: Rt/rT x rt/rt B. Count recombinant offspring Recombinants: red, tall AND white, short C. Calculate recombination frequency using total number of offspring. This is proportional to m.u.

An XY individual who is phenotypically female is probably lacking what gene?

SRY: sex determining region Y encodes a protein that causes the undifferentiated gonadal tissue to form testes (testis determining factor).

If the sequence was much shorter, such as GA and repeated 50 times in tandem, this would be known as a

STRS

ribosomes serve as a nonspecific workbench for the translation process. How do we get the information that is specific to a region of DNA translated from mRNA to proteins?

Same workbench all the time. Accepts all mRNA.

Two months after publishing this paper, they proposed a model for what?

Semiconservative model of replication: storage of genetic information in the sequence of bases and the mutations that would result from an alteration of the bases.

What is meant by the term gene interaction? Do the gene products have to physically interact?

Several genes influencing a particular characteristic No: cellular function of numerous gene products contributes to the development of a common phenotype

What is the DNA sequence like at the telomeres?

Short tandem repeats of TTGGGG. Present on one of two strands making up the telomere: the G-rich strand, and its complementary strand is the C-rich strand: AACCCC. The 3' strand is the G-rich one and extends as an overhang and have no complement. G-rich strands can loop back on themselves with G-G hydrogen bonds to make G-quartets. Bow like t-loops form and these properties make them inert.

What did they predict would happen if they put an O+ gene into a cell that was Oc ?

Should have no effect on constitutive enzyme production since regulation depends on the prescence of an O+ region immediately adjacent to the structural genes (O+ is cis-acting).

SNPs

Single nucleotide polymorphisms. Outside of the gene: might have an effect on the gene because it is upstream. They make an association between the SNP that is easily genotypes with a nearby gene variant.

How does RNA differ from DNA?

Single stranded, U instead of T, ribose, can fold back on themselves, some RNA viruses are double stranded.

Why doesn't this seem to make sense from an evolutionary perspective?

Skin cancer arises after peak reproductive years

small and large subunits

Small subunit decodes the triplets in the mRNA and the large subunit synthesizes peptide bonds.

degenerate.

Some triplet nucleotide sequences code for the same amino acids

tautomeric shifts

Spontaneous changes in base structure can cause mutations if they occur immediately prior to DNA replication.

PCR 3 steps

Step 1: denaturation: Reaction is heated to 95 and double stranded DNA is separated into single strands as hydrogen bonds break. Step 2: Hybridization/annealing : Reaction temperature reduced to approximately 55 to allow primer annealing. Step 3: Extension: Temperature is raised to 72 and Taq synthesizes DNA!

In the language of DNA, what are the three stop codons?

TAA, TAG and TGA

In the language of DNA, what is the start codon?

TAC

Eukaryotes consensus sequences:

TATA box: -30

True or false. Most eukaryotic genes contain introns.

TRUE

What does the DNA sequence look like at a telomere?

TTAGGG

What is the centromere and what does the DNA sequence look like at the centromere?

Tandem repeats/satellite around the centromere (alphoid family) each about 170 bp in length. In tandem arrays of up to 1 million bp. Within the repetitive DNA are sequences that are critical to centromere function.

What is a tautomeric shift?

Tautomers are two molecules with the same molecular formula but different connectivity - constitutional isomers, in other words - which can interconvert in a rapid equilibrium. Keto-enol forms of T and G and amino-imino forms of C and A. Shifts allow H bonding with non-complementary pairs. The mix-matched pairs are separated and become templates for normal complementary base in replication. Hence, it is a point mutation. A and G are purines and C and T are pyrimidines

Briefly list other functional RNAs that do not make proteins.

Telomerase RNA, snRNA, antisense RNA, microRNA, short interfereing RNA

Describe template binding:

Template binding when alpha recognizes DNA promoters that are upstream towards the 5' end and unwinds the helix to reveal the transcription start site.

Messelson and Stahl provided evidence that replication in prokaryotes was semi-conservative, what did Taylor-Woods-and Hughes demonstrate?

That semiconservative replication occurs also in eukaryotic organisms. Used root tips of a bean. They looked at the chromosomes in metaphase and found the radioactive thymidine in chromatids that had new DNA. In the presence of the isotope, both chromatids were labeled, but only one chromatid was labeled after it had grown in the unlabeled medium. This supports the semiconservative model.

With normal replication:

The 5' strand of a telomere will get shorter with each round of replication. The lagging strand will get shorter with each round of replication.

What can an Ames test tell us?

The Ames test uses different strains of salmonella typhimurium that can reveal the presence of types of mutations. Each strain contains a mutation in one of the genes of the histidine operon. Mutant strains cannot synthesize histidine (his-) and need it to grow. The assay measures the frequency of reverse mutations that occur, yielding (his+)

How are telomeres an example of repetitive DNA? Are there genes that code for proteins in the telomeres?

The DNA sequences here function to maintain the stability of the chromosomes by rendering the ends inert and with enzymes that use DNA as substrates. Have short tandem repeats that maintain the stability of the chromosome. 5'ttagggg3' repeated. The sequences are transcribed to make TERRA RNA that contributes to its heterochromatic nature and regulate telomerase by inhibiting it.

DNA TO MRNA

The RNA polymerase reads the sequence of DNA bases from only one of the two strands of DNA: the template strand. The RNA polymerase reads the code from the template strand in the 3' to 5' direction and thus produces the mRNA strand in the 5' to 3' direction. In RNA, the base uracil (U) replaces the DNA base thymine (T). Thus the base-pairing rules in transcription are A→U, T→A, C→G, and G→C, where the first base is the coding base in the template strand of the DNA and the second base is the base that is added to the growing mRNA strand.

Where does this gene normally function in the cell?

The SOD1 gene encodes superoxide dismutase-1 (EC 1.15.1.1), a major cytoplasmic antioxidant enzyme that metabolizes superoxide radicals to molecular oxygen and hydrogen peroxide, thus providing a defense against oxygen toxicity

chromatin

The complex of DNA and proteins that makes up eukaryotic chromosomes. When the cell is not dividing, chromatin exists in its dispersed form, as a mass of very long, thin fibers that are not visible with a light microscope

Law of independent assortment

The equal segregation of one allele pair is independent of the equal segregation of the other allele pair during gamete formation.

This hypothesis has since been refined by scientists later in history to:

The function of a gene is to dictate the production of a polypeptide

6. When did human skin begin to evolve to be darker? What kind of evidence was collected to answer this question?

The genome. When we became hairless. 1.2 mya

Garrod didn't work directly with genes, but what did he propose what the reason for different phenotypes in the individuals he was studying?

The inability to make a particular enzyme

What kind of molecules do the three structural genes code for?

The lac/lactose operon

. If one double-stranded DNA has a higher melting temperature than another, what does this tell us about the structure of this DNA?

The midpoint of the melting curve is the melting temperature ™ where 50% of the strands have unwound. The higher the Tm, the more G C pairs there are.

transformation

The name of the process to get a plasmid into a bacterial cell is called transformation. Derived from plasmid. Extrachromosomal, double stranded DNA molecules, replicate independently from the chromosomes within bacterial cells.

Termination.

The process ends when one of the stop codons UAG, UAA or UGA is encountered. A site is empty and GTP-dependent release factors cleave the polypeptide chain from the terminal tRNA, releasing it from the translation complex and tRNA is released from the ribosome and dissociates into subunits.

What are cis-acting sites?

The regulatory region that is on the same DNA molecule and upstream of the gene cluster it controls. Determines whether or not genes are transcribed into RNA and whether enzymes or proteins are synthesized from the RNA.

MSY

The rest is the male-specific region of the Y (MSY) that does not recombine with anything else:

Can also analyze the rate of reassociation in reassociation kinetics.

The single stranded DNA will collide, and form double strands if they are complementary. Occurs more slowly in larger genomes. Rapid reassociation may indicate the presence of repetitive DNA sequences. Why eukaryotic reassociation may take less time than prokaryotic.

lagging strand

The strand that is closest to the 3' end of the parent DNA is the lagging strand

If all offspring fail to develop wings, this means what? (Use genotypes from fig 4-9 to explain)

The two mutations affect the same gene and are alleles of one another. Complementation does not occur. Homozygous for ma and mb alleles.

. When you are cloning a fragment into the plasmid shown in 17-3, and you plate your transformed bacteria on plates containing Xgal and amp, which colonies will you be interested in choosing (i.e. which ones have your fragment inside the plasmid)?

The white ones

Why are loss of function mutations typically recessive?

There is still one wildtype allele with function and this is often "sufficient".

Where are promoters located relative to a gene?

They bind to one or more proteins that regulate transcription initation. Located immediately adjacent to the genes they regulate.

9. Native people living near the Arctic Circle would be predicted to have light skin, but they have dark skin. Why might this be so based on the second hypothesis?

They have the diet rich in folate and vitamin D

How did their experiments rule out dispersive replication?

They heated the DNA to separate it into single strands to determine the densities of the strands and found that they were either 14 or 15 N density, not an intermediate, which the dispersive replication model would suggest. It also would have suggested that all generations would have one band after.

linked SNPs

They make an ASSOCIATION between the SNP that is easily genotyped with a nearby gene variant. Gene X might help us guess what is inside

How did their experiments rule out conservative replication?

They would have had two distinct bands at Generation I, not one.

What is the leading hypothesis as to why someone with XXY genotype has a phenotype, if dosage compensation occurs in these individuals?

This chromosome inactivation does not normally occur in early stages of development. Not all genes on the X chromosome that becomes a barr body are inactivated (15% active).

Why would chromatin need to be remodeled?

To accommodate protein-DNA interactions. Needs to relax during activity, but re-compact during inactivity. Histone tails that make connections with adjacent nucleosomes and are potential targets for chemical modifications.

Why would bacteria need to regulate gene expression?

To adapt to their environment

Why would we use BLAST?

To compare a newly sequenced genomic DNA to the known sequences already stored in various databases.

A mismatch is seen (C-A) but which strand is the correct one? How does a cell know which strand needs to be fixed?

To determine which strand is taken out, DNA methylation occurs. Bacteria, with the enzyme adenine methylase, recognizes the DNA sequence as a substrate, adding a methyl group to each adenine residue. After replication, the new strand of DNA is temporarily unmethylated, where the repair enzyme binds to the unmethylated strand. The endonuclease enzyme creates a nick in the backbone of the unmethylated DNA strand either 5' or 3' to the mismatch. An exonuclease unwinds and degrades the nicked DNA strand. DNA polymerase uses the correct DNA strand as a template, and DNA ligase seals it together.

Why would you perform a chi square analysis?

To see if it is a chance deviation. Outcomes of independent assortment and fertilization, like coin tossing, are subject to random fluctuations from their predicted outcomes As sample size increases, average deviation decreases.

What is a promoter element, a cis or a trans factor?

Trans? Short nucleotide sequences that bind to regulatory factors.

What is a transcription factor? Is is a cis or trans element?

Trans? Transcription regulatory proteins. Some increase and are activators, some decrease and are repressors. transcription factors bind to cis acting sites and either positively or negatively effect the transcription initiation rate.

Watson and Crick model

Two chains, not three. Phosphate diester groups in 3' and 5' links. Bases on the inside, phosphate groups on the outside. Sugar is perpendicular to the base. High water content. Purine bonds to the pyrimidine. Purine 1 to pyrimidine 1, purine 6 to pyrimidine 6.

What is a thymine (pyrimidine) dimer and what is its effect on your DNA?

UV radiation of DNA causes the creation of pyrimidine dimers (that consist of two identical pyrimidines) They distort DNA conformation and prevent normal replication. Can cause cell death.

What pattern does she find globally in human skin color?

UV strong: skin is dark. Arose as diff populations adapted. 1.2 million years

If being dark-skinned offers an advantage, why aren't all humans dark-skinned?

UVB is needed for synthesis of vitamin D, needed for calcium. On equator, there is enough UVB with dark skin. As you move north and the sunlight goes away, you don't get enough UVB. Selection for the other MCR1 gene

How did Turner Syndrome and Kleinfelter syndrome phenotypes help determine how maleness is determined in humans?

Used them to see what happens when Y disappears

In situ molecular hybridization/FISH:

Uses DNA in chromosomal preparations. Mitotic cells are fixed to slides and put under hybridization conditions. Single stranded DNA and RNA is added (probe) and a fluorescent label is used (only in the centromeric region).

A sequence such as TATAGCGTAGCTAGCT repeated in tandem (next to each other) 75 times is an example of

VNTRs

G2 (3 hours) :

Volume of cell has doubled by the end of G2. DNA has been replicated

his is the product law in mathematics.

When we have two traits that independently assort, the combined probability is the product of the individual probabilities. T

What is rRNA, mRNA, and tRNA?

Which are non-coding "functional" RNAs that do not have instructions to make proteins? Ribosomal, messenger, transfer Ribosomal: 80% of all RNA.

How do we designate wildtype alleles in drosophila?

With + superscript. Lower case letters of the name of the trait. Recessive: lower. Dominant: uppercase. e+/e+ or +/+, e/+, e/e

The ribosome catalyzes the reaction that forms a peptide (covalent) bond between these two amino acids. Draw these two amino acids linked into a dipeptide:

Without the OH and the H. C bonds to the N. Peptide bond if O=C-N-H

Lesch Nyhan:

X linked recessive abnormal nucleic acid metabolism.

Radiation is often used to kill cancer cells. Why might this work?

X rays, gamma rays and cosmic rays are more energetic than UVR and can cause the ionizing radiation of cells, transforming molecules into free radicals, that can harm chromosomes and DNA. It can target the cancer cells and disrupt the DNA and the cell replication.

X-linked disorders revisited with mosiacism:

X(cb) = colorblind recessive allele (lacking a green opsin protein). Males: fully colorblind Females: carrier, partially colorblind (XCB/Xcb): some barr bodies are being expressed. Test this by crossing carriers and seeing how many male offspring are colorblind or not.

A female with has no Barr bodies in any of her somatic cells, what is her genotype?

XO

Turner syndrome:

XO

Klinefelter syndrome:

XXY

Skin cells were examined from several men. In one, a Barr body was found. What is unusual about this? What is his genotype?

XXY (interferes with the function of the y chromosome). Unusual because he should only have one X chromosome

Fruit flies:

XY (Double express all genes) and XX

Kangaroo:

XY and XX (turn of expression of all genes here; always paternal X: one X is inactive).

Humans:

XY and XX (turn of expression of all genes on either of these, but not both).

Xist

Xist gene makes mRNA transcript. It binds to the entire chromosome. Coding regions on the protein binds to the mRNA and histone molecules follow to coil it up = inactive gene, RNA polymerase cannot read it. Xist gene makes non-coding mRNA: no protein.

Y chromosome

Y chromosomes have much less information (75 genes) than X (900-1400). On both ends of the Y are pseudoautosomal regions (PARs) that can recombine with the X chromosome in meiosis.

piRNAs are small RNA molecules (26-31 nucleotides) that form RNA-protein complexes through interactions with piwi proteins. These complexes are important in regulation of gene transcription. Would you classify piRNA as a functional RNA? Why?

Yes

Do all eukaryotic cells express/produce telomerase?

Yes, but it is not always active.

Positive control means gene expression occurs only if

a regulator molecule directly stimulates RNA production.

GFP (green fluorescent protein)

a reporter gene to see in living tissues. Attached to the promoter.

merozygote:

a strain of bacteria that is made diploid by inserting F' factors (These are small circular pieces of DNA - plasmids that can be taken up by bacteria) .

cDNA

a stretch of DNA nucleotides that matches the RNA transcribed from a given gene. In other words, it does not contain the introns and the promoter of the original gene, but rather matches (i.e. complementary) to the mRNA.

Satellite DNA:

a variable proportion of the total DNA that does not have uniform density to the main-band (MB) DNA. Highly repetitive DNA (short sequences repeated a large amount of times).

hESCs have been at the center of debate for quite some time because retrieving them means destroying

a very early human embryo.

The process of science is:

a) Iterative: it circles back on itself to build upon and learn from to deepen our understanding. b) Not predetermined: could learn something that changes everything or takes it in a new direction

Let's talk termination... There are two mechanisms that bacteria can use that promote RNA polymerase dissociating from the DNA and RNA, they are:

a) hairpin secondary structure that causes the sequence of nucleotides in the termination region, held together by hydrogen bonds. b) termination factor p(rho) core polymerase enzyme dissociates

two types of melanin:

a) pheomelanin- looks reddish, yellow in color b) eumelanin- looks brown, black in color

There are two short RNA molecules involved in RNA induced gene silencing in the cytoplasm, they are:

a) small interfering RNAs (siRNAs) straight b) microRNAs (miRNAs) have double stranded stem-loop, but are spliced into liner by dicer Both are short, double stranded and 21-24 ribonucleotides long

Jacob and Monod made three major predictions to test the validity of their operon model

a. I gene makes a diffusible product. b. O region is involved in regulation but does not make a product c. O region must be adjacent to the structural genes in order to regulate transcription

There are two important sites on a tRNA, they are:

a. anticodon b. amino acid binding site

A fly carries a loss of function mutation in an enzyme, which is responsible for adding the 7-methylguanosine residue to the hnRNA. Suggest at least three potential ramifications to the presence of this mutation

a. nuclease attack b. cant travel though membranes c. wont translate

What are three ways that DNA can be made more accessible for transcription?

a. nucleosomes: slide/reorganize b. DNA: methylation c. histones: acetylation

RNA polymerase functions similiarly to DNA polymerase. However, there are two differences mentioned:

a. ribose sugar b. no primer needed to initiate synthesis, base is a nucleoside triphosphate

What does catabolite-activating protein (CAP) do?

activates expression of the lac operon but it is able to inhibit it when glucose is present=catabolite repression. Positive control. RNA polymerase transcribes the lac operon structural genes, but is not efficient unless CAP is there.

Down syndrome and XIST:

active Xist to make one of the three chromosomes inactive.

making cDNA

add aligoDT primer, add reverse transcriptase, digest RNA with RNAse H and add DNA pol I and ligase

Cis:

adjacent parts of the same DNA molecule

What does the cell theory state?

all organisms are composed of basic cells that are derived from preexisting structures

What if there was a mutation in the repressor gene such that it could no longer bind the operator (I-).

allows continuous transcription of structural genes because the repressor protein is altered or absent.

What if there was a mutation in the repressor gene such that it could no longer bind the operator (I-). Predict/explain phenotypic consequence on transcription of the structural genes:

allows continuous transcription of structural genes because the repressor protein is altered or absent.

Wobble pairing

allows for a single anticodon of a tRNA to interact with more than one mRNA codon. the third codon is the only one that is different in base pairing.

The code is nearly universal, meaning...

almost all prokaryotes, eukaryotes, viruses, archaea use it

to tell if something is mutagenic

ames test

charging of the tRNA is carried out by

aminoacyl-tRNA synthetase. 20 different types to add them. tRNA is specific based on the anticodon type. the enzyme has the active sites for the anticodon and the amino acid. ATP energies the intermediate and allows for the matching of the acids

Steady state level of mRNA:

amount in the cells as determined by a combination of the rate at which the mRNA is degraded. Amount available for translation.

Depurination:

an example of DNA damage that can lead to a spontaneous mutation. Occurs about 10,000 times per day in a typical human cell

When do sister chromatids separate?

anaphase

After being cut into fragments with restriction enzymes, the fragments can be

annealed (or "stuck together" via hydrogen bonds of complementary base pairs). Addition of an enzyme known as DNA ligase will then seal the phosphodiester bonds of the backbone.

blood type

antigens on the surface of red blood cells. Codominant. 4 phenotypes. Ia and Ib are codominant, but dominant to I

The growing RNA polynucleotide is parallel or antiparallel to its template DNA strand?

antiparallel

RITS (RNA induced initiation of transcription silencing complex:

antisense RNA strand targets RITS complex to specific gene promoters or larger regions of chromatin. Then, RITS gets chromatin remodeling enzymes to come and methylate histones and DNA, making heterochromatin.

Dosage compensation-

any mechanism that compensates for the differences in the number of copies of genes (dosage) due to the different chromosomes in males in females

Coiled chromatin fibers

are compacted into a chromatid (700 nm) to make the chromosome 1400 nm. Packing ratio of 500 to 1.

Regulatory functions of DNA replication

are composed of 20 proteins (prereplicatino complex: pre-RC), which assemble at replication origins. Recognized in G1 of the cell cycle as having a 6 protein complex known as the origin recognition complex (ORC). Distinguishes segments that have replicated from those that haven't.

SINES (short interspersed elements)

are less than 500 bp repeated 500,000 times Ex. Alu family (5% of genome. 200-300 bp long)

genes _______ proportional to genome size

are not

Aneuploidy:

arises by nondisjunction. The occurrence of one or more extra or missing chromosomes leading to an unbalanced chromosome complement.

What is the mode of inheritance in most families? ALS (Autosomal dominant, autosomal recessive, X-linked etc.)

autosomal dominant inheritance, rare cases of autosomal recessive inheritance have been reported.

albinism:

autosomal recessive

tay sachs

autosomal recessive lethal lipid metabolism disease with an abnormal enzyme. Normal for a couple months.

. The second major piece of evidence came from Hershey and Chase's experiments.

bacteriophage T2: virus coated in proteins with a core of DNA. Hexagonal head with a tail. Phage adsorbs to the bacterial cell and some component of the phage enters the cell and basically impregnates then lyses the cell. This phage is 50% protein and 50% DNA. Infection is initiated by the adsoption of the phage by its tail fibers to the bacterial cell.

Give an example of how a phenotype expression varies at one age relative to another within a single individual:

baldness

Histones:

basic, positively charges. 5 types, with lysine and arginine. They can bind to the PO3- in DNA. H2A H2B H3 and H4 Appear as tetramers: (H2A)2 * (H2B)2 and (H3)2 * (H4)2

dimensions of DNA

between base pairs: 3.4 A, between strands: 20 A

XYY:

bigger, dumber, in prison

Bacteria that have a plasmid without your cloned fragment of interest will be blue/white (circle one) when plated with X-gal.

blue

Lysozyme

breaks down the cell wall without destroying the bacterium.

Gyrase -

breaks phoshodiester on one of both strands far ahead of replication machinery.

The consensus sequences are the same in the liver and skin cells,

but TFs differ: they bind to the consensus sequences. Skin cells have the coding for fibrinogen, but they do not have the necessary TF to express them.

Proofreading increases accuracy

by 100 fold.

DNA polymerase I, II, and III

cannot initiate DNA replication, but they can elongate it. They can reverse their direction to proofread. Polymerase I is more stable and more present than III. III goes from 5 to 3 to elongate, then back 3 to 5 as an exonuclease to proofread. Polymerase I removes the primer and fills the gap and can repair DNA. Polymerase II, IV, and V repair DNA that has been damaged by external forces.

Mature mRNA:

cap/UTR, exons, UTR, AAAAAAA (for protection)

Cell cycle regulation:

cell division cycle (cdc) mutations. Products of these genes are enzymes called kinases that add phosphates to other proteins. 3 checkpoints for cell division.

S phase (7 hours):

cell growth and cell differentiation.

G1 (5 hours):

cell growth and cell differentiation. Length varies by species. Late in G1 the cell either enters G0 and stops dividing or it initiates DNA synthesis and continues the cycle.

Metaphase:

centromeres align on metaphase plate, Separase degrades cohesion once the chromatids are attached to the spindle fiber:

Anaphase:

centromeres split up and daughter chromosomes migrate to opposite poles, by the binding of the spindle fibers to the chromosome's kinetochore (proteins within the centromere). Motor proteins use the energy from ATP and constitutes the molecular motors in the cell. At the end of this: 46 chromosomes at each pole.

dominant negative mutations:

change that prevents polypeptides from interacting normally to make a functional protein.

Interchromosomal domains:

channels between chromosomes contain little or no DNA

When an amino acid is chemically linked to the 3' end of a tRNA, this process is known as

charging. Enzymes perform this chemical linking and they are known as aminoacyl tRNA synthetases. It is believed there are 20 different ones, one to link each different amino acid to a tRNA. 31 diff tRNAs

Chromatin:

chromatin remodeling in eukaryotes (has to be unwrapped from histones) no remodeling in prokaryotes

Prometaphase:

chromosomes are clearly double structures, centrioles reach the opposite poles and spindle fibers form

Interphase:

chromosomes are extended and uncoiled, forming chromatin

In eukaryotes an important consensus sequence in the promoter is called the TATA box. It is a cis or trans element?

cis

enhancer

cis

silencers

cis

Transcriptional regulation is controlled by

cis acting elements (DNA sequences) and trans-acting factors (diffusible molecules that interact with DNA or with other molecules)

TATA box:

cis-acting core-promoter element. -30 upstream from start point of transcription.

cis and trans mutations in lac

cis-acting mutations: affect the expression of genes on same chromosome. Example: Oc or P- trans-acting mutations: affect all structural genes regardless of what chromosome they are on. Example: Is or I- Oc: dominant repressor can't bind operator and lactose

What could patient-specific iPSCs be useful for?

cloning, differentiation, studying disease, therapies. examples for drug treatments.

all genes contain

coding region, regulatory region, transcription termination

TATA sequence is on

coding strand, not template strand. RNA polymerase binds to the promoter region to the template strand.

Oc

constitutive. transcription proceeds

I- mutant repressor gene:

constitutive. transcription proceeds.

coding region

contains the information for the structure of the expressed protein

Inheritance of feathers:

controlled by a single pair of autosomal alleles whose expression is modified by the individuals sex hormones.

B-galactosidas

converts lactose to glucose and galactose.

Nuclear reprogramming of somatic cells is the reverse of what process?

creating and isolating stem cells without an embryo. take differentiated cells and reprogram it to be undifferentiated

What is regenerative medicine?

creating cells, tissues, and organs for tissue or organ repair

reciprocal crosses:

crosses that can be made either from pollination from dwarf or tall plants (not sex dependent)

AluI and BalI:

cut at the same (blunt-end)

where does translation occur

cytoplasm

The position of the gene's promoter

determines where RNA polymerase II binds on the DNA, but it does not determine in which direction the polymerase will move along the DNA.

Bioinformatics:

develops hardware and software for processing nucleotide and protein data

STRs

di, tri, tetra and penta: CA is most common (repeats 5 to 50 times

4 ways to lengthen telomeres

diet, exercise, stress management, social support

missense-

different amino acid formed

Discontinuous variation:

discrete units (mendel)

if X linked disorder is lethal or debilitating,

disorder is exclusively occurs in males. Heterozygous female carriers. Pass to ½ female offspring.

termination transcription -

dissociation of RNA, RNAP, and DNA.

Map unit (m.u.)

distance between genes for which one product of meiosis out of 100 is recombinant (i.e. RF = 1 % = 1 m.u.)

Recombinant dna:

dna fragments from restriction enzymes + carrier DNA (vectors)

My phosphodiester bonds are broken and I need them repaired. Looking for someone with the right tools."

dna ligase

"Looking for someone with big machinery that can replicate my DNA quickly, without too many mistakes. Text me if you have what it takes."

dna polymerase

They arise during the process of _______________________. They are the only source of new ____________________ that are acted upon by evolution

dna replication, alleles

RNA primers

do not play a role in transcription; they are involved in DNA replication.

Middle repetitive DNA:

does include some duplicated genes, but most are noncoded. VNTRs: 15-199 bp found within and between genes (minisatellites) Microsatellites/STRs: di- tri- tretra- penta- nucleotides repeated 5-50 times

A p value < 0.05 means differences are

due to chance

2. What does the word recombination mean?

during the first meiotic prophase when homologs are paired, reciprocal exchange of chromosome segments

In interphase:

each chromosome occupies the chromosome territory.

Epigenesis:

each step of development increases the complexity of the sensory organ and is under the control and influence of one or more genes

Preformation:

egg has a miniature adult (homunculus)

If something doesn't complement anything:

either dominant mutation or haplo-insufficient so test is wrong. It won't complement correctly with homozygous recessive mutants Need to make sure they are homozygous recessive BEFORE complementation

viruses DNA

either linear or circular

elongation transcription-

elongation of RNA in the 5'→ 3' direction (nucleotides are added to the 3' end of the growing RNA).

lacA

encodes β-galactoside transacetylase (LacA), an enzyme that transfers an acetyl group from acetyl-CoA to β-galactosides.

Gain of function mutation:

enhance function of the wild-type product. Generally result in dominant alleles.

Activators bind to

enhancers. Repressors bind to silencer DNA elements. They inhibit the formation of a PIC, recruit chromatin-remodeling proteins

In the lac operon, the role of the catabolite activator protein is to...

ensure that glucose is used before lactose

Constitutive:

enzymes that are produced continuously regardless of the chemical makeup of the environment

imprinting occurs via

epigenetics (DNA is altered in a way that affects its expression). Methyl groups added to C5 of cytosine by DNA methyltransferase.

linear chromosomes

eukaryotes, nucleus, DNA and proteins to form chromatin

main difference between prokaryotic and eukaryotic dna

eukaryotic has to do pre-mRNA and splice out the introns

vectors for plant resistance

eukaryotic promoter, drought resistance, origin of replication, selection marker with eukaryotic promoter

Cis-elements and trans-acting factors:

eukaryotic system has more transcription factors (that recognize cis elements) and more cis elements and trans-acting. Trans-acting (proteins)

Autosomal dominant disease

every gen, equal sexes

Conditional mutations are

expressed under one condition but not another (temperature-sensitive mutation).

Permease:

facilitates the entry of lactose into the bacterial cell

This binding does what for RNA polymerase in the presence of lactose?

facilitating RNA polymerase binding at the lac operon promoter and transcription occurs.

A child is born that has the genotype XYY. In which parent did the non-disjunction occur and at which stage? Check any that work:

father meiosis II

Is an individual with Turner syndrome phenotypically male or female?

female Describe phenotype: ovaries are rudimentary. Sgirt, underdeveloped breasts.

Considering Watson-Crick base pairing rules, what will the secondary structure of this molecule look like? And how might this terminate transcription? Draw it:

folds on itself to make a RNA hairpin loop: one way to end transcription. Strong GC bonds hold structure together, causing a stalling of RNAP. When it stall, weak AU bonds are not strong enough to hold mRNA and DNA complex together.

Structural genes code

for the primary structure of enzymes.

Adaptor hypothesis:

francis Crick. Codon for amino acid. Anti-codon can base pair to the codon.

euchromatic regions that have

functional genes, and heterochromatic regions that lack genes

Negative control means that

gene expression occurs unless it is shut off by some form of a regulator molecules.

Constitutive mutants:

gene is produced continually.

heterochromatin

gene poor, less active, dark, condensed, repetitive DNA sequences.

Gain of function-

gene product with enhanced or new functions. Due to a change in the amino acid sequence of the protein that confers a new activity, or increases productivity. Usually dominant

euchromatin

gene-rich, transcriptionally active, light, dispersed appearance, unique DNA sequences

Define alternative splicing:

generate different forms of mRNA from identical pre-mRNA molecules. Increases the number of proteins that can be made from each gene.

What does it mean when we say two genes are linked?

genes on the same chromosome that are transmitted as a single unit. do not undergo independent assortment

The chromosome theory of inheritance explains how:

genetic information is transmitted from generation to generation. chromosomes are contributed to each individual via gametes (chromosomal theory of inheritance)

complete linkage

gives 1:2:1 ratio if two heterozygotes are mated. genes are close together and number of offspring is small can only form parental gametes

"Do you hate it when your DNA gets all tangled and coiled ahead of your replication fork? If so, let's journey ahead and fix these problems together."

gyrase (topoisomerase)

The Bombay phenotype

h/h; iA/iB will NOT have blood AB, they will be blood type O. Why? Homozygous recessive at one locus masks the expression of a second locus.

3. What does it mean when a stem cell is pluripotent?

has the potential to eventually differentiate into all the 220 different cell types

Protoplasts:

have only the cell membrane. Viruses don't have to be intact to infect.

sry

he protein it encodes is a DNA binding protein that regulates other genes. The normal action of the SRY protein is to induce transcription of a second DNA binding protein, SOX9. The SOX9 gene is located on the X chromosome. The SOX9 protein acts to induce transcription of other genes that lead to the development of testes. Mutations that disrupt SRY or SOX9 protein function thus block the formation of testes. XY individuals with these types of mutations develop as sterile females.

H-bonds. and denature me. Wink. "

helicase

Position effect:

heterochromatin next to a euchromatin may lead to both not getting expressed. Position of a gene or group of genes relative to other genetic material may affect their expression.

Collectively a pool of pre-RNAs in the nucleus is called:

heterogeneous nuclear RNA (hnRNA). Large and complexed with proteins. 25% are converted to mRNA

Stem cells can divide over and over and over...why?

high levels of telomerase.

replisome:

holoenzyme+proteins at replication fork.

Repeat sequences are

hot spots for DNA mutation and can contribute to hereditary diseases.

annotation:

identifying gene-regulatory sequences and other sequences of interest in the geneome so that gene maps can be developed.

Where can you find adult-derived stem cells (ASCs)?

in small numbers in the brain, intestine, hair, skin, pancreas, bone marrow, fat, mammary glands, teeth, muscle, blood. harvested from a biopsy.

Oogonia

in the ovaries begin meiosis.

In vivo and in PCR Name of enzyme that elongates new strand of DNA

in vivo: DNA polymerase in PCR: Taq or other thermophillic DNA polymerase

In vivo and in PCR What makes these two processes similar?

in vivo: Nucleotides are needed for elongation, DNA serves as template for new strand 5' 3' in PCR: Nucleotides are needed for elongation, DNA serves as template for new strand 5' 3'

In vivo and in PCR What the primers are made out of (DNA or RNA?)

in vivo: RNA in PCR: DNA

In vivo and in PCR what separates the two strands of DNA?

in vivo: helicase in PCR: heat

In vivo and in PCR Ligase needed, why or why not?

in vivo: yes to link okazaki fragments on the lagging strand in PCR: no, no lagging strand

The lactose metabolism system is ______ while the tryptophan expression system is _______.

inducable, repressive

I+

induced transcription if lactose is present. No transcription if lactose is not present. Normal.

In the lactose metabolism system, lactose is the

inducer.

The lactose metabolism system is _______ while the tryptophan expression system is ________

inducible, repressible

Transfection:

infection by only the viral nucleic acid

regulatory region

information on where and when a gene will be transcribed during development; usually upstream of the coding region

Glyphosate

inhibits an enzyme called EPSPS that builds three essential amino acids in plants and bacteria but, crucial to its widespread adoption, not in animals. The chemical attacks cells in the meristem, the growth bud at the tip of the plant. Within a day of application the plant stops growing, and death typically follows within a week or two

Crick noticed a pattern of degeneracy of the code, meaning it is the 3rd nucleotide of the codon that seems to differ and came up with the wobble hypothesis hypothesis.

initial two ribonucleotides of triplet codes are more critical than the third in attracting the correct tRNA during translation. Hydrogen bonding at the third position of the codon/anticodon interaction is less contrained and does not need to adhere as specifically to base-pairing rules.

5. What is a source of human embryos for hESC isolation?

inner cell mass. leftover embryos. ivf.

lines

interspersed 6,000 bp repeated 80,000 times

sines

interspersed: 500 bp. Repeating 10,000 times

Interphase:

interval between cell divisions. Replication of the DNA of each chromosome.

the mRNA length is about the same, what makes the gene length so different?

intron removal

folate

involved in DNA synthesis. Lack of folate: causes birth defects. UV damages folate and leads to poor reproductive success. Dark skin doesn't readily absorb UV rays that allow the absorption of Vitamin D.

lac operon order

ipozya

The turn of the helix

is 34 A, so 10 base pairs/turn. There are major and minor grooves along the axis

Testosterone

is a steroid hormone that acts by binding to the androgen receptor (AR). The AR binds testosterone, translocates to the nucleus, and binds the regulatory DNA of its target genes to induce their transcription. The effect of these target genes is to drive the development of male external genitalia.

1. Recombination frequency for two genes- (RF) -

is proportional to the physical length of DNA between them on the chromosome. a. RF = 50 %: b. RF < 50%: 2.

transcription termination

is the "stop"signal for where transcription should end; downstream of coding region

Sigma factor

is very specific: key to binding and initiating transcription. No RNA primer.

. If a trait is only ever seen in one of the two sexes,

it is a sex-limited inheritance.

Keep in mind that the mRNA transcript begins at

its 5' before the initial AUG start codon shown

Good markers:

lacZ, genes that are resistant to ampicillin

If lactose is present,

lactose binds to the repressor molecules and causes allosteric conformational change, rendering the repressor incapable of interacting with operator DNA. RNA polymerase, in the absence of repressor-operator interaction, transcribes the structural genes and the enzymes for lactose metabolism are produced.

Bacterial transposons (Tn elements):

larger than IS elements. Contain protein-coding genes. Mutations caused if inserted into gene-regulatory regions. Can induce drug resistance onto bacterial plasmid (R factors).

hypomorephic

leaky mutation. usually recessive and lethal

Replicon:

length of DNA that is replicated following one initiation event at a single origin.

Predict phenotypic consequence of a loss-of-function mutation in the receptor protein at the cell surface

less cell division

Premature stop codons =

less stability.

Let's conclude with an interesting fun fact... the human genome has about 20,000 functional genes. This DNA sequence only accounts for what percent of the entire human genome?

less than 2%

List a few of the traits that can be tested with PGD already. Categorize them in their severity if you can.

like cystic fibrosis and sickle cell anemia will afflict the children who carry the genetic mutation that causes them. The procedure has also been used to avoid passing on Huntington's disease, a severe neurological disease that typically does not surface until middle age but spares no one who carries the mutation that causes it. cancer

Why are liver enzymes added?

liver enzymes may activate some innocuous compounds, making them mutagenic. the bacteria requires the nutrients present in the liver extract for growth. a liver extract is necessary for the bacteria to produce histidine revertants. Substances are innocuous until activated by the metabolism in the liver.

Certain TFs are

localized to one part of the cell. Cells producing different set of proteins due to different trans-acting factors. Animal pole and vegetal pole (where TFs are). How cells are different from one another. Different cells have different TFs present.

shorter arm is the p,

longer is the q.

What is the danger of depurination of not corrected before DNA replication begins?

loss of one of the nitrogenous bases (normally G or A). Leaves an apurinic site on one strand. If not repaired, there will be no base at that position to act as a template during DNA replication. DNA polymerase will fix this blank with a random nucleotide.

. When glucose levels are high in a cell, cAMP levels are

low

In prokaryotes there is not

mRNA processing. In eukaryotes, the pre-RNA (immature transcript) is processed: 5' cap, 3' tail, remove introns

initiation translation

mRNA, ribosomes, charged tRNA, free amino acids, small subunits come together in the cytoplasm. and large subunit adds on top if the correct charged tRNA is bound to the mRNA 50S.

histone

made up of two tetromeres, connected by H1 (2 H2A and 2 H2B, 2 H3 and 2 H4) DNA wrapped around it. 147 base pairs.

Is an individual with Kleinfelter syndrome phenotypically male or female?

male Describe phenotype: tall, long arms, long legs, testes don't produce sperm, slight breasts, round hips

Polymorphic:

many forms, two or more common wildtype alleles in a population Ex. Blood (multiple alleles that are all common/wildtype)

Alternative splicing:

may generate two or more types of mRNA from the same transcript. Different forms of protein from the same coding. Alternative splicing is a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene.

Negative control

means that gene expression occurs unless it is shut off by some form of a regulator molecules.

Melanin is found inside melanosomes inside what cell type?

melanocytes

When cells are reprogrammed, what might be not quite right about these cells?

might have epigenetic shifts and memory that may not be totally reversible.

Why did Brenner suggest a triplet code, even without experimental data? (Why not doublet or a code with four nucletides = amino acid?)

minimal use of four letters to specify 20 AA. 2 = 16 AA, 4 = 256

Chromosomes are only visible in

mitosis. In interphase, the chromosomes uncoil and are chromatin, which disperse through the nucleus. DNA is replicated. Length contraction of 10,000 when they recoil in mitosis.

LINES and SINES

mobile sequences (can relocate within genome) SINES: 500 bp (preset 50,000 times or more) : eg. LINES; 6 k I legth ---preset 850,000 times

Trans:

molecules that bind to these DNA elements.

Eukaryotic cells have _______________DNA polymerase molecules than bacterial cells and use more types of them (14 kinds).

more

What do we call an individual who has some of their cells as 46, XX and some 45, X? How does this arise?

mosaics Somatic cells display different gene lines, each exhibiting a different karyotype

griffins experiment

mouse with IIIS (virulent) and IIR (avirulent) and heatkilled IIIS. IIR and IIIS heatkilled: living IIIS recovered

zygotes

multicellular diploid organisms begin life as single-celled fertilized eggs

D. 10. Summarize what two factors are in tension that drove human evolution of skin color variation:

need to protect skin from UV and need to use UVB for Vitamin D

Because transcription occurs only when the repressor FAILS to bind the operator, this is considered negative/positive control? (choose one.)

negative

Because transcription occurs only when the repressor FAILS to bind the operator, this is considered negative/positive control? (choose one.)

negative?

Why might scientists use directed differentiation of hESCs and what are a few examples of the types of cells that they can make?

neurons, gametes, liver cells, cardiac muscle, blood cells. growth factors, horomones, TFs, and small proteins can stimulate differentiation.

silent-

no change in amino acid produced

Prokaryotes cell:

no nuclear envelope or internal organelles. Circular DNA is present in the nucleoid area.does not extensively coil in mitosis.

Why are dominant lethal alleles so rare in a population?

no survivors (it cannot hide) so it leaves the population *Huntington disease

Is bacterial DNA compacted tightly around histones, like in eukaryotic cells?

no. Compacted into the nucleoid. DNA binding proteins. (HU and HI). Can bond to the PO3- parts of DNA. Does not compact to the same extent that histones do to DNA in eukaryotes. Not functionally inert

If all lactose is metabolized,

none is available to bind to the repressor, which is again free to repress transcription.

Z+

normal. Transcription if lactose, repressed if none.

Non-transformed (without marker) will

not grow, but X-gal (similar to lactose) will be cleaved by lacZ, turns blue.

You are asked to find the location of a DNA sequence resulting in a protein that is being overexpressed during in a disease state. This sequence most likely resides within: heterochromatin a long interspersed element (LINE) a short tandem repeat (STR) likely to be any of these not likely to be be any of these

not likely any of them

What will happen if an enhancer is: • moved from one side of a gene to another? • inverted its orientation? • moved beside an entirely different gene?:

nothing, nothing, newly adjacent gene is enhanced

Genetic material is passed into daughter cells during

nuclear division/karyokinesis.. followed by cytoplasmic division ( cytokinesis) that encloses cell in plasma membrane.

Transcription factory:

nuclear sites at which most RNA polymerase II transcription occurs and contains active RNA polymerase and transcription factors

ribozyme

nucleic acid that can do enzyme catalysts of peptide bond formation.

NOR:

nucleolous organizer region (areas of DNA that endode rRNA).

Chromatin can be remodeled in two general ways by acting on either

nucleosomes or DNA.

inosine

nucleotide. modifide purine. found in tRNA but not in mRNA and DNA

amorphic mutation

null, no expression

linkage groups

number of linkage groups should correspond to the haploid number of chromosomes. when large numbers of mutant genes present in a species are investigated, genes on the same chromosome show evidence of linkage.

Proteome =

number of proteins an organism can (but does not necessarily) make

Positive control means gene expression

occurs only if a regulator molecule directly stimulates RNA production.

EcoRI and HindIII make

offset cuts: leaves one end over handing (cohesive ends)

Continuous variation:

offspring are a blend (widespread belief)

When we have about 20, we call this an

oligonucleotide

Monocistronic:

one gene/protein

Open reading frames (ORF):

open reading frame has a stop codon

The inducer, lactose, has two binding sites:

operator binding region (gets altered when bound to lactose) and lactose binding side.

Prokaryotic gene regulation

operons, repressors, cis acting, operators, promoters

Epigenesist:

organism develops from the egg

Centrioles:

organization of spindle fibers that function in mitosis and meiosis. From the basal body (associated with formation of cilia and flagella).

In a prokaryote, such as E.coli, where does replication begin?

oriC. Replicon is the entire genome. bi-directional.

Glycocalyx:

over the pm and is made up of glycoproteins and polysaccharides. Provides biochemical identity at the surface of cells (for ex: ABO, AB, Rh and MN antigens on red blood cells). Receptor molecules, antigens, etc.

tetrad

pairing of dyads (i.e., replicated homologs or four chromatids)

Dispersive:

parental strands are dispersed into two new double helices after replication. Each strand has new and old DNA.

Penetrance:

percentage of individuals who show at least some degree of expression of a mutant genotype

XXX:

perfectly normal, or can be mentally retarded

What enzyme helps bring lactose into the cell? Gene name? If gene is mutated, we abbreviate this as:

permease, lac Y, lac Y-

Parental origins affect

phenotype expression.

Criss cross pattern of inheritance:

phenotypic traits are controlled by recessive X-linked genes that are passed from homozygous recessive mothers to son: sons express same X linked traits as their mother.

self ligation:

plasmid cut with a restriction enzyme closes back on itself.

Complexes brought to the 3' untranslated region (UTR) cause

poly A tails to shorten which leads to: short half-lives and rapid degradation

DNA is a _______________ of repeating monomers. In this case, the __________ is the monomeric unit. And each monomer is made up of 3 components.

polymer, nucleotide

4. As the distance between two linked genes increases...

porportion of recominant genes increases and parental gametes decreases

molecules in the cytoplasm:

posttranscriptional modification of a eukaryotic RNA transcripts 7mG cap added at the 5' end before transcritption is completed. Protects it from nuclease attack. Transports mRNA across the nuclear membrane into the cytoplasm.

What is PGD? What is the basic procedure?

preimplantation genetic diagnosis, or P.G.D., for more than a decade to screen for genes certain to cause childhood diseases that are severe and largely untreatable. In vitro fertilization. in which eggs are extracted from the mother and fertilized with the father's sperm in a petri dish. When the resulting embryos are three days old, doctors remove a single cell from each and analyze its DNA. Only embryos without the defective gene are then considered candidates to implant in the mother's uterus

shugosin

prevents cohesion from being degraded by separase at the centromeric region.

sex ratios

primary sex ratio: proportion of males to females conceived in a population. Secondary sex ration: proportion of each sex that is born. Theoretical ratio of 1 assumes that males produce equal numbers of x and y bearing sperm, equally viable sperm, egg is equally receptive to x and y bearing sperm. More males than females.

hypermorphic:

produce more gene activity per allele than wild type. Dominant. Homozygotes get it worse.

restriction enzymes:

produced by bacteria as a defense against infection by viruses by degrading their DNA. Recognizes and binds to DNA at a specific nucleotide sequence (restriction site: present randomly in genome, 4-6 nucleotides long, some are 8).

circular chromosomes

prokaryotes and some eukarotes. in cytoplasm, mitochondria, chloroplasts, packaged loosely without histomes

Two key stages that produce variation in meiosis:

prophase 1 for crossing over. metaphase 1 for independent assortment

Rho dependent mechanism:

protein dependent is the other way. Induces an unwinding of RNA/DNA complex. Recognizes a sequence of RNA, glides along, and can recognize a termination sequence. Helps uncouple the RNA/DNA duplex. Hexomeric protein (6 subunits).

three major cellular classes of RNA,

rRNA: 80% of all RNA in a cell. Structural component of ribosomes. mRNA: transcripted then taken to translation tRNA: recognizes amino acids for translation

Expressivity:

range of expression of mutant genotype.

The other three cis elements are regulatory and affect:

rate of transcription Proximal-promoter elements Enhancers silencers

cloverleaf

read from 5' to 3'. ends with CCA and OH at the 3' end and the amino acid attachment site.

A person has one allele with a loss-of function mutation and the other allele is wild type. There is no phenotype. Yet if both alleles are loss-of-function, then there is a sever phenotype. Is this loss-of-function mutation dominant or recessive in this case?

recessive

complementation only works for

recessive traits

anticodon region

recognizes mRNA

Methyl transferase

recognizes parent methylated GC sequences and attaches a methyl group on complementary daughter CPG sites. makes it coiled tightly

Loss of function mutation:

reduce or eliminate the function of the affinity of a substrate to an enzyme. Complete = null

Loss of function-

reduces or eliminates the function of the gene product

post-transcriptional regulation:

regulation of splicing and processing, regulation of transport, degradation of mRNA, translation regulation, protein modifications, rate of translation,

RITS

remodels chromatin and silences transcription

Transacetylase:

removes toxins

When scientists were first looking for the genetic material, they knew it had to possess four major characteristics, they were:

replication, storage of information, expression of information, variation by mutation

What trans-acting element binds the operator? Where does it come from, environment or synthesis?

repressor Synthesis from I gene

Lactose must bind to the

repressor and CAP (a dimer that binds to adjacent regions of DNA) must be bound so that it can bend the DNA

When the repressor protein is bound to the operator:

repressor is allosteric (reversibly interacts with another molecule, causing both a conformational change in the repressor's 3D space and a change in its chemical activity. Repressor normally binds to the DNA sequence of the operator region. It inhibits the actions of RNA polymerase, repressing the transcription of the structural genes.

Trans acting factor binds to it (like a

repressor or activator)

Recombinant DNA technology began with two key tools:

restriction enzymes and cloning vectors

plasmid vectors have been genetically engineered to have

restriction sites for enzymes in the multiple cloning site. Allows scientists to clone a range of diff fragments.

a. Reverse transcriptase

reverse transcriptase is then used to generate a doublestranded DNA molecule called cDNA, using the mRNA as a template. Finally, this cDNA is incorporated into the cloning vector

inducible:

role of a substrate that induces enzyme production.

What has been the major concern with injecting stem cells into animals?

scientists cannot fully control the spread of stem cells to other places in the body. has formed tumors, trisomy,

2. What are two basic characteristics of stem cells?

self renewal indefinately by mitosis differentiation into specialized cell types

SRY:

sex determining region Y encodes a protein that causes the undifferentiated gonadal tissue to form testes (testis determining factor).

However if the trait is possible in both sexes but more prevalent or influenced by the organism's sex it is a

sex-influenced inheritance trait (like baldness, horn formation, coat patterns).

+1 reading frame:

shifts it by 1

Linkers:

short, double-stranded oligonucleotides with a restriction enzyme sequence.

What did they predict would happen if a I+ gene was introduced into this cell?

should restore inducibility (normal wild-type repressor is a trans-acting factor)

RISC

siRNA. degrades mRNA and inhibits translation

eukaryotic gene regulation

silencers, repressors, chromatin remodeling, nucleosomes, transcription complexes, epigentic marks, cis acting, NO OPERATORS OR OPERONS, promoters, enhances

XXXY:

similar to kleinfelters, but more extreme

What is a SNP?

single nucleotide polymorphisms (SNPs; pronounced "snips"). SNPs are single-nucleotide substitutions of one base for another that occur in more than one percent of the general population. SNPs on the gene that codes for the protein that the drug targets could render the drug useless if the protein is manufactured differently than what the drug was intended to do.

"Its fun without commitment. I just want to be single forever. Text me if you feel the same way."

single stranded binding proteins

Autosomal recessive disease

skips generations, equal in both sexes

HnRNA (heterogeneous nuclear RNA):

smaller mRNA

break 50S unit

smaller unit where catalyst takes place.

why does the nuclear envelope dissolve?

so the proteins in the centromeres can attach to the chromatids

snRNA and proteins

spliceosome to remove introns in the nucleus. need RNA to recognize the introns

Recombinant DNA technology:

splicing eukaryotic DNA into bacterial DNA and inserted into a bacterial cell. Eukaryotic proteins are produced.

snRNA + proteins And where in the cell would you find these functioning?

splicosome that removes the loop-like regions. Their function is to process mRNA and remove introns nucleus

single stranded binding proteins (SSBPs)-

stable the open conformation of DNA

termination translation

stop codon is reached, A site is empty, mRNA and polypeptide chain is released, and large and small subunits break.

non-sense-

stops coding prematurely

tRNA has a secondary

structure due to base pairing.

a. Marker gene

such as genes for antibiotic resistance, are often engineered into plasmids. These marker genes enable researchers to know which bacteria have the plasmids. The antibiotic is added to the media used to grow the bacteria. Cells that do not contain the plasmid will fail to reproduce. In addition to marker genes, plasmids typically contain one or more genes of interest.

Is

super repressed. No transcription even if I+ is there.

What gene is mutated in most cases of familial ALS?

superoxide dismutase-1 gene (SOD1;147450) on chromosome 21q22.1.

Endosymbiotica hypothesis:

symbiotic relationship between organelles lead to the cell

ER:

synthesizes fatty acids and phospholipids

elongation

tRNA is released from the P site and the large subunit and moves to the E (exit) site and the complex shifts towards the P site by 3 nucleotides, helped by elongation factors (EFs) and GTP. Following the shift, the P site contains a tRNA attached to a peptide chain and A has the tRNA with an amino acid attached.

List the molecular players in translation:

tRNA, free amino acid, ribosomes, mRNA, large and small subunits, aminoacyl tRNA synthetases

. Linkage maps-

tell us the distance between genes of interest

non-linear process of science

testing ideas, exploration and discovery, benefits and outcomes, community analysis and feedback

UV lights can be used to mutate the genome. Make an absorption spectrum and compare it to

the action spectrum. The molecule absorbs at mutagenic wavelengths.

Telophase:

the centromeric region is split in two, signaling the beginning of anaphase. daughter chromosomes arrive at the poles and cytokinesis commences. Chromosomes uncoil and diffuse into chromatin. Nuclear envelope reforms. Spindle fibers disappear and nucleolus reforms. Cells enter interphase.

What is the phenotype of someone with ALS?

the death of motor neurons in the brain, brainstem, and spinal cord, resulting in fatal paralysis. ALS usually begins with asymmetric involvement of the muscles in middle adult life. The first form they delineated is characterized by rapidly progressive loss of motor function with predominantly lower motor neuron manifestations and a course of less than 5 years. Pathologic changes are limited to the anterior horn cells and pyramidal tracts. The second form is clinically identical to the first, but at autopsy additional changes are found in the posterior columns, Clarke column, and spinocerebellar tracts. The third form is similar to the second except for a much longer survival, usually beyond 10 and often 20 years.

Some proteins in eukaryotes will be secreted from the cell and these proteins are built on ribosomes that are associated with

the endoplasmic reticulum. Absent from the cytoplasm of prokaryotic cells. Facilitates secretion of new proteins from the ribosomes directly into the ER via a tunnel in the large subunit.

telomerase

the enzyme is a ribonucleoprotein that has a short piece of RNA inside that guides attachment of the enzyme to the telomere, and a template for the synthesis of its DNA complement (reverse transcription). The extension of the 3' overhang provides the 3-OH group necessary for the initiation of synthesis to fill the gap

Beadle and Tatum came up with the hypothesis:

the function of an individual gene is to dictate the production of an enzyme

Mutation rate:

the likelihood that a gene will undergo a mutation in one generation

What if the operator sequence is altered such that the repressor can't bind it (Oc)?

the nucleotide sequence of the operator DNA is altered and will not bind with a normal repressor molecule so structural genes are always transcribed.

The position effect:

the physical location of a gene in relation to other genetic material may influence its expression. Translated near heterochromatin, expression of the allele is modified.

Structural genes code for

the primary structure of enzymes.

genome

the totality of all the genetic material in a given organism

If DNA was the genetic material,

then they would find radioactive protein in empty phage coats at the end of their experiment.

if protein was the genetic material,

then they would find radioactive protein in the cell at the end of their experiment.

What happens if an individual has only a Y and no X?

they do not survive.

Why are scientists optimistic that spinal cord injuries might one day be treated with stem cells?

thought spinal cord cannot grow new neurons, but they did itttttt

Each cell is a different environment, and

thus has a different set of transcription factors that may or may not bind the regulatory elements of different genes.

Anticodon loops

to which the nitrogenous bases can pair

activators

trans

repressor

trans

RNA Pol II:

transcribes mRNA and snRNA: main one, only one that does coding

RNA Pol I:

transcribes rRNA

RNA Pol III:

transcribes tRNA nad 5S rRNA

In prokaryotes, the critical step in regulation is:

transcription (binding of RNA pol to promoter) Repress: to turn down the expression of genes encoding enzymes that are not needed. Induce: to turn up the expression of genes encoding enzymes that are needed.

When the consensus sequences are mutated,

transcription levels decrease.

List the basic steps to clone DNA into a plasmid and transfer the plasmid into bacteria:

treat cells with calcium ions and using brief heat shock to pulse DNA into cells. Electroporation: brief, high intensity pulse of electricity to move DNA into bacterial cells. Many plasmids increase their copy number to make hundreds in the host cell. 1. cut plasmid DNA and DNA to be cloned with the same restriction enzyme (usually cut once within the multiple cloning site to make a linear vector) 2. DNA restriction fragments from the DNA that will be cloned are added to this vector by DNA ligase. 3. sticky ends anneal, joining DNA with the plasmid 4. DNA ligase seals the DNA backbone 5. replicates to make many copies

When three nucleotides are bound together we call this a

trinucleotide

Reading frame:

triplet sequences of nucleotides

If the ratio is expressed in 16 parts, it suggests that

two gene pairs are interacting

A complementation analysis involves crossing

two homozygous recessive mutants.

monohybrid:

two true breeding individuals

If two linked genes are far enough apart and the result is a 1:1:1:1 ratio (50% parental and 50% recombinant) this would be indistinguishable from what?

two unlinked, independent assorment

Serotypes:

type of bacteria determeined by the chemical structure of the polysaccharide. Identified by roman numerals.

give an example of how the genetic code is

unambiguous: each one codes for something sepecific

UTR

untranslated region.

RNA can fold

up on itself and form loops to bind to itself.

What kind of organs have been created in vitro?

urinary bladder, skins

Why was it important in the methodology of the Messelson-Stahl experiment that they used 15N?

used bacteria cells to produce new DNA molecules. 15 ammonium chloride. A heavy isotope and more dense, and is stable. Almost all E. coli cells had the heavier isotope. Used sedimentation equilibrium centrifugation in which samples are forced through a density gradient. First generation: one band of intermediate density (suggests semiconservative). After, two bands, one heavier and one lighter.

Restriction enzymes:

used by bacteria to cut the DNA of invading viruses. Can be used to cut DNA to make a set of reproducible fragments.

How can sickle cell disease be cured in mice with iPSCs and maybe humans in the future?

used homologous recombination to correct the iPSCs by replacing alleles.

One type of reprogrammed cells are induced pluripotent stem cells (iPSCs). How were they first made?

used retroviruses to deliver transgenes into mice that encoded TFs in cell development that reprogrammed the fibroblasts back to an earlier stage of development.

electroporation,

uses a short electrical pulse to open pores in the plasma membrane, allowing the plasmid to pass through.

If we look at the same gene in different cell types,

we will see the exact same DNA- including the promoter and all its regulatory elements.

If we look at two different genes in one cell,

we will see they have different DNA sequences- including the promoter and all its regulatory elements.

transforming principle

what turned dead S pneumococcus to live S when injected into a live R mouse in Griffith's experiments

What is the dilemma presented in this article? Is there a fix?

when customers face ambiguous or alarming results needing expert interpretation, and they heed the timeless suggestion: ask your health care provider for more information. each basic question about genetic testing was answered incorrectly by over half of physicians, irrespective of receipt of the educational mailer. Improve education

the linkage ration

when two completely linked genes whos parents are heterozygous at both loci mate: offspring are 1:2:1

How do we define personalized medicine?

where a patient's personal genetic and environmental information is used collectively to predict individual risks of disease and responsiveness to drugs, promises to revolutionize the medical management of many illnesses

One type of gene interaction is epistasis,

where one gene or gene pair masks or modifies the expression of another gene or gene pair.

Bacteria that have a plasmid with your cloned fragment of interest will be blue/white (circle one) when plated with X-gal.

white

Transformed:

white, won't cleave X-gal, clones of each other.

Positive control:

will yield the expected outcome

What happens when you cross A/a; B/b x A/a; B/b? Why is this called recessive epistasis?

¼ are albino: bb (recessive) masks or suppresses the expression of the A gene. AABB, AABb, AaBB, AaBb: agouti 1/16, 2/16, 2/16, 4/16 (9/16) AAbb, Aabb, aabb: albino (1/16, 2/16, 1/16) 4/16 aaBB, aaBb: black (3/16) 1/16 + 2/16

Prophase:

½ of time in mitosis. Centrioles migrate to opposite ends of the cell (one new, one mature). Located in the centrosome. Nuclear envelope disappears. Nucleolus disintegrates within the nucleus. Chromatin fibers condense and chromosomes become visible. Sister chromatids are held together by a protein complex, cohesion, beginning in the S phase.