Bio 97

Epigenetics

"above the genome" heritable changes that regulate gene expression without altering DNA sequence

Which end does the 3' end on?

(OH) group

DNA backbone is made up of

1 phosphate: dNMP (N = ACGT) 3 phosphates: dNTP

How many base pairs are in the human genome?

10^9

How many bp of DNA is each nucleosome composed of?

146

How many Histone proteins are there of each type in a nucleosome?

2 H3/H4 Dimers 2H2A/ H2B Dimers 146 bp of core DNA

How many genes are in the human genome?

20,000 genes

How many chromosomes does the human genome have?

23 x 2 chromosomes ( 46 chromatids )

Which direction does the exonuclease go in?

3' to 5'

If there are five molecules of DNA containing the target region at the beginning of a PCR reaction, how many copies of the target will be present after three rounds of amplification?

40 The number of target sequences is doubled with each replication cycle.

Which end terminates on the phosphate group?

5' end

Which direction does polymerization occur in?

5' to 3' direction

Primers always synthesize in the...

5' to 3' direction New bases are always added to the 3' end of the primer, so the GFP gene sequence is to the right of the forward primer and to the left of the reverse primer.

A large gene-containing region of DNA in the fruit fly Drosophila melanogaster‎ is 92,672 base pairs long. The length of linker DNA in Drosophila‎ is 35 base pairs. Approximately how many nucleosomes are required to organize this region of DNA into the 10nm fiber structure?

512 nucleosomes Each nucleosome repeat is composed of the DNA (146 bp) wrapped around the core nucleosome particle plus the linker DNA (35 bp in this case). Therefore each repeat accounts for 181 (146 + 35) base pairs of DNA. Since the region is 92,672 bp long, then approximately 512 nucleosomes (92,672/181) would be required to organize the region into the 10nm fiber structure.

Chromosome

A DNA containing structure containing a centromere

Purine How many Hydrogen Bonds?

A and G 2 hydrogen bonds

silent mutation

A mutation that changes a single nucleotide, but does not change the amino acid created.

Histone modifications

Acetylation and methylation

Frameshift Mutation

Addition or Removal of a base pair

Which of the following are present in your liver cells?

All enhancers are present in your liver cell. it just depends whether they are turned on or off.

Which of the following statements best describes the function of aminoacyl tRNA synthetase? It attaches a specific amino acid to a tRNA molecule. It helps tRNA synthesize proteins. It synthesizes tRNA molecules. It provides the energy required to attach a specific amino acid to a tRNA molecule.

Aminoacyl tRNA synthetase catalyzes the charging reaction that links a specific amino acid to a tRNA molecule.

Carriers

An individual heterozygous for a recessive allele (Cc)

Methylation of DNA (CpG)

C and G on some strand of DNA. On CpG islands you get repeated CGs, methylation of Cytosine itself. When DNA is methylated on cytosine, then expression is suppressed.

Pyramidines How many hydrogen bonds?

C and T 3 hydrogen bonds

forward mutation

Changes the wild-type phenotype to a mutant phenotype

Chromatin consists of..

DNA and proteins and is the material of which chromosomes are composed

Chromatid

DNA molecule

What does PCR do?

DNA replication in a test tube

The hierarchy of chromosome organization

DNA, nucleosomes, histones, solenoid, chromatin fiber, chromatid

A standard PCR cycle includes three steps: denaturation (95°C), annealing (55°C), and elongation (65°C).

Denaturation (95 degrees C) = Template DNA Annealing ( 55 degrees C) = primers Elongation (65 degrees C) = dNTPs (deoxyribonuleotieds) Taq Polymerase

When are 3 phosphates used in DNA?

During the copying of DNA

How can nucleosomes be repositioned or removed?

Enzymes move them out of the way Histone/ DNA modifiction, epigenetics "above the genome", heritable changes that regulate gene expression without altering DNA sequence

dominant negative mutation

Exerts a dominant effect. A heterozygote produces a nonfunctional altered protein that also prevents the normal gene product from functioning

T or F, Enhancers increase the rate of transcription?

FALSE

The 4 daughter cells of meiosis are genetically identical True or False?

False

Equation that explains the relative proportions of each base in a DNA macromolecule?

G+A=T+C

Interphase is split into three phases...

G1 , S phase, G2

Half of DNAs proteins are composed of...

Histone proteins

Transmission Genetics

How traits are inherited

What were mendels conclusions?

Inheritance does not involve "blending" of traits the F1 plants are not true breeding and they contain two different traits

Is H1 part of the nucleosome core?

NO

Below is a partial mRNA sequence from a mutant gene in E. coli. used to answer the following questions. 5'... ACCCGCCACGCC... 3' Assume the reading frame contains the codon ACC. Which partial amino acid sequence is encoded within the partial mRNA sequence

Nterm...T-R-H-A...Cterm

What is the role of primers in PCR?

Primers bind to end of the target DNA strands, then taq polymerase synthesizes a new strand using the target DNA as a template.

What does RNA have on its sugar that DNA doesn't?

RNA has two hydroxyl groups DNA has one hydroxyl group and one H

What is genotype ratio?

Ratio of genotypes being expressed

What is phenotype ratio?

Ratio of phenotypes being expressed

What are examples of heterochromatin?

Repetitive DNA Centromeric DNA Barr body Telomeric DNA

Which phase is the longest and why?

S phase and it is the longest because this is where DNA synthesis occurs

Where is the promoter found?

Side that starts transcribing in 5' to 3' direction The promoter is located in the DNA that is adjacent to the start site of transcription. The start site corresponds with the 5' end of the RNA (or the 3' end of the DNA template strand). Return to Assignment

What is the function of the H1 Histone?

Stabilizes the 30 nm fiber

Which region of a tRNA molecule binds to amino acids?

The 3′ end of a tRNA molecule contains the amino acid binding site.

Which of the following statements about manual Sanger sequencing is true?

The DNA fragments produced in sequencing reactions are synthesized by DNA polymerase to be complementary to the template strand. Return to Assignment

DNA methylation

The addition of methyl groups to bases of DNA after DNA synthesis; may serve as a long-term control of gene expression.

While the introduction of the mutant synthetase gene restored some of the growth characteristics, this strain still does not grow as fast as wild-type E. coli. Which of the statements support this observation? The mutant synthetase gene allows histidine tRNA to be charged with asparagine, therefore histidine could not be present in any protein. If the the histidine residue was important to the function of various other proteins growth may not be completely restored. The mutant synthetase gene allows histidine tRNA to be charged with asparagine, but sometimes this tRNA could deliver asparagine in the place of histidine to other proteins where the histidine residue was important to the function of the protein and growth. The codon for histidine has not changed in the mutant variant, therefore only the mutant variant of the protein is produced resulting in slow growth. The normal synthetase that charges histidine tRNA with histidine is still present resulting in the mutant variant of the protein. Not having enough of the normal protein may still limit growth. Submit

The normal synthetase that charges histidine tRNA with histidine is still present resulting in the mutant variant of the protein. Not having enough of the normal protein may still limit growth. Since the mutant synthetase gene allows histidine tRNA to be charged with asparagine and the normal synthetase that charges histidine tRNA with histidine is still present, the result will be the same tRNA charged with either histidine or asparagine. Either of these charged tRNAs can recognize the CAC codon. Therefore sometimes a histidine will be incorporated as expected, but other times an asparagine will be incorporated. When the mutant variant of the gene for the growth is transcribed and translated with the histidine tRNA charged with asparagine, this will produce the normal protein (Nterm...T-R-N-A...Cterm) and be beneficial for the cell. But not all transcripts from this gene will produce the normal protein since histidine can be incorporated as well. Other proteins in the cell where the histidine residue is important for function may now have asparagine incorporated likely making these proteins non-functional and possibly impacting growth. Since histidine can still be incorporated into these proteins using the correctly charged tRNA, some functional protein can still be produced.

Speculate about why enhancers are not part of transcription of bacterial genes. The high level of mutation in bacterial genomes would likely alter these conservative sequences rendering them nonfunctional. Bacteria mostly regulate gene expression at the level of translation, making transcription enhancers unnecessary. There is little to no intergenic space on bacterial chromosomes, which makes long-range-acting enhancer sequences unnecessary. Enhancers often provide a mechanism for cell-specific transcription of genes, and most bacteria lack differentiated cell types. Bacterial operons make coordinate regulation of protein synthesis by enhancers unnecessary.

There is little to no intergenic space on bacterial chromosomes, which makes long-range-acting enhancer sequences unnecessary. Enhancers often provide a mechanism for cell-specific transcription of genes, and most bacteria lack differentiated cell types. Bacterial operons make coordinate regulation of protein synthesis by enhancers unnecessary

Each aminoacyl tRNA synthetase enzyme recognizes only one amino acid, but each enzyme can often recognize several tRNAs because there is usually more than one codon for each amino acid.

True

True or False, Enhancers bind transcription factors that stimulate transcription of one or more genes.

True

Histones are positively charged, and DNA is negatively charged.

True or False

Sister Chromatids

Two copies of the same DNA molecule, joined by a centromere

Haplosufficient

When the amount of units needed for a phenotype is met

Haploinsufficient

When the amount of units needed for a phone type is not met

Functional types of mutations/alleles

Wild Type Loss of Function -null or anamorphic -Hypomorphic -Dominant negative Gain of function -hypermorphic -neomorphic

When a trait is X-linked dominant the phenotype is visible in:

XAXA, XAXa females and XA____ males

Female chromosomes are

XX

Males chromosomes are

XY

When a trait is X-linked recessive, the phenotype is visible in

XaXa females and Xa__ males

Methylation

a biochemical process that influences behavior by suppressing gene activity and expression

Epistasis

a gene at one locus alters the phenotypic expression of a gene at a second locus

During meiosis the products receive

a haploid amount of DNA

neomorphic mutation

a mutant expressing a new or novel function not seen in the wild type

What does PCR require?

a sequence specific DNA primer a special polymerase piece of DNA four nucleotides dideoxynucleotides

Missense

a single nucleotide change results in a codon that codes for a different amino acid

Pure breeding strains

all round offspring , all wrinkled offspring

What does DNA polymerase need to begin?

an RNA primer

Proband

an individual with a disorder who is the first subject in a study

DNA forms an

antiparallel double helix

Euchromatin

areas of active expression, not tightly condensed

In mammals, the different dosage of X chromosomes between males and females is compensated

by X chromosome inactivation in females this occurs two weeks after fertilizations During development, 1 X chromosome condenses into a Barr body

reverse mutation

changes a mutant phenotype back to the wild-type phenotype or close to the wild type

Nonsense Mutation

changes the amino acid to a stop codon

In eukaryotes DNA is organized as...

chromatin

Which strand does the reverse primer hybridize

coding strand in the 5' to 3' direction

Null/amorphic mutations

completely block function of a gene product (e.g. deletion of an entire gene)

During Mitosis, chromosomes ...

condense

During interphase, DNA can be ...

condensed to different degrees

Histones are typically modified on their tails

end terminal of their tails

hypermorphic mutation

enhanced gene function (protein functions more efficiently) -extremely rare -usually dominant

Fruit flys, red eyes, where is the chromatin

euchromatin is near the centromere, heterochromatin is far from the centromere

hypermorphic mutation

excessive expression of gene product leads to excessive gene action

How does polymerase proofread?

exonuclease chews back on strand of DNA

What are the two types of Heterochromatin?

facultative and constitutive

Heterochromatin

few active genes, tightly condensed

Homologous chromosomes

found in diploid cells. They pair during meiosis and contain the same genes, but possibly different alleles.

Environmental Impact

genetically identical individuals show different phenotypes as a result of environmental factors.

Meiosis takes place in

germ line cells

Each chromosome has..

half DNA and half protein

Meiosis produces

haploid gametes from diploid cells

Incomplete dominance

heterozygotes have a phentype intermediate between two alleles Red x White = Pink

synaptonemal complex

holds together non sister chromatids. It forms during zygotene and dissolves during diplotene

Pure breeding strains are

homozygous

A test cross is

homozygous recessive

Epressivity

how strongly a. phenotype is expressed

Enhancers _____________ the level of transcription of genes in an orientation independent manner.

increase

Enhancers__________ the level of transcription of genes in an position independent manner.

increase

Fruit fly, white eye with red patches white patches explanation red patches explanation

inversion moved some of the heterochromatin to the euchromatin area centromeric heterochromatin spreads across to the euchromatin side = no gene expression

epigenetic differences

is heritable, passed on through mitosis but has no effect on DNA sequence

Where heterochromatin is located on the centromere is

key to gene expression

Multiple alles

more than two alleles affect a phenotype

X chromosome inactivation gives rise to

mosaicism

Polygenetic inheritance

multiple genes influence characteristics

leaky/hypomorphic mutation

mutation resulting in partial loss of gene function

DNA is made up of

nucleotides

reverse mutation - second - site reversion

occurs by mutation in a different gene that compensates for the original mutation, restoring the original to WT.

reverse mutation - intragenic mutation

occurs through second mutation elsewhere in the same gene

Pleiotropy

one gene affects changes amino acid, producing a different protein, which changes the phenotypic character

Nucleosomes can be displaced to

open chromatids

Mendel chose traits that were dichotomous which means...

plants either showed one trait or the other (easy to distinguish)

chiasmata

points at which crossing over occurs, allowing exchange of genetic material between homologous chromosomes

Mitosis

produces two identical diploid daughter cells

Heterochromatin surpresses gene expression by compacting

promoters and the whole gene body

Lethal alleles

recessive homozygotes cannot survive

Constitutive heterochromatin

remains condensed throughout the cell cycle and development. No gene expression.

What forms the backbone of DNA

sugar

Reciprocal crosses

swap the identity of the male and female parents produces identical results

What does DNA polymerase do?

synthesizes DNA; proofreads and repairs DNA

This gene is a mutant variant that severely slows the growth of the bacteria. The normal version of the encoded protein should contain the partial amino acid sequence (Nterm...T-R-N-A...Cterm). It's known that mutant forms of tRNA synthetases can charge tRNAs with a different amino acid than expected. If a mutant synthetase gene was introduced into the E. coli, which one could produce the normal version of the encoded protein? synthetase that charges a histidine tRNA with histidine synthetase that charges an asparagine tRNA with asparagine synthetase that charges an asparagine tRNA with histidine synthetase that charges a histidine tRNA with asparagine Submit

synthetase that charges a histidine tRNA with asparagine Since the mutant sequence (Nterm...T-R-H-A...Cterm) contains a histidine instead of an asparagine in the normal sequence (Nterm...T-R-N-A...Cterm), then a tRNA is needed that recognizes the histidine codon (CAC), but can deliver an asparagine amino acid. Therefore a mutant synthetase that charges a histidine tRNA with asparagine will be needed.

Why are test crosses used...

tells you the genotype of the F1 phenotype if unknown

Which strand does the forward primer hybridize

template strand

neomorphic mutation

the mutant allele has novel function that produces a mutant phenotype in homozygous and heterozygous organisms. s

Co-dominance

the phenotype of both alleles is fully expressed in heterozygotes Red x White = Red + White patches

Penetrance

the probability that a mutation will manifest its phenotype

Facultative heterochromatin

the regions of euchromatin are converted into heterochromatic state

Immediately after the primers have annealed to the target sequence, _______.

the temperature is raised so that taq polymerase can extend the primers

The -10 and -35 consensus sequences are important because of:

their location relative to one another their nucleotide content their location relative to the start of transcription

Acetylation

usually of lysine amino acid, makes less positively charged chromatin decondensed, genes activated