EXAM 3 REVIEW FINAL GENETICS

In mammalian cells, the _____ strand folds over and pairs with a short stretch of DNA to form a t-loop.

G-rich

Orphaned Romanian Children who grew up in orphanages had shorter telomeres than children who grew up with biological or foster parents. Shortened Telomeres are associated with shorter ____ ___ and increased incidence of disease

life span

These results suggest that early ___ ___ from severe psychosocial deprivation may be embedded at the molecular genetic level through accelerated telomere shortening.

adverse care

Telomere length is ___ ___ to blood lead level in children. Shorter relative telomere length in peripheral blood is a risk marker for some types of cancers and cardiovascular diseases.

inversely proportional

Children exposed to lead had ___ telomeres than children not exposed to lead

shorter

Telomere length is inversely associated with ____

aging

To understand the role of telomere biology in ageing-related diseases, it is essential to expand telomere research to newborns and children and seek further insight into the underlying causes of the variation in TL due to ____and geographical location.

ancestry

Recent research has converged on the premise that TL might be an active determinant in adult-onset ____

disease

The _____ is the chromosomal locus essential for chromosome inheritance and genome stability.

centromere

The physical role of the centromere is to act as the site of assembly of the ______- a highly complex multiprotein structure that is responsible for the actual events of chromosome segregation

kinetochore

The kinetochore protein, CENPF, is mutated in human ciliopathy and _____ phenotypes.

microcephaly

Histones are highly alkaline proteins found in eukaryotic cell _____that package and order the DNA. Histones have a positive charge and DNA is negatively charged – hence the attraction.

nuclei

_____ has a highly complex structure with several levels of organization

Chromatin

What is less condensed, on chromosome arms, unique sequences, many genes, replicated throughout S phase, transcription happens often, and crossing over is common?

Euchromatin

What is more condensed, at centromeres, telomeres, and other specific places, repeated sequences, few genes, replicated in late S phase, transcription is infrequent, and crossing over is uncommon?

heterochromatin

DNase I sensitivity is correlated with the transcription of globin genes in___ _____. The U gene encodes embryonic hemoglobin; the αD and αa genes encode adult hemoglobin. The red arrows indicate sites of DNase I digestion

chick embryos

_____ is a heritable alteration of phenotype because of altered chromatin structure (histone modification, acetylation) or the modification of DNA (methylation) without changing the DNA sequence

Epigenetics

These mice are genetically identical but have different levels of methylation of the DNA at the agouti locus which controls ___ ___

coat color

Moderately repetitive DNA: 150 ~ 300 bp long – Tandem repeat sequences – Interspersed repeat sequences » Short interspersed elements: ____s: Alu element » Long interspersed elements: _____s

SINE, LINE

Mapping with microsatellites. Fragments are amplified and separated based on size by electrophoresis. Each person has a unique “fingerprint” of microsatellites - very useful in _____

forensics

Neutralizing their positive charges would have which effect on the histone proteins?

The attraction to DNA would be reduced

Sequences that can move about the genome

Transposable Elements

Movement of the transposons

Transposition

Transposable Elements Cause _____

Mutations

What are features of transposons?

•Flanking direct repeats •Terminal inverted repeats

Mobile DNA sequences found in the genomes of all organisms. • Make up at least 45% of human DNA • Most are able to insert at many different locations. • Rely on mechanisms distinct from homologous recombination • Often cause mutations

Transposons

Short flanking repeats from 3 to 12 bp long are present on both sides of the____ _____ . • Do not travel with the transposable element • Regenerated at the point of insertion

transposable elements

Terminal, inverted repeats (9 to 40 bps) are found at ends of many ____ ____

transposable elements

Only DNA transposons are found in bacteria; they include: • Insertion sequences: • Common in bacteria but also infect ____ ___ ___

plasmids and viruses

Mu is a transposing ______

bacteriophage

Why is this process referred to as “copy and paste” transposition? • A new copy of the transposable element is introduced at a new site while the old copy remains at the original site.

Replicative Transposition

• Single copy of the transposable element is on one DNA molecule • Two DNA molecules are joined • Transposable element is replicated • Results in the production of a cointegrate structure: • Two DNA molecules plus two copies of the transposable element

events necessary for co-integrate formation

• Crossing over at regions within the copies of the transposable element produces two molecules, each with a single copy of the transposable element = ____ ___ ___ ___

resolution of the cointegrate.

What are the enzymes involved in replicative transposition?

Transposase, Resolvase

An enzyme that binds to the end of a transposon and catalyzes the movement • May be encoded by cellular gene or often by transposable element • Makes single-strand breaks at each end of the transposable element and on either side of the target sequence where insertion occurs

Transposase

An enzyme which brings about the separation of two transposons contained in a cointegrate during the process of replicative transposition • Encoded either by cellular genes or by transposable element • Responsible for resolution

Resolvase

Why is this process referred to as “cut and paste” transposition?

• Transposable element is excised from old site and inserted into a new site • Does not increase number of copies.

• Cleavage requires a transposase enzyme produced by the transposable element. • Joining of the transposable element is carried out by normal replication and repair enzymes. • Original site is typically repaired using homologous template on sister chromatid.

non-replicative transposition

Chromosomal rearrangements are a consequence of ___ ____

transposed sequences

One of her ideas was the notion of genetic recombination by crossing over during meiosis. During the 1940s and 1950s, McClintock discovered _____(transposons) and used it to demonstrate that genes are responsible for turning physical characteristics on and off.

transposition

_____ _____ discovered transposable elements (TE).

Barbara McClintock

Transposition results in _____ maize kernels

variegated

The discovery of the first known active human L1 element was the result of its retrotransposition into the factor VIII gene, causing a de novo case of _____

hemophilia

The mechanisms that ensure developmental progression in the early human embryo remain largely unknown. These results indicate that LINE1 RNA and PRC2 maintain H3K27me3-mediated gene repression and 3D nuclear organization to prevent ____ ___ of hESCs

developmental reversion

Evolution: Transposons may have coordinated progesterone responsiveness that led to the evolution of ____ in mammals

pregnancy

Mammals very likely have a progesterone-responsive _____because of these transposons.

uterus

Emerging lines of evidence suggest that cancers driven by p53 mutations could represent ‘transposopathies’, i.e. disease states linked to eruptions of ____ ____

mobile elements.

When p53 is mutated, retroelement activity is dramatically increased, which could potentially drive tumorigenesis and other transposopathies

p53 is an important tumor suppressor.

ORF1p shares little to no homology to known proteins, leaving its origins and its role in _____ unknown

retrotransposition

At the time of submission, we found 96 retrotransposition events in the literature resulting in ____ ____ disease

single-gene

Overview of retrotransposon–aging interactions. Defense mechanisms are weakened with age, allowing the deprepression of retrotransposons (inner layer). The direct molecular consequences of retrotransposon activity (middle layer) drive several cellular and tissue-level processes (outer layer) which collectively ___ ____

promote aging.

Encoding proteins tha are not regulatory (for example: tubulin or enzymes)

structural genes

Encoding products that interact with other sequences and affect the transcription and translation of these sequences (for example: transcription factors)

Regulatory genes

DNA sequences that are not transcribed but play a role in regulating other nucleotide sequences

regulatory elements

Continuously expressed under normal cellular conditions

Constitutive expression

Stimulate gene expression

Positive Control

Inhibit gene expression

Negative Control

~ 60-90 amino acids, responsible for binding to DNA, forming hydrogen bonds with DNA

Domains

Within the binding domain, a simple structure that fits into the major groove of the DNA‒ Distinctive types of DNA-binding proteins based on the ____

motif

Promoter + additional sequences that control transcription (operator) + structural genes

Operon

A region of DNA that initiates transcription of a particular gene, located near the transcription start site of gene, on the same strand and upstream of the start codon. ➢____ can be about 100 -1000 base pairs long

promotor

DNA sequence encoding products that affect the operon function but are not part of the operon

regulator gene

Changes in a relatively small number of regulatory sequences help produce the large phenotypic differences between humans and ______

chimpanzees

− Stimulate and stabilize basal transcription apparatus at core promoter − Mediator - is a multiprotein complex that functions as a transcriptional coactivator in all eukaryotes. The main function of mediator complexes is to transmit signals from the transcription factors to the polymerase. − Regulation of galactose metabolism through GAL4

Transcriptional Activators and Coactivators

Transcriptional ______ proteins bind to sites on DNA and stimulate transcription.

activator

The _____sequences in the promoters of three eukaryotic genes illustrate the principle that different sequences can be mixed and matched in different combinations.

consensus

Transcription is activated by GAL4 in response to_____. GAL4 binds to the UASG (upstream activation sequence) site and controls the transcription of genes in galactose metabolism

galactose

DNA sequence stimulating transcription a distance away from promoter

enhancer

DNA sequence that blocks or insulates the effect of enhancers

Insulator

An insulator _____the action of an enhancer on a promoter when the insulator lies between the enhancer and the promoter.

blocks

Rare variation in non-coding regions with evolutionary signatures contributes to ___ ___ __ risk

autism spectrum disorder

Likely recessive, rare, inherited variants in HARs, VEs, and CNEs substantially contribute to ASD risk in probands whose parents___ ____ , which enriches for recessive contributions, but modestly contribute, if at all, in simplex family structures.

share ancestry

___ ___ ___ __ are found in the upstream region of the metallothionein gene. MTs have the capacity to bind both physiological heavy metals (such as zinc, copper, selenium) and xenobiotic heavy metals (such as cadmium, mercury, silver, arsenic). The basal transcription apparatus binds near the TATA box. In response to heavy metals, activator proteins bind to several MREs and stimulate transcription.

Multiple response elements (MREs)

Alternative splicing leads to the production of the small t antigen and the large T antigen in response to the mammalian virus ____

SV40

Gene function can be regulated by ____ ____

alternative splicing

Alternative splicing occurs in every category of ____ hallmarks

cancer

____ alternative splicing regulates angiogenesis in tumor cells

VEGF

A microRNA (miRNA) is a ___ ___ ___RNA molecule (containing about 22 nucleotides) found in plants, animals and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression.

small non-coding

Primarily transcription control, has cascade of gene regulation, DNA-binding proteins important, no chromatin structure, has operons, has negative and position controls, relatively simple initiation of transcription, less common enhancers, transcription and translation occur simultaneously, and rare regulation by small RNAs?

Bacterial Gene Control

Many levels of regulation, has cascades of gene regulation, DNA-binding proteins are important, role of chromatin structure is important, uncommon presence of operons, has negative and positive control, relatively complex initiation of transcription, enhancers are more common, transcription and translation occur separately, and has common regulation by small RNAs?

Eukaryotic Gene Control

Most transcriptional activator proteins affect transcription by interacting with _____.

The basal transcription apparatus

How do amino acids in DNA-binding proteins interact with DNA?

By forming hydrogen bonds with DNA bases

What is the difference between a structural gene and a regulator gene?

Structural genes encode proteins that function in the structure of the cell; regulator genes control transcription of other genes.

In RNA silencing, siRNAs and miRNAs usually bind to which part of the mRNA molecules that they control?

3′ UTR

The concept of ____suggests that a continuous sequence of nucleotides in DNA encodes a continuous sequence of amino acids in a protein.

collinearity

The coding sequences (exons) of most eukaryotic genes are disrupted by noncoding _____

introns

Alternative splicing of mRNA is an important modifier of gene function.The family of Tsar Nicholas Romanov II of Russia. Defect in splice site caused inactivation of _____ ____

hemophilia gene

The royal disease was likely caused by a point mutation in F9, a gene on the X chromosome that encodes blood coagulation ___ __

factor IX.

• A mature mRNA contains a 5′ untranslated region (5′ UTR, or leader sequence) • Protein-coding region • 3′ untranslated region (site of microRNA binding)

Messenger RNA

Three primary regions of mature mRNA are the 5′ untranslated region, the ____ ___ region, and the 3′ untranslated region

protein-coding

‒ A nucleotide with 7-methylguanine; 5′-5′ bond is attached to the 5′ end of the RNA.

The addition of the 5′ cap

‒ ~ 50-250 adenine nucleotides are added to the 3′ end of the mRNA.

The addition of the poly(A) tail

Most ______ mRNAs have a 5′ cap.

eukaryotic

Most eukaryotic mRNAs have a ___ poly(A) tail.

3′

‒Consensus sequences: • 5′ consensus sequence: GU A/G AGU: 5′ splice site • 3′ consensus sequence: CAGG • Branch point: the adenine “A”: ~18-40 nucleotides upstream of 3′-splicing site

RNA splicing

five RNA molecules + 300 proteins

Spliceosome

The _____ _____ of the gene for human interleukin 2 includes the TATA box, transcription start site, start and stop codons, introns, exons, poly(A) consensus sequence, and 3′ cleavage site.

nucleotide sequence

MicroRNA genes are transcribed by RNA polymerase II as large primary transcripts (pri-microRNA) that are processed by a protein complex containing the RNase III enzyme Drosha, to form an approximately 70 nucleotide precursor microRNA (pre-microRNA). This precursor is subsequently transported to the cytoplasm where it is processed by a second RNase III enzyme, DICER, to form a mature microRNA of approximately 22 nucleotides (Figure 1). The mature microRNA is then incorporated into a ribonuclear particle to form the RNA-induced silencing complex, RISC, which mediates gene silencing. MicroRNAs have been shown to be involved in a wide range of biological processes.

Transcription and processing of microRNAs

Originate in mRNA, transposon, or virus, cleavage of RNA duplex or single-stranded RNA that forms long hairpins, 21-25 nucleotides, action is degradation of mRNA, inhibition of transcription, chromatin modification, and target genes from which they were transcribed?

siRNA

Originate from RNA transcribed from distinct gene, cleavage of single-stranded RNA that forms short hairpins of double-stranded RNA, 21- 25 nucleotides, action is degradation of mRNA, inhibition of translation, chromatin modification, and target genes other than those form which they were transcribed?

miRNA