Mod 8-10 Flashcards by Paolo Dominic Elizon

whole set of genes of individuals

genome

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modification of ________ leads to changes in gene expression and may alter individul traits or phenotype

base sequences

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alterations that do not involve changes in an individual’s base sequence but still effect gene expression

epigenome

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“epi” in epigenome means

above

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________________ can detect the turning on and off of genes

epigenetic marks

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changes in the regulation of gene activity and differential expression of genes including differences in the pattern and timing of genetic switches are considered

epigenetic

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the term “epigenetics” was coined by ________________

Conrad Waddington

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epigenetics follows <blank> which proposed that the early embryo was undifferentiated</blank>

theory of “epigenesis”

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the branch of biology which studies the causal interactions between genes and their products which brings the phenotype into being

epigenetics (Waddington)

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the study of mechanism of temporal and spatial control of gene activity during the development of complex organism

epigenetics (Holliday)

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study of changes in gene expression that occur not only by changing DNA sequence but by modifying DNA methylation and remodeling chromatin

Epigenetics [Holliday (?)]

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Mitotically and/or meiotically heritable changes that could not be explained by DNA base sequence changes

Epigenetic changes (Wu and Morris)

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TRUE OR FALSE: Most cells in a multicellular organism like man, have an identical genome, however, these cells do not become differentiated and commit to specific functions

FALSE: they become differentiated

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includes stable and long-term alteration in the transcriptional potential of a cell that MAY NOT necessarily be heritable

epigenetics

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affects the ACCESSIBILITY of the genome at the right place and at the right time

Epigenetic mechanisms

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determine which genes will be turned off or on. It also regulates the degree of expression at a particular time given a particular environmental condition

Epigenetic factors

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<blank> is stable and reveals our inherited genetic identity.
</blank>

DNA Structure

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TRUE or FALSE: There is an interplay between our genome and the environment and signals from the environment that can lead to such epigenetic marks effecting the differential switching of genes even among twins

True

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<blank> attached to DNA and epigenetic factors in histone tails activate or repress genes
</blank>

Methyl groups

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attachment of methyl groups (in cytosine) by the DNA transferase machinery to bases of the DNA which significantly influences GENE EXPRESSION and CELL FUNCTION

DNA Methylation

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causes a blockage for binding of transcription factors, silencing or inactivation of genes

Methyl groups or moities

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<blank> is an INTERFACE between the dynamic environment and the static genome
</blank>

DNA Methylation (Szyf)

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Methyl is added by <blank> in methyl transferase in the Cytosine of 5' - CG - 3' dinucleotides</blank>

methyl transferase

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TRUE or FALSE: High frequency of METHYLATED CpG islands within or in the vicinity of a gene’s promoter region REDUCES transcriptional activity of that gene

TRUE

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accounts for the very specific patter of activating and silencing genes in every cell

Methylation

genes are less methylated (also evident pattern in EARLIEST ZYGOTIC STAGES)

Active

hypermethylated

TRUE OR FALSE: Methylation may not be inherited per se

TRUE

TRUE or FALSE: Patterns are generated during gestation in accord with the signals from the environment

TRUE

TRUE or FALSE: Mistakes in methylation do not cause the same effect as a mutated gene

FALSE: causes the same effect

expression of depends on the ORIGIN OF INHERITANCE whether derived maternally or paternally.

Imprinted genes

TRUE or FALSE: There are cases when only maternal alleles of the imprinted genes are transcribed and the paternal alleles are silenced (VICE VERSA)

TRUE

TRUE or FALSE Epigenetic modifications cannot be passed across generations

FALSE: may be passed (Kaati, Bygren, and Edvinsson) There is a "memory" of environmental influence on the genome

WHICH MECHANISM Genetically identical mice may have different phenotypes (Agouti viable yellow gene causing yellow fur color, tendency to become obese, develop tumors) The methylated agouti gene has a brown fur color and is healthy

DNA Methylation Heavy methylation suppresses the expression of trait as observed in identical twin mice

TRUE or FALSE: Maternal diet can be affected by the environment

TRUE

TRUE or FALSE: Epigenetic factors other than foods, drugs, and environmental chemicals cannot change a developing organism's expression

FALSE

"Superman" gene

Arabidopsis thaliana (Jacobsen & Meyerowitz) (DNA Methylation)

Floral development is regulated by

homeotic genes (DNA Methylation)

encodes for a transcription factor that affects one of these homeotic genes

"Superman" gene (DNA Methylation)

(2) It controls the boundary between reproductive and accessory plant structures specifically to develop into carpels

"Superman" gene fourth whorl of A. thaliana flowers (DNA Methylation)

in the superman gene, just after the promoter region, causes variation in the formation of STAMEN and the CARPEL

Cytosine methylation (DNA Methylation)

'superman' gene bring about the and restricts the effect of another gene (APETALA 3)

clk allele ('Clark Kent' gene) (DNA Methylation)

endemic to Mendoza province, Argentina

S. ruiz-lealii (shows recurrent flower malformations in its inflorescence within the same plant) hypermethylation in S. ruiz-lealii (DNA Methylation)

DNA associates with of histones

Octamer

modification can either support or suppress genes

Histone

The tighter the association of histone tails to the DNA, the

less accessible the DNA is for DNA PROCESSING and TRANSCRIPTION (or gene is silenced) (HISTONE MODIFICATION)

Addition of methyl groups to histone tail =

restriction (tighter wound) (HISTONE MODIFICATION)

TRUE or FALSE: Transcription factors can readily bind to genome promoters

FALSE: cannot (HISTONE MODIFICATION)

Acetylation of histones

relaxes and unravels compact DNA (genes are more available as chromatin is more exposed and accessible to DNA binding proteins) (HISTONE MODIFICATION)

combination of signals (causing methylate/demethylate, acetylate/deacetylate) =

lead towards modification of histones (HISTONE MODIFICATION)

TRUE or FALSE: The area within nucleus where the modifications reside could convey information

TRUE (HISTONE MODIFICATION)

TRUE or FALSE: Methylated DNA and acetylated histones are found in same components or territories in the nucleus

FALSE: different* (HISTONE MODIFICATION)

TRUE or FALSE: Methylated DNA is associated with acetylated histones (vice versa)

FALSE: Methylated DNA recruits proteins that cause deacetylation of histones, resulting to shutdown of gene (HISTONE MODIFICATION)

Third mechanism of epigenetic change which can silence a gene is

RNA interference (RNAi)

RNA interference discoverers

Andrew Z. FIRE & Craig C. MELLO

can regulate the stability of mRNA and can be used to silence the expression of TARGET GENES

Short (21-25bp in length), double-stranded non-coding RNA (dsRNA) or small interfering RNA

used for RNAi. Both pairs with specific target mRNA, causing inhibition of translation or degradation of mRNA

short, single stranded RNAs or microRNA (miRNA) and short interfering RNAs (siRNA)

is involved in signaling, cell differentiation, and timing of cell development as well as programmed cell death (apoptosis)

miRNA (microRNAs)

can directly base pair mRNA degradation instead of inhibition

siRNA (short interfering RNA)

recognizes and cuts dsRNA into siRNA and miRNA

dicer

binds and unwinds the double-stranded siRNA or miRNA, producing single stranded siRNA or miRNA

RNA-induced silencing complex (RISC)

TRUE or FALSE: Epigenomes can be affected by environmental factors such as diet, stress, and prenatal nutrition among others

TRUE

TRUE or FALSE: Diet and stress can influence the epigenome of an individual by changing epigenetic marks

TRUE (strong expression of genes for obesity)

TRUE or FALSE: Low folate food are recommended during pregnancy

FALSE: High. Folate is a strong METHYL DONOR which can prevent the developing embryo to have neural tube defects

Neural tube develops on which day of pregnancy

28th (Pregnant mothers are advised to take folic acid (vit B9 supplements for recommended 400g folate per day)

TRUE or FALSE: Epigenome is likely to be most vulnerable to environmental factors during embryogenesis because DNA synthetic rate is high, and the elaborate DNA methylation patterning for normal tissue development is established during this period

TRUE (Dolinoy, et al. 2006)

Study of molecular relationships between nutrition and response of genes

Nutritional genomics (nutrigenomics)

5 Tenets of Nutrigenomics

1. Diet can be a serious risk factor 2. Gene expression and structure of human genome can be (directly or indirectly) altered by chemicals in our diet 3. Degree to which diet influences the balance between healthy and disease states may depend on the genetic make-up 4. Diet-regulated genes are likely to play a role in the onset, incidence, progression, and/or severity of chronic diseases 5. Dietary intervention based on knowledge of nutritional requirement, nutritional status, and genotype can be used to prevent, mitigate, or cure chronic diseases

Metabolic disorders that can be managed through diets

phenylketonurics, galactosemics, phenylalanine-free and milk-free diet, respectively

TRUE or FALSE: Nutrients cannot reverse or change epigenetic phenomena by DNA methylation and histone modification

FALSE: it can modify expression of critical genes

investigates the role of bioactive components such as tea polyphenols, genistein from soybean, and isothiocyanates from plant foods

Nutritional epigenetics

can be utilized for intervention, including preventive therapy

Nutriepigenomics

TRUE or FALSE: Epigenetic modifiers such as resveratrol, curcumin, and green tea hold promise for preventing cancer and treating metabolic disorders

TRUE

TRUE or FALSE: Food rich antioxidants are used to delay aging, may regulate cancer as they reduce DNA methylation in critical genes associated with the disease

TRUE

change in the genetic material that is HERITABLE and PERMANENT

Mutation

3 Types of Chromosomal Mutation

Euploidy Aneuploidy Structural changes involving one or more chromosomes

change involving WHOLE GENOME or THE ENTIRE SET of chromosomes

Euploidy (multiplication of one or more genome)

known as the basic chromosome number

Genome (X)

complete set of chromosomes or genes

Genome (X)

X=n n = ???

n = haploid number

TRUE or FALSE: In polyploid, X is also equal to n

FALSE: X not equal to n

Types of Euploidy

Monoploid (X) Polyploid (3X-6X)

One set of genome or whole set of chromosomes

Monoploid (X)

More than two sets of genome

Polyploid (3X-6X)

Types of Polyploid

Autopolyploid Allopolyploid

Basic genome is identical

Autopolyploid

Basic genome is not identical

Allopolyploid

Types of segregation in autotetraploid

1. Random chromosome type 2. Random chromatid type

type of segregation where genes are close to the centromere (to find the gametes assign alleles in a FIGURE)

Random chromosome type (Autotetraploid)

type of segregation where genes are far from the centromere (to find the gametes, use the GAMETIC SERIES)

Random chromatid type (Autotetraploid)

Types of addition (Aneuploidy)

1. Trisomic (2n +1), page 40 Module 9 2. Double trisomic (2n +1 +1) 3. Tetrasomic (2n+2)

Types of subtraction (Aneuploidy)

1. monosomic (2n -1) 2. double monosomic (2n -1 -1) 3. nullisomic (2n-2)

Types of structural aberrations

1. deletion 2. duplication 3. translocation 4. inversion

missing chromosome segment

deletion Types of deletion: interstitial (2), terminal (structural aberrations)

repeated chromosome segment

duplication Types: tandem, reverse tandem, displaced, transposition (structural aberrations)

exchange of chromosome segments involving NON-HOMOLOGOUS chromosomes

translocation (structural aberrations)

chromosome segment is inserted in a different order

inversion (structural aberrations)

two chromosomes in homologous pair are affected (structural aberrations)

Homozygous

only one of the chromosomes in the homologous pair is affected structural hybrids (structural aberrations)

Heterozygous

Types of inversion (structural aberrations)

1. Paracentric 2. Pericentric

centromere is not included in the inverted segment

Paracentric (structural aberrations)

centromere is included in the inverted segment

Pericentric (structural aberrations)

what is formed for heterozygous for paracentric inversion

bridge acentric fragment

what is formed for heterozygous for RECIPROCAL TRANSLOCATION

IV (quadrivalent) results to ring or chain

Adjacent 1 Adjacent 2 (segregation of ring and chain)

sterile gametes, with deletion and duplication

3. alternate or zigzag (segregation of ring and chain)

fertile gametes no deletion and duplication

change A-T to C-G during replication (associated with DNA POL II

Treffers mutator gene

genes or mobile genetic elements

Transposons or jumping

can move and insert itself into gene loss of gene function

Transposons or jumping

revertible mutants in corn Noble prize winner 1983 35 years after publication

Barbara Mc Clintock

encodes a transposase

suppressor of color formation

TRUE or FALSE: Ds cannot move without AAc

True

TRUE or FALSE: Ac can't transpose to location of gene C (color) anthocyanin

False

Ac-Ds stationary produces

purple kernel (no transposition occuring)

Ac-Ds transposed into C (Activate Ds transposition)

White kernel (colorless)

Activates Ds transposition out of C in a few cells during kernel development

Spotted kernels

change in a single nucleotide (or few adjacent nucleotides)

Gene mutation or Point mutation

Types of gene mutation

1. Base pair substitution (a. transition, b. transversion) 2. Frameshift mutation

Types of amino acid substitution

nonsense same sense missense

pu -> pu py -> py

transition

pu <-> py

transversion

no effect on amino acid sequence

same sense

change in amino acid sequence

missense

formation of STOP codon

nonsense

Transient maternal influence causes

Delayed chromosomal inheritance

- Temporary maternal influence (F1) - Differences in reciprocal crosses (influence of maternal cytoplasm) - Delayed expected Mendelian segregation Principle of segregation is disregarded

Delayed chromosomal inheritance

Outside the nucleus

Extranuclear

cytoplasm is donated by the

mother

- Cytoplasmic factors - capable of self perpetuation - independent transmissions

Extranuclear inheritance

cytoplasmic factors are called

plasmagenes plasmons plasmids cytogens

account for hybrid vigor

Epistasis (genetic basis of heterosis)

accumulation of favorable dominant genes in the hybrid

Dominance (Davenport) (genetic basis of heterosis)

heterozygous are more vigorous and more productive than homozygous parents

Overdominance (genetic basis of heterosis)

Mirabilis jalapa, four o'clock plants observation of cytoplasm (plastids inside cytoplasm)

Carl Correns

Chromosomals follow

Dominant gene

If gene is extrachromosomal, it follows

maternal inheritance (expression of gene is not from nuclear)

nucleus: cytoplasm:

Nucleus : maternal and paternal DNA cytoplasm: maternal DNA

extrachromosomal genes are unable to show linkages with known nuclear genes

non-mappability

superiority of F1 hybrid over its parents in terms of yield or some characteristics

Heterosis or Hybrid Vigor

TRUE or FALSE: Selfing or pure-breeding parentals does not result to heterozygote F1

TRUE

to prevent selfing, must be done

emasculation

anthers are removed to render the plant

male sterile

requirement for preventing emasculation

CMS or cytoplasmic male sterile female CMS x male restorer gene