Unit 2 Gene Expression Test

One way that researchers are identifying cancerous cells is to detect the degree of methyl groups that are present on several cancer-causing genes. One gene, RSSF2, appears to be a tumor suppressor and produces a protein that is involved in stopping the cell from dividing. Doctors would expect to see ________ levels of the RSSF2 protein in these abnormally dividing ovarian tumor cells because DNA for the gene had a(n) ________ in methyl groups

(low, lower, smaller) (increase)

Tertiary sources of scientific information

-Articles in a newspaper (NY Times) or magazine written by identified journalists. Rarely contain complete citations. -Government warnings a s consumer updates. -Encyclopedia entries such as Wikipedia that contain some citations and references, but the content of the article may or may not have been fact checked.

how chromatin structure or chemical modification of DNA - known as epigenetics - affect gene expression

-Epigenetics is the study of heritable changes in gene expression (active versus inactive genes) that do not involve changes to the underlying DNA sequence — a change in phenotype without a change in genotype — which in turn affects how cells read the genes.

The PU Test

-P: check for Previous work -U: go Upstream/laterally from the source

protein involved in winding DNA into chromatin

-all DNA is wrapped around special proteins called Histones -methyl makes it more tightly wound and turns it off -acetyl makes it more loosely wound and turns it on making it open to transcription

micro ray- explain what color spots you would expect to see for genes that are expressed in normal cells or over-expressed or under-expressed in cancer cells

-colors: -red: it is bound to gene that is expressed more frequently in a cancerous cell -green: it is bound to a gene that is expressed more frequently in normal cells -yellow: it is bound to a gene that is expressed more frequently in both types of cells (cancerous, normal) -grey: it is bound to a gene that is not expressed in either type of cells (cancerous, normal)

Epigenome and its affects on cells

-is made up of chemical compounds and proteins that can attach to DNA and direct such actions as turning genes on or off, controlling the production of protiens in particular cells. When epigenomic compounds attach to DNA and modify its function, they are said to have "marked" the genome. -ex: The Agouti Mouse model

difference between active and inactive genes in terms of chromatin winding and chemical modifications (methylation and acetylation)

-more methyl- more tightly wound: inactive -more acetyl- less tightly wound: active

base pairing rules of DNA

A pairs with T; G pairs with C

Researchers collected mRNA transcripts from rapidly-dividing cancerous breast cells and from normal breast cells. Based on the function of the proteins made from these genes, which gene would be most likely to have higher levels of mRNA expression in breast cancer cells compared to normal cells?

CDCA3

how changes to the epigenome can be responsible for cancer

Certain chemicals consumed can overstimulate the proto-oncogenes which result in rapid reproduction of cells

What is the relationship between DNA and proteins?

DNA encodes for proteins, and protein enzymes replicate and maintain DNA.

how microarrays are produced and used to detect differences in gene expression between cells

DNA microarray is a technique that scientists use to determine whether genes are on or off. Microarray analysis involves breaking open a cell, isolating its genetic contents, identifying all the genes that are turned on in that particular cell, and generating a list of those genes.

Only cells in the digestive system have genes for digestive enzymes

False

order of organization of genetic material, from largest to smallest.

Genome, chromosome, gene, nucleotide

Queen bees are genetically identical to worker bees, however queen bees have a single gene silenced which impacts expression of numerous traits. The two bee types also differ in their diet as larvae, with individuals fed royal honey developing into queen bees. Based on your understanding of epigenetics, you might expect royal honey to be:

High in methyl compounds.

Epigenetic inheritance

Inheritance of traits by mechanisms not directly involving nucleotide sequence is called

The GR gene, which codes for a protein that results in anxious behavior in rats, can be inactivated by:

Injecting a drug that results in tightly winding the section of DNA that contains the GR gene.

how chemotherapy drugs might take advantage of methylation to re-activate gene

It methylates the parts of the gene that shouldn't be expressed so it suppresses that gene. It stops tumor growth if it methylates the thing that was causing the growth.

Which of the following is the main difference between a primary and secondary source?

Primary sources describe a single research study about a phenomenon or question, secondary sources present several research studies about that same phenomenon

Specifically, which of the following is the MOST important reason an expert would use to rank this food reactions site least reliable?

Purpose: The site sells products designed to treat disorders and offers "affiliates" who wish to link to the site a commissions when users buy products from the site.

If researchers added red-labeled copies of mRNA from rapidly-dividing cancerous breast cells, and green-labeled copies of mRNA from normal cells from and from normal breast cells, what color spots would indicate a gene that had increased expression in cancer cells compared to normal cells?

Red

Primary source of scientific information

Research studies performed, written, and then submitted for peer-review to a scientific journal that build upon and include references to previous research studies (original data)

Secondary source of scientific information

Reviews of several research studies written up as a summary article with references. Can appear in peer-reviewed academic journals or government

The KRT8 gene contains an estrogen response element and produces the protein keratin in secretory epithelia in the breast and uterus. Since the KRT8 gene is present in all cells and estrogen travels throughout the body, why is this keratin protein only produced in epithelial breast cells but not in other cells in the breast, for example, in skin cells?

Skin cells do not produce the estrogen receptor protein necessary to stimulate transcription.

which pairs most closely resemble each other in size and shape?

T most closely resembles C and A most closely resembles G

selective gene expression

The basis of cellular differentiation (e.g. kidney cells functioning and appearing different than nerve cells) is

If a cell were unable to produce histone proteins, which of the following would be expected to occur?

The cell's DNA could not be packed into its nucleus.

Which of the following statements concerning the eukaryotic chromosome (found in animals, plants, fungi, and protists) is FALSE?

The number of genes on each chromosome is different in different cell types.

You find an article in the media about how sleep deprivation affects judgment when it comes to making healthy food choices. You want to use this source in a paper you are writing about the topic. There are many benefits of using a tertiary source, but what is a valid concern you might have about this type of source?

The source may not report any limitations of the original studies it describes

One strand of DNA is the template for the synthesis of another strand

The template specifies the bases on the nucleotides of the strand being made.

chromatin tightly wound (heterochromatin)

Transcription OFF

methylated DNA

Transcription OFF

methylated histones

Transcription OFF

acetylated histones

Transcription ON

chromatin loosely wound (euchromatin)

Transcription ON

Brain cells and liver cells are genetically identical

True

Genes can be switched on and off in each particular cell type.

True

In our cells, gene expression can be controlled by numerous mechanisms beyond transcription factors or epigenetic tags.

True

Portions of DNA that have few methyl tags will be loosely wound around histones and can be transcribed.

True

Studies examining epigenetic tags in twins have been useful in identifying variation in gene expression in humans. Which of the following patterns would you expect to be true based on epigenetics.

Younger identical twins have more similar epigenetic tags on their DNA because they have a more common life experiences.

Most differentiated cells (i.e. cells that develop into specific types such as nerve or muscle cells) retain

a complete set of their genes, an retain the ability to express those genes under certain circumstances

Different cell types, for example a muscle or a blood cell in the same organism retain

a complete set of their genes, and retain the ability to express those genes under certain circumstances into mRNA

regulatory proteins and their role in adding tags to the epigenome

a gene regulatory proteins attach to a specific sequence of DNA on one or more genes. once there, it acts like a switch, activating gene transcription or shutting them down

If you were able to look very closely at a portion of DNA and find methylated histones (histones with methyl groups), you would:

be looking at a region of inactive DNA

Which of the choices below best demonstrate the pattern of mRNA expression you would observe if you used cells from these same tissues from a woman who was past menopause (very low estrogen levels).

breast uterus skin ○○○

Women who have been diagnosed with breast cancer are often given tamoxifen which binds the estrogen receptor and blocks transcription of estrogen responsive genes in the breast. In uterine cells, however, tamoxifen stimulates transcription of estrogen responsive genes. Which of the expression patterns would you expect in a woman taking tamoxifen?

breast uterus skin ○●○

mRNAs were extracted from the following cell types in the same individual and added to three identical microarray spots all containing DNA from the KRT8 gene. (Breast and uterus cells contain the estrogen receptor protein, but skin cells do not.)

breast uterus skin ●●○

how epigenetic changes can occur in response to the environment

epigenetic regulation has to do with the genes passed down to you from your parents. Part of it is inheritance and the other part is the environment - if you have a nurturing environment ... mouse experiment. What you eat, if it has methyl or acetyl groups in it can affect it.

CRAP test

evaluates the quality of a source of information C-currency R- reliability A-authority P- purpose/POV

why all the cells in an individual are genetically identical, yet have distinct functions and characteristics

every cell has the exact same genes and DNA. depending on the location of the cell, the histones are either methylated (tightly wrapped) or acetylated (loosely wrapped) which allows them to express their specific function.

A densely staining region of highly compacted chromatin is known as _____ and is generally____.

heterochromatin; not transcribed

teeth holding together the two strands of the double helix consist of

hydrogen bonded nitrogen-containing bases

Which of the following are true about DNA methylation?

it leads to genomic imprinting, which is reversible

when "epigenetic regulation" normally occurs and why

it occurs by adding either methylation histones or acetylation histones. methylation histones wind the DNA up more (which makes DNA unreadable for transcription) and Acetylation histones unwind the DNA (which makes DNA readable for transcription)

Comparing DNA sequences for the KRT8 gene in a breast and a skin cell would show

no differences

Which of the following has a beads on a string structure

nucleosomes

Epigenetics describes the effect of __________ on gene expression

parental care diet environment

The term "gene expression" refers to the

process by which genetic information flows from genes to proteins.