Lesson 3.

4 Learning Task Worksheet

These questions should help you to review the content and skills that you learned by reading Concept
20.2 of your textbook and completing all of the lesson activities.

● Read each question carefully.

● Complete each question thoroughly.
● Turn in your completed worksheet to your teacher.

1.

A . Define transcription. Where does it occur?

Transcription is the process of making RNA from DNA in order to transfer genetic information out of
the nucleus and to the site of protein synthesis (the ribosomes). RNA polymerase “rewrites” the DNA
information and creates a new copy in the form of mRNA.

Transcription happens in the nucleus of human cells

The process of Transcription takes place in the cytoplasm in prokaryotes and in nucleus in
eukaryotes. It uses DNA as a template to make an RNA (mRNA) molecule. During transcription, a
strand of mRNA is made that is complementary to a strand of DNA.

B. Define translation. Where does it occur?

Translation is the process by which RNA is used to make proteins. tRNA “reads” the mRNA strand and
“translates” it into a chain of amino acids (a protein).

Translation is the process in living cells in which proteins are produced using RNA molecules as
templates. The generated protein is a sequence of amino acids. This sequence is determined by the
sequence of nucleotides in the RNA. The nucleotides are considered three at a time.

Translation happens in the cytosol.

Translation can't start until transcription and RNA processing are fully finished.

C. What is the transcriptome of a cell?

Transcriptome refers to the protein-coding part of an organism's genome. It refers to the set of RNA
molecules such as messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and other
noncoding RNA molecules that are present in cells.

Transcriptome data obtained from different types of cells can help researchers to gain a deeper
understanding of what constitutes a specific cell type, how that type of cell normally functions, and
how changes in the normal level of gene activity may reflect or contribute to disease.
D. What is the proteome of a cell?

A proteome is the complete set of proteins expressed by an organism. The term can also be used to
describe the assortment of proteins produced at a specific time in a particular cell or tissue type. The
proteome is an expression of an organism's genome.

A proteome is a set of all expressed proteins in a cell, tissue, or organism, and a systematic analysis of
proteins within a defined system for their identity, quantity, and function is called proteomics.

E. Define gene expression.

Gene expression is the process by which the information encoded in a gene is used to direct the
assembly of a protein molecule, by which information from a gene is used in the synthesis of a
functional gene product that enables it to produce end products, proteins or non-coding RNA, and
ultimately affect a phenotype.

2. Explain why the transcriptome of one cell may be different from the transcriptome of another
cell.

In multicellular organisms, nearly every cell contains the same genome and thus the same genes.
However, not every gene is transcriptionally active in every cell — in other words, different cells show
different patterns of gene expression.

3. Give an example of a type of a gene that is probably expressed in most or all cell types of the
human body. Justify your expectation.

An example of gene expression is the differential expression of genes in human cells. All human cells
contain the same DNA but have very different structures and functions. Liver cells and neurons in the
brain contain the same DNA yet are very different in structure and function.

4. You are a researcher who has found a gene in dogs involved in the development of muscles. How
could you use the known sequence of this gene to determine whether humans have and utilize this
same gene?

To determine the function of human genes, researchers can look for similar genes in other animals
whose functions are known. If scientists have identified a gene in the dog involved in the
development of muscles, they can search the human genome for a gene with a similar sequence and
surmise that the human gene probably has a function similar to the one in the dog.

This is part of annotating describing the experimental and inferred information about a gene or
protein. In its most elementary form, the human genome may be described as a shorthand list of
three billion “letters”—A, T, C, and G—each of them representing one of four nucleic acid bases:
adenine, thymine, cytosine, and guanine, respectively. Bases are small, nitrogenous molecules, which
in DNA occur in base pairs. This base sequence information, or code, is useful only to the extent that
researchers can interpret and apply it, which is why having other genomes available to study is so
valuable.
 5. Why would a researcher apply the same probe to the same cell but at different times?

Utilizing different animals will allow us to get at the true function of that gene, and then allow us to
break down what that gene product (or protein) is doing in that biochemical pathway, and to look across
different organs and tissues at different developmental moments in the organism's life, to really identify
how it's regulated and how it functions.

6. Why is it important to use the sequence of a cDNA, instead of the sequence of the gene itself, in
order to produce a probe for use in in situ hybridization?

The most important advantage of cDNA clones is that they contain the uninterrupted coding sequence of
a gene.

Techniques have been developed in which nucleic acid probes are used in much the same way as labeled
antibodies to locate specific nucleic acid sequences in situ, a procedure called in situ hybridization. This
procedure can now be done both for DNA in chromosomes and for RNA in cells. Labeled nucleic acid
probes can be hybridized to chromosomes that have been exposed briefly to a very high pH to disrupt
their DNA base pairs.

7. Outline the steps used to produce a cDNA.

The process of making cDNA from eukaryotic genes involves the following five steps:

1. Isolate mRNA from a sample of cells.

2. Add reverse transcriptase to the mRNA in a test tube. Reverse transcriptase makes the first DNA
strand using the mRNA as a template and a short poly-dT as a DNA primer.
3. Degrade the mRNA using another enzyme.
4. Synthesize the second DNA strand using DNA polymerase and a primer in the reaction mixture.
5. The result is cDNA, which carries the complete coding sequence of the gene but no introns.

The cDNA can be used to study gene expression and function, and can be amplified using PCR for
further analysis.

8. Why do researchers use a cDNA in gene cloning in prokaryotic cells to obtain the protein product of
a particular gene?

cDNA libraries are used to express eukaryotic genes in prokaryotes. Prokaryotes do not have introns in
their DNA and therefore do not possess any enzymes that can cut it out during transcription process.
cDNA does not have introns and therefore can be expressed in prokaryotic cells.

9. What does GWAS stand for, and what are they?

A genome-wide association study (GWAS) is a research approach used to identify genomic variants that
are statistically associated with a risk for a disease or a particular trait. It involves rapidly scanning
markers across the complete sets of DNA, or genomes, of many people to find genetic variations
associated with a particular disease. Once new genetic associations are identified, researchers can use
the information to develop better strategies to detect, treat and prevent the disease. Such studies are
particularly useful in finding genetic variations that contribute to common, complex diseases, such as
asthma, cancer, diabetes, heart disease and mental illnesses.

GWAS involve scanning markers across the genomes of many people to find genetic variations associated
with a particular disease.

With the completion of the Human Genome Project in 2003 and the International HapMap Project in
2005, researchers now have a set of research tools that make it possible to find the genetic contributions
to common diseases. The tools include computerized databases that contain the reference human
genome sequence, a map of human genetic variation and a set of new technologies that can quickly and
accurately analyze whole-genome samples for genetic variations that contribute to the onset of a
disease.

10. Polygenetic traits are genetic traits that result from the combined expression of many genes. List at
least three examples of human traits you would expect to be polygenetic.

In humans, height, skin color, hair color, and eye color are examples of polygenic traits.

11. Genomic studies allow researchers to uncover the causes of many multifactorial diseases.

If you were a researcher studying schizophrenia and wanted to find out how the transcriptome of a
person with schizophrenia differed from the transcriptome of a person without schizophrenia, how
would you go about researching this? Explain how you could use a microarray to begin to answer this
question.

Microarray studies can be used to examine expression levels for large numbers of genes simultaneously
and may be applied to identify genes involved in schizophrenia.

screening gene expression from identified schizophrenia patients in the dorsolateral prefrontal cortex
(DLPFC) from three pools of patients with schizophrenia (n=15) and three matched control pools (n=15).
Pooling of tissue samples was employed as a strategy to detect changes in gene expression that are
consistently found across individual cases of schizophrenia. Differences in gene expression were
examined by z-ratios in addition to traditional normalized ratios.

12. Many microarrays use green dots to show that gene expression is turned on in normal cells; red
dots to show genes are turned on in cancer cells; and yellow dots to show gene expression in both
cell types. If you wanted to compare the microarrays from a group of breast cancer patients with
those from a group of control subjects, on which genes would you focus your research: the green
dots, yellow dots, and/or red dots? Explain your answer.
 If the expression of a particular gene is higher in the experimental sample than in the reference
sample, then the corresponding spot on the microarray appears red. In contrast, if the expression in
the experimental sample is lower than in the reference sample, then the spot appears green.

Starting by focusing on the red dots with cancer cells and compare against green dots of the normal
cells. Comparative gene expression in the two samples could easily be determined by quantitating
the ratio of red and green fluorescence in the spot corresponding to each gene. Microarrays can then
be used to gain insight into whether gene expression changes could be correlated with cancer
treatment outcomes.

13. Microarrays have been a valuable technology. However, as sequencing methods become more
efficient and inexpensive, new technologies are replacing older ones. RNA-sequencing (RNA-seq;
pronounced “RNA-seek”) is rapidly replacing the use of microarrays.

RNA-seq accomplishes basically the same thing as microarrays do. It allows a researcher to
determine which RNA sequences are found in a specific cell type at a specific time.

Explain the basic procedures involved in this technology.

mRNA-Seq offers improved specificity, so it's better at detecting transcripts, and specifically isoforms, than
microarrays.

RNA sequencing (RNA-seq) is a genomic approach for the detection and quantitative analysis of messenger
RNA molecules in a biological sample and is useful for studying cellular responses.

The basic steps of an RNA-seq experiment involve RNA extraction, RNA fragmentation, cDNA generation,
library amplification, and sequencing on an NGS platform to get strings of continuous sequence data in
“reads”. The most common approach is short-read sequencing (read lengths ≤ 300 bp; RNA-seqlopedia).