MCQ

Fill in the blanks.

1. The conversion of the information in RNA into protein is translation

2. There are 4 different nucleotides in mRNA and 20 different types of amino acid in protein.

3. What is the universal genetic code? same mRNA codons specify the same amino acids in all living
organisms.

4. Each group of three consecutive nucleotides in mRNA is called a codon

5. RNA sequence can be translated in any one of three different reading frames, depending on
where the decoding process begins. However, only one of the three possible reading frames in an
mRNA encodes the required protein.

6. The adaptors consist of a set of small RNA molecules known as transfer RNAs.

7. a set of three consecutive nucleotides that pairs with the complementary codon in an mRNA
molecule is anti-codon.

8. Eucaryotic tRNAs are synthesized by RNA polymerase III.

9. What signals the end of the protein-coding message? Stop codons (UAA, UAG, UGA)

10. What does wobble position refer to? the 3rd nucleotide more flexible to achieve the same
amino acid.

11.How do tRNAs link amino acids to codons during translation? most cells have a different
synthetase enzyme for each amino acid .

12. The genetic code is translated by 2 adaptors that act one after another; what are the first and
second adaptors? 1- aminoacyl-tRNA-synthetase 2- tRNA

13. What is the function of aminoacyl-tRNA-synthetase? the synthetase couples a specific amino
acid to its corresponding tRNA.

14. What does a tRNA anticodon base pair with? mRNA codon

15. Editing by tRNA synthetase has high binding affinity between correct amino acid and the active
site of its synthetase.

16. In editing by tRNA synthetase, what happens to incorrect amino acids? the amino acid is
attached to AMP, tRNA binds, synthetase forces the adenylated amino acid into a second pocket
"editing pocket of the enzyme".

17. Editing pocket excludes the correct amino acid

18. protein synthesis is performed in the ribosome.

19. ribosome is a complex catalytic machine made from more than 50 different proteins: ribosomal
proteins, several RNA molecules and rRNA.

20. Eucaryotic and procaryotic ribosomes are composed of one large and one small subunit.

21. The small subunit provides the framework on which the tRNAs can be accurately matched to the
codons of the mRNA, while the large subunit catalyzes the formation of the peptide bonds that link
the amino acids together into a polypeptide chain.
22. What is the APE site of a ribosome? A site: amino acid (amino acyl), P site: protein (peptidyl) ,E
site: exit.

23. What are the functions of elongation factors? drive translation forward and improve accuracy

24. Elongation factors bind to DTP and hydrolyze GTP which causes conformational changes in the
factor proteins.

25. Binding and hydrolysis of EF-G leads to rearrangement of the ribosome structure moving the
mRNA exactly 3 nucleotides through it.

26. The factors are called EF-Tu and EF-G in bacteria, and EF1 and EF2 in eucaryotes.

27.All of our cells have the same genes but, They are not expressed at the same time in the
different types of cells.

28. What tool do use to compare the size and charge to follow protein in a cell? Gel electrophoresis.

29. Enhancer consist of Cis regulatory sequences that regulate transcription.

30. proteins that bind to DNA and control gene transcription is Transcription regulators

31. Regulators bind in major groove.

32. How transcription regulators bind to cis regulatory sequences to turn genes on/off is
Dimerization

33.repressor turn the gene off, and activator turn the gene on.

34. repressors and activators are proteins that bind DNA and regulates expression.

35.inducer and co-repressor are small molecules that may participate in gene regulation by altering
the the function of repressor and activator.

36.prokaryotic genes are often organized into operons.

37. operons is cluster of gene that are transcribed as a single unit. Allow regulation of expression of
entire cluster through single transcription switch.

38. DNA looping is Transcription regulators communicate with proteins that assemble at the
promoter.
 Long answer

1.Types of RNA used in translation and their function.

2. Describe a tRNA molecule and identify the T, D, and anticodon loops and the end that attaches
to the amino acid.

3. explain the two adaptors used in translation.

4.Describe the two mechanisms of which ensure that the correct amino acid is added to its
equivalent tRNA molecule.

Several mechanisms working together ensure that the tRNA synthetase links the correct amino acid
to each tRNA. The synthetase must first select the correct amino acid, and most synthetases do so by
a two-step mechanism.

• First, the correct amino acid has the highest affinity for the active-site pocket of its synthetase and
is therefore favoured over the other 19. In particular, amino acids larger than the correct one are
effectively excluded from the active site. However, accurate discrimination between two similar
amino acids, such as isoleucine and valine (which differ by only a methyl group), is very difficult to
achieve by a one-step recognition mechanism.

• A second discrimination step occurs after the amino acid has been covalently linked to AMP. When
tRNA binds the synthetase, it tries to force the amino acid into a second pocket in the synthetase, the
precise dimensions of which exclude the correct amino acid but allow access by closely related
amino acids. Once an amino acid enters this editing pocket, it is hydrolysed from the AMP, and is
released from the enzyme

5. What is the process of incorporation of an amino acid into a protein?

-peptide bond forms between the carboxyl group at the end of a growing polypeptide chain and a
free amino group on an incoming amino acid

-the growing end remains "activated" by covalent attachment to tRNA

-the addition of a new tRNA disrupts high energy linkage, but replaces it with an identical linkage

6. Describe translation as four steps cycle .

1) -growing polypeptide (3 amino acids) linked to tRNA in P site

-next tRNA with amino acid 4 binds to A site (anticodon of tRNA base pairs with codon of mRNA)

2) -carboxyl end of polypeptide released from tRNA at P site (breakage of bond between tRNA and its
aa)

-carboxyl end joins to amino acid in A site (new peptide forms); peptidyl transferase in the ribosome
catalyzes this step

3) -large ribosomal subunit moves relative to mRNA held by small subunit

-shifts 2 bound tRNAs to E and P sites

4) conformational changes move small subunit and its bound mRNA exactly 3 nucleotides, ejecting
spent tRNA (E site)

-ribosome is ready to receive the next amino acid and the cycle continues from step 1
7. Describe initiation (start), elongation and termination (stop) of translation. What type of factors
do they use?

Slide 63-72
8. Seven steps at which eukaryotic gene expression can be controlled.

1. transcriptional control

Regulation by a cell of gene expression by controlling when and how often a given gene is
transcribed.

2. RNA-processing control

Regulation by a cell of gene expression by controlling the processing of RNA transcripts, which
includes their splicing.

3. RNA transport and localization control

Regulation by a cell of gene expression by selecting which completed mRNAs are exported from the
nucleus to the cytosol and determining where in the cytosol they are localized.

4. translational control

Regulation by a cell of gene expression by selecting which mRNAs in the cytoplasm are translated by
ribosomes.

5. mRNA degradation control

Cell regulation of gene expression by selectively preserving or destroying certain mRNA molecules in
the cytoplasm.

6. protein degradation control

The means by which the concentration of a protein in the cell can be reduced by selectively
degrading it in response to external signals or to stages of the cell division cycle.

7. protein activity control

The selective activation, inactivation, degradation, or compartmentalization of specific proteins after

they have been made. One of the means by which a cell controls which proteins are active at a given
time or location in the cell.
9. What are the 4 different types of transcription regulators and define them

 Helix-turn -helix: twists DNA

 zinc-finger: Zn holds alpha helix and beta pleated sheets to maintain a DNA loop. Work
efficiently as monomers
 Leucine Zipper: Series of leucine dimerize by binding to both sides of DNA (scissoring)

 Helix loop Helix: similar to helix turn helix except is forms a loop around the leucine zipper

10. the assembly of transcription factors can result in these 2 types of activators

Transcription activators: Turn genes on and increase transcription.

Transcription repressors: Turns genes off and decreases transcription.

11. describe what happens in lac operon in E coli

Lac operon in E coli is controlled by Lac repressor and CAP activator causing it to be expressed only
when needed. Operon in this case encode protein required to import and digest lactose to
disaccharides and glucose. When lactose is absent, lac repressor binds to cis regulator sequence
called lac operator and shuts off expression of operon. When glucose is absent, the cyclic AMP is
produced by a cell which is required for CAP to bind to DNA and active transcription.

Operon is on only when lactose is present, and glucose is absent.

12. Difference between Control Gene Transcription in Eucaryotes and prokaryotes

1. Eucaryotic RNA polymerase II, which transcribes all the protein-coding genes, requires five general
transcription factors, whereas bacterial RNA polymerase needs only a single general transcription
factor, the sigma subunit.

2. Eucaryotic cells lack operons - sets of related genes transcribed as a unit - and therefore must
regulate each gene individually.

3. Each bacterial gene is typically controlled by one or only a few gene regulatory proteins, but it is
common in eucaryotes for genes to be controlled by many (sometimes hundreds) of different
regulatory proteins. This complexity is possible because many eucaryotic gene regulatory proteins
can act over very large distances (tens of thousands of nucleotide pairs) along DNA, allowing an
almost unlimited number of them to influence the expression of a single gene.

4. A central component of gene regulation in eucaryotes is Mediator, a 24-subunit complex, which

serves as an intermediary between gene regulatory proteins and RNA polymerase. Mediator
provides an extended contact area for gene regulatory proteins compared to that provided by RNA
polymerase alone, as in bacteria.

5. The packaging of eucaryotic DNA into chromatin provides many opportunities for transcriptional
regulation not available to bacteria.

13. Eucaryotic gene control region describes what?

the whole expanse of DNA involved in regulating and initiating transcription of a gene, including the
promoter, where the general transcription factors and the polymerase assemble, and all of the
regulatory sequences to which gene regulatory proteins bind to control the rate of the assembly
processes at the promoter.

14. Four ways eukaryotic activator proteins can direct local alterations in chromatic structure to
stimulate transcription initiations.

Slide 53

15. Explain how histone modification during transcription initations

Slide 54

16. Six of the ways in which eukaryotic repressor proteins can operate.

1.Types of RNA used in translation and their function.

 mRNA: a Type of RNA that carries a protein-building message. "Genetic messenger" between
DNA and protein.
 rRNA: becomes machine that translates message in mRNA. Works with ribosomal proteins to
build proteins out of amino acids building blocks of proteins.
-make up the ribosome along with proteins

-RNA with enzymatic activity. The rRNA of a ribosome, not the protein, catalyzes the formation of a
peptide bond between amino acids. As the amino acids are delivered, ribosome joins them via
peptide bonds into new polypeptide.

- Order of codons in an mRNA becomes translated into a new protein.

 tRNA: carries amino acids (individual) amino acids to cite that protein is being built.
- -delivers amino acids to growing polypeptide chains
- -Has 2 attachment sites: anticodon and site that binds to an amino acid (the one specified by
the codon)
- -They Fold up into each other. move amino acids.
- -Anticodon loop
- -20 tRNA's. can only carry specific amino acid. Individual made for another
- -Binds to codons
- 2. Describe a tRNA molecule and identify the T, D, and anticodon loops and the end that
attaches to the amino acid.
- A tRNA molecule has a cloverleaf structure with the complementary base pairing
that creates the double-helical regions of the molecule. The anti-codon is the
sequence of three nucleotides that base pairs with a codon in mRNA. The amino
acid that matches the codon/anti codon pair is attached at the 3' end of tRNA.
tRNAs contains some unusual bases that are produced by chemical modification
after the tRNA has been synthesized. For example the bases denoted
Ψ(pseudourdine) and D(dihydrouridine) are derived from uracil. Y=pyrimidine C/U;
R=purines A/G
- The T loop is a specialized region on the tRNA molecule which acts as a special regognition site for the
ribosome to allow a tRNA-ribosome complex to form during hte process of protein biosynthesis. The D
loops main function is recognition. It is thought that the D loop will act as a recognition site for
aminoacyl-tRNA synthetase(an enzyme involved in the aminoacylation of the tRNA molecule)