Test 3: Compare and Contrast

Question 1

Peptidyl transferase/ guaninyl transferase**

Answer 1

Both of these are enzymes involved in gene expression.

Peptidyl transferase: associated with the large subunit of the ribosome during translation, breaks an amino acyl bond between the tRNA and amino acid, & adds the amino acid to the growing polypeptide chain by forming a peptide bond.

Guaninyl transferase: is involved in post-transcriptional modification (capping) of mRNA, catalyzes the addition of guanine to the 5’ end of the mRNA transcript in a 5’ to 5’ manner, & forms phosphotriester bonds.

Question 2

Transition/ transversion**

Answer 2

Both of these refer to substitutional point mutations in DNA.

Transition: substitution of a purine for another purine or a pyrimidine for another pyrimidine occurs more often than transversions

Transversion: substitution of a purine for a pyrimidine or a pyrimidine for a purine, & consequences are much more severe than transition.

Question 3

EF-G/ RF1

Answer 3

Both of these are factors that play a role in translation.

Elongation Factor G (EF-G): mediates the translocation step in the elongation phase, causes the simultaneous movement of the ribosome (one codon down the mRNA), the movement of de-acylated tRNA from P-site to E-site, the movement of new peptidyl tRNA from A-site to P-site, & requires energy from the hydrolysis of GTP.

Release Factor 1 (RF1): mediates the release of the polypeptide chain during the termination phase, binds to A-site on ribosome and triggers the peptidyl transferase to release chain into cytoplasm, & doesn’t require energy.

Question 4

Nucleosome/ platysome**

Answer 4

Both of these terms refer to DNA packaging in eukaryotes

Platysome: contained within the nucleosome, consists of 4 types of histone proteins that come together to form an octamer, resemble just the “bead” portion of beads on a string under electron microscopy.

Nucleosome: consists of the platysome, 146 bp of DNA wrapped around the platysome, 5th type of histone protein that serves as a linker protein, & resembles beads on a string under electron microscopy.

Question 5

Recombination repair/ excision repair**

Answer 5

Both of these are repair mechanisms utilized by the cell to repair occurrences of dimers in DNA.

Excision repair: involves the physical removal of the dimer, cuts out the segment of DNA containing the dimer and degrades it, segment is replaced using the undamaged strand as template. Permanent repair.

Recombination Repair: doesn’t actually remove dimer from DNA, leaves a gap in the daughter strand where the dimer would be during replication, corresponding identical SS region on undamaged template is cut out and placed into gap, gap on the undamaged template is filled by using the newly made daughter strand as a template, a short term fix.

Question 6

Tautomerization/ intercalation**

Answer 6

Both of these terms refer to the occurrence errors in DNA as the result of mutations.

Tautomerization: spontaneous mutation involving an isomerization between the normal and tautomerized forms of nitrogenous bases, causes disruption of complementarity and leads to point mutations.

**Intercalation: ** induced mutation involving an outside agent that forms stacks between adjacent base pairs in DNA, causes distortions of the DNA helix, confuses polymerase, & leads to frameshift mutations or possible denaturing in high concentrations.

Question 7

Nuclear amplification/ cytoplasmic amplification**

Answer 7

Both terms refer to gene expression in eukaryotes.

Cytoplasmic amplification: involves polysomal translation where multiple ribosomes translate the same mRNA simultaneously in cytoplasm

**Nuclear Amplification: ** involves the multiple transcription of the same gene on DNA by RNA polymerase in the nucleus due to tandem repeats sequences in DNA, & only one ribosome is involved.

Question 8

Alkylating agent/ intercalating agent

Answer 8

Both of these agents are DNA reactive chemical mutagens that interact with nitrogenous bases and chemically alter them.

**Alkylating Agents: ** add alkyl groups to the rings in nitrogenous bases and alter the complementarity, high exposure can cause SOS activation and depurination, can cause transition mutations.

Intercalating Agent: tri-ringed flat molecules that stack themselves between adjacent base pairs and distort the DNA helix, high exposure can cause denaturation.

Question 9

Intron/ exon

Answer 9

Both of these terms refer to post-transcriptional modification in eukaryotic gene expression. Both are transcribed into mRNA in the nucleus.

**Introns: ** non-coding regions of an mRNA transcript that are cut out and degraded

**Exons: ** coding regions of the transcript that are spliced together and make up the functional mRNA that is translated by the ribosome

Question 10

Positive effector/ negative effector

Answer 10

Both of these are effector molecules that are also referred to as trans-acting elements in bacterial gene regulation. Both of these effector molecules bind to cis-acting elements, and both have an impact on gene expression through their effects on transcription.

• *Positive effectors: ** enhance transcription
• *Negative effectors: ** inhibit transcription

Question 11

Repressible operon/ inducible operon**

Answer 11

Both of these terms describe sets of genes that are functionally related and located in close proximity to each other on the bacterial genome. Both can be switched to either on or off under the right set of conditions.

Inducible operons: usually code for non-essential functions and are generally turned off, usually associated with catabolic pathways, are not attenuated

Repressible operons: code for critical functions and are generally turned on, usually associated with anabolic pathways, are attenuated.

Question 12

Class I genes/ class II genes

Answer 12

Both of these terms refer to divisions of genes in eukaryotes.

Class I genes: are small set, transcribed by RNA polymerase I, consists mostly of rDNA, more primitive and similar to bacterial genes.

Class II genes: large set, transcribed by RNA polymerase II, responsible for most of the HnRNA pool and are more advanced.
Class III genes: small set, transcribed by RNA polymerase III, responsible for tRNA, smRNA, 5S rRNA genes, unusual promoter downstream from the start

Question 13

Histones/ non-histones

Answer 13

Both of these terms refer to categories of nucleoproteins.

Non-histone: proteins are very acidic, containing a high concentration of amino acids with acidic R groups, vary in their number and in the timing of their synthesis

**Histones: ** very basic, containing high concentrations of amino acids with basic R groups, histone concentration is directly proportional to concentration of DNA, synthesis is linked to DNA replication.

Question 14

Transition/ frameshift

Answer 14

Both of these terms describe instances of mutations in DNA.

**Transition: ** substitutional point mutation, involves the substitution of one purine for another purine or one pyrimidine for another pyrimidine, & can alter one amino acid

Frameshift: mutation caused by an addition/deletion of one base in a codon, alters the reading frame of the triplet codon and changes the entire amino acid sequence from the point mutation, much more disruptive and detrimental than transition

Question 15

Spliceosome/ ribozyme

Answer 15

Both of these terms refer to post-transcriptional modification of primary transcripts to produce functional mRNA. Both involve the removal of introns and joining together of exons.

Spliceosome: joins with smRNA to form snRNP complex that edits the transcript using signal sequences that mark boundaries between introns & exons.

**Ribozyme: ** catalyzes its own self-excision process in which introns are removed in a manner similar to that of an episome.

Question 16

Monocistronic/ polycistronic

Answer 16

Both of these terms refer to expression of genes.

**Monocistronic: ** refers to an mRNA transcript coding for a single polypeptide, eukaryotic genomes consist of genes that are monocistronic.

**Polycistronic: ** refers to an mRNA transcript coding for more than one polypeptide, prokaryotic genomes consist primarily of polycistronic genes.

Question 17

Cis-acting elements/ trans-acting elements

Answer 17

Both of these elements are components of bacterial gene regulation.

Cis-acting elements: are actual portions of the gene that act as binding sites, can be either operators or promoters and are involved with RNA polymerase

**Trans-acting elements: ** molecules not part of the gene that bind to the cis-acting elements, can be either positive (enhance transcription) or negative (inhibit transcription)

Question 18

IF3/ EF-Tu

Answer 18

Both of these are factors that take part in prokaryotic translation of mRNA into polypeptides.

**IF3: ** is involved in both the initiation stage and the termination stage, aids in the binding of the small ribosomal subunit to the mRNA transcript and stabilizes it, later causes the ribosomal subunits to dissociate, not involved with GTP

**Ef-Tu (temp. unstable): ** involved in the elongation stage, shuttles a charged tRNA into the A site of the ribosome, hydrolyzes GTP, plays a screening role in translation

Question 19

Endonuclease/ exonuclease

Answer 19

Both of these refer to enzymes that involved in cleaving elements of polynucleotide chains.

**Exonuclease: ** degrades polynucleotide chains from the end, can degrade in the 5’-3’ or 3’-5’ direction, involved with DNA polymerase

**Endonuclease: ** internally cuts polynucleotide chains, can either nick one strand of DNA or can cut both strands, involved with DNA repair

Question 20

Pribnow/ Shine-Delgarno

Answer 20

Both of these terms refer to conserved sequences in bacterial gene expression.

Pribnow sequence: is involved in initiation of transcription, located on DNA and is -10 bp upstream from start point, involved with RNA polymerase

**Shine-Delgarno: ** involved in initiation of translation, located on mRNA and is -7 bases upstream from the start codon, involved with the ribosome

Question 21

IF1/ IF3

Answer 21

Both of these are initiation factors that take part in translation and are associated with the assembly of ribosomes.

**Initiation Factor 1 (IF1): ** is involved in only the initiation stage, guides the large ribosomal subunit into place on mRNA, only involved with assembly of ribosome

Initiation Factor 3 (IF3): involved in the initiation stage and termination stage, assists the small ribosomal subunit in binding the mRNA transcript, later causes the dissociation of the ribosome – ending translation.

Question 22

Conservative Transposon/ Replicative Transposon

Answer 22

Both of these terms refer to mobile elements within the genome that can lead to alteration of gene expression and mutations, and are characterized by inverted repeat sequences in front of and behind an internal sequence that codes for transposase.

Conservative transposons (jumping genes): insert themselves into the genome, remain there for a period of time, and excise themselves and relocate.

Replicative transposons: insert themselves into the genome and replicate themselves. The original sequence remains, and the replicated sequence relocates to another position in the genome.

Question 23

Complementation/ Non-complementation

Answer 23

Both of these terms refer to experimental outcomes and are associated with the work of Benzer and the rII locus of defective viruses that lacked the ability to lyse the host cell. Benzer was seeking to determine whether or not genes were indivisible units, and simultaneously infected host cells with two viruses, each lacking lytic ability. Both results contributed to the conclusion that genes can be subdivided

Complementation: resulted when the host cell was lysed because each virus contributed a functional product that the other lacked.

Non-complementation: resulted when the cell was not lysed because each defective virus was defective for the same functional product.

Question 24

Prokaryotic ribosome/ Eukaryotic ribosome

Answer 24

Both types of ribosomes are composed of ribosomal RNA and ribo-proteins, and both consist of one large subunit and one small subunit. Both are highly conserved among their respective organism.

Prokaryotic: large subunits are 50S (Svedberg units), small subunit is 30S, consists of 3 rRNAs and 52 ribo-proteins

**Eukaryotic: ** large subunits are 60S, small subunits are 40S, consists of 4 rRNAs and 82 ribo-roteins

Question 25

Capping/Tailing

Answer 25

Both refer to post-transcriptional processing in Eukaryotes.

**Capping- ** Guaninyl transferase adds a guanine cap in the 5’ to 5’ direction to RNA. All of RNA is capped.

**Tailing- ** poly-A tail is added to the RNA and degraded over time. Not all RNA is tailed

Question 26

What is the definition of mutation?

Answer 26

Mutation is sudden, random, heritable change
Mutations based on tissue type:
Somatic: local consequences, not passed on to offspring
Germinal: no consequence to carrier, are passed on to offspring (larger impact on pop.)

Mutations based on causes:

• *Spontaneous:** can never be eliminated, no outside causative agent, due to inherent qualities of genetic system
• *Induced:** caused by an outside agent, classified as mutagens

Question 27

What is the c-value paradox?

Answer 27

The c in the c-value paradox refers to the concentration of DNA. This refers to the fact that there is much more DNA present in eukaryotic genomes than seems necessary. The amount of DNA in the eukaryotic genome is thousands-fold more than what is needed to code for the genes it contains.