VERGARA, FRANZ MIGUEL A.

DENT-1L
Instructions: To prepare yourself for the future modules, you must answer these questions
together (by group). When responding, be brief and to the point. It will be analyzed by
a plagiarism detector.

1. What exactly is a genome and what makes it up? What is the fundamental tenet of
molecular biology?
The genome is the complete collection of DNA instructions contained in a cell. In
humans, the genome is made up of 23 pairs of chromosomes in the nucleus and a
single tiny chromosome in the mitochondria. A genome contains all of the
information that a person needs to grow and function.
2. Define complementary and antiparallel in relation to DNA.
Two biopolymers are antiparallel in biochemistry if they run parallel to each other but
in the opposite direction (alignments). A DNA double helix has two complimentary
strands that run in opposite directions beside each other.
3. Why is supercoiling important in bacterial cells? What enzyme aids in this process?
Because it regulates all DNA-related functions, DNA supercoiling is crucial for all
living cells. The competing activities of topoisomerase I, which relaxes DNA, and
DNA gyrase, which compacts DNA, cause worldwide DNA supercoiling in bacteria.
4. In base pairs, how big is the Escherichia coli genome? How many genes are there?
E. coli genome coli (sequenced in 1997) has around 4 million base pairs and
approximately 3000 genes. These figures are typical for bacteria, which typically
have genomes of several million base pairs and a few thousand genes.
5. What exactly are viruses and plasmids?
Unlike viruses, which encase their genetic material in a protective protein coat known
as a capsid, plasmids are "bare" DNA and do not encode the genes required to encase
the genetic material for transfer to a new host; however, some types of plasmids do
encode the conjugative "sex" pilus required for their own transmission.
6. What characteristics does a R plasmid impart on its host cell?
The plasmid can self-replicate, be taken up from the environment, and be transferred
between bacteria. Plasmids are used by host organisms to address stress-related
conditions. For example, many plasmids carry genes that encode the production of
enzymes that inactivate antibiotics and toxins.
7. What is the difference between a template and a daughter strand of DNA?
Bacteria can uptake new plasmids from other bacterial cells (during conjugation) or
from the environment.
8. DNA polymerase adds a nucleotide to which end (5′ or 3′) of a freshly produced
strand of DNA?
During elongation, an enzyme called DNA polymerase adds DNA nucleotides to the
3'end of the template. Since DNA polymerase can add new nucleotides only at the
end of the backbone, it adds RNA nucleotides that are complementary to the primer
sequence that provides this starting point.
9. What is the primer made of in DNA replication, and why are there leading and
lagging strands?
Because DNA polymerase can most effectively synthesize DNA in a 5′ to 3′
 direction, the opposite new strand is prepare in quick portions referred to as Okazaki
fragments. The Okazaki fragments every require a primer fabricated from RNA to
begin the synthesis. The strand with the Okazaki fragments is called the lagging
strand.
10. What roles do DNA Pol I and III, DNA helicase, and DNA ligase play?
Primase synthesizes RNA primers that are complementary to the DNA strand. DNA
polymerase III expands the primer by adding it to the 3'end to take full advantage of
the new DNA. Remove the RNA primer and replace it with DNA polymerase I. The
gap between DNA fragments is closed by DNA ligase.
11. What is a replisome, and what are its components?
Replisomes are DNA copying machines containing helicases to untie DNA duplexes,
polymerases to copy DNA, and nucleases and ligases to handle discontinuous
stretches of DNA on subsequent strands (Bell & Dutta, 2002).). From: Methods in
Enzymology, 2017.
12. How are the replisome's actions halted?
The presence of lesions in DNA, such as lesions that form after exposure to UV light,
can cause replisome activity to cease, leading to the destruction of replisomes, which
can be life-threatening for cells.
13. How are mistakes in DNA replication maintained to an absolute minimum?
The quantity is saved so low through a proof-studying device that assessments newly
synthesized DNA for mistakes and corrects them whilst they're found.
14. What enzyme is responsible for transcription?
RNA polymerase is an enzyme this is answerable for copying a DNA series into an
RNA series, during the technique of transcription.
15. What is a promoter, and what protein in Bacteria identifies promoters?
Each gene (or, in bacteria, each group of genes that are transcribed together) has its
own promoter. Promoters contain DNA sequences that allow RNA polymerase or its
helper proteins to attach to DNA. Once a transcription bubble is formed, the
polymerase can initiate transcription.
16. What exactly is the function of messenger RNA (mRNA)? What are the other two
RNA classes?
Messenger RNA (mRNA) molecules carry the coding sequence for protein synthesis
and are called transcripts. Ribosomal RNA (rRNA) molecules make up the core of a
cell's ribosome (the structure in which protein synthesis takes place). Transfer RNA
(tRNA) molecules transport amino acids to the ribosome during protein transfer.
17. How does polycistronic mRNA enable gene families to be regulated collectively?
Polycistron mRNA has a ribosome binding site near the starting site of each cistron.
Translation initiation begins at one of these multiple internal sites and produces
multiple proteins. Eukaryotic mRNA has a unique start and end site that produces a
single type of polypeptide.
18. What structures cause transcription termination?
Transcription termination involves a secondary structure mechanism, and in eukaryotic
cells, RNA signals direct polyadenylation and termination. ... end of transcription
19. RNA polymerase. Polyadenylation. RNA polymerase II. End factor. Riboswitch. Nested
Gen.Rloop. Polymerase.
20. What are the three primary components of an archaeal promoter?
The TATA-, BRE-, and (Inr) initiator elements are the three archaeal promoter
elements that have been identified so far as having defined roles in transcription
initiation.
21. What eukaryotic enzyme is the archaeal RNA polymerase similar to?
Although Archaea and Bacteria use only one kind of RNA polymerase (RNAP) to
transcribe all genes, their subunit makeup and architecture are surprisingly similar to
that of eukaryotic RNAPII.
22. What stages are included in the eukaryotic RNA processing?
Capping at the 5' end.
Addition of a poly A tail at the 3' end. and.
Splicing to remove introns
23. Distinguish between the various protein structural classes.
Peptide bonds are formed when amino acids are combined to form protein structures.
The main structure of a protein is the sequence of amino acids. The dihedral angles of
peptide bonds determine the secondary structure, while the folding of protein chains
in space determines the tertiary structure.
24. What is denaturation, and why is it damaging to cells?
Denaturation occurs when a protein's shape is altered by an external stress (for
example, heat, acid, or alkali) to the point where it can no longer perform its
biological function.
25. What is the role of a tRNA's anticodon?
A tRNA anticodon couples with its complementary codon on the mRNA molecule
each time an amino acid is added to a developing polypeptide during protein
synthesis, guaranteeing that the correct amino acid is put into the polypeptide.
26. What is the role of a tRNA's acceptor stem?
The tRNA base encodes the size and polarity of the amino acid separately. The
acceptor stem encodes the amino acid size. The anticodon base encodes the polarity
of the amino acid. Therefore, amino acid properties determine how tRNA bases are
recognized by aminoacyl-tRNA synthetases.
27. What actions must be taken to create a charged tRNA?
How do tRNA interact with mRNA and ribosomes when loading the correct amino
acids to build brand new proteins? To see how this process works, see the next article
on the translation stage.
28. What exactly are start and stop codons?
The start codon marks the site at which translation into protein sequence begins, and the stop
codon marks the site at which translation ends.
29. What is the significance of the ribosome reading "in frame"?
Once the gene has been sequenced, it is important to identify the correct open reading
frame (ORF). Each region of DNA has six possible reading frames, three in each
direction. The reading frame used determines which amino acids will be encoded by
the gene.
30. What exactly is codon bias?
Codon utilization bias refers to variations withinside the frequency of incidence of
synonymous codons in coding DNA. A codon is a sequence of 3 nucleotides that
encodes a particular amino acid residue in a polypeptide chain or for the termination
of translation.
31. How would you locate ORFs if you were given a nucleotide sequence?
Locate a chain similar to a begin codon with the intention to decide the analyzing
frame – this may be ATG (experience strand). Read this sequence in the base triplet
until the stop codon is reached (TGA, TAG or TAA).
32. What exactly are the parts of a ribosome?
Ribosomes are product of proteins and ribonucleic acid (abbreviated as RNA), in
nearly same amounts. It contains sections, referred to as subunits. The tinier subunit
is the area the mRNA binds and decodes, while the larger subunit is the area the
amino acids are included.
33. What functions does rRNA serve in protein synthesis?
The main function of RNA is to produce proteins by translation. RNA carries genetic
information that is translated by the ribosome into various proteins required for
cellular processes. mRNA, rRNA, and tRNA are the three major types of RNA
involved in protein synthesis.
34. A full polypeptide chain is released from the ribosome in what way?
The release factor binds to the stop codon at the A site and stimulates the hydrolysis
of the bond between the tRNA and the polypeptide chain at the P site, resulting in the
release of the full-length polypeptide from the ribosome.
35. What effect does tm RNA have on stopped ribosomes?
Ribosomes are responsible for translating encoded messages from messenger RNA
molecules to synthesize proteins from amino acids. The ribosome translates each
codon or set of three nucleotides in the mRNA template and adapts it to the
appropriate amino acid in a process called translation.
36. What exactly are molecular chaperones, and why are they required?
Molecular chaperones promote protein folding and are especially required for large
proteins and protein complexes. Therefore, E coli cell-free protein synthesis systems
are complemented by E. coli or eukaryotic molecular chaperones to achieve correct
folding of product proteins.
37. Heat shock proteins protect which macromolecules?
Some heat shock proteins act as intracellular chaperones for other proteins. They play
an important role in protein-protein interactions such as folding, establishing the
correct protein conformation and preventing unwanted protein aggregation.
38. How do chaperones help the cell of Escherichia coli produce nitrate reductase?
Nitrate reductase (NR) catalyzes the reduction of nitrate to nitrite, the first reaction of
nitrate assimilation. Nitrate reductase requires molybdenum (Mo) as a cofactor.
39. What exactly is the signal sequence, and what does it indicate?
Signal transduction sequences are found at the N-terminus of some proteins, which
allow them to find the correct location outside the cell membrane. The signal
sequence marks proteins that are transported extracellularly through the cell
membrane.
40. What makes up the signal recognition particle?
SRP has three known functions: signal peptide recognition, inhibition of elongation,
and promotion of translocation (55, 56, 80-83). The particles are composed of 6-
component polypeptides with molecular weights of 72, 68, 54, 19, 14, and 9 kDa and
7 SLRNAs (80, 84).
41. How do the chemicals secreted by the translocases Sec and Tat differ?
42. Why is it vital for gram-negative bacteria to have more secretion routes in
comparison to gram-positive bacteria?
The main difference between the SEC and TAT pathways is that the SEC pathway
carries unfolded proteins, whereas the TAT pathway carries folded proteins. The SEC
route is the most common in animals. The TAT pathway is most common in plants,
archaea, and bacteria.
43. How do the secretion pathways of types I–VI vary from Sec and Tat secretion?
The bacterial secretion system is a protein complex that resides in the bacterial cell
membrane for the secretion of substances. Specifically, it is a cellular device used by
pathogens to secrete virulence factors (mainly proteins) and invade host cells.
44. What gives the injectosome its name?
Injectsomes are transmembrane complexes used by Gram-negative bacteria to
transfer so-called effector proteins to eukaryotic host cells, where effectors influence
the host's behavior in favor of the bacterium [12, 13].