Test 1

Where are restriction enzymes primarily located?

Bacteria and archaea

What precise DNA sequences do restriction enzymes target?

Recognition sites or restriction sites

What defines a palindromic sequence in DNA?

Sequences that read the same forward and backward

What is the term for DNA ends characterized by overhanging,

single-stranded regions?

Sticky ends

What is the outcome when sticky ends from different DNA

fragments, produced by a restriction enzyme, interact?

Base-pair with each other

What happens when HindIII and KpnI act on a plasmid

containing their recognition sites?

They cleave the plasmid DNA, producing linearized

DNA fragments with sticky ends.

What is the purpose of DNA ligase in molecular biology?

To join DNA fragments with compatible sticky ends.

What type of bond does DNA ligase catalyze the formation of?

Phosphodiester bonds

What is the result of the annealing of complementary sticky ends

of the plasmid and insert?

Creation of a circular recombinant plasmid

How is the recombinant plasmid introduced into bacterial

cells?

Via a procedure called transformation

In the process of preparing recombinant DNA, what crucial

function do bacterial cells serve?

Replicating the recombinant plasmid

How do plasmids replicate in relation to the bacterial

chromosome?

They replicate independently of the bacterial

chromosome

What is one of the primary uses of PBR322 or pUC18 in

molecular biology research?

DNA cloning and gene expression studies

What is the size of PBR322 in base pairs (bp)?

Approximately 4,361 bp

What are the antibiotic resistance markers present in PBR322?

Ampicillin resistance and tetracycline resistance

What is the function of the polylinker in PBR322 or

pUC18/19?

It contains multiple unique restriction enzyme

recognition sites.

How does the size of pUC18 compare to PBR322?

pUC18 is considerably smaller than PBR322.

What selectable marker is present in pUC18?

Ampicillin resistance

Why is the presence of the ampicillin resistance gene important

in pUC18?

It serves as a selectable marker for plasmid-

containing cells.

How does the polylinker in pUC18 compare to the one in

pBR322 in terms of versatility?

The polylinker in pUC18 is more versatile.

What key feature of pUC18 makes it particularly

advantageous for cloning experiments?

Its extensive multiple cloning site (MCS)

What is the purpose of LacZ α-complementation in bacterial

plasmids like pUC18?

To allow for blue-white screening of transformed

colonies

Which enzyme's activity is central to LacZ α-complementation

screening?

β-galactosidase

When bacterial colonies contain the recombinant pUC18

plasmid with a disrupted lacZ gene, what color will they produce

on X-gal plates?

White

Why is LacZ α-complementation important in molecular

biology?

It facilitates the screening of recombinant plasmids

with inserted DNA fragments.

In blue-white screening of bacterial colonies using X-gal and

IPTG, what is the purpose of X-gal?

To act as a substrate for β-galactosidase

Why do colonies containing the intact pUC18 plasmid (without

an inserted DNA fragment) produce blue colonies on X-gal

plates?

They can produce functional β-galactosidase.

What is the role of IPTG in blue-white screening using X-gal?

To act as a molecular mimic of allolactose and induce

lac operon expression

Which of the following is NOT a purpose of blue-white

screening in molecular biology research?

A) identifying bacterial colonies containing recombinant plasmids

B) detecting the presence of functional lacZ genes

C) confirming successful, DNA transformations

D) synthesizing chromogenic substrates

Synthesizing chromogenic substrates

Which plasmid would be more suitable for cloning larger DNA

fragments?

PBR32217

What type of functional groups are usually absent in

hydrophobic side chains of amino acids?

Hydroxyl groups (-OH) and amino groups

(-NH2)

How do hydrophobic amino acids behave within a

protein's structure?

They cluster together in the interior of

proteins, away from water.

What is the primary role of hydrophobic side chains in

proteins?

Stabilizing the protein's three-dimensional

structure.

Which of the following elements are predominantly

present in hydrophobic side chains of amino acids?

Carbon (C) and hydrogen (H)

Why do hydrophobic amino acids cluster together in

the interior of proteins?

To minimize their interactions with water.

Which type of functional groups are typically present in

uncharged polar side chains of amino acids?

Hydroxyl groups (-OH) and amino groups

(-NH2)

Why are uncharged polar amino acids more likely to be

found on the surface of proteins rather than in the

protein's hydrophobic core?

They form hydrogen bonds with water and

other polar molecules.

Which of the following statements is true regarding the

net charge of uncharged polar amino acids at

physiological pH?

They have neither a net positive nor net

negative charge.

Which amino acid contains a thiol (-SH) group in its

side chain, allowing it to form disulfide bonds with

other cysteine residues?

Cysteine (Cys)

Which amino acid has a side chain consisting of

just a single hydrogen atom, making it highly flexible

and often referred to as a "flexible hinge" in protein

structures?

Glycine (Gly)

Proline (Pro) is unique among amino acids because

its side chain forms what type of structure?

A five-membered ring structure

What is the key characteristic of glycine (Gly) that

allows it to be highly flexible in protein structures?

A small size and lack of a bulky side chain

What distinguishes charged polar amino acids

from other amino acids at physiological pH?

They have a net electric charge.

Which type of interactions can charged polar

amino acids engage in due to their net electric charge?

Ionic interactions

Which amino acid has a positively charged

guanidino group (-NH-C(NH2)(NH2)) in its side chain

and is known for forming ionic bonds with negatively

charged groups?

Arginine (Arg)

What is the pKa approximate value of the

guanidino group in arginine (Arg), indicating that it is

predominantly protonated (positively charged) at pH

values below this value?

pH 12.5

At what pH range is the carboxyl group in

glutamic acid (Glu) predominantly deprotonated

(negatively charged) based on its pKa value?

Above pH 4.1

Histidine (His, H) is unique among amino acids

because its side chain contains an imidazole group. What is

the approximate pKa value of histidine's imidazole group?

pH 6.0

Why is histidine considered important in various

biological processes, especially in proteins and

enzymes?

Its dual ionization state allows it to function

as a buffer and participate in proton transfer reactions.

How is a peptide bond formed between two amino

acids during protein synthesis?

Through a condensation reaction involving

the removal of a water molecule (H2O).

What is the primary structure of a protein

primarily determined by?

The linear sequence of amino acid residues

linked together by peptide bonds.

Which of the following are the two most common

secondary structures found in proteins?

Alpha helices and beta sheets

Tertiary structure refers to:

The overall three-dimensional shape of a

protein.

Which amino acid residue is known for forming

disulfide bonds that can contribute to tertiary

structure?

Cysteine

The hierarchical structure of hair, visible under

various magnifications, is primarily composed of which

fibrous structural protein?

α-Keratin

Hemoglobin, a globular protein, is known for its

function in:

Transporting oxygen in the blood

What does the prefix "Myo" in "myoglobin"

indicate?

Its presence in muscle cells

How many heme groups with Fe2+ ions can be

found in a single myoglobin molecule, allowing it to

bind oxygen?

One

How many polypeptide subunits make up a

complete hemoglobin molecule?

Four

Which structural protein heavily relies on

hydroxylation of proline for stability and strength?

Collagen

Scurvy is primarily caused by a deficiency in which

vitamin that plays a critical role in the hydroxylation of

proline residues in collagen synthesis?

Vitamin C

What is carboxylation in the context of

prothrombin and blood clotting?

The addition of carboxyl groups specifically

to certain glutamate residues in prothrombin.

What role does prothrombin play in the blood

clotting cascade?

It converts fibrinogen into fibrin to stop

bleeding.

What can occur if there are problems with the

carboxyl groups in prothrombin or other clotting

cascade proteins?

Hemorrhage or excessive bleeding.

Where are glycoproteins with N-linked

glycosylation commonly found, and what functions do

they serve?

On the cell membrane, serving in cell

adhesion, signaling, and immune responses.

What is the primary difference between chain-

terminating dideoxynucleotides (ddNTPs) and normal

deoxynucleotides (dNTPs)?

ddNTPs lack a 3' hydroxyl group.

In DNA sequencing, why are chain-terminating

dideoxynucleotides (ddNTPs) used?

To terminate DNA strand elongation

at specific bases.

What role does the lack of a 3' hydroxyl group in

ddNTPs play in DNA sequencing?

It prevents the formation of

phosphodiester bonds, leading to chain

termination.

Why is Sanger sequencing considered a serial process?

Because only one chain-terminating

ddNTP can be added at a time.

In Sanger sequencing, why is it necessary to add one

ddNTP at a time to the growing DNA chain?

To ensure that each termination event

corresponds to a specific base.

In DNA sequencing, why is it necessary to load the

generated DNA fragments onto a polyacrylamide gel?

To separate DNA fragments by size

for sequencing.

What distinguishes real-time sequencing with reversible

terminators (NGS) from traditional Sanger sequencing?

Real-time sequencing allows for the

monitoring of nucleotide incorporation as it

happens, while Sanger sequencing does not.

Which of the following is a key feature of Prism

capillaries in automated DNA sequencers?

A) They use radioactive labels for DNA fragments.

B) They allow for larger DNA fragment sizes.

C) They facilitate DNA synthesis reactions.

D) They have a narrow inner diameter for efficient DNA

separation

They have a narrow inner diameter for

efficient DNA separation.

In automated DNA sequencers, which method relies on

fluorescently labeled dideoxynucleotides (ddNTPs) to

terminate DNA strand synthesis at specific bases?

Sanger sequencing

What role do different fluorescent tags play in

sequencing?

They provide a unique color code for each

nucleotide.

What does it mean to "multiplex" samples on the

ABI PRISM 3700 DNA sequencer?

To combine multiple samples into a single

sequencing run.

What is Next-generation sequencing (NGS)?

A high-throughput DNA sequencing

technology.

Which NGS platform is known for its sequencing-

by-synthesis method?

Illumina

In NGS, what is the role of adapters?

They connect DNA fragments to the

sequencing platform.

What is the primary purpose of the glass surface

on Illumina flow cells?

To immobilize DNA fragments for

sequencing reactions

Where are primers used for DNA amplification

usually positioned within Illumina flow cells?

On the glass surface within the

sequencing adapters

What is the significance of the clustering area on

Illumina flow cells?

It allows for the spatial separation of

DNA clusters for parallel sequencing.

How do sequencing adapters contribute to cluster

formation in NGS?

They attach DNA fragments to the flow

cell surface.

How does the emitted fluorescent signal during

SBS help determine the DNA sequence?

By analyzing the emitted light

signals and their positions.

In NGS, what is the significance of dual-indexed

sequencing adapters?

They enable the pooling of multiple

samples.

In Illumina sequencing, what is the SBS

(Sequencing by Synthesis) process primarily based on?

Fluorescently tagged-reversible

terminator nucleotides

How does the SBS process use fluorescently tagged

nucleotides to determine DNA sequences?

By recording the emitted

fluorescent signals during nucleotide

incorporation

In cancer research, what is a common application

of NGS technology?

Identifying genetic mutations in

cancer genomes

During Illumina's SBS process, how are

nucleotides incorporated into the growing DNA strand?

By reversible termination with

fluorescently tagged nucleotides

When was the Human Genome Project (HGP)

officially launched?

1990

What was the primary goal of the Human Genome

Project (HGP)?

To map and sequence the entire

human genome

Approximately how many base pairs are there in

the human genome?

3 billion base pairs

What major milestone was achieved in 2003 as a

result of the Human Genome Project?

The complete sequencing of the

human genome

What is the primary purpose of PCR (Polymerase Chain Reaction)?

To amplify and make multiple copies of DNA

Why is Taq polymerase, derived from Thermus aquaticus, commonly used

in PCR?

It can function at high temperatures, surviving the denaturation step.

What would be the consequence of using a DNA polymerase that is not heat-

stable, instead of Taq polymerase, in PCR?

The enzyme would degrade at high temperatures.

Why is it crucial to design PCR primers with high specificity?

To minimize non-specific amplification

How many primers are typically used in a standard PCR reaction?

Two

How does Taq polymerase contribute to the extension step of PCR?

It synthesizes new DNA strands complementary to the template.

What is the primary function of the buffer in a PCR reaction?

To control the reaction's pH and maintain optimal

conditions