Ligase Enzymes

Correct answer: A. Cut DNA fragments will not join permanently

Restriction enzymes can cut DNA but ligase makes the permanent join. Therefore ligase is essential in cloning.

Correct answer: A. After cutting DNA with a restriction enzyme

In cloning, a restriction enzyme first cuts the vector and the desired DNA fragment at suitable sites. DNA ligase then forms phosphodiester bonds between their ends and joins the insert to the vector. Introducing DNA into bacteria and selecting colonies occur after ligation. Exam tip: remember the sequence—cutting, ligation, transformation, selection.

Correct answer: A. It joins DNA ends

The main function of DNA ligase is joining DNA ends. Remember it as the joining enzyme in gene cloning.

Correct answer: A. 3 prime hydroxyl and 5 prime phosphate

DNA ligase joins a 3 prime hydroxyl end with a 5 prime phosphate end. It forms a phosphodiester bond.

Correct answer: A. 5 prime phosphate

In ligation 5 prime phosphate and 3 prime hydroxyl are required. A new phosphodiester bond forms between them.

Correct answer: A. Sealing broken nicks

DNA ligase can seal nicks in the DNA backbone. Thus it is useful in both replication and repair.

Correct answer: D. Cutting DNA at a recognition site

DNA ligase seals nicks in the sugar-phosphate backbone by forming phosphodiester bonds. Thus, it joins DNA fragments, including Okazaki fragments formed during replication. Cutting DNA at a specific recognition site is carried out by a restriction endonuclease, not by ligase. Exam tip: remember ligase as the DNA “joining” enzyme and restriction enzymes as DNA “cutting” enzymes.

Correct answer: A. Ligase joins fragments and polymerase extends a new strand

Polymerase extends a strand by adding nucleotides. Ligase seals nicks between already formed fragments.

Correct answer: A. Joining the cut vector and insert

In recombinant-DNA construction, restriction enzymes first cut the vector and the desired DNA insert at selected sites. The resulting ends are brought together, and DNA ligase then seals the sugar-phosphate backbones by forming phosphodiester bonds. This produces a covalently closed recombinant plasmid or another recombinant DNA molecule. Thus option A is correct because it identifies the joining or ligation step. Option B describes the earlier cutting step performed by a restriction enzyme, not by ligase. Gel electrophoresis separates DNA fragments for analysis, and boiling a protein has no role in ligating DNA fragments. The sequence of cutting followed by ligation is central to cloning.

Correct answer: A. Phosphodiester bond

DNA ligase completes the sugar-phosphate backbone by catalysing formation of a phosphodiester bond between a 3′-hydroxyl group and a 5′-phosphate group on adjacent DNA ends. This is a covalent bond, so it creates a stable, permanent connection rather than merely holding the strands together through temporary base pairing or weak molecular forces. Option A is therefore correct. Hydrogen bonds between complementary bases help hold the two DNA strands together, but they are not the new backbone bond made by ligase. The other listed ‘bonds’ are not recognised chemical bonds involved in DNA ligation and are biologically irrelevant.

Correct answer: A. DNA ligase

DNA ligase joins breaks (nicks) in the sugar-phosphate backbone between short DNA fragments by forming phosphodiester bonds. Thus, it joins Okazaki fragments during replication to make a continuous strand. DNA polymerase adds new nucleotides, but DNA ligase performs the key function of sealing the nick between fragments. Exam tip: Choose DNA ligase when the question mentions joining fragments or sealing nicks.

Correct answer: A. To form a new phosphodiester bond

DNA ligase joins DNA ends by catalysing formation of a new phosphodiester bond in the sugar-phosphate backbone. Creating this covalent linkage is not energetically free, so the ligase reaction uses an activated substrate and chemical energy. Depending on the enzyme source, the energy may be supplied through ATP or NAD+; for example, many common laboratory ligases use ATP, whereas some bacterial ligases use NAD+-dependent activation. Option A is correct because the energy supports formation of the new DNA backbone bond. DNA colouring, freezing water and dissolving fat are unrelated to the biochemical purpose of ligation.

Correct answer: A. It can join both sticky and blunt ends

Direct answer: A, T4 DNA ligase can join both sticky and blunt ends. DNA ligase joins DNA backbones by forming phosphodiester bonds, using energy supplied by the reaction system. T4 DNA ligase, obtained from bacteriophage T4, is widely used because it can efficiently join compatible sticky ends and can also join blunt-ended DNA, although blunt-end ligation is usually less efficient and may need suitable conditions or higher DNA concentration. Option A is correct because it states this broad usefulness. Option B is wrong: cutting DNA is the role of restriction enzymes, not ligase. Option C is wrong because starch digestion is performed by amylase, not T4 DNA ligase. Option D is wrong because ligase does not color proteins. In cloning, this enzyme seals the insert to the vector after their ends have been prepared. Exam cue: ligase joins; T4 ligase handles sticky and blunt ends.

Correct answer: A. Compatible and adjacent DNA ends

For joining by ligase DNA ends should be close and chemically proper. Compatible ends make ligation easier.

Correct answer: D. It cuts DNA at palindromic sites

Cutting at palindromic sites is linked with restriction enzymes. Ligase does not cut DNA but joins it.

Correct answer: A. DNA ligase

Direct answer: A, DNA ligase. When DNA is cut, sticky ends may first meet through temporary complementary base pairing. These hydrogen-bond interactions hold the fragments near each other, but they do not make the sugar-phosphate backbones continuous. DNA ligase completes the repair by catalyzing formation of phosphodiester bonds between the proper 3′ hydroxyl and 5′ phosphate groups. This seals the nick and makes the recombinant DNA strand stable. Option A is correct. Option B, chlorophyll, captures light energy in plants and does not join DNA. Option C, a ribosome, helps translate mRNA into protein and does not seal DNA. Option D, a fatty acid, is a lipid building block and is not a DNA enzyme. The same ligase principle operates in cloning and during DNA replication, where separate pieces must be joined. Memory cue: base pairing brings DNA together; ligase seals the backbone.

Correct answer: A. DNA replication

In DNA replication ligase joins fragments on the lagging strand. It is not only a laboratory enzyme.

Correct answer: A. Plasmid vector and insert DNA

The direct answer is option A: a plasmid vector and insert DNA must be joined to form a recombinant plasmid. A plasmid is a small circular DNA molecule that can carry an inserted gene. The insert is the desired DNA fragment. Restriction enzymes can open the vector and prepare compatible ends, and DNA ligase joins the vector backbone to the insert by forming phosphodiester bonds. The resulting DNA molecule contains DNA from two sources and is therefore called recombinant DNA. Option A is correct because both the vector and insert are essential parts. Option B is wrong because water and fat are not DNA components in plasmid construction. Option C is wrong because chlorophyll and soil do not form a recombinant plasmid. Option D is wrong because proteins and starch are different biological materials, not the DNA pieces joined in cloning. The ligase is the joining tool, not a replacement for either DNA part. Memory cue: recombinant plasmid equals vector plus insert, sealed by ligase.

Correct answer: A. Because it joins DNA fragments by forming phosphodiester bonds

DNA ligase joins broken DNA ends or DNA fragments by forming phosphodiester bonds. It is called a ligase because it carries out ligation, the joining of DNA pieces. An enzyme that cuts DNA at specific sites is a restriction endonuclease, not a ligase. Exam tip: remember ligase as the enzyme that ‘joins DNA fragments’.

Correct answer: A. Joining insert DNA with a plasmid vector

DNA ligase joins an insert DNA fragment to a plasmid vector by forming phosphodiester bonds between DNA fragments. Therefore, it is used to make recombinant DNA during gene cloning. Cutting DNA at specific sites is done by restriction enzymes, not ligase. Exam tip: remember that restriction enzymes cut DNA, whereas ligase joins DNA fragments.

Correct answer: D. Cutting a specific sequence in DNA

The direct answer is D: ligase does not cut a specific DNA sequence. DNA ligase is a joining enzyme. It joins DNA ends and seals breaks, called nicks, in the sugar-phosphate backbone by forming phosphodiester bonds. During DNA replication, it also joins Okazaki fragments on the lagging strand after the separate pieces have been made. Option A is therefore a true ligase function. Option B is also true because sealing a nick is exactly a repair or joining action performed by ligase. Option C is true because ligase connects Okazaki fragments to make a continuous strand. Option D is correct as the exception: recognizing and cutting a particular DNA sequence is the role of a restriction endonuclease, not ligase. The word “not” is the key in this question. Memory cue: ligase is like molecular glue; restriction enzyme is the molecular scissors.

Correct answer: A. Sugar-phosphate backbone

Ligase completes the sugar-phosphate backbone of DNA by forming a phosphodiester bond. This is permanent joining.

Correct answer: A. DNA ends are compatible and ligase is active

Successful ligation needs compatible DNA ends and active ligase. Wrong conditions can reduce joining.

Correct answer: A. For bond-forming action of ligase

Ligase needs energy to make a new phosphodiester bond. Therefore ligation buffer contains an energy source.

Correct answer: A. It uses ATP to join DNA ends

T4 DNA ligase joins broken DNA ends by forming phosphodiester bonds, and it uses ATP for this reaction. DNA ligase that uses NAD+ is typically found in bacteria such as E. coli. Cutting DNA at recognition sequences is done by restriction endonucleases, whereas adding new nucleotides is the role of DNA polymerase. Exam tip: Remember T4 DNA ligase as an ATP-dependent ligase.