Q.EcoRI recognises the sequence 5'-GAATTC-3' and cuts between G and A on each strand, leaving single-stranded overhangs. Draw/describe the products of this cut and explain why the overhangs are called 'sticky ends'.

Only 5' GAATTC 3' / 3' CTTAAG 5' -- the real EcoRI site -- is a true palindromic sequence, cut near its centre by a restriction enzyme.

Working

Most Type II restriction enzymes recognise short, palindromic sequences of double-stranded DNA -- sequences where the base sequence on one strand, read 5' to 3', is identical to the sequence on the complementary strand, also read 5' to 3'. Such symmetry lets the enzyme (which usually acts as a symmetrical dimer) bind and cut both strands near the axis of symmetry, close to the middle of the recognition site.

Testing option (a): top strand 5'-GAATTC-3'; the bottom strand written 3'-CTTAAG-5' is, read 5'->3', GAATTC -- identical to the top strand. This is a true palindrome. It is, in fact, the actual recognition sequence of the well-known restriction enzyme EcoRI (from E. coli), which cuts between the G and the A on each strand (G^AATTC), i.e. almost exactly at the middle of the six-base-pair site, producing sticky ends.

The remaining sequences (b) CGTTCG/ATCGTA, (c) CACGTA/CTCAGT, and (d) GATATG/CTACTA are not complementary palindromes in the required sense -- reading their bottom strands 5'->3' does not reproduce the top strand -- so they are not genuine restriction-enzyme recognition sites of this type.

Restriction endonuclease recognition sites are typically short palindromic sequences of 4 to 8 base pairs.

Restriction enzymes recognize specific, usually palindromic, DNA sequences and cleave the DNA at or near that site. Most commonly used restriction enzymes (like EcoRI, BamHI, HindIII) recognize sequences that are 4 to 8 nucleotides long, which is short enough to occur reasonably often in a genome yet specific enough to give reproducible, useful cuts for cloning and genetic engineering.

Restriction enzymes are both nucleases that cut DNA at specific sites AND an essential tool in genetic engineering, so both (b) and (c) are correct -- option (d).

Working

Restriction endonucleases (restriction enzymes) are bacterial enzymes that recognise specific, usually palindromic, short DNA sequences (recognition sites) and cleave the DNA backbone at or near those sites. This is exactly what option (c) states: "Nucleases that cleave DNA at specific sites" -- a correct description of their mechanism. Because they can cut DNA at precise, predictable locations, restriction enzymes are one of the foundational tools of recombinant DNA technology, used to cut both the DNA of interest and the vector so that they can be joined together -- making option (b), "Essential tool in genetic engineering," also correct. Option (a), stating they are "not always required," is incorrect, since restriction digestion is a standard and generally necessary step in constructing recombinant DNA. Since both (b) and (c) are independently true and complementary descriptions of the same enzymes, the fully correct answer is that both apply.

Exonuclease cuts DNA at the terminus, endonuclease cuts it in the middle, alkaline phosphatase adds/removes a phosphate group, and ligase joins DNA fragments -- matching to (c).

Working

These four enzymes are all classic tools of recombinant DNA technology, each with a distinct site and mode of action on a DNA molecule:

1. Exonuclease -- removes nucleotides progressively starting from the free end (terminus) of a DNA strand, either from the 5' or 3' end. So (1) matches (iii) "cut the DNA at terminus".
2. Endonuclease -- recognises a specific internal sequence and cleaves the DNA strand in the middle of the molecule, not at an end. Restriction endonucleases (e.g. EcoRI) are the best-known example. So (2) matches (iv) "cut the DNA at middle".
3. Alkaline phosphatase -- catalyses the removal (or, in reverse reactions, transfer) of a terminal 5'-phosphate group from DNA, commonly used to prevent unwanted self-ligation of a vector. So (3) matches (i) "add or remove phosphate".
4. Ligase -- catalyses formation of a phosphodiester bond between the 3'-OH end of one DNA fragment and the 5'-phosphate end of another, sealing nicks and joining fragments together -- essential for constructing recombinant DNA molecules. So (4) matches (ii) "binding the DNA fragments".

Putting these together gives (1)-(iii), (2)-(iv), (3)-(i), (4)-(ii).

Nucleases are the class of enzymes that cut/degrade nucleic acids (DNA/RNA); restriction endonucleases are the sequence-specific nucleases used in genetic engineering.

Nucleases are enzymes that catalyse the cleavage (hydrolysis) of phosphodiester bonds in nucleic acid chains (DNA or RNA). They include exonucleases (which remove nucleotides from the ends of a strand) and endonucleases (which cut within the strand, often at specific recognition sequences, as in restriction enzymes used in genetic engineering). Ligase JOINS DNA fragments (the opposite function), proteases cleave proteins (not nucleic acids), and polymerases synthesise new nucleic-acid strands rather than cleave them.

Restriction endonucleases cut DNA at specific sites; among the options only EcoRI is one — the answer is (d).

Let us classify each enzyme:

• (a) Taq polymerase — a DNA polymerase from Thermus aquaticus used in PCR (synthesises DNA); not a nuclease.

• (b) DNA polymerase — synthesises new DNA strands; not a restriction enzyme.

• (c) Ligase — joins DNA fragments (seals nicks); it is a joining enzyme, not a cutter.

• (d) EcoRI — a restriction endonuclease from E. coli that recognises the palindromic sequence 5'-GAATTC-3' and cuts within it, producing sticky ends. This is the true restriction endonuclease.

Restriction endonucleases are 'molecular scissors' that cut DNA at specific recognition sequences.

Restriction endonucleases are bacterial enzymes that recognize specific short palindromic nucleotide sequences on DNA and cleave the DNA strand at or near that specific site, often producing 'sticky ends'. They are essential tools in recombinant DNA technology for cutting out a gene of interest and opening up a vector at a matching site so the two can be joined. DNA polymerase synthesises new DNA strands, alkaline phosphatase removes phosphate groups, and DNA ligase joins DNA fragments together — none of these cut DNA at a specific sequence the way a restriction endonuclease does.

Restriction enzymes cut DNA at specific recognition sequences.

Restriction endonucleases are bacterial enzymes (part of their restriction-modification defence system against phage DNA) that recognise a specific, usually palindromic, short nucleotide sequence (e.g. EcoRI recognises GAATTC) and cleave the DNA backbone at or near that site, generating either sticky or blunt ends. This sequence-specific cutting is what makes restriction enzymes indispensable tools for constructing recombinant DNA. They do not cut based on gene ends, methyl groups (in fact methylation of the host's own DNA at the recognition site protects it from its own restriction enzyme) or the timing of replication.