Basic processes in DNA replication, transcribtion & translation I, II & III

Question 1

DNA replication

Answer 1

The process in which DNA is copied, that is translated and transcribed.

Question 2

Transformation

Answer 2

The phenomenon transformation is now defined as a change in genotype and phenotype due to the assimilation of external DNA by a cell. The transforming substance is DNA.

Question 3

Bacteriophages

Answer 3

Viruses that infect bacteria is called bacteriophages, or phages.

Question 4

Phages

Answer 4

Viruses that infect bacteria is called bacteriophages, or phages. Phages have been widely used as tools by researchers in molecular genetics.

Question 5

Virus

Answer 5

Viruses are much simpler than cells. A virus is little more than DNA (sometimes RNA) enclosed by a protective coat, which is often simply protein. To produce more viruses, a virus must infect a cell and take over the cells metabolic machinery.

Question 6

The structure of a DNA strand

Answer 6

Each DNA nucleotide monomer consists of a nitrogenous base (T, A, C or G), the sugar deoxyribose and a phosphate group. The phosphate group of one nucleotide is attached to the sugar of the next by a covalent bond, forming a backbone of alternating phosphates and sugars from which the bases project. The polynucleotide strand has directionality, from the 5’ end (with the phosphate group) to the 3’ end (with the -OH group of the sugar). 5’ and 3’ refer to the numbers assigned to the carbons in the sugar ring.

Question 7

Double helix

Answer 7

The two DNA strands are organized in a double helix. Two strands that spiral around each other.

Question 8

Antiparallel

Answer 8

The two sugar phosphate backbones are antiparallel, which means that their subunits run in opposite directions.

Question 9

Key features of DNA structure

Answer 9

The helix is righthanded, curving up to the right in the front. Adenine pairs with Thymine because it can form 2 hydrogen bonds and has the right diameter. Cytosine pairs with Guanine, because it can form 3 hydrogen bonds and also has the right diameter. The diameter of the double helix is 2nm, there are 10 base pairs per complete circle and the length of a full circle is 3.4nm.

Question 10

Partial chemical structure

Answer 10

Strong covalent sugar-phosphate bonds link the nucleotides of each strand, while weaker hydrogen bonds between the bases hold one strand to the other. From top to bottom, the left strand is oriented in 5’ to 3’ direction, and the right strand in 3’ to 5’ direction.

Question 11

Base pairing in DNA

Answer 11

The pairs of nitrogenous bases in a DNA double helix are held together by hydrogen bonds.

Question 12

Semiconservative model

Answer 12

This semiconservative model can be distinguished from a conservative model of replication, in which the two parental strands come together after the process, (the original structure is conserved). The semiconservative model suggests that the two strands of the parental molecule separate, and each functions as a template for synthesis of a new, complimentary strand.

Question 13

Conservative model

Answer 13

The conservative model of replication, the two parental strands come together after the process, (the original structure is conserved).

Question 14

Dispersive model

Answer 14

Each strand of both daughter molecules contain a mixture of old and newly synthesized DNA.

Question 15

Origins of replication

Answer 15

The replication of chromosomal DNA begins at particular sites called origins of replication, short stretches of DNA that have a specific sequence of nucleotides.

Question 16

Replication fork

Answer 16

Proteins that initiate DNA replication recognize this sequence and attach tot he DNA, separating the two strands and opening up a bubble. At each end of the bubble is a replication fork, a Y shaped region where the parental strands of DNA are being unwound. Several kinds of proteins participate in the unwinding.

Question 17

Helicases

Answer 17

Helicases are enzymes that untwist the double helix at the replication forks, separating the two parental strands and making them available as template strands.

Question 18

Single-strand binding proteins

Answer 18

After the parental strands separate, single-strand binding proteins bind to the unpaired DNA strands, keeping them from repairing. The untwisting of the double helix causes tighter twisting and strain ahead of the replication fork.

Question 19

Topoisomerase

Answer 19

Topoisomerase helps relieve the strain of untwisting the strands by breaking, swiveling and rejoining DNA strands.

Question 20

Primer

Answer 20

The initial nucleotide chain produced during DNA synthesis is a short stretch of RNA, not DNA. This RNA chain is called a primer and is synthesized by the enzyme primase. Primase starts a complementary RNA chain with a single RNA nucleotide and adds RNA nucleotides one at a time, using the parental DNA strand as a template. The completed primer, generally 5-10 nucleotides long, is thus base-paired to the template strand. The new DNA strand will start from the 3’ end of the RNA primer.

Question 21

Primase

Answer 21

This RNA chain is called a primer and is synthesized by the enzyme primase. Primase starts a complementary RNA chain with a single RNA nucleotide and adds RNA nucleotides one at a time, using the parental DNA strand as a template.

Question 22

DNA polymerases

Answer 22

Enzymes called DNA polymerases catalyze the synthesis of new DNA by adding nucleotides at the 3’ end of a preexisting chain. It is DNA polymerase III that starts to synthesize the leading strand. Polymerase I is also important.

Question 23

Antiparallel elongation

Answer 23

Because of their structure, DNA polymerases can add nucleotides only to the free 3’ end of a primer or growing DNA strand, never to the 5’ end. Thus, a new DNA strand can elongate only in the 5’ to 3’ direction. Since the strands are antiparallel, this poses a problem since the DNA chain forks open in only one direction.

Question 24

Leading strand

Answer 24

Along one template strand DNA polymerase III can synthesize a complimentary strand continuously by elongating the new DNA in the mandatory 5’ to 3’ end direction. DNA pol III remains in the replication fork on that template strand and continuously adds nucleotides to the new complementary strand as the fork progresses. The strand made by this mechanism is called the leading strand. Only a primer is required for DNA pol III to synthesize the entire leading strand.

Question 25

Lagging strand

Answer 25

To elongate the other new strand of DNA in the mandatory 5’ to 3’ direction, DNA pol III must work along the other template strand in the direction away from the replication strand. The DNA strand elongating in this direction is called the lagging strand. In contrast to the leading strand, which elongates continuously, the lagging strand is synthesized discontinuously, as a series of segments. These segments are called Okazaki fragments, and they are about 1,000-2,000 nucleotides long in E. coli and 100-200 long in eukaryotes.

Question 26

Okazaki fragments

Answer 26

In contrast to the leading strand, which elongates continuously, the lagging strand is synthesized discontinuously, as a series of segments. These segments are called Okazaki fragments, and they are about 1,000-2,000 nucleotides long in E. coli and 100-200 long in eukaryotes.

Question 27

DNA ligase

Answer 27

Whereas only one primer is required on the leading strand, each Okazaki fragment on the lagging strand must be primed separately. First, primase joins RNA nucleotides into a primer. Secondly, DNA pol III adds DNA nucleotides to the primer, forming Okazaki fragment 1. Third, after reaching the next RNA primer to the right, DNA pol III detaches. Fourth, fragment 2 is primed, then DNA pol III adds DNA nucleotides, detaching when it reaches the fragment 1 primer. Fifth, DNA pol I replaces the RNA with DNA, adding nucleotides to the 3’ end of fragment 1 and 2. Sixth, DNA ligase forms a bond between the newest DNA and the DNA of fragment 1. Then it is complete, and the process repeats till the lagging strand is complete.

Question 28

DNA polymerase I

Answer 28

Whereas only one primer is required on the leading strand, each Okazaki fragment on the lagging strand must be primed separately. First, primase joins RNA nucleotides into a primer. Secondly, DNA pol III adds DNA nucleotides to the primer, forming Okazaki fragment 1. Third, after reaching the next RNA primer to the right, DNA pol III detaches. Fourth, fragment 2 is primed, then DNA pol III adds DNA nucleotides, detaching when it reaches the fragment 1 primer. Fifth, DNA pol I replaces the RNA with DNA, adding nucleotides to the 3’ end of fragment 1 and 2. Sixth, DNA ligase forms a bond between the newest DNA and the DNA of fragment 1. Then it is complete, and the process repeats till the lagging strand is complete.

Question 29

DNA polymerase III

Answer 29

Whereas only one primer is required on the leading strand, each Okazaki fragment on the lagging strand must be primed separately. First, primase joins RNA nucleotides into a primer. Secondly, DNA pol III adds DNA nucleotides to the primer, forming Okazaki fragment 1. Third, after reaching the next RNA primer to the right, DNA pol III detaches. Fourth, fragment 2 is primed, then DNA pol III adds DNA nucleotides, detaching when it reaches the fragment 1 primer. Fifth, DNA pol I replaces the RNA with DNA, adding nucleotides to the 3’ end of fragment 1 and 2. Sixth, DNA ligase forms a bond between the newest DNA and the DNA of fragment 1. Then it is complete, and the process repeats till the lagging strand is complete.

Question 30

Mismatch repair

Answer 30

Mismatched nucleotides sometimes do evade proofreading by a DNA polymerase. In mismatch repair, other enzymes remove and replace incorrectly paired nucleotides resulting from replication errors. They are quite important as some errors are associated with some types of cancer, like colon cancer.

Question 31

Nuclease

Answer 31

Most cellular systems for repairing incorrectly paired nucleotides, whether they are due to DNA damage or to replication errors, use a mechanism that takes advantage of the base-paired structure of DNA. In many cases, a segment of the strand, containing the damage, is cut out (excised) by a DNA cutting enzyme called nuclease, and the resulting gap is then filled in with nucleotides, using the undamaged strand as template. The enzymes involved in filling in the gap are DNA polymerase and DNA ligase. One such DNA repair system is called nucleotide excision repair.

Question 32

Nucleotide excision repair

Answer 32

Most cellular systems for repairing incorrectly paired nucleotides, whether they are due to DNA damage or to replication errors, use a mechanism that takes advantage of the base-paired structure of DNA. In many cases, a segment of the strand, containing the damage, is cut out (excised) by a DNA cutting enzyme called nuclease, and the resulting gap is then filled in with nucleotides, using the undamaged strand as template. The enzymes involved in filling in the gap are DNA polymerase and DNA ligase. One such DNA repair system is called nucleotide excision repair.

Question 33

Telomeres

Answer 33

Eukaryotic chromosomal DNA molecules have special nucleotide sequences called telomeres at their ends. Telomeres do not contain genes; instead, the DNA typically consists of multiple repetitions of one short nucleotide sequence. In each human telomere, for example, the sequence TTAGGG is repeated a 100 to a 1000 times. Telomeric DNA acts as a buffer zone that protects the organisms genes. They do not prevent the erosion of genes near ends of chromosomes, they just postpone it. Shortening of telomeres is proposed to play a role in the aging process of some tissues and even of the organism as a whole.