DNA (Deoxyribonucleic acid) DNA structure DNA replication DNA repair

DNA (Deoxyribonucleic acid) DNA is the storage site of genetic information Functions of DNA 1- Replication (i.e. makes copy of itself): the stored information are transmitted from parent DNA to daughter DNA during cell division by a process called: replication. 2- Makes all proteins that cells needed through gene expression [(transcription and translation (protein synthesis)] DNA (Deoxyribonucleic acid) 2

Gene expression

Site: Human DNA (eukarytotic) is present in the nucleus(linear) and mitochondria ( 1 circular). Bacterial DNA (procaryotic) is circular (number is 1)

Structure of DNA: Human DNA consists of two strands. Each strand is a polymer of deoxyoribonucleotides (dAMP, dGMP, dCMP, dTMP). The nucleotides are arranged in each strand linked together by 3'→5′ phosphodiester bond; a bond in which phosphate group links between C3′ of one deoxyribose to C5′ of the next deoxyribose in the strand. Each DNA strand has two ends: 5′ end (the end with free phosphate group attached to C5′ of the first pentose) and 3′ end (the end with free OH group on C3′ of the last pentose.

This is a tetranucleotide written as 5`-GCTA-3` or GCTA

The nucleotides in the polynucleotide chain is always written from 5′ → 3′ direction This part of polynucleotide is written 5`-ATC-3` or ATC

Base pairing: The two strands are linked together through hydrogen bonding formed between purine bases in one strand with pyrimidine bases in the other resulting in two types of base pairing: - Adenine is always paired with thymine by 2 hydrogen bonds (A=T) - Guanine is always paired with cytosine by 3 H-bonds (G ≡ C) _

So in the double stranded DNA: 1- The content of adenine equals to that of thymine and the content of guanine is equal to that of cytosine 2- Total purine content is equal to pyrimidine content 3- The two strands are complementary to the other i.e. each base of one strand is matched by a complementary hydrogen bonding base on the other strand. 4- The two strand are antiparralel (opposite in direction)

The two strands are complementary to each other in opposite directions as shown

DNA double helix: The two strands of DNA wind arround each other forming double helix which stabilize DNA. Also abundance of hydrogen bonds between bases help to stabilize DNA. Watson and Crick model

DNA replication (DNA synthesis): DNAs have the ability to reproduce themselves by the process of replication, thus ensuring the transfer of genetic information from one generation to the next. DNA replication is the process in which DNA is duplicated before cell division. DNA synthesizes replicate of itself by using its own structure as a template. Each strand of the double helix serves as a template for constructing a complementary daughter strand. The resulting double helix contains one parental and one daughter, and the mode of replication is thus called: Semi-conservative

DNA polymerases The enzyme responsible for DNA synthesis (replication) and repair is called DNA polymerase In Prokaryotes (bacteria): 3 enzymes Polymerase I replicating and repair enzyme Polymerase II repair enzyme Polymerase III replicating enzyme In Eukaryotes (human) there are 5 enzymes) α, β, γ, δ and ε (epsilon) - Pol α and pol δ: are replicating enzymes for nuclear DNA. Pol α synthesize lagging strand while pol δ synthesize leading strand. - Pol γ replicate mitochondria DNA - Pol β and pol ε are involved in DNA repair.

Nucleases: classified as: Exonuclease • Cut phosphodiester bond from the ends • Remove single nucleotide 5' →3' exonuclease 3' → 5' exonuclease Endonuclease In the middle • Produce a nick • Does not remove nucleotide

Steps of prokarytic DNA replication: 1- Separation (unwinding) of double strands: Unpairing (separation, unwinding) of the two strands of the DNA double helix by: helicase enzyme with the formation of “replication fork ”. This separation is necessary because DNA polymerase III enzyme that responsible for replication use only one single stranded DNA as a template.

TWO problems arise from unwinding step: Problem 1 is Repairing or rewinding Solution: The separation is maintained by Single stranded DND binding (SSB) proteins: that bind to single stranded DND and keep two strands separated and prevent rewinding

Problem 2: supercoils As the two strands of the double helix are separated, a problem is found, called “ positive supercoil or supertwist”. Accumulation of supercoils interfere with further unwinding of the double helix. Solving the problems of supercoils: To solve this problem there is a group of enzyme called DNA topoisomerases which are responsible for removing supercoils in the helix. Two types are found: Type I and Type II topoisomerases. DNA gyrase enzyme: is a type II topoisomerase found in bacteria and plants.

Supercoiling can be demonstrated by tightly grasping one end of telephone cord 20

Topoisomerase I Remove supercoilingby cutting (endonuclease activity} and sealing (ligase activity) a single strand Topoisomerase II Remove supercoiling by cutting (endonuclease activity} and sealing (ligase activity) a double strand

Etoposide: is an anticancer drug Etoposide: is an anticancer drug. It is topoisomerase inhibitor that prevent the action of type II topoisomerase and lead to DNA strand to break. Cancer cells will be affected by this drug more than healthy cells because they divide more rapidly. Therefore This causes errors of DNA synthesis and lead to death of cancer cells. Quinolones (e.g. Ciprofloxacin): are antimicrobial agents that inhibit bacterial DNA gyrase

3- Direction of replication: The enzyme responsible for replication is called: DNA polymerase III which forms a complementary copy from DNA template. DNA polymerase III read nucleotide sequence on DNA template from 3′ → 5′ direction so the direction of synthesis of the new DNA strand will be antiparallel i.e in 5′ → 3′ direction. Therefore DNA polymerase III has 5′ → 3′ polymerase activity

4-Starting synthesis of complementary strand by DNA polymerase III: This need RNA primer, because DNA polymerase III can’t join the first two nucleotides to start the new strand (can’t act de novo), it adds the nucleotides to the existing RNA primer. RNA primer is a short segment of RNA (8-10 nucleotides with free 3' OH end) consisting of RNA nucleotides (AMP, GMP, CMP, UMP) Primase: is the enzyme responsible for synthesis of RNA primer Primase is of key importance in DNA replication because no known DNA polymerases can initiate the synthesis of a DNA strand without initial RNA primers.

When DNA polymerase III recognizes RNA primer, it begins to synthesize new DNA strand using the 3' OH of RNA primer as the acceptor of the first nucleotide. As we said before each DNA template is read from 3′ → 5′ and each new strand is synthesized from 5′ → 3' (5′ → 3' polymerase activity) The 2 new strands grow in opposite direction, one in 5′ → 3′ direction toward replication fork and called “leading strand” which is synthesized continuously and need only one RNA primer. The other strand called “Lagging strand” which is synthesized also in 5′ → 3′ direction but away from replication fork and synthesized discontinuously as small fragments of DNA called Okazaki fragments and so need many RNA primers

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5- Proofreading of newly synthesized DNA: (3'→5’ exonuclease activity of polymerase III) It is highly important for the survival of an organism that the nucleotide sequence of DNA be replicated with a few errors as possible. Misreading of the template could result in mutation and damage and could be lethal. To ensure correct replication, DNA polymerase III enzyme has the function of proofreading activity i.e. check that each nucleotide added to the new strand is correctly matched to its complementary nucleotide on the template. If DNA polymerase III mispairs a nucleotide (add false nucleotide that not match with the template ). it will excise (remove) the wrong nucleotide (exonuclease activity) using its 3'→5’ exonuclease activity.

So DNA polymerase III has two functions: Polymerase function (5' → 3' polymerase activity) Proofreading function (3' → 5' exonuclease activity)

6- Removal of RNA primers by DNA polymerase I: When DNA polymerase III finishes synthesis of new DNA on lagging strand, RNA primers are removed by DNA polymerase I (5' → 3' exonuclease activity) and the gap produced is filled by DNA synthesized by also DNA polymerase I (5' → 3' polymerase activity) and check the added nucleotides (proofreading) using 3'→5’ exonuclease activity. So DNA polymerase I has 3 functions: Removal of primers (5' → 3' exonuclease activity) Filling gaps with new DNA (5' → 3' polymerase activity) Proofreading (3'→5’ exonuclease activity) 7- DNA ligase: Connect (ligase) the newly synthesized DNA (Oazaki fragments) together

Removal of RNA primers and filling the resulting gap by DNA polymerase I

As a result of replication, 2 double stranded DNA is formed, each of which contain one old and one new strand, This is called: Semiconservative manner of replication.