Amalia Tristiana _ 4401412063_ rombel 1 pendidikan biologi

STRUKTUR DARI DNA POLIMERASE

DNA polymerase memainkan peran penting dalam memperbaiki informasi genetic. DNA polimeraseadalah enzim penting dalamreplikasi DNAmaupun dalamreparasi DNA. DNA polimerase pertama kali ditemukan pada tahun 1957. olehArthur Kornberg. DNA polimerase membaca rantai DNA utuh sebagai cetakan (templat) dan menggunakannya untuk membentuk rantai baru. Molekulpolimeryang baru terbentuk merupakan komplemen atau pasangan dari rantai yang digunakan sebagai cetakan, dan identik dengan pasangan dari rantai cetakan sebelum terjadi reaksi.

DNA Polimerase berperan dalamelongasidanproofreading.

Elongasi. Elongasi atau pemanjangan rantai menentukan kecepatan berlangsungnya reaksi polimerisasi (nukleotida per detik), yang dinyatakan sebagai prosesivitas yaitu jumlah nukleotida yang ditambahkan sebelum enzim DNA polimerase ini melepaskan dirinya dari rantai cetakan.

Proofreadingmerupakan aktivitas mengenali kekeliruan pengkopian dan memperbaikinya. Penelitian pada awal tahun 2010 pada sel jaringan ikat manusia menyatakan ada tiga jenis DNA polimerase yang terlibat dalam terjadinya pemotongan nukleotida, dalam rangka koreksi terhadap DNA, yaitu DNA polimerase , , dan

DNA polimerase dalam pemanjangan rantai dan koreksi cetakan

DNA Structure

DNA in cells exists as adouble-stranded helix.

Asingle strandof DNA is a chain ofnucleotidesjoined by covalent bonds between the phosphate of one nucleotide and the pentose sugar of the adjacent nucleotide.

Anucleotideconsists of aphosphate groupbound toa pentose(a five carbon sugar; in DNA the sugar isdeoxyribose)with anitrogenous base(A, T, C, or G) also bound to the pentose.

The carbons in the pentose are numbered to make it easier to talk about them.

The phosphate attached to the number 5 carbon of the pentose is called a 5' ("five prime") phosphate.

The hydroxyl group (O-H) attached to the number 3 carbon is called the 3' ("three prime") hydroxyl

Because the nucleotides in a strand of DNA are always joined together in the same way (5' phosphate to 3' hydroxyl) the strands have direction, sort of a head and a tail, if you want to think about it that way.

Of course the proper way to think about it is "DNA strands have a 5' end and a 3' end".

The two strands of a double stranded DNA molecule are held together by hydrogen bonds between specific nitrogenous base pairs: adenines on one strand form hydrogen bonds with thymines on the opposite strand (A-T) and guanines on one strand form hydrogen bonds with cytosines on the opposite strand (G-C)

The strands are oriented in opposite directions.

This is the only way the bases can line up across from each other to form the hydrogen bonds that hold the strands together.

Because the two strands of a double stranded DNA molecule are oriented in opposite directions a double stranded DNA molecule is said to beantiparallel.

This is "helical"

During DNA replication, the two strands of the double helix separate and each strand is used as a template byDNA polymeraseto synthesize two new strands of DNA. (Click the "DNA polymerase" link and read)

DNA polymerase "reads" the existing strand that serves as a template from 3' to 5' and synthesizes the new strand 5' to 3'.

The new strands are synthesized according to the rules of nitrogenous base pairing (A pairs with T and G pairs with C) - wherever the polymerase reads "A" on the template strand it inserts "T" in the growing new strand (and inserts "A" where it reads "T", inserts "G" where it reads "C", and inserts "C" where it reads "G").

The result of DNA replication is two new strands of DNA, each having a base sequence complementary to one of the original strands.

Because each double-stranded DNA molecule contains one original and one new strand, the replication process is calledsemi-conservative

Langkah kerja DNA polimerase

The DNA strands will remain bound together to prevent breakage until the replication enzymes open the helix and separate the strands.

The site where the DNA strands separate and replication begins is called the replication fork

Another property of DNA polymerase: DNA polymerase can't synthesize a new strand de novo, it can only extend from an existing nucleotide with a free 3' hydroxyl.

This would present a problem but there is an RNA polymerase, called primase, which can synthesize a strand of RNA without having a nucleotide already in place.

Primase also reads the template strand of DNA 3' to 5' and synthesizes a short complementary strand of RNA 5' to 3', leaving a . This short piece of RNA is called a primer and has a free 3' hydroxyl for DNA polymerase to use as a starting point for synthesis of new DNA - it extends from the primer to produce a new DNA strand.

Because DNA is anti-parallel (the template strands are oriented in opposite directions), and because new DNA strands are synthesized in one chemical direction (5 to 3), at the replication fork something a little odd has to happen.

One new strand is synthesized continuously from a starting RNA primerintothe opening replication fork (the DNA polymerase is reading the template strand 3' - 5' and synthesizing the new strand 5' - 3'). This is the continuous, or leading strand.

other new strand is also synthesized 5' - 3' butaway fromthe opening replication fork, since the template strand, (which is also being read 3' - 5') runs in the opposite direction of the other template strand (they're anti-parallel).

Every time the replication fork opens a little more primase has to put another RNA primer in and DNA polymerase has to synthesize another fragment of DNA. The strand that is synthesized away from the opening replication fork is synthesized discontinuously and is called the lagging strand.

The discontinuous strands of DNA are called Okazaki fragments. DNA polymerase will digest the RNA primers and replace them with DNA and the enzyme DNA ligase will join them to the 5' end of the Okazaki fragments.

how the polymerase/primase works???

DNA polymerase proofreads new molecules of DNA and removes mismatched bases before continuing DNA synthesis.

Each daughter bacterium receives a chromosome identical to the other

Struktur dari Famili A, B, X, Y, dan RT polymerase.

Structures of family A, B, X, Y, and RT polymerases. The proteins are inribbon representation. Thefingers, palm, and thumb subdomains are colorcoded ingold, red, and green, respectively. (A) Structure of apo Klentaq1 (family A). The 3-5vestigial exonuclease domain is indicated in silver. (B) Structure of apo RB69 DNApolymerase (family B). The 3-5 exonuclease domain and the Nterminal domain are indicated in grey and silver, respectively. (C) Structure of apo pol bDNA polymerase(family X). The lyase domain is indicated grey. (D) Structure of the Dpo4 DNA polymerase (family Y ). The littlefinger subdomain is indicated in silver. (E) Structure of the p66 subunit of reverse transcriptase (RT family). The RNAseH and connection subdomains are indicated in grey and silver, respectively.

Structure of the p/t DNA bound Klentaq1. (A) Overall structure of the Klentaq1 bound to a p/t DNA. The protein is in ribbon representation, whereas the p/t DNA is in both ribbon and ballandstick representation. The fingers, palm, and thumb subdomains are colorcoded as inFig. 2, whereas the vestigial 3-5exonuclease is colored grey. The primer strand ribbon is in cyan, and the template strand ribbon is in magenta. (B) Superimposition of the apo (red) and p/tbound (cyan) Klentaq1. Only the protein is shown and is in ribbon representation. The DNAbound structure differs from that of the apo form by a conformationalchange in the thumb subdomain. (C) Location of Tyr 671 and the templating base in theE:p/t complex. The Ohelix is labeled and is shown in red ribbon representation. Theprimer and template strands are in both ribbon and ballandstick representation.The primer and template strands are in silver and cyan, respectively. Thefirst singlestranded template base (the templating base) is in deep blue. Tyr 671 is seen stacked ontop of the template base of thefirst duplex base pair, and the templating base isflipped out. (D) Model of a dNTP bound to the Ohelix of Klentaq1 in the E:dNTP complex and its position relative to active site. The subdomains are colorcoded as inFig. 3A. The various subdomains are in ribbon representation with lined instead offilledin ribbons for thefingers subdomain. This allows the visualization the Ohelix in pale green in the fingers domain. The distance between the base of the dNTP and the active site residues is indicated.

Schematic diagram of active sites showing two metal ions, the nucleotide binding ion (site A), and the catalytic ion (site B) (1, 2).

Sources :

1. Insight into the Catalytic Mechanism of DNA Polymerase: Structures of Intermediate Complexes (Biochemistry2001,40,5368-5375)

2. STRUCTURE AND MECHANISM OF DNA POLYMERASES By PAUL J. ROTHWELL AND GABRIEL WAKSMAN.

3. http://classes.midlandstech.edu/carterp/Courses/bio225/chap08/lecture2.htm

Amalia Tristiana

_ 4401412063_ rombel 1 pendidikan biologi

STRUKTUR DARI DNA POLIMERASE

DNA

polymerase

memainkan peran penting dalam memperbaiki informasi

genetic

.

DNA

polimeras

e

adalah enzim penting dalam

replikasi DNA

maupun dalam

reparasi DNA

.

DNA

polimerase pertama kali ditemukan pada tahun 1957

.

oleh

Arthur Kornberg

.

DNA polimerase

membaca rantai DNA utuh sebagai cetakan

(

templa

t

) dan menggunakannya untuk membentuk

rantai baru. Molekul

polimer

yang baru terbentuk merupakan komplemen atau pasangan dari

rantai yang digunakan sebagai cetakan, dan identik dengan pasangan dari rantai cetakan sebelum

terjadi reaksi

.

DNA polimerase dalam pemanjangan rantai dan koreksi cetaka

n

DNA Polimerase berperan

dalam

elongasi

dan

proofreading

.

Elongasi

. Elongasi atau

pemanjangan rantai

menentukan kecepatan

berlangsungnya r

eaksi

polimerisasi (nukleotida per

detik), yang dinyatakan sebagai

prosesivitas yaitu jumlah

nukleotida yang ditambahkan

sebelum enzim DNA polimerase

ini melepaskan dirinya dari

rantai cetakan.

Proofreading

merupakan

aktivitas mengenali kekeliruan

pengkopian dan

memperbaikinya. Penelitian

pada awal tahun 2010 pada sel

jaringan ikat manusia

menyatakan ada tiga jenis DNA

polimerase yang terlibat dalam

terjadinya pemotongan

nukleotida, dalam rangka

koreksi terha

dap DNA, yaitu

DNA polimerase d, e, dan ?

Amalia Tristiana _ 4401412063_ rombel 1 pendidikan biologi

STRUKTUR DARI DNA POLIMERASE

DNA polymerase memainkan peran penting dalam memperbaiki informasi genetic. DNA

polimerase adalah enzim penting dalam replikasi DNA maupun dalam reparasi DNA. DNA

polimerase pertama kali ditemukan pada tahun 1957

.

oleh Arthur Kornberg. DNA polimerase

membaca rantai DNA utuh sebagai cetakan (templat) dan menggunakannya untuk membentuk

rantai baru. Molekul polimer yang baru terbentuk merupakan komplemen atau pasangan dari

rantai yang digunakan sebagai cetakan, dan identik dengan pasangan dari rantai cetakan sebelum

terjadi reaksi.

DNA polimerase dalam pemanjangan rantai dan koreksi cetakan

DNA Polimerase berperan

dalam elongasi dan proofreading.

Elongasi. Elongasi atau

pemanjangan rantai

menentukan kecepatan

berlangsungnya reaksi

polimerisasi (nukleotida per

detik), yang dinyatakan sebagai

prosesivitas yaitu jumlah

nukleotida yang ditambahkan

sebelum enzim DNA polimerase

ini melepaskan dirinya dari

rantai cetakan.

Proofreading merupakan

aktivitas mengenali kekeliruan

pengkopian dan

memperbaikinya. Penelitian

pada awal tahun 2010 pada sel

jaringan ikat manusia

menyatakan ada tiga jenis DNA

polimerase yang terlibat dalam

terjadinya pemotongan

nukleotida, dalam rangka

koreksi terhadap DNA, yaitu

DNA polimerase d, e, dan ?