ȭа Ʈ-2: 4 ۿ ( )

 

- -

 

I.

 

II. Һ

1. 帧

2. Һ

3.

 

III. DNA

1. DNA ݺ

2. DNA

3. ټ (bacteria) DNA

4. ټ Ϲ DNA

5. ټ chromatin

 

IV. (transcription)

1. ټ

2. ټ

 

V. (translation)

1. Ribosome

2. Shine-Dalgarno sequences

3. ܹ ռ

4. ܹ ռ

5. ܹ ռ

6. rRNA

7. ܹ 3

 

 

- -

 

I.

 

 

overall of view

- coupled transcription & translation

- RNA modification

- post-translation

DNA duplication

- DNA helicase

- DNA single strand binding protein   (DNA ssbp)

- DNA gyrase

- DNA polymerase I, II & III

- Primase

- DNA ligase

?

transcription

- RNA polymerase

- sigma factor

- promoter

- mRNA (polycistronic mRNA)

- tRNA

- RNA polymerase I, II & III

- Ribozymes

translation

- ribosome: 50S + 30S 70S

- ribosome: 60S+40S 80S

post -tanslation

-

- protein modification

 

 

II. Һ

1. 帧 Ϲ: DNA mRNA protein

 

2. Central dogma (Һ )

(1)

    1) DNA duplication: DNA-dependent DNA polymeration

    2) transcription : DNA-dependent RNA polymeration

    3) translation : RNA (DNA)-dependent protein synthesis

    img1.gif

 

(2) Һ

    1) reverse transcriptase ( ȿ)

        a. HIV (human immunodeficiency virus)

        b. RNA virus (ڰ RNA)

        img2.gif

    2) Virus

genome

intermediate

mRNA

transcription

dsDNA (±)

-

mRNA (+)

normal

ssDNA (+)

dsDNA (±)

mRNA (+)

dsDNA intermediate & transcription

ssDNA (-)

dsDNA (±)

mRNA (+)

dsDNA intermediate & transcription

ssRNA (±)

-

mRNA (+)

transcription of (-) strand

ssRNA (+)

-

ssRNA (+)

directly use

ssRNA (-)

-

mRNA (+)

transcription of (-) strand

 

3.

(1) ټ

        img3.gif

 

(2) ټ

    img4.gif

 

(3) ټ RNA splicing mechanism

: http://www.web-books.com/MoBio/Free/Ch5A4.htm

: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.1020

    img5.gif

 

III. DNA : http://www.johnkyrk.com/DNAreplication.html

1. DNA ݺ

    img6.gif

 

2. DNA

(1) DNA ̸ (template)

(2) 3' -OH group

    img7.gif

 

3. ټ (bacteria) DNA

http://www.mun.ca/biochem/courses/3107/Lectures/Topics/DNA_polymerases.html

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/D/DNAReplication.html   

(1)

    1) κ bacteria ü

    2) Ư initiation proteins ִ 300bp

    3) ̰ DNA double-helix Ǯ single-strands

    img8.gif

 

(2) DNA ʿ ȿ ܹ

     1) (E. coli) DNA polymerase

        a. DNA pol I: RNA primer DNA ü

        b. DNA pol II: DNA repair

        c. DNA pol III: replicating fork ϴ ֵ ȿ

 

    2) helicase

        a. ss-DNA ܹ ȿ

        b. ATP ϸ replication fork ̵Ŵ

 

    3) single-strand binding protein

        a. ss-DNA ȭŴ

        b. intrastrand hydrogen bond

 

    4) topoisomerase

        a. replication fork Կ DNA supercoil° ȭ

        b. DNA DZ ؼ unwinding Ͼ Ѵ.

        c. supercoiled DNA strain unwindingȴ

        d. degree of supercoiling Ͽ DNA

    img9.gif

 

(3) leading strand lagging strand

    1) leading strand

        a. DNA 5'3' ռǴ

        b. DNA罽 ( primer ʿ)

 

    2) lagging strand

        a. DNA 3'5' ռǴ

        b. leading strand ݴ DNA ռ ҿ Ͼ 罽

        c. replication fork ̵ ݴ

        d. primase 11bp ¥ RNA primer ʿ

 

    3) lagging strand ռ

        a. primase DNA 3'ܿ RNA ռ (RNA primer) Ŀ

        b. DNA polymerase III Ͽ DNA ռ

        c. Ǹ, DNA pol III DNA pol I ۿ

        d. DNA pol I exonucleaseۿ뵵 Ͽ RNA primer ְ DNA ռ

        e. DNA DNA pol I DNA ligase DNA

 

    4) Okazaki fragments

        a. DNA pol III ռϴ ª DNA ( 1000bases long)

        b. Okazaki ϳ RNA primer ʿ

        img10.gif

 

4.  ټ Ϲ DNA

img11.gif

    img12.gif

 

5. ټ chromatin

    - chromatin DNA

    - H1 nucelosome ̿ ġ nucleosome packing

     img13.gif

 

IV. (transcription): http://www.biostudio.com/d_%20Transcription.htm

img14.gif

 

1. ټ

(1) Initiation: (transcription = DNA mRNA)

    1) RNA polymerase(RNA pol) DNA promoter Ư κп

    2) RNA pol DNA promoter ϴ DNA

    3) DNA coiling Ǯ鼭 RNA polymerase

    4) RNA pol (RNA ռǰ ), ٽ

 

(2) promoter: RNA polymerase DNA template ó ϴ DNA

    1) Ȯ ܹ ؼ RNA pol ϴ Ȯ ġ

    2) ٿ , 밳 DNA major groove

    3) RNA pol ſ ū ܹ̾ DNA ÿ

    4) promoter ⼺ DNA Ǵ 罽

    5) Ǵ 罽 (template) ̿Ǹ antisense (template strand) Ѵ

    6) sense strand mRNA

    7) promoters پ ְ ݴ Ųٸ

        a. promoter ڿ 簡 Ͼ

       b. ٸ promoter ٸ ڿ ݴ 簡

 

(3) Elongation: (transcription)

    1) RNA polymerase (RNA pol)

    2) RNA pol ribonucleotide phosphodiester ˸ ۿ

    3) RNA ü(precursors) nucleoside triphosphate: ATP, GTP, UTP, CTP

    4) RNA polymerase DNA template ̵ϸ

 

(4) Termination: http://utminers.utep.edu/rwebb/html/transcription__termination.html

    1) hairpin loop

        a. inverted repeat sequence + central non-repeating segment

        b. intrastrand stem-loop structure

        c. ̷ U ݺǸ 簡 ȿ

 

    2) intrinsic terminators:

        a. GC-rich AT-rich )

        b. ٸ (factors) 簡

img16.gif

 

    3) Rho-dependent termination

        a. Rho ܹ RNA Ͽ 縦

        b. RNA pol Rho-dependent termination site ٴٸ

        c. Rho ܹ RNA pol ̵ RNA pol DNA и

 

(5) Bacterial RNA polymerase

    1) Bacteria, Archaea, Eukarya RNA pol

    2) (E. coli) RNA pol 4 subunits: , ', ,

        * ϰ 2' ߽ (core enzyme)

    3) sigma factor() 縦 ϴ DNA promoter ġ

         * factor ó RNA pol-DNA ü

         * ª κ RNA ռ

    4) κ (RNA ռ) core enzyme(2')

 

(6) Bacterial Promoters

    1) RNA ռ Ȯ ۿ ſ ߿

        a. Ư DNA ( promoters)

        b. factor promoter

 

    2) promoter

        a. promoter ſ

        b. ϳ ̵ θ ( ü ִ)

        c. Ư ſ Ǿ ִµ, upstream

            * upstream: 簡 ۵Ǵ (=1) , ǥ (-35 = 35 base )

            * Pribnow (-10 regions): consensus = TATAAT

            * -35 regions: consensus = TTGACA

            * factor -10 -35 ÿ

 

(7) Messenger RNA (mRNA)

    1) (prokaryotes) mRNA

        * mRNA ܹ

        * polycistronic mRNA: ȿҵ Բ ־ mRNA

        * ̷ mRNA Ǹ (ܹ ռ), ܹ ռ

        * polycistronic mRNA ,

 

    2) Operon: ÿ Ǵ

        * 밳 polycistronic mRNA rRNA ϳ operator

 

(8) Transfer RNA (tRNA)

    1) mRNA ܹ (translation)ϴ

    2) codon ű⿡ ´ amino acid ִ ߰ (adaptor molecule)

    3) aminoacyl-tRNA synthetase: tRNA Ư ƹ̳

    4) tRNA

        a. bacteria: 60

        b. (mammalian cells): 100-110

 

    5) tRNA : 䳢Ǯ ǥ

        * ª (73-93 nucleotides) ܻ罽(single strand) RNA ( intrastrand pairing)

        * Ư 2 (conserved sequence)

        * RNA ʹ ٸ, ȭ purines pyrimidines ߰ߵ

        * ̷ tRNA ʼ

    7) tRNA

        * TC loop, anticodon loop, D loop acceptor end

        * anticodon loop ( ) mRNA

        * accepter end (3'-end of tRNA): ׻ CCA a.a. ester

    img17.gif

 

2. ټ

(1) RNA Polymerases in Eukarya

    1) ٿ RNA polymerase 3: subunits

        a. RNA pol I: κ rRNA ռ

        b. RNA pol II: mRNA ռ (bacterial RNA pol )

        c. RNA pol III: tRNA rRNA ռ

    2) ̷ ϴ RNA pol Ư promoters ϱ

        a. bacteria ܹ ڳ tRNA ڰ promoter

        b. bacteria κ ڰ ܹ

             κ ڸ RNA pol II

 

    4) RNA pol promoter Ư ʿ

        * ׷ ܹ (RNA pol II )

 

(2) RNA Processing and Ribozymes

    1) (transcription) mRNA ٷ mature mRNA

    2) 쿡 intron

        a. Ŀ RNA precursor RNA (= pre-mRNA)

        b. intronκ ߶ mature mRNA Ȱ ܹ ռ

        c. intron ܹ κ(exon) ߰ ǹ

        d. intron

 

    3) splicing: ܹ ռ ʿ intron ߶

    4) self-splicing

        a. κ ribozyme self-splicing intron

        b. : ribozyme ˸ Ȱ RNA Ī

 

    5) 5'-capping

    6) 3'-tailing: polyA tail

 

V. (translation): ܹ ռ

1. (ribosome: ܹ ռ ⱸ)

(1) ribosomes

    1) 2 subunits: 50S (Svedberg unit) + 30S 70S ribosomes

    2) subunit ribonucleoprotein (= ribosomal RNAs + ribosomal proteins)

    3) 50S subunit = 5S rRNA + 23S rRNA + 34 proteins (ڷ; 1,600,000)

    4) 30S subunit = 16S rRNA + 21 proteins (ڷ; 900,000)

 

(2) ribosomes ٺ ũ

    1) 2 subunits: 60S (Svedberg unit) + 40S 80S ribosomes

    2) subunit ribonucleoprotein (= ribosomal RNAs + ribosomal proteins)

    3) 60S subunit = 28S rRNA + 5.8S rRNA + 5S rRNA + 49 proteins (ڷ; 2,800,000)

    4) 40S subunit = 18S rRNA + 33 proteins (ڷ; 1,400,000)

img18.gif

 

2. Shine-Dalgarno sequences

(1) mRNA ϴ Ư ⼭ (AUG codon տ )

(2) ܹ ռ , ribosome ϴ 16S rRNA binding ⼭

(3) Ϲ ⼭ AGGAGG, (E. coli 쿡 AGGAGGU)

(4) anti-Shine-Dalgarno sequence

    1) 16S rRNA 3 end ϴ ⼭

    2) mRNA Shine-Dalgarno sequence ȣ ⼭

    img19.gif

 

3. ܹ ռ

(1) ܹ ռ :

http://www.biostudio.com/demo_freeman_protein_synthesis.htm

http://www.johnkyrk.com/DNAtranslation.html

    img20.gif

 

 

(2) amino acid activation

    img21.gif

 

(3) ܹ ռ (Initiation of protein synthesis)

img22.gif

    1) (free) 30S ribosome subunit ׻ ۿ

    2) ü (initiation complex)

        = 30S subunit + mRNA + formylmethionine (fMet) tRNA + initiation factors

        - guanosine triphosphate (GTP) ʿ

    3) ü 50S subunit Ȱ 70S ribosome (ռ и)

    4) Shine-Dalgarno sequence

        a. mRNA 5'-end ϴ Ư : 3-9 nucleotides

        b. 16S rRNA 3'-end ribosome-mRNA ü ʼ

        c. polycistronic mRNA S-D initiation

 

    5) : ribosome 밳 mRNA 5'-end cap

        a. mRNA ó initiation codon ã

        b. polycistronic mRNA (translation)

 

    6) codon (start codon) = AUG

        a. κ start codon fMet-tRNA ش

        b. N-terminal end formyl ߿

        c. protein ù a.a. ׻ Met

        d. Met 밳 ߿ ŵ ù a.a. Met ƴ

 

4. ܹ (Elongation of protein synthesis)

    img23.gif

(1) mRNA ַ 30S subunit յǾ

(2) ⿡ a.a. Ű ִ tRNA 50S subunit A-site, P-site ȣ ۿ

    1) A-site (accepter site): ο AA-tRNA ó ϴ

    2) P-site (peptide site): ڶ󳪴 polypeptide tRNA پ ִ

 

(3) ο ܹ (peptide bond) , ڶ peptide P-site ̵

    1) non-ribosomal 뼺(soluble) elongation factors GTP ʿ

    2) A-site ٽ ο AA-tRNA

(4) translocation

    1) elongation factors GTP

    2) mRNA 3 nucleotides ŭ ( codon A-site )

    3) Ȯ 3 nucleotides ̴ ſ ߿

    4) a.a. ϰ tRNA E-site ̵ Ż recycle

 

(5) polysomes

    1) ϳ mRNA ribosomes ÿ ϴ

    2) ribosome ӵ (mRNA ȿ )

    3) ribosome 翡 polypeptide ̰ ٸ

        img24.gif

 

5. ܹ ռ (Termination of protein synthesis)

    img25.gif

 

(1) stop codon (130, ׸ 11.9)

    1) stop codon: Ǵ AA-tRNA

    2) nonsense codon̶

 

(2) ϴ tRNA Ƿ ̻ ܹ ϰ

(3) release factors ȣ о ռ polypeptide tRNA

(4) polypeptide ribosomes subunits иǾ

(5) recycle initiation complex ִ free subunit

 

6. rRNA (Role of ribosomal RNA in protein synthesis)

(1) 16S rRNA: (translation) ݿ

    1) (initiation) Shine-Dalgarno

    2) (elongation) ϴ

    3) (termination) : mRNA release factors ȣ ۿ

 

(2) 23S rRNA: translocation ϴ

    - elongation factors 23S rRNA ȣ ۿ

 

(3)

    1) subunits Ż

    2) tRNA ġ (A-site P-site Ȯ ϴ )

        a. codon:anticodon ֿ ȣ ۿ

        b. anticodon stem/loop 16S rRNA ȣ ۿ,

        c. accepter end 23S rRNA ȣ ۿ

    3) peptide ˸ : peptide ϴ 23S rRNA (ribozyme Ȱ)

 

7. ܹ 3 (Protein folding)

(1) ռǸ鼭 ڹ Ȱ ִ 3 ٰ Ǿ

(2) ܹ molecular chaperones ܹ ʿ

    1) Ȯ 3

    2) ü

 

(3) molecular chaperones

    1) protein folding , ü ܹ 3 Ե

    2) chaperonin

    3) ҿϰ (folding) ܹ ⼭ ATP ҸϿ ϰ

    4) ռ ܹӸ ƴ϶, denature ܹ refolding

 

(4) production of active insulin

        img26.gif

    1) preproinsulin (Leader, B chain, C chain, and A chain)

    2) preinsulin consists of BCA without L.

    3) spontaneous folding

    4) A and B chains linked by sulphide bonds.

    5) Leader and C chain are cut off.

    6) Insulin molecules remains.