RNA

RNA

- held together by 3’-5’ phosphodiester bonds

 Single stranded

 3 classes of RNA in living cells: rRNA, mRNA, tRNA

consists of four varying bases : uracil, cytosine, adenine and guanine

rRNA, mRNA, tRNA

 3 classes of RNA in living cells:

Ribosomal RNA (rRNA)

- structural and functional components of ribosomes

- Functions is to decode / translation (process in which proteins are made)

- where protein synthesis takes place

Messenger RNA (mRNA)

- provides genetic information for proper assembly of amino acids into proteins

- Has a poly A tail- long sequence of adenine nucleotides on the 3’ end of the RNA chain

- Has a ‘cap’- consists of a molecule of 7- methylguanosine on the 5’ end

Transfer RNA (tRNA)

- 10-15%

- serves as a link (or adaptor) between the messenger RNA (mRNA) molecule and the growing chain of amino acids that make up a protein

- smallest RNA

Small nuclear RNA (snRNA)

processes initial mRNA to its mature form in eukaryotes

micro RNA (miRNA)

affects gene expression'; important in growth and development

Small interfering RNA (siRNA

affects gene expression; used by scientists to knockout a gene being studied

Human Cell

46 chromosomes; total DNA is 1-meter long

46

Human cell has _______ chromosomes

Histones

small proteins which serve to arrange the DNA into basic structural units called nucleosomes (beads on a string)

Nucleosomes

- (histones+DNA) made up of 2 molecules each of H2A, H2B, H3 and H4

H1, H2A, H2B, H3, H4

Classes of Histones

 form the structural core of the nucleosome beads

H1

 aids packing of nucleosome into more compact structures.

 not found in nucleosome core.

DNA SYNTHESIS

Substrate

Template

Primer

Enzymes

deoxynucleoside triphosphate

Substrate:

- dATP (adenosine triphosphate)

- dGTP (guanosine triphosphate

- dCTP (cytosine triphosphate)

- dTTP (thymidine triphosphate)

Template

- DNA chain that provides precise information

Primer

- initial portion of a linear molecule

- short nucleic acid sequence that provides a starting point for DNA synthesis

Oligoribonucleotide

- formed with DNA as the template

Primase

- catalyze formation of primer

1. REPLICATION

2. TRANSCRIPTION

3. TRANSLATION

4. REVERSE TRANSCRIPTION

CENTRAL DOGMA

REPLICATION

- parental DNA duplex is copied by base pairing

- made possible by DNA polymerase

TRANSCRIPTION

- information contained in DNA is copied to form complementary sequence of ribonucleotides

- RNA polymerase

TRANSLATION

- transcribed from DNA into mRNA

- in the ribosomes

REVERSE TRANSCRIPTION

- RNA can be transcribed into DNA

- enzyme reverse transcriptase; retrovirus RNA

Watson & Crick

○ DNA is a duplex of 2 strand of polydeoxyribonucleotide chain

3H

C forms ______- bonds with G

2H

T forms _____- bonds with A

Complementary

(opposite polarity)

Genome

○ encodes genetic blueprint for building the organism

○ entire set of DNA instructions found in a cell

DNA REPLICATION

● Entire genome is copied and passed on to a new cell

● Basis of heredity

is semiconservative

Prokaryotic Replication

● DNA double helix - when separated, each of 2 strand serve as a template for replication of a new complementary strand

● allows for the genetic blueprints of a cell to be passed on to daughter cells in cell division

○ without loss of genetic information

● allows for protein synthesis ○ how genes are expressed ○ Begins with transcribing the specific gene – section of DNA

SEMI-CONSERVATIVE REPLICATION

○ Each strand of the 2 double helices formed would have 1 old and 1 new strand

CONSERVATIVE REPLICATION

○ Replication produces one helix made entirely of old DNA (parent strand) + one helix made entirely of new DNA (daughter strand)

I. INITIATION

II. ELONGATION

III. ELONGATION

IV. TERMINATION

DNA REPLICATION

DnaA protein

INITIATION

 20-50 monomers

 bind to specific nucleotide sequence at Ori C

 initiates DNA replication by forming a specific DnaA-oriC complex

DNA Helicases (DnaB protein)

INITIATION

separates the DNA strands

 helix stabilizing proteins

 binds cooperatively to single strands of DNA stabilizing the single-stranded state

 protect the DNA from nucleases

 enzyme that bind to single-stranded DNA near the replication fork

 forcing strands apart

 unwinding the double helix

10 deoxyribonucleotides

For every ____________- added during replication → parental double-helix makes one complete turn around its axis

DNA Topoisomerase

- introduces ‘swivel’ points along the double helix → avoid need for entire strand to rotate

reduces torsional strain and positive supercoils

Type I DNA Topoisomerase

ELONGATION

forms a ‘nick’ through which the complementary strand passes

Type II DNA Topoisomerase (I)

ELONGATION

 relieves both positive and negative supercoils

 make transition breaks in both strands

 DNA Gyrase

- subclass of Type II topoisomerases that relieves positive supertwisting in replication fork

Primase (DnaG protein)

ELONGATION

 RNA polymerase → synthesizes short stretches of RNA

 uses 5’ – ribonucleoside triphosphates as building blocks

Primer

ELONGATION

 short, double-stranded region with free -OH group on the 3’ end of the shorter strand

OH Group

ELONGATION

first acceptor of a nucleotide by action of DNA polymerase

DNA Polymerase

ELONGATION

Reads parental nucleotide sequence in the 3’ → 5’ direction; synthesizes new DNA strands in the 5’ → 3’ direction

Okazaki Fragments

ELONGATION

 short DNA segments found during DNA replication in the lagging strand (3’ → 5’ direction)

Leading Strand

 copied in the direction of the advancing replication fork

Lagging Strand

 copied in the direction of the replication fork

5’ - 3’ polymerase activity

activity that synthesizes DNA

3’ - 5’ exonuclease activity

will freeze newly synthesized DNA chain

5’ - 3’ exonuclease activity

removes the RNA primer

DNA polymerase I

exercises/removes the RNA primers and replaces them with DNA

DNA Ligase (III)

III. ELONGATION

 joins the DNA chain synthesized by DNA polymerase III

 seals the nick after DNA pol I fills in the gap

Type II DNA Topoisomerase

III. ELONGATION

 relieves both positive and negative supercoils

 make transition breaks in both strands

TERMINATION In prokaryotes

 replication ends when the forks meet

TERMINATION In Eukaryotes

 replication ends at telomere regions

Telomere

: regions at the end of chromosomes with repetitive nucleotides such as TTAGGG sequences

DNA Ligase

 joins the DNA chain synthesized by DNA polymerase III and the chain made by the DNA polymerase I after removal of RNA primer.

 seals the nick after DNA pol I fills in the gap

Prokaryotic DNA replication

chromosomes are circular and are usually smaller in number

DNA replicates in the cytoplasm

LARGE okazaki fragments

DNA gyrase is required

Eukaryotic DNA replication

chromosomes are linear and usually larger in number

replicates in the nucleus

small okazaki fragments

does not require DNA gyrase

DNA Pol III

(prokaryotic)

strand elongation and proofreading

DNA Pol I

(prokaryotic)

excises the RNA primer and fills in the gap

DNA Pol alpha (α)

synthesize the RNA primer

DNA Pol (delta) δ

elongates the leading strand

DNA Pol (epsilon) ε

elongates the lagging strand

DNA Pol (beta) β

cuts off primers DNA pol I in bacteria

carries out repairs

DNA Pol (gamma) γ

carries out replication within the mitochondrion