N.A. -- Central Dogma

• Nucleus — Replication, Transcription, Reverse transcription

• Cytoplasm (Ribosome) — Translation (protein synthesis)

Where does Replication, Transcription, Translation, and Reverse Transcription occur?

Reverse Transcriptase (RNA directed DNA polymerase)

This enzyme is used by retroviruses for reverse transcription (mRNA to DNA)

1. DNA Replication

2. Transcription

3. Translation

4. Reverse Transcription

It is the process where:

1. DNA is copied itself

2. DNA → mRNA

3. mRNA → Protein (Amino acid chain)

4. mRNA → DNA

• hnRNA, snRNA, mRNA — RNA in Transcription

• mRNA, rRNA, tRNA — RNA in Translation

What RNAs are involved in Transcription? Translation?

• Transcription — mRNA

• Translation — Protein (Amino Acid chain)

What is the end product of Transcription? Translation?

DNA replication

It is the biochemical process by which DNA molecules produce exact duplicates of themselves.

1. Helicase unwind the parent double helix

2. Single-Stand binding protein stabilizes the separated DNA (prevent reattachment)

3. DNA polymerase synthesizes new DNA strand in leading strand in a 5’→3’ direction

4. In the lagging strand, RNA primer is extended by DNA polymerase to form an Okazaki fragment

5. RNA is replaced by DNA, the gaps are glued by Ligase

Explain the process of DNA replication

1. REPLICATION FORK- The point at which the DNA double helix is unwinding, which is constantly changing (moving)

2. LEADING STRAND- The strand that grows continuously

3. LAGGING STRAND- The strand that is synthesized in small segments

4. OKAZAKI FRAGMENTS- short segments, (after their discoverer, Reiji Okazaki), as the DNA unwinds

5. NICKS- The breaks or gaps in the daughter strand

IDENTIFY:

1. The point at which the DNA double helix is unwinding, which is constantly changing (moving)

2. The strand that grows continuously

3. The strand that is synthesized in small segments

4. short segments, (after their discoverer, Reiji Okazaki), as the DNA unwinds

5. The breaks or gaps in the daughter strand

Reiji Okazaki

He discovered the Okazaki Fragments

5’→3’ direction

In what direction is the leading strand synthesized?

DNA polymerase III recognized the RNA primer and begins to synthesize DNA

What happens during the elongation?

1. RNA primer is elongated by DNA polymerase III until another RNA is encountered

2. RNA primer is cut out by DNA polymerase I, one ribonucleotide at a time

3. DNA polymerase I fills the Gap

4. The remaining NICK is sealed by DNA-Ligase

What happens during RNA primer removal and filling of gaps by DNA polymerase I

DNA Helicase

It influences the unwinding of DNA double helix, and the hydrogen bonds between complementary bases are broken

DNA polymerase III

• Verifies that the base pairing is correct and then catalyzes the formation of a new phosphodiester linkage between the nucleotide and the growing strand. R

• Recognizes the RNA primer & begins to extend it with DNA.

Primase

Synthesizes a short stretches of RNA (primers) that are completely complementary and antiparallel to the DNA template

RNA Primer

is RNA that lay down short strand of ribonucleotide and initiates DNA synthesis.

1. DNA Primer — Used for PCR (polymerase chain reaction) amplification

2. RNA Primer — Main ingredient of replication

DNA Primer or RNA Primer

1. Used for PCR (polymerase chain reaction) amplification

2. Main ingredient of replication

DNA Polymerase I

It removes RNA primers from fragments and replace it the required nucleotides.

DNA Ligase

• Connect two strands of DNA together by forming a bond between the phosphate group and deoxyribose group of each strands.

• It is used in cells to join together the Okazaki fragments which are formed on the lagging strand

1. Phosphate group —— DNA Polymerase III

2. Deoxyribose group —— DNA Polymerase I

1. Phosphate group

2. Deoxyribose group

Which is synthesized by DNA POLYMERASE III and DNA POLYMERASE I

1. Sequence of Deoxyribonucleotides in its deoxyribonucleic acid (DNA)

2. Ribonucleic Acid (RNA)

1. In what sequence is the genetic master plan of an organism contained?

2. It is considered as the “working copies” of the DNA, and it is through this that the master plan is expressed through transcription and then translated.

RNA

DNA or RNA

• Contains equal amount of specific bases and molecules (small), ranging from 75 nucleotide to a few thousand nucleotides

Central Dogma

It is a theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein.

Heterogenous nuclear RNA (hnRNA)

TYPE OF RNA:

• Formed directly by DNA transcription

• Post-transcription processing converts “RNA” into mRNA.

Small nuclear RNA (snRNA)

TYPE OF RNA:

• Facilitates the conversion of heterogeneous nuclear RNA to messenger RNA.

• It contains from 100 to 200 nucleotides.

Messenger RNA (mRNA)

TYPE OF RNA:

• Carries instructions for protein synthesis (genetic information) to the sites for protein synthesis.

Ribosomal RNA (rRNA)

TYPE OF RNA:

• Combines with specific proteins to form ribosomes, the physical sites for protein synthesis.

• Most abundant type of RNA in a cell (75% to 80% by mass)

Transfer RNA (tRNA)

TYPE OF RNA:

• Delivers amino acids to the sites for protein synthesis.

• Are the smallest of the RNAs, possessing only 75–90 nucleotide units.

Transfer RNA (tRNA)

It is the smallest RNA

Ribosomal RNA (rRNA)

It is the most abundant type of RNA

Transcription

It is the process by which DNA directs the synthesis of hnRNA/mRNA molecules that carry the coded information needed for protein synthesis.

1. hnRNA molecule is produced

2. It is then “edited” to yield the desired mRNA

What is the “two-step” process of mRNA production (transcription)?

Gene

It is segment of a DNA strand that contains the base sequence for the production of a specific hnRNA/mRNA molecule.

Genome

It is all of the genetic material (the total DNA) contained in the chromosomes of an organism.

1. RNA polymerase temporarily unwinds the DNA double helix

2. Free ribonucleotides align along the exposed DNA bases (template strand) forming new base pairs — _{^{Now: U + A, not T; Ribose, not Deoxyribose}}

3. RNA polymerase links ribonucleotides to the growing hnRNA molecule

4. The process continues until RNA polymerase encounters stop signal —END OF TRANSCRIPTION

5. formed hnRNA & RNA polymerase is released

6. DNA rewinds to reforms double helix

Explain the process of transcription from a gene

hnRNA

What is produced after gene transcription? It is the precursor for mRNA.

Template Strand

It is the strand of DNA that is used for hnRNA/mRNA synthesis

Information Strands

• The other DNA strand, although not involved in RNA synthesis, gives the base sequence present in the hnRNA strand being synthesized (with the exception of U replacing T)

1. Template Strand — used for hnRNA/mRNA synthesis

2. Information Strand — gives the base sequence present in hnRNA being synthesized

TRANSCRIPTION:

What are the two strands that are formed from the separated DNA double helix by RNA polymerase?

POST TRANSCRIPTION: Conversion of hnRNA into mRNA

• Introns are spliced, and remaining exons are joined together

• snRNA (shortened RNA) is formed —— this caused by splicing of introns, making the segments shorter

• snRNA combines with protein particles snRNPs (snurps)

• A large complex is formed, called spliceosomes

• mRNA is produced —— serves for protein synthesis _{^{(will form TRANSCRIPTOME)}}

Explain what happens during Post-Transcription

EXON (ExpressiON of genetic informatiON)

This is a gene segment that conveys (codes for) genetic information

INTRON (INTeRruptiON of genetic information)- i

This is a gene segment that does NOT conveys (codes for) genetic information

• SPLICING — removal of introns

• ALTERNATIVE SPLICING — exons from the same gene are joined in different combinations, leading to different, but related, mRNA transcripts

What are the 2 types of splicing?

SPLICING

The process of removing introns from an hnRNA molecule and joining the remaining exons together to form an mRNA molecule.

small nuclear ribonucleoprotein particle (snRNPs or Snurps)

It is a complex formed from an snRNA molecule and several proteins.

SPLICEOSOMES

It is a large assembly of snRNA molecules and proteins involved in the conversion of hnRNA molecules to mRNA molecules

Alternative Splicing

It is a process by which several different proteins that are variations of a basic structural motif can be produced from a single gene

TRANSCRIPTOME

It is all of the mRNA molecules that can be generated from the genetic material in a genome.

genetic code

It is the assignment of the 64 mRNA codons to specific amino acids (or stop signals)

codon

a three nucleotide sequence in an mRNA molecule that codes for a specific amino acid

• 64 in total

  • 61 codes for A, C, G, U bases combinations

  • other 3 are termination/stop codons

How many codons are there?

tRNA

function as intermediaries that deliver amino acids to the mRNA

• Cloverleaf _{^{(3’ end open part)}} — where amino acid attaches through ester bond

• Loop _{^{(opposite to cloverleaf)}} — site for a sequence of three bases [anticodon]

What are the two features of tRNA structure and their importance?

aminoacyl tRNA synthetase

This is the enzyme that recognizes different tRNA molecules, also recognize the one kind of amino acid that “belongs” with the particular tRNA and facilitates its bonding to the tRNA

Anticodon

These are three nucleotide sequence on a tRNA molecule that is complementary to a codon on an mRNA molecule

• Codon — in the mRNA; code for specific amino acid

• Anticodon — in the tRNA; complementary to codon

What is the difference between codon and anticodon?

Translation

It is process by which mRNA codons are decode and a particular protein molecule is synthesized

• mRNA

• tRNA

• amino acids

• ribosomes

• different enzymes

What are needed for the translation phase?