DNA_RNA_Protein Synthesis_Mini lecture Thn 1.pptx

RNA DNA SINTESIS

1. DNA, RNA & Protein Synthesis Yunia Sribudiani Universitas Padjadjaran

2. Structure of Human Genome

3. Genome

4. Human Genome Project (HGP): 1990 -2003 VS Francis Collins J. Craig Venter Non-private (NIH & DOE) Private (Celera Genomics, 1998) Method: Shotgun sequencing (2000 – 10.000 bp ) Clone-based sequencing (150.000 – 200.000 bps) 20.000 BAC Clones James Watson

5. Human Genome 22 pairs autosome + 2 pairs of sex chromosomes (XX or XY) = 46 chromosomes Prediction: 3 billion base pairs (haploid)  1 pg 30.000 – 300.000 genes ~ 2000 books containing 1.5 millions letters each 10 letters/minute, 8 hours/day, 50 years to type the entire human genome DNA in one cell ~ 6ft long DNA whole body ~ Earth --> Moon 6000X

6. http://www.lhsc.on.ca/_images/Genetics/centraldogma.jpg Transfer of genetic information goes on one direction Central Dogma in Genetic Transcription: RNA synthesis from DNA (DNA  RNA) Translation : Protein synthesis from RNA (RNA  Protein)

7. Deoxyribonucleic Acid (DNA) DNA is: Molecule of Life Consist of two strands twisted around of each other (double helix)  looks like twisted staircase Build in by combination of Sugars ( Deoxyribose ), Phosphates and Nitrogen Bases Nitrogen Bases: Guanine (G), Cytosine (C ), Thymine (T) and Adenine (A) A + T + G + C = ALL LIFE

8. Deoxyribonucleic Acid (DNA)

9. 46,XY /XX Genome An organism’s complete set of DNA Chromosome A thread-like structure containing DNA  and a  protein of living organism,   that  form in the nucleus when the cell begins to divide and  that carry  the genes which determine  an  individual's hereditary  traits (http:// www.thefreedictionary.com/chromosome) Gene a segment of DNA that provides the  coded instructions   for RNA synthesis   ,  which, when translated into protein,  leads  to  the expression  of hereditary character ( http:// dictionary.reference.com/browse/gene ) Locus A specific location of a gene or  DNA  sequence on a chromosome . Genome - Chromosome - Gene Human genome: 3 billion base pairs (haploid)  1 pg 20.000 – 40.000 genes

10. All somatic cells in an organism contains the same set of DNA/Chromosome However not the same set of genes are expressed in all those cells/organs Set of genes express in the heart will be different with those express in the muscle or in the brain, although part of those genes could be equally expressed in all three organs (overlap) Genes turned ON determine Cells fate (differentiation) and function Genome - Chromosome - Gene

11. DNA Replication

12. http://cmapspublic2.ihmc.us/rid%3D1L3QS6XDK-2Q283Z-1PSM/DNA%2520Replicaion.jpg DNA Replication

13. Replication Fork DNA Replication

14. Eukaryotic chromosome replication Because of their large size, eukaryotic chromosome have multiple origins Replication begins at specific sites where the two parental strands separate and form replication bubbles. The bubbles expand laterally, as DNA replication proceeds in both directions. Eventually, the replication bubbles fuse, and synthesis of the daughter strands is complete. 1 2 3 Origin of replication Bubble Parental (template) strand Daughter (new) strand Replication fork Two daughter DNA molecules In eukaryotes, DNA replication begins at many sites along the giant DNA molecule of each chromosome. In this micrograph, three replication bubbles are visible along the DNA of a cultured Chinese hamster cell (TEM). (b) (a) 0.25 µm

15. DNA Replication DNA replication occurs only when cells are dividing

16. Crossing Over during Meiosis

17. Crossing Over during Meiosis

18. Transcription

19. RNA Vs DNA: Uracil (U) replace Thymine (T) Single stranded Has different sugar (Ribose ) There ~4 different RNA types : mRNA (messenger) tRNA (transfer) rRNA (ribosome) siRNA Transcription

20. Transcription There are 3 steps in Transcription process : Initiation Transcription factors bind to the promoter and help RNA polymerase recognized and bind to DNA Elongation RNA polymerase opens DNA strands and synthesizes mRNA along template strand Reads 3’-5’ --- makes mRNA 5’-3’ mRNA grows at a rate of 30-60 nucleotides/second Termination Specific nucleotide sequences signal “stop” and cause RNA polymerase to release DNA; this “stop” sequence called terminator (also known as poly-A signal sequence) , usually AAUAA on the mRNA in eukaryotes (do not confuse this with a stop codon)

21. RNA Processing Control http://www.uic.edu/classes/bios/bios100/lecturesf04am/lect15.htm

22. RNA Processing Control These two different protein isoforms could be expressed in different cells or in the same cells at different time point DNA of Eukaryotic cells not as prokaryotic cells have exon /coding region (part that will be translated into protein/functional RNA) and intron /non-coding region. The Introns part will be spliced out of pre-mRNA and produce mRNA, although sometimes (few) exons will also be spliced out (alternative splicing) This alternative splicing process will produce different RNA isoforms  produce different protein isoforms Exon Intron 1 ) Splicing

23. 2 ) Capping at 5’- end Synthesis of the “Cap” is a modified guanine (G) which is attached to the 5’ of the pre-mRNA. This process occurs only in the nucleus  hence mRNA from mitochondria is un-cap The functions of the 5’-Cap : Regulation of nuclear export Inhibit the mRNA degradation Promotion of translation (Binds to Ribosomes) RNA Processing Control

24. RNA Processing Control 3)

25. mRNA & tRNA Structure mRNA t RNA

26. RNA Structure

27. Translation

28. Translation Is the actual synthesis of a polypeptide, which occurs under the direction of mRNA Occurs on ribosomes Codons blocks of 3 nucleotides decoded into the sequence of amino acids Codons must be read in the correct reading frame For the specified polypeptide to be produced Translation

29. The code For ALL life! strongest support for a common origin for all life Code is redundant In Total we have 64 codons ( 3 are stop codon) several codons for each amino acid Why is this a good thing? Start codon AUG methionine Stop codons UGA, UAA, UAG

30. Most cells have 40 different tRNA molecules; this is less than the 61 amino-acid-coding codons and more than the 20 different aminoacids . Some tRNAs can pair with more than one codon as long as first two positions are correct  called ‘ wobble hypothesis’ (Francis Crick,1966) *I is used for hypoxanthine because hypoxanthine is the nucleobase of Inosine transfer RNA ( tRNA )

31. rRNA Structure

32. The role of ribosomal RNA ( rRNA ) Structure of a Ribosome: Consist of a small and a large subunit Made in nucleolus 60% rRNA , 40% protein Has 3 binding sites for tRNA A site: Amino acid site P site: Peptide site E site: Exit site Has 1 binding site for mRNA Large subunit Small subunit P E A

33. Building a polypeptide Initiation brings together mRNA, ribosome subunits, proteins (initiation factors) & initiator tRNA Elongation Termination

34. Elongation: growing a polypeptide catalyzed by peptidyl transferase peptydil tRNA

35. Termination: release polypeptide Release factor “release protein” bonds to A site bonds water molecule to polypeptide chain Now what happens to the polypeptide?

36. Function of a ribosome tRNA binding sites facilitate base pairing between tRNA anticodons and mRNA codons rRNA joins amino acid as a polypeptide Multiple ribosomes can translate same mRNA simultaneously; complex called a polyribosome

37. The signal mechanism for targeting proteins to the ER Figure 17.21 Ribosome mRNA Signal peptide Signal- recognition particle (SRP) SRP receptor protein Translocation complex CYTOSOL Signal peptide removed ER membrane Protein ERLUMEN Polypeptide synthesis begins on a free ribosome in the cytosol. 1 An SRP binds to the signal peptide, halting synthesis momentarily. 2 The SRP binds to a receptor protein in the ER membrane. This receptor is part of a protein complex (a translocation complex) that has a membrane pore and a signal-cleaving enzyme. 3 The SRP leaves, and the polypeptide resumes growing, meanwhile translocating across the membrane. (The signal peptide stays attached to the membrane.) 4 The signal- cleaving enzyme cuts off the signal peptide. 5 The rest of the completed polypeptide leaves the ribosome and folds into its final conformation. 6

38. Translation in Prokaryotes Transcription & translation are simultaneous in bacteria DNA is in cytoplasm no mRNA editing needed

39. Chromosomal abnormalities & Types of Mutation

40. Chromosomal abnormalities & Types of Mutation

41. Chromosomal abnormalities & Types of Mutation

42. Chromosomal abnormalities & Types of Mutation

43. Chromosomal abnormalities & Types of Mutation

44. Epigenetics

45. Histone Modification https://www.broadinstitute.org/news/1504 Chromatin in eukaryote cell is not served only for structural role BUT Chromatin is also important for gene expression regulation HOW ???? By open up OR close the chromatin structure

46. Histone Modification

47. Histone Acetylation  by Histone Acetylfransferases (HATs)  loosening chromatin structure ( Euchromatin ) Transcription factors/trans-acting elements have access to the DNA and initiate transcription process  Transcriptional activation Histone Modification

48. Histone Modification Deacetylation  by Histone deacetylases (HDACs)  tighten up chromatin structure (Heterochromatin)  Chromatin can inhibit access of transcription factor to the DNA Transcriptional deactivation

49. DNA Methylation DNA Methylation  occurs in the CpG island (CG-rich sequence) in the promoter  transcription is off

50. DEFECT in EPIGENETICS REGULATION

51. GENETIC IMPRINTING DISEASES Prader-Willi Syndrome : Maternal imprinting of Chr.15 X X X X X X   Symptoms: weak muscles, poor feeding, and slow development. In childhood the person becomes constantly hungry which often leads to obesity and type 2 diabetes.

52. GENETIC IMPRINTING DISEASES Angelman Syndrome : Paternal imprinting of Chr.15 Mother Father Symptoms: Developmental delays, including no crawling or babbling at 6 to 12 months. Intellectual disability. No speech or minimal speech. Difficulty walking, moving or balancing well ( ataxia )  Frequent  smiling and laughter. Happy, excitable personality

53. GENETIC IMPRINTING DISEASES DNA  hypomethylation  can activate oncogenes and initiate  chromosome  instability, whereas DNA  hypermethylation  initiates silencing of tumor suppressor genes. CANCERS