DNA and Protein Synthesis: Basic Definitions and Biochemistry

1. Chapter IV Genetics DNA and Protein Synthesis Yalun Arifin

2. Basic definitions DNA: The molecule that encodes genetic information. DNA is a double-stranded molecule held together by weak bonds between base pairs of nucleotides. The four nucleotides in DNA contain the bases: adenine (A), guanine (G), cytosine (C), and thymine(T). In nature, base pairs form only between A and T and between G and C; thus the base sequence of each single strand can be deduced from that of its partner. RNA: A chemical found in the nucleus and cytoplasm of cells; it plays an important role in protein synthesis and other chemical activities of the cell. The structure of RNA is similar to that of DNA. There are several classes of RNA molecules, including messenger RNA, transfer RNA, ribosomal RNA, and other small RNAs, each serving a different purpose.

3. DNA and RNA

4. Biochemistry of DNA • Double Helix Two DNA strands are antiparallel. Held together by base pairs: • Hydrogen bonds between the nitrogen-containing bases • A = T, and G = C • DNA Structure Reveals Key to Replication Each of the two original strands serves as a template for construction of a new matching strand.

5. DNA and RNA • In RNA, thymine is replaced by uracil Nucleotides joined by covalent bonds between sugar and phosphate to make a chain Bases are laid out in specific and highly varied order, carrying code for protein synthesis

6. S S S S P P P P S S S S P P P P S S S S P P P P S S S S P P P P S S S S P P P P DNA G C Nucleotide A T P C S G O G C O C G S A T T A P T A P G C S O T A T A O S A T P A C G P A T S O A T O A T S P T A C G

7. DNA: Central dogma

8. Central dogma in cells

9. In the absence of a nuclear membrane, DNATranscription and RNATranslation are not physically separated.

10. DNA undergoes replication and transcription in the nucleus; proteins are made in the cytoplasm.RNA must therefore travel across the nuclear membrane before it is translated: transcription and translation are physically separated. The primary transcript, heterogeneous RNA (hnRNA), undergoes extensive post-transcriptional processing to make mRNA.

11. How do DNA keep the information? • The genetic information in DNA in kept in the sequences of bases in the nucleotides (A ,T, G, C). This code consists of 3 nucletiodes (e.g. ATG, AAA, TAA) that encodes a certain amino acid. Thus, 64 codes are possible to give the infinite number of genetic sequences. • DNA Replication New helices are composed of half old (original) and half new nucleotides. Process catalyzed by enzymes: • DNA polymerase catalyzes addition of matching bases, and proofreads. • DNA ligase permanently attaches short sections to make one chromosome.

12. Protein Synthesis How Proteins Are Made: Genetic Transcription, Translation, and Regulation • Proteins: Polypeptides • Strands of amino acids (20 different) joined by peptide bonds. • Every protein has a unique amino acid sequence.

13. H O H H3N C C O O– H3N C C CH O– CH2 H CH3 glycine (gly) isoleucine cys ile asn cys glu ala val ser tyr leu O C H3N O– gly cys ser val gln cys leu gln glu asn tyr

15. Protein Synthesis: Two Stages • Stage 1—DNA contains information for protein but resides in the nucleus; proteins are made in the cytoplasm. Solution: Copy DNA into small strands of RNA (transcription). • Stage 2—Amino acids added in correct order by using the information on the RNA (translation).

16. OVERVIEW OF TRANSCRIPTION AND TRANSLATION DNA TRANSCRIPTION (in nucleus) mRNA ribosomes tRNA mRNA TRANSLATION (in cytoplasm) protein

17. RNA nucleotide DNA nucleotide O O H3C H H C H C O– O– uracil (base) thymine (base) N N H N H P O CH2 N HO O P O CH2 HO O O O O O ribose (sugar) deoxyribose (sugar) Phosphate group Phosphate group H H H H OH OH H OH RNA strand DNA strand C G C sugar- phosphate handrail sugar-phosphate handrail S U S A T P P S S P P S Bases: cytosine (C) guanine (G) adenine (A) uracil (U) C S G Bases: cytosine (C) guanine (G) adenine (A) thymine (T) C P P S G S C G S P P P S A S A T S P U T A S P S P A T U S C G C

18. Basic definitions Intron: The DNA base sequences interrupting the protein- coding sequences of a gene; these sequences are transcribed into RNAbut are cut out of the message before it is translated into protein. Exons: the sequences in the DNA molecule that code for the amino acid sequences of corresponding proteins. Messenger RNA: the template for protein synthesis; the form of RNA that carries information from DNA in the nucleus to the ribosome sites of protein synthesis in the cell Transfer RNA: short-chain RNA molecules present in the cell (in at least 20 varieties, each variety capable of combining with a specific amino acid) that attach the correct amino acid to the protein chain that is being synthesized at the ribosome of the cell (according to directions coded in the mRNA) Ribosomal RNA: RNA found in ribosome

19. Three Types of RNA Transcribed • mRNA (messenger RNA) carries instructions for sequence of amino acids in a protein. • rRNA (ribosomal RNA) important component of ribosomes. • tRNA (transfer RNA) involved in matching correct amino acid to specific instructions in mRNA.

20. Table 14.2 Types of RNA Type of RNA Functions in Function Messenger RNA (mRNA) Nucleus, migrates to ribosomes in cytoplasm Carries DNA sequence information to ribosomes Transfer RNA (tRNA) Cytoplasm Provides linkage between mRNA and amino acids; transfers amino acids to ribosomes Cytoplasm Ribosomal RNA (rRNA) Structural component of ribosomes

21. Transcription Uses Base Pairing • DNA used as a template to match complementary bases. • C to G and A to U (not T). • RNA polymerase catalyzes addition of new nucleotides into a single strand of RNA (called a transcript) from one strand of the double helix.

22. A C U U G G mRNA C G U U C A RNA nucleotides G G C A A G T A C C T A DNA mRNA mRNA

23. RNA Processing • mRNA is edited. • Parts to be cut out are called introns. • The remaining pieces (called exons) are joined together to make the finished product.

24. exon 1 INTRON exon 2 INTRON exon 3 enzyme enzymes cut into the introns edited mRNA transcript

25. Making Sense of “Junk” DNA • Only 1.5% of our DNA codes for proteins (1 inch out of 6 feet). • Rest is noncoding DNA—housekeeping (regulatory) sequences, tips of chromosomes, and “junk”: • Introns • Repetitive Sequences • “Selfish DNA” • Primates have 1 million Alu (280 base pairs long) repeats, 10% of DNA, congregate in gene-rich areas.

26. Genetic Code: How DNA Codes for Amino Acid Sequence • Four bases in DNA, 20 amino acids in protein, not one-to-one code. • Not two to one either—There are only 16 possible combinations of two bases of DNA (AA, AT, AC, AG, CA, etc.). • Triplet code—three nucleotides (called a codon) signifying one amino acid.

27. THE TRIPLET CODE G G C A A G T A C C T A DNA TRANSCRIPTION mRNA C G U U C A U G G A C U codon codon codon codon TRANSCRIPTION protein arg ser trp thr

28. Codon Table • 64 different possible combinations of the four nucleotides—more than enough for the 20 different amino acids. • Redundant = several different codons signify the same amino acid. • Carries instruction codons for stopping (UGA, UAA, UAG) and starting (AUG) translation. • Universal

29. Second Base U C A G UUU UCU UAU UGU U tyr phe cys UUC UCC UAC UGC C ser U UUA UCA UAA stop UGA stop A leu UUG UCG UAG stop UGG trp G CUU CCU CAU CGU U his CUC CCC CAC CGC C pro arg leu C CUA CCA CAA CGA A gln CUG CCG CAG CGG G First Base Third Base AUU ACU AAU AGU U ser asn AUC ACC AAC AGC C ile thr A AUA ACA A AAA AGA lys arg AGG AUG ACG AAG G met (start) GUU GCU GAU GGU U asp GUC GCC GAC GGC C val G ala gly GUA GCA GAA GGA A glu GUG GCG GAG GGG G

30. Translation Requires Translator • mRNA carries the instructions in the codons for each of the amino acids. • tRNA molecules (transfer RNA) are “translator” molecule. • tRNA can match the appropriate amino acid with the codon in the mRNA.

31. tyr asp phe ser leu glu gly thr mRNA ribosome

32. Structure of Transfer RNA • Part of the molecule binds an amino acid. • The other end has three nucleotides (anticodon) that form a base pair with the codon in the mRNA.

33. amino acid amino acid attached site tRNA molecule G U C mRNA attachment site anticodon C G A mRNA codon

34. Ribosomes: The Location of Protein Synthesis • Large conglomerate of enzymes and ribosomal RNA (rRNA) in two subunits. • A site—binds tRNA-carrying amino acids. • P site—binds tRNA attached to growing chain of polypeptides.

35. mRNA large subunit protein P A small subunit protein large subunit mRNA P site A site small subunit

36. Steps of Translation

37. met met UCA AUG mRNA leu start codon leu met met GAC CUG A site A site P site P site

38. met met leu leu A site A site P site P site thr met leu Polypeptide chain A site P site

39. Genetic Regulation: Lac Operon • Operon = multipart genetic system. • Bacteria (E. coli) synthesize certain enzymes only if substrate is present. • Example—lactose, called an inducer • Genes involved: • y (permease enzyme to help lactose enter the cell) • z (-galactosidase enzyme to cut lactose into galactose and glucose) • a gene • i (codes for repressor protein)

40. lac operon regulator gene promotor operator p i gene o z gene y gene a gene DNA binding site of RNA polymerase codes for repressor protein codes for b-galactoseidase, which clips lactose molecules codes for permease enzyme that transports lactose into cells

41. Lac Operon: Regulatory DNA Sequences • Upstream promoter (acts as a binding site for RNA polymerase) • Between promoter and first gene is operator. • Repressor binds operator: prevents RNA polymerase from binding to the promoter. • No transcription, so no enzymes made.

42. RNA polymerase o p i gene z gene y gene a gene DNA no transcription repressor protein blocks binding of RNA polymerase repressor protein

43. Lac Operon: Lactose Inducer Present • Cell needs to make enyzmes only when lactose is present. • Repressor binds lactose; it will not bind the operator, so transcription ensues.

44. 2 RNA polymerase binds to promoter o p i gene z gene y gene a gene DNA transcription proceeds 3 repressor mRNA transcript lactose b-galactosidase 1 lactose the (inducer) inactivates the repressor so that it cannot bind to the operator permease galactose glucose cell membrane lactose

45. Magnitude of Metabolic Operations • Human cells have between 50,000 and 100,000 genes. • But one cell usually makes only 5,000 to 20,000 specifically required proteins. • Some are made continuously, and others are inducible.