Overview of Molecular Biology

1. Overview of Molecular Biology • Each species has a uniquely fundamental set of genetic information, its genome. • The genome is composed of one or more DNA (deoxyribonucleic acid) molecules (46 in human beings), each organized as a chromosome. • Prokaryotic genomes are mostly single circular chromosomes. • Eukaryotic genomes consist of usually two sets of linear chromosomes confined to the nucleus. • A gene is a segment of DNA that is transcribed into a RNA molecule used to make proteins. • Introns interrupt many eukaryotic genes. • Viral genomes consist of either DNA or RNA.

3. The Cell: Storehouse of Hereditary/Genetic Information

4. The Cell • Origin of life on Earth about 3.5 billion years ago • Organisms are made up of cells, which can be decomposed into organelles, then into molecules. • The Cell Theory: • all living things are composed of one or more cells • cells are basic units of structure and function in an organism • cells come only from the reproduction of existing cells • Two basic classes of cells • prokaryotic (pro = before, karyon = nucleus) cell: simpler, represented by bacteria and blue algae • eukaryotic (eu = true, karyon = nucleus) cell: structurally more complex, all other organism types, such as protists, fungi, plants and animals • Both prokaryotic and eukaryotic cells share a similar molecular chemistry. Most important molecules are proteins and nucleic acids.

5. Protein Structure • Proteins are polypeptides of 70-3,000 amino acids. • This structure is (mostly) determined by the sequence of amino acids that make up the protein. • There are 20 amino acids commonly found in proteins

8. Amino Acid Families

9. DNA and RNA are polymers of nucleotides • DNA is a nucleic acid, made of long chains of nucleotides Phosphate group Nitrogenous base Nitrogenous base(A, G, C, or T) Sugar Phosphategroup Nucleotide Thymine (T) Sugar(deoxyribose) DNA nucleotide Polynucleotide Sugar-phosphate backbone

10. DNA has four kinds of bases: A, T, C, and G • DNA has four kinds of bases: A, T, C, and G Thymine (T) Cytosine (C) Adenine (A) Guanine (G) Pyrimidines Purines • DNA molecules consist of double helix strands, which are antiparallel • complementary base pairing rules: adenine (A) only pairs with thymine (T), and guanine (G) only pairs with cytosine (C) • the pairs of bases form base pairs (bp) • reverse complementation of s = AGCTAAC in the 5’ 3’ direction is = GTTAGCT

11. Hydrogen bond Three Representations of DNA Ribbon model Partial chemical structure Computer model Figure 10.3D

12. The Human Genome • 22 pairs of chromosomes called autosomes • Two sex chromosomes (X,Y): XY in males and XX in females

13. Relative Size of Genomes

15. Genes: The Functional Part of DNA A gene is certain region of DNA which is converted during a process called transcription into an intermediate sequence of chemically distinct nucleotides called an RNA (different types such as mRNA, tRNA, etc.) In a process called translation, RNA is then used to produce proteins that can be used by the cell to maintain its activity. The entire process is sometimes called the “central dogma” of molecular biology.

16. Structure of Genes

17. Introns and Exons in Genes • Exons: coding regions of genes • Introns: noncoding regions (“junk” DNA)

18. RNA has a slightly different sugar: ribose rather than deoxyribose • RNA has U instead of T to bind with A • RNA does not form a double helix; three-dimensional structure of RNA is far more varied than that of DNA RNA is also a nucleic acid Nitrogenous base(A, G, C, or U) Phosphategroup Uracil (U) Sugar(ribose) Figure 10.2C, D

19. Questions About Proteins • Given a strings of amino acids, determine if similar sequences are in the database. • Given a strings of amino acids, predict secondary structure. • Given a strings of amino acids, predict interactions with other macromolecules, i.e. identify sequence motifs. • Given a strings of amino acids, predict function.

20. Questions About DNA • Given a string of nucleotides, determine if there are similar sequences in the database. • Given a string of nucleotides, determine if it is informational: (1) find exons, (2) find splice junctions, (3) find promoters, (4) find regulatory sequences, and (5) evaluate for taxa-specific codon bias (different organisms often show particular preferences for one of the several codons that encode the same given amino acid; how these preferences arise is a much debated area of molecular evolution). • Given a string of nucleotides, find RNA secondary structure. • Given a string of nucleotides, find repeated sequences.

21. The “Central Dogma” of Molecular Biology • Replication: DNA copies itself into two identical strings although copying errors may occur called mutations. • Transcription: A gene is converted into an intermediate sequence of chemically distinct nucleotides called an RNA (different types such as mRNA, tRNA, rRNA, etc.). • Translation: RNA is further decoded to produce the functional activity of a gene which usually takes the form of a protein.

22. Central Dogma of Molecular Biology (in flowchart form)

23. The “Central Dogma” in Prokaryotes and Eukaryotes

24. Transcription Basics • RNA molecule is synthesized from a segment of DNA that includes a gene • RNA nucleotides are similar to DNA nucleotides but have a (slightly) different backbone. In particular, DNA and RNA are composed of repeating units of nucleotides. Each nucleotide consists of a sugar, a phosphate and a nucleic (nitrogenous) acid base. The sugar in DNA is deoxyribose. The sugar in RNA is ribose, the same as deoxyribose but with one more OH (oxygen-hydrogen atom combination called a hydroxyl). • T is replaced with U (U = Uracil) GAUUACA GATTACA

25. RNA polymerase DNA of gene Promoter DNA Terminator DNA Initiation • RNA nucleotides line up along one strand of the DNA following the base-pairing rules • The single-stranded messenger RNA peels away and the DNA strands rejoin • In transcription, the DNA helix unzips Elongation Area shownin Figure 10.9A Termination GrowingRNA Completed RNA RNApolymerase

26. Eukaryotic RNA is processed before leaving the nucleus Exon Intron Exon Intron Exon DNA • Noncoding segments called introns are spliced out • A cap and a tail are added to the ends TranscriptionAddition of cap and tail Cap RNAtranscriptwith capand tail Introns removed Tail Exons spliced together mRNA Coding sequence NUCLEUS CYTOPLASM

27. Different Types of RNAs • Messenger RNA (mRNA): Encodes protein sequences. Each three-nucleotides group, called a codon, translates to an amino acid (the protein building block). • Transfer RNA (tRNA): Decodes the mRNA molecules to amino acids. It connects to the mRNA with one side and holds the appropriate amino acid on its other side. • Ribosomal RNA (rRNA): Part of the ribosome, a machine for translating mRNA to proteins. It catalyzes (like enzymes do) the reaction that attaches the hanging amino acid from the tRNA to the amino acid chain being created.

28. What is a Code? • System by which information is represented by strings of coding symbols (length of strings is determined by the number of objects being represented) • Enables the efficient transfer and storage of information • Many different types in common usage, for example, ...

29. Braille

30. Morse Code

31. Ascii Code

32. To encode n objects (items of information) using k coding symbols, strings of length logkn + 1 are needed.

33. There are 20 amino acids used to make proteins. Which amino acids make up the protein to be produced are encoded in the RNA molecule. Since there are four bases {A,U,C,G} to use as coding symbols, the length of the code words must be at least log420 + 1 = 3 symbols long! The code words are called codons.

34. Codons

35. Codons Encode Amino Acids

36. The Genetic Code Of the 64 codons, 61 specify one of the 20 amino acids. The other 3 codons are chain-terminating codons and do not specify any amino acid. AUG, one of the 61 codons that specify an amino acid, is used in the initiation of protein synthesis.

37. Genetic Code Representations

40. Translation Basics • Translation is mediated by the ribosome. • Ribosome is a complex of protein and rRNA molecules. • Ribosome attaches to the mRNA at a translation initiation site. • Ribosome moves along the mRNA sequence and in the process constructs a sequence of amino acids (a polypeptide molecule) which is released and folds into a protein.

41. Ribosome build polypeptides Next amino acidto be added topolypeptide Growingpolypeptide tRNA molecules P site A site Growingpolypeptide Largesubunit tRNA P A mRNA mRNAbindingsite Codons mRNA Smallsubunit Figure 10.12A-C

42. mRNA, a specific tRNA, and the ribosome subunits assemble during initiation Largeribosomalsubunit Initiator tRNA P site A site Startcodon Small ribosomalsubunit mRNA 1 2

43. Amino acid Polypeptide Asite P site Anticodon mRNA 1 Codon recognition mRNAmovement Stopcodon Newpeptidebond 2 Peptide bond formation 3 Translocation Figure 10.14

44. DNAdoublehelix(2-nmdiameter) Histones “Beads ona string” Nucleosome(10-nm diameter) Tight helical fiber(30-nm diameter) Supercoil(200-nm diameter) 700nm Metaphase chromosome

45. Mutations in DNA What is a Mutation? A mutation is a permanent change in the DNA sequence of a gene. Mutations in a gene's DNA sequence can alter the amino acid sequence of the protein encoded by the gene. How does this happen? Like words in a sentence, the DNA sequence of each gene determines the amino acid sequence for the protein it encodes. The DNA sequence is interpreted in groups of three nucleotide bases, called codons. Each codon specifies a single amino acid in a protein. Mutations introduce genetic diversity into populations and facilitate the processes of natural selection and evolution.

46. Transitions and Transversions DNA substitution (point) mutations are of two types. Transitionsare interchanges of purines (A and G) or of pyrimdines (C and T), which therefore involve bases of similar shape. Transversionsare interchanges between purine and pyrmidine bases, which therefore involve exchange of one-ring and two-ring structures. Although there are twice as many possible transversions, because of the molecular mechanisms by which they are generated, transition mutations occur at higher frequency  than transversions.

47. Point mutations Defined at DNA level Defined at codon level Defined at protein level

48. Questions About DNA • Given a string of nucleotides, determine if there are similar sequences in the database. • Given a string of nucleotides, determine if it is informational: (1) find exons, (2) find splice junctions, (3) find promoters, (4) find regulatory sequences, and (5) evaluate for taxa-specific codon bias (different organisms often show particular preferences for one of the several codons that encode the same given amino acid; how these preferences arise is a much debated area of molecular evolution). • Given a string of nucleotides, find RNA secondary structure. • Given a string of nucleotides, find repeated sequences.

49. Questions About Proteins • Given a strings of amino acids, determine if similar sequences are in the database. • Given a strings of amino acids, predict secondary structure. • Given a strings of amino acids, predict interactions with other macromolecules, i.e. identify sequence motifs. • Given a strings of amino acids, predict function.