Overview of Overview of Molecular BiologyMolecular 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.

The Cell: Storehouse of The Cell: Storehouse of Hereditary/Genetic InformationHereditary/Genetic Information

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.

Protein StructureProtein 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

Amino Acid Amino Acid FamiliesFamilies

DNA is a nucleic acid, made of long chains of nucleotides

DNA and RNA are polymers of nucleotides

Nucleotide

Phosphate group

Nitrogenous base

Sugar

Polynucleotide Sugar-phosphate backbone

DNA nucleotide

Phosphategroup

Nitrogenous base(A, G, C, or T)

Thymine (T)

Sugar(deoxyribose)

DNA has four kinds of bases: A, T, C, and G DNA has four kinds of

bases:

A, T, C, and G

Pyrimidines

Thymine (T) Cytosine (C)

Purines

Adenine (A) Guanine (G)

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

= GTTAGCTs

Three Representations of DNA

Figure 10.3D

Ribbon model Partial chemical structure Computer model

Hydrogen bond

The Human GenomeThe Human Genome

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

Relative Size of GenomesRelative Size of Genomes

Genes: The Functional Part Genes: The Functional Part of DNAof 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.

Structure of GenesStructure of Genes

Introns and Exons in GenesIntrons and Exons in Genes

•Exons: coding regions of genes•Introns: noncoding regions (“junk” DNA)

RNA is also a nucleic acid 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

Figure 10.2C, D

Phosphategroup

Nitrogenous base(A, G, C, or U)

Uracil (U)

Sugar(ribose)

Questions About ProteinsQuestions 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.

Questions About DNAQuestions 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.

The “Central Dogma” of The “Central Dogma” of Molecular BiologyMolecular 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.

Central Dogma of Molecular Biology (in flowchart form)

The “Central Dogma” in The “Central Dogma” in Prokaryotes and EukaryotesProkaryotes and Eukaryotes

Transcription BasicsTranscription 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)

GATTACA GAUUACA

In transcription, the DNA helix unzips

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

RNA polymerase

DNA of gene

PromoterDNA Terminator

DNAInitiation

Elongation

Termination

Area shownin Figure 10.9A

GrowingRNA

RNApolymerase

Completed RNA

Noncoding segments called introns are spliced out

A cap and a tail are added to the ends

Eukaryotic RNA is processed before leaving the nucleus

DNA

RNAtranscriptwith capand tail

mRNA

Exon Intron IntronExon Exon

TranscriptionAddition of cap and tail

Introns removed

Exons spliced together

Coding sequence

NUCLEUS

CYTOPLASM

Tail

Cap

Different Types of RNAsDifferent 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.

What is a Code?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, ...

Braille

Morse Code

Ascii Code

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

• 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.

CodonsCodons

Codons Encode Amino Acids Codons Encode Amino Acids

The Genetic CodeThe 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.

Genetic Code RepresentationsGenetic Code Representations

Translation BasicsTranslation 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.

Ribosome build polypeptides

Figure 10.12A-C

Codons

tRNAmolecules

mRNA

Growingpolypeptide

Largesubunit

Smallsubunit

mRNA

mRNAbindingsite

P site A site

P A

Growingpolypeptide

tRNA

Next amino acidto be added topolypeptide

mRNA, a specific tRNA, and the ribosome subunits assemble during initiation

1

Initiator tRNA

mRNA

Startcodon Small ribosomal

subunit

2

P site

Largeribosomalsubunit

A site

Figure 10.14

1 Codon recognition

Amino acid

Anticodon

AsiteP site

Polypeptide

2 Peptide bond formation

3 Translocation

Newpeptidebond

mRNAmovement

mRNA

Stopcodon

DNAdoublehelix(2-nmdiameter)

Metaphase chromosome

700nm

Tight helical fiber(30-nm diameter)

Nucleosome(10-nm diameter)

Histones

“Beads ona string”

Supercoil(200-nm diameter)

Mutations in DNAMutations 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.

DNA substitution (point) mutations are of two types. Transitions are interchanges of purines (A and G) or of pyrimdines (C and T), which therefore involve bases of similar shape. Transversions are 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.

Transitions and TransversionsTransitions and Transversions

Defined at DNA level

Point mutationsPoint mutations

Defined at codon level

Defined at protein level

Questions About DNAQuestions 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.

Questions About ProteinsQuestions 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.