DNA, RNA, replication, translation, and transcription

DNA, RNA, replication, translation, and transcription

DNA structure

One monomer unit = deoxyribonucleic acid

Ø  Composed of a base, a sugar (deoxyribose), and a phosphate

Ø  Directionality along the backbone 5’ (phosphate) to 3’ (OH) Double-strand pairing:

Ø  Complementary base-matching

Ø  Base-matching achieved by H-bonding and geometry (long vs short nucleotides)

Ø  Antiparallel (one strand 5’  3’, the other 3’  5’)

Helical shape

Ø  10.4 nucleotides per turn

Ø  Diameter = 2 nm

Ø  Both major and minor grooves

Ø  Called B-DNA. The helix twist and diameter can also change under dehydrating conditions and methylation to A-DNA and Z-DNA

Base-pairing and strand interactions

Ø  A, G are long (double ring purines)

Ø  C,T are short (single ring pyrimidines)

Ø  Need one long and one short nucleotide per pair

Ø  C-G have three hydrogen bonds (slightly stronger matching)

Ø  A-T have two hydrogen bonds (slightly weaker matching)

Ø  Base stacking of aromatic rings allows sharing of pi electrons and adds stability to interior structure of DNA some hydrophobic driving force as well

Ø  Pair structure allows template for semi-conservative copying

Information in DNA sequence is the genome

Ø  Genes are stretches of information in the sequence that encode for particular function (usually a particular protein, but sometimes also an RNA sequence)

Ø  About 20,000 genes in humans

Ø  Typically 1000s of nucleotides long

Ø  Genes can be expressed (use to make proteins) or repressed (not used)

Ø  Regions of DNA are divided into coding and non-coding segments

Ø  Over 50% of human DNA is non-coding

Ø  Genes can be spliced together

Ø  Genes are organized in the large-scale structure of the DNA in the nucleus

In bacteria, genome usually circular

The genome in eukaryotes is organized into chromosomes

Ø  Each chromosome a separate DNA molecule

Ø  Human cells contain 46 chromosomes (22 each from mother and father)

Ø  Chromosomes are extended and replicated during interphase portion of the cell cycle extended allows for gene expression

Ø  Chromosomes are condensed, visible with light during cell division (M phase)

Special DNA sequences exist in each chromosome

Ø  Replication origins – multiple locations where the replication machinery first binds to start replication

Ø  Centromere – center “pinch point” of a chromosome that allows one copy of each to be pulled apart into two daughter cells during division.

Ø  Telomere – specialized sequences at the chromosomes end that facilitate replication there.

Higher-order DNA structure

ü  How do cells efficiently store very long chains of DNA?

ü  DNA wraps around protein “spools” to form nucleosomes

ü  Nucleosomes are made of histone proteins

ü  Spools organize into chromatin fibers that pack in regular ways, on different length scales

Replication

DNA replication is semi-conservative one strand from each of the initial two strands end up in a daughter strand

Each strand serves as a template for a new strand

New strand is formed by complementary base-pairing of the correct nucleotide plus formation of a phosphodiester bond

Synthesis begins at replication origins

ü  About 100 nucleotides long rich in A-T, which are easier to pull apart because have 2 rather than 3 hydrogen bonds

ü  1 in bacteria

ü  10000 in humans

Initiator proteins bind at replication origins and recruit DNA replication machinery proteins

·         DNA polymerase is responsible for catalyzing synthesis of new strands Replication forks form and involve a leading and a lagging strand

Ø  DNA is directional; two strands are antiparallel

Ø  DNA polymerase can only synthesize from 5’ to 3’ direction, adding new nucleotides to the 3’ end

lagging strand must be synthesized by first spooling out some template strand and then     synthesizing in reverse

Error-correction machinery

Ø  Mutations occur 1 in 10

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 nucleotides copied   evolution, cancer

Ø  Much better error rates than expected simply from base-pairing energetics

Ø  DNA polymerase proofreads to make sure correct nucleotide is added if not, it excises and goes back to add the correct one

Ø  Mismatch repair machinery fixes incorrectly added nucleotides not found by DNA polymerase detects nicks in newly created strand

Damage to DNA continuously occurs

Ø  Homologous recombination uses similar sequences in nearby strands in order to fill in excised damaged DNA

Ø  Also the basis of heredity

Transcription

Messenger RNA, or mRNA, is the RNA “copies” of genes ultimately used to synthesize proteins, although some RNA are the final product themselves

RNA has some distinctions from DNA

Ø  Ribose rather than deoxyribose sugar (differs in an OH group)

Ø  Uracil instead of thymine (loss of a methyl group)

Ø  single-stranded, and typically folds into unique shapes, like proteins

less chemically stable

Other kinds of RNA

Ø  Ribosomal RNA, rRNA, is RNA that becomes part of the ribosome, the big molecular machine responsible for synthesizing proteins

Ø  Transfer RNA, tRNA, is used to bring correct amino acids to the ribosome during protein synthesis

Ø  Micro RNAs (mRNAs) are important in regulating gene expression

Transcription involves the synthesis of rRNA from DNA using RNA polymerase

Ø  RNA polymerase must unpair and unwind DNA as it is reading it

Ø  Much less accurate than replication   errors of 1 in 10

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Ø  Protein synthesis can tolerate more errors

Ø  Multiple RNAs can be sequenced from the same gene at the same time

Translation

Information transmission

Ø  4 bases in DNA/RNA to 20 amino acids in proteins

Ø  “Translation” since the chemical language is different

Ø  How many nucleotides needed to specify each amino acid?

Ø  Two = 16 combinations   not enough!

Ø  Three = 64 combinations   plenty!

Processed (e.g., spliced) mRNA is read in groups of three nucleotides

Ø  Called codons

Ø  Redundancy of codons for different amino acids typically the last nucleotide is variable

Ø  Three possible reading frames depending on starting nucleotide

Transfer RNAs (tRNAs) are the intermediates between nucleotides and amino acids

Ø  About 80 nucleotides long

Ø  At one end: anticodon that base-pairs with mRNA.At the other end: covalently coupled amino acid

Ø  tRNAs are charged with an amino acid by aminoacyl tRNA synthetases that ensure correct addition of individual amino acids to corresponding tRNA

General process for synthesis of proteins

Ø  Binding sites for mRNA and three tRNA amino acid carriers in ribosome

Ø  Correct tRNA binds at A site through base pairing with mRNA

Ø  High-energy covalent bond attaching amino acid is added to growing chain

Ø  Ribosome shifts over one tRNA unit, placing the tRNA in the P and then E site

Initiation of protein synthesis

Ø  All proteins begin with a methionine start codon that signals initiation of protein synthesis (methionine typically removed in post-translational processing)

Ø  Initiation factor tRNA binds first with small subunit to mRNA

Ø  Large subunit then binds

Ø  Synthesis continues until a stop codon is reached, which bind release factor proteins

After synthesis

Many proteins undergo post-translational modifications

Ø  Disulfide bond formation

Ø  Phosphorylation

Ø  Binding of small molecule cofactors

Ø  Association with other protein subunits into large functional structures

Ø  Glycosylation = addition of sugars to the surface to create glycoproteins

Ø  Proteases are proteins that degrade other proteins

Ø  The proteosome is a large cylindrical protein complex that is responsible for degrading most proteins in eukaryotic cells in its interior

Ø  The proteosome recognizes proteins that need to be degraded because they are “tagged” with ubiquitin – a protein that can be attached to proteins to signal that they are destined for degradation

Manipulating DNA, proteins, cells

Manipulation of DNA

Ø  Restriction nucleases – proteins that cleave DNA at particular locations, enabling fragmentation into smaller parts in a predictable way

Ø  Gel electrophoresis – separation of DNA fragments of different sizes

Ø  Hybridization – double strands can be separated by heating just below boiling temperature cooling then allows re-association to correct base pairing strands

Ø  Probe sequences of nucleotides can be used to hybridize to certain sequences of DNA

Ø  Recombinant DNA can be joined to existing DNA using DNA ligase

Cloning DNA using bacteria

Ø  Plasmids are typically used circular DNA molecules that exist independently of the bacterial chromosome

Ø  Plasmids also occur naturally, but those carrying foreign DNA are termed vectors

Cloning DNA using chemistry

Ø  Polymerase chain reaction (PCR) is a much quicker tool for duplicating DNA without cells, developed in 1980s

Ø  Uses a heat resistant DNA polymerase isolated from hot-springs bacteria to then make copies

Ø  Repeated cycles of cooling and heating then enable repeated replication

Ø  Amplicifation from one to billions of the same molecule

Sequencing DNA

 Ø  DNA polymerase used to make copies of a sequence

Ø  Dideoxy DNA sequencing use of small amounts of dideoxyribonucleotides that terminate a growing copy

Ø  Four separate experiments use either an A, T, C, G dideoxy base in addition to the four usual ones

Ø  Each experiments produces many copies of different lengths, but each terminated at a specific kind of nucleotide

Ø  Gel electrophoresis gives the molecular weight distribution in each of the four cases and can be used to show the sequence .Highly automated