What is the Structure of DNA?

•  DNA structure must be compatible with its 4 roles:
• – Make copies of itself
• – Encode information
• – Control cells & tell them what to do
• – Change by mutation

DNA is a Double Helix

• Nucleotides that make up DNA have 3 components:
• – Phosphate group
• – 5-C sugar (deoxyribose)
• – Nitrogen-containing organic base
• Four Bases of DNA Nucleotides
• Adenine (A) - purines
• Guanine (G) - purines
• Thymine (T) - pyrimidines
• Cytosine (C) - pyrimidines

Characteristics of Four Bases

• Watson & Crick assumed  that the phosphate group & sugar connect the bases together
• Thus, nitrogenous bases could occur in any order without changing basic molecular structure
• Consistent with role as repository of information

3D Structure of Proteins

• Linus Pauling made the discovery using X-ray crystallography:
• – Tiny bit of crystallized sample is bombarded with X-rays
• – Spots & areas thus formed reveal atomic arrangement in the sample
• – Some proteins have a regular structure
• Pauling made paper models to resemble amino acids & assembled them into protein model
• Model looked like twisted helix winding around axis (elongated spiral)
• Pauling called the model alpha helix

Research of DNA Structure

• M. Wilkins’ research confirmed DNA was a helix
• E. Chargaff found relative amounts of 4 bases conform to rule regardless of DNA source  -
• Chargaff’s Ratios
• Amount of adenine always equals thymine
• Amount of cytosine always equals guanine
• Amount of A+T together is independent of C+G

Watson & Crick’s Research

• Considered there could be 2 helices with adenine on one & thymine on the other
• Proposed pairing relationships – sequence on one chain is complement of sequence on other
• Used Pauling’s model building approach to make a metal model
• Their model was sugar-phosphate backbone (like rails on ladder), twisted into helix as predicted by pictures
• Paired bases projecting from backbone formed rungs of a ladder projecting from rails & satisfied Chargaff’s ratios
• Found bonds holding nucleotides together were covalent
• Bonds holding base pairs – relatively weak, but many together – strong

DNA Replication

• Replication – process by which DNA copies itself
• – Precedes cell division
• – Watson & Crick said replication begins when weak bonds connecting parental strands break
• Strands separate as halves of a zipper
• Watson & Crick exposed bases attract new mates (T pairing with A, C pairing with G, etc.)
• Each strand acts as a blueprint upon which a new partner is assembled
• As each new strand forms, nucleotides are lined together to form a complete strand
• Double Helix of DNA
• Result is two double-stranded daughter helices
• – Each composed of one parental strand & one newly synthesized strand
• This mechanism is called semiconservative replication
• Watson & Crick proposed this solely on basis of logic, no scientific evidence

How is Info in DNA Expressed?

• A. Garrod, 1902, proposed connection between genes & proteins
• Proteins – amino acid polymers that fold, twist into 3D structures
• – Amino acids differ form each other in side group (R group composition)
• – The genes determine protein primary structure

· RNA as an Intermediary

• DNA codes for protein through related polymer of ribonucleic acid nucleotides or RNA
• DNA that encodes protein is copied into sequence of RNA nucleotides
• Smaller, more mobile RNA goes to the part of the cell where sequence is decoded into protein

· Decoding DNA

• Two separate processes involved:
• – Transcription – DNA used as the template to make RNA
• – Translation – RNA serves as the template for the sequence of amino acids in a protein

Structure of RNA

Nucleotides & Polynucleotides

• Composed of phosphate group, nitrogenous base (A, G, C, U [instead of T]) & ribose sugar
• Nucleotides are joined together into single-stranded molecule by covalent bonds

Differences: DNA & RNA

• They contain different sugars
• – DNA contains deoxyribose
• – RNA contains ribose
• Nitrogenous bases
• – DNA contains A, G, T, & C
• – RNA contains A, G, U, & C
• Uracil (U) replaces thymine (T) in RNA, thus A pairs with U when DNA is used as a template to make RNA
• DNA – most stable as double helix, RNA most often exists as a single strand of nucleotides
• Some RNAs fold back on themselves, forming intrastrand pairings giving molecule distinctive shape; These shapes are important to RNA function
• Size
• – DNA molecules are larger
• – RNAs are smaller
• Mobility
• – DNAs are basically immobile
• – RNAs are highly mobile
• Life span
• – DNAs are long-lived
• – RNAs are broken soon after their job is done

Transcription

All RNAs are transcribed from DNA in nucleus

• Messenger RNA (mRNA) carries genetic info from DNA (nucleus) to cytoplasm where it is translated into protein
• All RNAs are transcribed from DNA in nucleus
• Transfer RNA (tRNA) is interpreter molecule that brings amino acids to site where mRNA translated into protein
• Transfer RNA (tRNA) brings amino acids to site where mRNA is translated into protein
• All RNAs are transcribed from DNA in nucleus
• – Ribosomal RNA (rRNA) - >80% of RNA in most eukaryotes
• – Several rRNAs & many proteins combine to form ribosomes
• Enzymes involved in and control transcription
• – The enzyme RNA polymerase catalyzes assembly of RNA & places appropriate complimentary RNA nucleotides into new RNA

– Other enzymes separate DNA double helix strands to allow transcription

Translation

• Proteins are synthesized in translation – assembly of protein from mRNA template
• More complex & machinery of translation is far more elaborate than that of transcription

Steps in translation

• Long m RNA strand joins small subunit of ribosome
• mRNA ribonucleotides found in sets of 3 (codon)
• Pair with anticodon portion of tRNA

The Genetic Code

• 3 RNA nucleotides code for 1 amino acid
• The language of genes is written in sequence of nitrogenous base
• Can be translated 3 at a time into amino acid words
• Need code to stand for 20 amino acids
• Alphabet for code has 4 letters (A, G, C, T or U)
• Can only make 4 one-letter words (41), 16 two-letter words (42), 64 three-letter words (43)
• To code unambiguously for 20 amino acids
• – Need at least 20 words
• – Three-letter words would be the minimum
• M. Nirenberg & H. Matthaei, 1960s, developed a technique for cracking code

Features of code

• – Code is universal, applies to humans & all other living things
• – Most amino acids have 2 and many have 4 triplet codons that code for them

What Makes Cells Different from Each Other?

• During lifetime a person may manufacture as many as 100,000 different proteins, but
• – Only ~5000 are found in any one cell at any given time
• Prokaryotes regulate genetic expression mostly in transcription
• Eukaryotes regulate genetic expression at many levels
• Transcription is important in eukaryotes as well but there are other levels of regulation

DNA Mutations

• Mutations are essential for life
• Mutation is the sudden appearance of a new allele
• Some mutations involve whole chromosomes
• – Polyploidy arises as genetic accident, but can be advantageous
• – Aneuploidy is a change in chromosome number involving single chromosome or single homologous pair
• B. McClintock showed that DNA molecules did not always remain intact from generation to generation
• – Called this genetic rearrangement transposition &
• – Called moved bits of DNA
• Transposable genetic element, later transposons
• While sequences of transposon DNA are not random
• – Target sites are thought to be random, so that
• – Transposon can land anywhere
• Can create new combinations of genes & can introduce errors in genetic material
• Inversions
• – Piece of chromosome broken, then reincorporated in chromosome in reversed order
• Deletions
• – Parts of chromosome spontaneously deleted
• Micromutations that involve single DNA bases or just a few bases
• – Called point mutations
• Neutral mutations
• – Most mutations are harmful, but
• – Many have little or no impact on recipients

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