DNA & Proteins: Foundations and Discoveries

DNA & Proteins

• DNA and proteins are fundamental to life.
• Early theories proposed a hereditary agent, but concrete macromolecules weren't identified.
• Darwin studied heredity, but lacked the mathematical tools to interpret his findings.
• Mendel's experiments on plant phenotypes exposed patterns of heredity.

Discovery of DNA's Purpose

• Frederick Griffith (1928) experimented with bacteria (streptococcus pneumoniae).
• He experimented with two types of bacterial cells:
  • S strain bacteria (smooth): pathogenic
  • R strain bacteria (rough): non-pathogenic
• A key finding was when heating-killed S strain bacteria and mixing it with live R bacteria, the R bacteria transformed into S bacteria.
• This suggested a transfer of genetic material.

Designed and ran 4 Experiments

• Four key experiments were conducted.
• Live R cells did not cause pneumonia
• Live S cells did cause pneumonia
• Killed S cells did not cause pneumonia
• Killed S cells plus live R cells DID cause pneumonia

What happened?

• The possibility of R cells mutating was discussed.
• The possibility of some S cells surviving was discussed.
• It was concluded that DNA transferred and changed the R cells.

Later Studies

• Further experiments used non-lethal forms of strains to infectious ones.
• Early belief was that proteins were hereditary.
• Biochemical experiments showed strains with protein digesting enzymes still developed more proteins.
• Experiments with DNA digesting enzymes showed cell functionality stopping.
• These affirmed DNA as the hereditary molecule.

Viruses

• In 1952, molecular biologists studied bacteriophages (viruses that infect bacteria).
• Electron micrographs showed viruses had protein coats and nucleic acids inside.
• When viruses infect cells, the protein coat remained outside, while nucleic acids entered.

The structure of DNA

• Rosalind Franklin used X-ray crystallography to study DNA structure.
• X-ray diffraction patterns revealed the DNA molecule's structure.
• Watson and Crick used Franklin's data and made significant deductions.

Fame and Fortune

• Watson and Crick received the Nobel Prize.
• Rosalind Franklin, who did much of the foundational work, was not recognized.

DNA

• DNA is a very stable molecule with a double helix structure that's more stable than RNA.
• Each gene codes for one protein.
• Genes are composed of 4 nucleotides: adenine, thymine, guanine, and cytosine.
• The sequence of nucleotides is the genetic code, determining protein structure.
• Nucleotides form codons of three, each specifying specific amino acids.

DNA Structure

• DNA is double-stranded and helical, adding stability.
• Base pairs (A-T, G-C) are complementary.
• Two hydrogen bonds link A and T.
• Three hydrogen bonds link G and C.
• The sugar-phosphate backbone forms the DNA’s structure.

Nucleotides

• Pyrimidines are single rings.
• Purines are double rings.
• DNA's structure is like a ladder — a pyrimidine pair bonded to a purine.

DNA Backbone Structure

• Nucleotides are bonded together via phosphodiester bonds.
• The phosphate groups of nucleotides form the DNA backbone.
• Phosphate groups are negatively charged, so the backbone aligns on opposite sides.

RNA

• DNA is the blueprint. RNA is the worker.
• Three main types of RNA:
  • Messenger RNA (mRNA)
  • Transfer RNA (tRNA)
  • Ribosomal RNA (rRNA)
• All RNA is manufactured in the nucleus of eukaryotes or the nucleoid region of prokaryotes.

RNA and DNA Comparison

• DNA: Deoxyribose sugar, contains thymine, double-stranded double helix, genetic material for most organisms.
• RNA: Ribose sugar, contains uracil, instead of thymine, single-stranded, genetic material for some viruses.

Basic DNA to Protein Scheme

• DNA—Transcription—RNA—Translation—Protein

Transcription

• DNA information is converted into RNA information.
• The "alphabet" is the same -- just the "letters" (nucleotides) differ (Thymine → Uracil)

Translation

• mRNA's information is converted to protein.
• Codons on mRNA are converted into amino acids form the protein by translating the genetic alphabet.

mRNA

• Messenger RNA carries genetic information from DNA to ribosomes
• Accounts for 5-10% of the total RNA in a cell at any given point
• Consists of a chain of nucleotides
• Used for protein production but is temporary.

rRNA

• Used in constructing ribosomes.
• Ribosomes contain primarily rRNA and some proteins;
• rRNA makes up 60-65% of the ribosome mass and proteins make up roughly 35-40%.
• rRNA constitutes 75-80% of the total RNA in a cell at any given moment.

Ribosome Structure

• Ribosomes have a small and a large subunit
• Involved in assembling amino acids according to mRNA instructions.

Promoter

• Transcription begins at a region called a promoter
• RNA polymerase recognizes the specific promoter region to start transcription
• Promoters are found upstream (before) the gene to be transcribed.

RNA Polymerase

• Responsible for mRNA synthesis, based on a DNA template
• There are specific RNA polymerases for different RNA types: -RNA Polymerase I (rRNA) -RNA Polymerase II (mRNA)
  -RNA Polymerase III (tRNA)

Construction of RNA

• RNA polymerase uses a DNA template and environmental nucleotides to build RNA molecules.
• The template is a particular strand of DNA, selected with a promoter.

mRNA

• Post-transcriptional processing adds a "cap" and "tail" to the finished mRNA.
• This modified mRNA is transported outside the nucleus toward ribosomes for protein synthesis.
• "Tail" protects the mRNA from enzymatic degradation.

Junk DNA

• DNA contains portions that are not coding for protein.
• Exons code for proteins.
• Introns are non-coding regions that are spliced out.
• Introns can create alternative mRNA versions allowing for many proteins from a single gene.

Genetic Code

• The genetic code uses triplets of nucleotides (codons) to specify amino acids.
• AUG codes for methionine (start codon).
• UAA, UAG, and UGA are stop codons.

tRNA

• tRNA molecule carries amino acids to the ribosome.
• They contain specific anti-codons that recognize mRNA codons.
• The anticodon sequence determines which amino acid is attached to the tRNA.

Ribosomes

• Ribosomes are the protein synthesis machinery, binding mRNA and tRNA molecules
• The ribosome functions to orient the mRNA and tRNA in relation to one another so they can bond effectively, effectively acting as an enzyme.

Translation (Stages)

• Initiation: start codon, mRNA and tRNA, assembly of ribosomal units.
• Elongation: tRNA brings in amino acids to each codon on mRNA.
• Termination: stop codon reached, release of amino acid chain.

Mutations and Proteins

• Changes in DNA sequences (mutations) may affect protein formation.

Point Mutations

• Changes in one or a few base pairs.
• Substitution mutations: replacing one nucleotide with another.
• Insertion/deletion mutations: adding or removing nucleotides, which causes a major structural change.

Mutagens

• External factors causing mutations (U/V light, chemicals).
• Recent research shows high diversity in surface oceans and organisms.
• Limited diversity in deep-earth organisms, suggestive of a slower rate of evolution in such an environment.

Mutations important for evolution

• Mutations introduce variation, which allows organisms to adapt over generations and develop useful metabolic processes and body structures.
• Gene replication in the genome allows for multiple copies of genes to evolve over generations without interfering with the primary function.

Some Examples of Mutations

• Single base-pair changes can lead to significant differences, as evidenced in the evolution of birds' beaks and fruit flies' development.