Molecular Biology Review

Nucleotide vs. Nucleoside

• A nucleotide has a phosphate group, while a nucleoside does not.
• Both nucleotides and nucleosides contain a ribose sugar.
• RNA has ribose.
• DNA has deoxyribose (missing an oxygen atom).

Ribose vs. Deoxyribose

• Ribose has an oxygen group. Deoxyribose is missing an oxygen group.

Pyrimidines

• Longer word, smaller molecule.
• CUT: Cytosine, Uracil, and Thymine.
• Uracil is found in RNA, and Thymine is found in DNA. Therefore, they cannot be in the same sequence (in carbon-based life).

Purines

• Shorter word, bigger molecule.
• A and G: Adenine and Guanine.

ADP vs. ATP

• ADP: Diphosphate (two phosphate groups).
• ATP: Triphosphate (three phosphate groups).
• ATP is responsible for energy production in the cell by breaking a phosphodiester bond to release a phosphate group, converting ATP to ADP.

Phosphate Backbone

*Gives DNA a negative charge.
*A negatively charged DNA is crucial for cellular function because the cellular wall is also negatively charged so it doesn't attach to the cell wall.

DNA Strands

• Original strand: 3' to 5'.
• Complementary strand: 5' to 3'.
• They are antiparallel, which allows them to form a double helix.

Central Dogma of Molecular Biology

• DNA is transcribed into RNA.
• RNA is translated into protein at the ribosome for protein synthesis.

DNA Replication

• Parent DNA (template strand) is used to create a new, complementary strand.
• A pairs with T (or U in RNA).
• G pairs with C.
• Replication occurs in one direction but must be antiparallel.

RNA

• RNA is a single-stranded molecule.
• RNA does not form a double helix.
• RNA is shorter than DNA.
• Estimated DNA length in one cell: about a mile long.

Types of RNA

• Ribosomal RNA (rRNA): Provides the site within the ribosome where polypeptides bind for protein synthesis.
• Messenger RNA (mRNA): Carries information from the nucleus to the ribosome.
• Transfer RNA (tRNA): Brings specific amino acids to the ribosomes for protein synthesis.

Transfer RNA (tRNA)

• Has a cloverleaf shape.
• Has an acceptor end on the 3' end (yellow) which carries the needed amino acid to the anticodon.
• The anticodon identifies the needed amino acid.

Transcription

• DNA is transcribed into RNA, which involves changing the language from DNA (T) to RNA (U).
• During a quiz, determine if you are making a new DNA strand or an RNA strand. If making an RNA strand, change all T's to U's.

Genetic Code

• Three nucleotides (triplets) form a codon, which codes for an amino acid.
• Nucleotides are smaller than amino acids; three nucleotides are needed to make one amino acid.
• Example: UAC codes for serine, UGC codes for cysteine.
• A chart is used to look up which codon corresponds to which amino acid.
• Multiple codons can code for the same amino acid.
• Mutations that change a codon to another codon that codes for the same amino acid may not cause significant problems. Changing the codon to one that codes for a different amino acid will cause a mutation.
• The genetic code has a start codon (methionine) and stop codons, which signal when to start and stop making a protein.
• mRNA contains the sequence of codons that determines the amino acid sequence in the protein.
• Proteins are made of amino acids.
• Analogy: Amino acids are like Lego pieces, proteins are like a house or car built from Legos, and the genetic sequence is like the Lego manual.

Codon vs. Anticodon

• Codons (mRNA) and anticodons (tRNA) must be complementary for an amino acid to be produced.
  The positive charge is codon while the negative charge is anticodon.
• tRNA is needed to help make a protein from mRNA.
• mRNA and tRNA must have base pairs opposite of each other to fit perfectly.

Protein Synthesis

• Three steps: initiation, elongation, and termination.
• Initiation: start codon.
• Elongation: building the protein strand.
• Termination: stop codon.

Ribosomes

• The ribosome has a small subunit and a large subunit.
• tRNA is located inside the ribosome.
• mRNA enters the ribosome, and the ribosome starts to elongate and create a protein.
• Analogy: Ribosome is like a Polaroid camera: mRNA is the picture, and the ribosome spits out the image.
• Human (eukaryotic) ribosomes are different from bacterial ribosomes.
• Eukaryotic ribosomes: 80S.
• Bacterial ribosomes: 70S.
• Antibiotics can target bacterial ribosomes (e.g., tetracycline or aminoglycoside) without harming human cells.
• Anticancer drugs attack all cells, while some antibiotics only attack bacterial cells.

From DNA to Protein

• DNA strand → template DNA → mRNA → anticodons → polypeptide (protein).

Mutations

• Changes in the nucleotide sequence.
• Some mutations are random (mutagens) due to errors during DNA replication.

Types of Mutations:

• Point Mutation: Substitution of a nucleotide.
• Deletion Mutation: Deletion of a nucleotide or amino acid, causing a shift in the reading frame.
• Insertion Mutation: Addition of an extra nucleotide, also causing a shift in the reading frame.
• Silent Mutation: A change in the nucleotide sequence that results in the same amino acid being coded for; therefore, there is no effect on the protein.

Recombinant DNA

• Involves cleaving human DNA and inserting it into another DNA (e.g., bacterial plasmid).
• Used in cloning.

PCR: Polymerase Chain Reaction

• Invented by a guy who, after making millions of dollars and winning the Nobel Prize, spent his time surfing.
  DNA has a negative charge, and DNA can move using electricity.
• Each persons DNA weighs differently.
• The process involves using an electro rod to have DNA travel. In a solution you put a negative electro rod and a positive electro rod. DNA will repel and travel downwards until it stops in a certain area.
• A gel is needed that can have electricity pass through. Example Ten percent Tris.
• PCR amplifies copies of DNA.
• DNA is separated using temperature, and primers are added to make copies.
• Even with one drop of blood, PCR can make enough DNA to run multiple tests.
• The results must be replicated multiple times to be conclusive.
• Uses: Identify pathogens (viruses, bacteria), develop vaccines, and study retroviruses (HIV).