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Class Notes

DNA and RNA Structure

• DNA and RNA belong to a class of macromolecules called nucleic acids.
• Nucleic acids are polynucleotides which means they contain many nucleotides joined together.
• A nucleotide consists of:
  • One cyclic five-carbon sugar (The carbons found in this sugar are numbered 1' through to 5')
  • One phosphate
  • One nitrogenous base
• The sugar is deoxyribose in DNA and ribose in RNA. The only difference between the sugars is that ribose has a hydroxyl group (OH) on the 2' carbon and deoxyribose does not. This makes deoxyribose more stable than ribose.
• The phosphate is linked to the 5' carbon of the sugar in both RNA and DNA.
• The nitrogenous bases are adenine(A), guanine(G), cytosine(C), thymine(T), and uracil(U).
  • Adenine and guanine are purines (contains a six membered ring of carbon and nitrogen fused to a five membered ring).
  • Adenine and guanine are both found in DNA and RNA.
  • Cytosine, thymine and uracil are pyrmidines (contains a six membered ring of carbon and nitrogen).
  • Cytosine is found in both DNA and RNA, but thymine is only found in DNA and uracil is only found in RNA.
• A nucleotide is formed when a phosphate attahes to the 5' carbon of the sugar and one of the nitrogenous baseses attaches to the 1' carbon of the sugar.
• A strand of DNA or RNA consists of nucleotides linked together by phosphodiester bonds.
  • A phosphodiester bond exists between the phosphate of one nucleotide and the sugar 3' carbon of the the next nucleotide.
  • This forms a backbone of alternating sugar and phosphate molecules known as the "sugar-phosphate backbone".
• RNA, in most cases, consists of one strand of nucleic acids linked together by phosphodiester bonds.
• A DNA molecule consists of two strands of nucleotides twisted together to form a double helix.
  • The sugar-phosphate backbone is found on the outside of this helix and the bases are found braching towards the middle.
  • Hydrogen bonds join the the nitrogenous bases and hold the two strands together.

Complementation

• The two strands of DNA are complementary to one another because of the properties of base pairing:
  • A will only pair with T by two hydrogen bonds
  • G will only pair with C by three hydrogen bonds
  • For example: If one strand is ACGTA the other strand is TGCAT
  • Complementation is important for storage and transmittance of genetic information

Antiparallel Strands

• The two strands of DNA are also antiparallel(run in opposite directions) to one another.
  • A strand of DNA can have the direction 5'-3' or 3'- 5'. One strand in the DNA molecule is 5'-3' and the other strand is 3'-5'. A DNA strand is assigned direction based on what is found at the end of the strands.
    • The end of the strand with a free phosphate is the 5' end because phosphate attaches to the 5' carbon of the sugar.
    • The end with a free OH group is the 3' end because the OH group is attached to the 3' carbon of the sugar.

Gene Definition

• A gene is a sequence of nucleotides in DNA that codes for a functional product.

Bacterial Chromosome

• A chromosome is an association of genes and some protein.
• A bacteria usually has a single circular chromosome. The chromosome is about 1mm long which is about 1000 times longer than the typical bacterial cell. Therefore, it is looped, folded and packed tightly inside the cell.

Protein Structure

• Proteins are macromolecules that play many functions in the cell.
• They are used for support, storage, transport of other substances, defense against invaders, and catalytic enzymes.
• This is just a brief overview of protein structure.
  • Proteins are composed of repeating units called amino acids.
    • An amino acid consists of a carbon atom bonded to a hydrogen, a carboxyl group and an R side chain.
  • There are 20 different amino acids that can be found in proteins.
    • The R side chain is the varible part that makes amino acids different from one another.
    • It is also the properties of the R group that determines how amino acids will interact with each other.
  • Amino acids are linked by peptide bonds to form polypeptide chains.
    • The sequence of amino acids in this chain in known as the primary structure of the protein.
  • A protein consists of one or more of these polypeptide chains folded and coiled together.
    • The conformation depends on the R groups present and how they interact.