DNA Structure and Function

DNA Structure and Function

Introduction

• In the 1860s, Friedrich Miescher isolated phosphate-rich chemicals from white blood cells (leukocytes).
• He named these chemicals "nuclein" because they were isolated from the nuclei of the cells; these chemicals would eventually be known as DNA.

Basic Features of DNA

1. A double-helix structure.
2. The specific base-pairing of nitrogen bases.
3. The repetitive sugar and phosphate units.

Nucleic Acids: DNA and RNA

• DNA and RNA are organic molecules that belong to the nucleic acids group.
• DNA stands for deoxyribonucleic acid.
• RNA stands for ribonucleic acid.
• Both DNA and RNA are composed of nucleotides, which are the small subunits or monomers of nucleic acid polymers.

Why Scientists Initially Doubted DNA as Hereditary Material

1. DNA was thought to be too simple.
2. Early studies suggested viruses lacking DNA could still pass on genetic traits.
3. DNA was believed to be made of only four kinds of subunits.

Nucleotide Composition

• Each nucleotide in DNA is composed of three parts:
  1. A phosphate group.
  2. A sugar called deoxyribose.
  3. One of four possible nitrogen-containing bases (A, T, C, G).

Relationship Among DNA, Gene, and Chromosome

• A chromosome contains hundreds of genes, which are composed of DNA.

Nitrogen Bases

• The nitrogen bases and their sequences are the structure of DNA that serves the function of genes.
• Example:
  • Height:
    • Tall = TT or Tt
    • Short = tt

Genetic Code

• These 3 nucleotide bases (ATG) code for a specific amino acid.
• These 3 nucleotide bases (GCC) code for a specific amino acid.
• TT = the nucleotide strand - homozygous dominant
• Tt = the nucleotide strand - heterozygous
• tt = the nucleotide strand - homozygous recessive

Base-Pairing

• The bases are adenine, guanine, cytosine, and thymine; they are found in specific base-pairs.
• It is called base-pairing because there are equal amounts of adenine and thymine, and equal amounts of guanine and cytosine.
• $A$ always pairs with $T$, and $G$ always pairs with $C$.
• A purine always pairs with a smaller-sized pyrimidine.
• $A$ & $G$ are purines and are larger in size.
• $T$ & $C$ are pyrimidines and are smaller in size.
• The base pairs are linked together by hydrogen bonds.
• The amount of DNA differs between species, but the amount of cytosine is always equal to the amount of guanine, and the amount of adenine is always equal to the amount of thymine.
• The order of nucleotides in DNA can encode vast amounts of information.
• It’s not the number of different bases, but their sequence that’s important.
• Each sequence of bases represents a unique set of genetic instructions (like Morse code).

DNA Structure: Double Helix

• Organisms typically have millions (bacteria) to billions (plants or animals) of nucleotides.
• DNA is a double helix of two nucleotide strands.
• DNA consists of 2 separate strands linked by nucleotides – looking much like a twisted ladder – that is twisted (helix).
• In comparison of a DNA molecule to a twisted ladder, the rungs of the ladder would be the nitrogenous bases linked together, and the uprights or sides of the ladder would be the deoxyribose sugar linked to the phosphates (the sugar-phosphate backbone).

DNA Replication

• DNA replication occurs in interphase prior to mitosis.
• The production or replication of new DNA occurs in the nucleus.
• DNA replication is called semi-conservative replication because this process produces two DNA double helices, each with one old strand and one new strand.

Mechanism of DNA Replication

• DNA helicase enzymes pull apart the parent DNA double helix, breaking apart the hydrogen bonds.
• DNA polymerase takes free nucleotides and base pairs them up with the new strands that have been pulled apart.
• DNA ligase enzymes glue each of the individual pieces of DNA into their new double strands to finally form 2 newly synthesized DNA strands each containing one old strand and one new strand, which is important because now each carries the original genetic code.
• Then each strand twists together to form a double helix.

Mutations

• If the Sequence of one strand is: TCGCACAT what would the complimentary strand or matching base-paired strand would be? AGCGTGTA
• A gene mutation is a change in the nucleotide sequence of DNA.
• These mutations or mistakes are most significant in meiosis.
• If a mutated DNA molecule is replicated, the gene mutation can be passed on to offspring through the gametes.
• There are different kinds of mutations:
  • Point mutations – change in an individual nucleotide: AACGCAGTG à AACCCAGTG
  • Insertion mutations – when one or more extra nucleotides are inserted into a strand. AACGCAGTG à AATAGCGCAGTG
  • Deletion mutations – when one or more nucleotides are removed from a gene. AACGCAGTG à AACGGTG

Gene Interpretation

• Each gene (genotype) gives instructions for or encodes the information for a single protein.
• Proteins are responsible for building cellular components and carrying out chemical reactions (phenotype).
• Protein synthesis occurs on the ribosomes outside the nucleus.
• RNA – carries the information from DNA in the nucleus to the ribosomes.

RNA vs. DNA

• RNA is similar to DNA, but there are 3 main differences:
  1. RNA is single-stranded.
  2. RNA has the sugar ribose instead of deoxyribose.
  3. RNA has the base uracil instead of thymine.
• DNA codes for the synthesis of three major types of RNA:
  • Messenger RNA (mRNA)
  • Ribosomal RNA (rRNA)
  • Transfer RNA (tRNA)
• These all are involved in converting the nucleotide sequence of genes into the amino acid sequence of protein.

DNA Transcription and Translation

• Because each base pairs with a complementary base, in every DNA molecule the amount of cytosine equals that of guanine.
• The Required Steps:
  1. DNA undergoes transcription - the information in DNA is copied into a complementary single stranded mRNA
  2. mRNA leaves the nucleus and undergoes translation - pairing up with a complementary tRNA molecule on a ribosome
  3. tRNA carries with it amino acids - during the process of translation, a sequence of amino acids create a protein
• FYI: In RNA, the thymine is replaced with a uracil, so that adenine base-pairs with uracil in RNA.
• EXAMPLE: DNA to mRNA to tRNA to Protein
  • If the DNA strand is: ATGCGCTGCAATTAG (DNA Template)
  • the complementary mRNA strand would be: AUGCGCUGCAAUUAG (mRNA)
  • the complementary tRNA strand would be: UACGCGACGUUAAUC (tRNA)
• The tRNA carries the amino acids, but it is the mRNA that carries the code for the amino acids.

Genetic Code and Translation

• Every three mRNA letters code for one amino acid.

  • EX:
    • AUG = Methionine (Start codon)
    • CGC = Arginine
    • UGC = Cysteine
    • AAU = Asparagine
    • UAG = Stop codon

• DNA undergoes transcription and the information in the DNA template is copied into an mRNA transcript (copy), which then undergoes translation by pairing up with tRNA, making sequences of amino acids into a protein.

mRNA Elongation and Termination

• Elongation of mRNA continues until RNA polymerase comes to a DNA terminator sequence.
• Terminator sequence causes RNA polymerase to release the mRNA strand or transcript.

mRNA Processing

• mRNA transcript contains exons and introns.
• Portions of the primary mRNA transcript, called introns, are removed, leaving only the exons.
• Intron is non-coding segment of DNA removed by spliceosomes before mRNA leaves nucleus.
• Exons are the parts of mRNA that can code for the protein and exit the nucleus.

RNA Splicing

• Spliceosomes are enzymes that cut the primary mRNA transcript and then rejoin adjacent exons.
• Enzymes in the nucleus remove introns from the mRNA molecule.

Translation (Protein Synthesis)

• The process where the sequence of bases of mRNA assembles (synthesizes) specific amino acids into a protein by using tRNA as a translator.
• Translation is a second step by which gene expression leads to protein synthesis.

Role of Transfer RNA (tRNA)

• Transfer RNA (tRNA) are attached to amino acids.
• The tRNA carry these amino acids to the ribosomes to find the complementary mRNA.
• tRNA has anticodons that bind to mRNA codons.
• An anticodon is group of nucleotides on tRNA complementary to codon on mRNA.
• There is at least one tRNA molecule for each of the 20 amino acids found in proteins.
• There are fewer tRNA's than codons because some tRNA's pair with more than one codon.
• tRNA synthases are enzymes that recognize which amino acid should join which tRNA molecule
• An amino acid-tRNA complex forms, then travels into the cytoplasm to a ribosome for protein synthesis.

Role of Ribosomal RNA (rRNA)

• Ribosomal RNA (rRNA) is produced from a DNA template in the nucleolus of nucleus.
• Ribosomal RNA (rRNA) combines with dozens of proteins to form a complex structure called a ribosome.
• rRNA is packaged with a variety of proteins into ribosomal subunits, one larger than the other.
• Subunits move separately through nuclear envelope pores into cytoplasm where they combine.
• Ribosomes can float free in cytosol or attach to rough endoplasmic reticulum.
• Ribosomes have one binding site for mRNA and two binding sites for transfer RNA (tRNA) molecules.
• They facilitate complementary base pairing between tRNA anti-codons and mRNA codons; rRNA reads the codons.
• Ribosomes move down the mRNA molecule, new tRNA's arrive; amino acids join; and a polypeptide (protein) forms.
• Translation terminates once the polypeptide is formed; and the ribosome dissociates into its two subunits.
• Ribosomes are first free in the cytoplasm ; once synthesis begins, some have a series of amino acids called a signal sequence that enables the ribosome to bind to the endoplasmic reticulum.
• Nearly all polypeptide (proteins) have a signal sequences that target them for a final location in a cell.

Process of Translation

1. Chain Initiation
   • A small ribosomal subunit attaches to mRNA in the vicinity of the start codon: a base triplet (AUG).
   • The initiator tRNA pairs with this codon.
   • Then the large ribosomal subunit joins to the small subunit.
2. Chain Elongation
   • tRNA matches complimentary anitcodons with the mRNA codons
3. Chain Termination
   • Termination of protein synthesis occurs at a stop codon that does not code for an amino acid.
   • The protein is cleaved by an enzyme and released from the last tRNA.
   • tRNA and the protein leave the ribosome, which dissociates into its two subunits.

Genetic Code Qualities

• Universal for all organisms
• Based on 64 codons
• Comes with start and stop codons
• Redundant (more than 1 codon can represent the same amino acids)

Mutations and Their Effects

• The protein is unchanged – the new codon may specify the same amino acid as the old codon. Ex: UUU mutates to UUC, but both codons code for phenylalanine.
• The new protein may be similar to the original one – the new codon may specify a different amino acid, but may not change the function of the new protein produced
• The new codon and resulting amino acid may produce a non-functional protein.
  • EX: The original strand is: UUUAAACCCGGG which codes for the amino acids: Phenylalanine, Lysine, Proline, and Glycine, but there is a deletion mutation and one of the Us is deleted so now the strand is: UUAAACCCGGG, which codes for Lysine (UUA), Asparagine (AAC), Proline (CCG).

Impact of Mutations on Evolution

• Approximately 1 in $10^5$ – $10^6$ eggs or sperm carry a mutation
• Most mutations are harmful or neutral
• Mutations create new gene sequences and are the ultimate source of genetic variation
• Mutant gene sequences that are beneficial may spread through a population and become common

Examples of Genetic Sequences

• If the DNA triplets were GAT-TCA, the mRNA codons would be? CUA-AGU
• If a segment of DNA had the sequence C-G-A-T-G-C-T-A-C, the messenger RNA complementary to it would have what sequence? GCUACGAUG
• If the DNA triplets were AAG-CAT, the tRNA anticodons would be? AAG-CAU

Gene Regulation

• The human genome contains ~ 30,000 genes
• A given cell “expresses” (transcribes) only a small number of genes
• Some genes are expressed in all cells
• Other genes are expressed only:
  • In certain types of cells
  • At certain times in an organism’s life
  • Under specific environmental conditions