DNA, Genes, and Transcription Vocabulary

DNA Packaging and Structure

• The DNA in each of your cells is approximately six feet long.
• DNA needs to be structured to avoid becoming a tangled mess.
• Proteins help compact DNA within the cell's nucleus.

Histones

• Histones are proteins that compact DNA.
• A histone is made up of eight individual polypeptides.
• Polypeptides are chains of amino acids that fold into secondary, tertiary, and quaternary structures.
• A histone octamer consists of two copies each of four unique polypeptides.
• DNA wraps around the histone octamer approximately 1.6 times.

Chromatin

• Chromatin is compacted DNA wrapped around histones.
• DNA is most compacted when cells are dividing.
• When cells are not dividing DNA is less compacted so it is accessible for transcription.

Genome vs. Gene

• The genome is all of an individual's DNA, including all chromosomes.
• A gene is a sequence of DNA nucleotides that is transcribed to produce a functional RNA. It doesn't have to encode for a protein but it has to encode for an RNA.
• Genes also include regulatory sequences.

Transcription and Gene Expression

• Transcription is the process of making an RNA copy from DNA.
• DNA stays in the nucleus, so RNA copies are needed to leave the nucleus for protein synthesis.
• Not all genes are made into RNA at all times, especially in multicellular organisms.
• Gene expression refers to a gene being made into a protein.
• The ability to control transcription is crucial for multicellular organisms to ensure proteins are made in the correct tissues and at the appropriate times.

DNA Directionality

• DNA is read in the 3' (three prime) to 5' (five prime) direction.
• The 3' end has the third carbon of the sugar closest to it, while the 5' end has the fifth carbon closest to it.
• Genes can be located on either strand of the DNA molecule.
• RNA polymerase starts at the 3' end and moves to the 5' end of the DNA during transcription.

RNA Directionality

• If DNA is read in the 3' to 5' direction, RNA is made in the 5' to 3' direction.
• RNA is complementary to the DNA strand.
• New nucleotides are added to the 3' end of the growing RNA molecule.
• The antiparallel nature of DNA and RNA binding means RNA runs in the opposite direction of the gene it was transcribed from.
• RNA is built one nucleotide at a time, adding new nucleotides to the three prime end.
• RNA is identical to DNA with the exception of an oxygen atom and the presence of uracil (U) instead of thymine (T).
• Phosphodiester bonds between nucleotides are the same in RNA and DNA.

Gene Structure: Prokaryotes vs. Eukaryotes

• Prokaryotes lack membrane-bound organelles and a nucleus; their DNA is in the cytoplasm.
• Eukaryotes have a membrane-bound nucleus.

Prokaryotic Gene Structure

• Prokaryotic genes have two regulatory regions: a promoter and an operator.
• Promoter: The region where RNA polymerase attaches to DNA.
  • RNA polymerase is the enzyme that makes RNA from DNA.
  • Sigma factors are proteins that guide RNA polymerase to the promoter.
• Operator: Has three structural genes all attached to or controlled by the same promoter. The three genes will always be made into RNA at the same time.
  • Regulator Gene: A gene that is not expressed on the same promoter, encodes for a protein that controls expression of the structural gene.
  • The regulator gene makes a protein that can bind to the operator sequence.
  • The Operator Sequence is a segment of DNA where a repressor binds.
  • Repressor proteins control whether structural genes are made or not.
    • If the repressor protein binds to the operator, the gene is not made.
    • If it is unbound, then the gene is made.

Eukaryotic Gene Structure

• Eukaryotic genes also have a promoter where RNA polymerase binds.
• Eukaryotes have enhancers and silencers.
  • Enhancers: Regions of DNA where transcription factors bind to increase the likelihood of gene transcription. Transcription factors are proteins.
    • Enhancers can be located before or after the coding sequence.
  • Silencers: Regions of DNA that bind to transcription factors to prevent or decrease the likelihood of gene transcription.
• Example:
  • REST is a transcription factor that binds to a silencer before neuron genes.
  • This prevents neuron genes from being expressed in non-neuron cells.
  • Mutations in the silencer sequence or REST can lead to neuron genes being expressed in the wrong places, such as colon cancer, Huntington's disease, etc.

Untranslated Regions (UTRs)

• Five Prime (5') UTR
  • Located on the 3' end of the gene and the 5' end of the RNA.
  • Involved in mRNA binding and attachment to the ribosome, as well as mRNA export from the nucleus.
• Exons: The part of the gene that actually encodes for the amino acid sequence.
• Introns: Sections of the strand that are removed from the RNA before it leaves the nucleus.
  • Alternative splicing involves cutting out varying sections of the strand depending on the circumstance.
• Three Prime (3') UTR
  • Located on the tail end of the mRNA.
  • Involved in mRNA stability, export from the nucleus, and addition of the poly-A tail.