Chapter 4.5-4.7

Chapter 4 Continued: Cellular Metabolism

4.5 DNA (Deoxyribonucleic Acid)

  • Definition: DNA is the genetic material; it is a molecule that stores information on its sequence of nucleotides.

  • Function: Instructs a cell on how to synthesize certain proteins, which include:

    • Enzymes

    • Blood proteins

    • Structural proteins of muscle and connective tissue

    • Antibodies

    • Cell membrane components

Genetic Information

  • Gene: A segment of a DNA molecule that encodes the information to synthesize a protein; serves as a unit of inheritance.

  • Chromosome: Long molecules of DNA wrapped around proteins, organized to form chromosomes.

  • Genome: The complete set of genetic instructions for an organism; all cells (except sex cells) contain two copies of the genome.

  • Exome: The small portion (2%) of the genome that codes for proteins.

  • Gene Expression: The control of which proteins are produced in each cell type, in what amounts, and when.

Structure of DNA

  • Nucleotides: The building blocks of DNA, consisting of:

    • A 5-carbon sugar (deoxyribose)

    • A phosphate group

    • A nitrogenous base (adenine, cytosine, guanine, or thymine)

  • DNA Structure:

    • Double-stranded molecule made up of two chains of nucleotides.

    • The structure resembles a ladder twisted into a spiral (double helix).

    • Bases from the two complementary strands are linked together by hydrogen bonds.

Base Pairing in DNA

  • Complementary Base Pairing: Bases pair only with specific counterparts:

    • Adenine (A) pairs with Thymine (T)

    • Cytosine (C) pairs with Guanine (G)

  • Purines and Pyrimidines:

    • Purines: Adenine (A) and Guanine (G)

    • Pyrimidines: Cytosine (C) and Thymine (T)

    • A purine binds only to a specific pyrimidine.

DNA and Histones

  • Histones: Proteins around which DNA double helix is wound.

  • Chromatin: A group of 8 histones that influence the configuration of chromatin and the accessibility of genes for protein synthesis under certain conditions.

DNA Replication

  • Definition: The process in which an exact copy of a DNA molecule is made, occurring during interphase (specifically the synthesis phase, S).

  • Steps in DNA Replication:

    1. Hydrogen bonds break between base pairs.

    2. Strands unwind and separate via DNA helicase.

    3. New nucleotides pair with exposed bases under the direction of DNA polymerase.

    4. DNA polymerase links new sugar-phosphate backbone through hydrogen bonds.

4.6 Protein Synthesis

  • Overview: A sequence of three DNA nucleotides provides a template for complementary RNA; each unit of three RNA nucleotides is called a codon, representing genetic code.

  • The order of bases in a gene determines the amino acid sequence in a polypeptide chain. Each sequence of three nucleotides can signify:

    • An amino acid

    • A signal to start

    • A signal to stop

  • There are 20 unique amino acids.

  • Processes of Protein Synthesis: Involves enzyme-catalyzed processes of transcription and translation.

RNA Molecules

  • Differences from DNA:

    • RNA is single-stranded.

    • Contains the sugar ribose instead of deoxyribose.

    • Contains Uracil (U) instead of Thymine (T); other bases are Adenine (A), Guanine (G), and Cytosine (C).

    • RNA molecules are generally much shorter than DNA.

  • Types of RNA:

    • Messenger RNA (mRNA)

    • Transfer RNA (tRNA)

    • Ribosomal RNA (rRNA)

Transcription

  • Definition: The process of copying information from DNA into an RNA sequence.

  • Nuclear Pores: Only RNA can exit the nucleus; mRNA is synthesized from the DNA strand.

  • Process of mRNA Synthesis:

    1. RNA Polymerase recognizes the correct strand of DNA to copy and binds to the promoter (a DNA sequence that signals the beginning of a gene).

    2. A section of DNA unwinds to expose the gene coding for the needed protein.

    3. Complementary mRNA nucleotides pair with the DNA bases of the template strand. The mRNA is identical to the non-template (coding) strand, except for the base Uracil (U) in place of Thymine (T).

    4. A termination signal indicates the end of the gene, and the new mRNA strand is released. The DNA rewinds into a double helix.

    5. The mRNA exits the nucleus through a nuclear pore and attaches to a ribosome in the cytoplasm.

Translation

  • Definition: The process of converting the genetic code carried by mRNA into a sequence of amino acids that ultimately forms a protein.

  • Each amino acid is specified by a sequence of three bases (codons) in DNA.

  • Protein Synthesis Location: Occurs in the cytoplasm (either at free ribosomes or rough endoplasmic reticulum).

  • The ribosome uses the genetic code from mRNA to synthesize a protein.

Genetic Code Table

  • Refer to Table 4.2 for specific codons and their corresponding amino acids (e.g.,

    • UUU: Phenylalanine (Phe)

    • UUA: Leucine (Leu)

    • AUG: Start Methionine (Met)

    • UAA, UAG, UGA: Stop codons).

Protein Synthesis and tRNA

  • Process of tRNA: Transfer RNA aligns amino acids during translation along the mRNA strand on the ribosome.

  • tRNA Binding: Each tRNA binds to its specific amino acid and transports it to a ribosome. At the ribosome, it binds to the mRNA and adds its amino acid to the growing polypeptide chain.

  • Chaperones: Proteins that assist in folding the newly synthesized proteins into their unique shapes for functionality.

  • Proteasomes: Spool-shaped structures that process misfolded proteins; proteins can be re-folded or destroyed as necessary.

  • Energy Requirement: Protein synthesis is powered by ATP; 3 ATP molecules are required to link each amino acid to the growing chain.

Gene Expression Regulation

  • Protein synthesis is controlled by the rate at which mRNA is transcribed and the enzymatic degradation of mRNA in the cytoplasm.

  • Transcription Factors: Proteins that activate specific genes during gene expression.

  • Epigenetics: The field of biology focused on modifications of gene expression that do not involve changes in the DNA sequence; can switch a gene on or off.

4.7 Changes in Genetic Information: Nature of Mutations

  • Mutations: Changes in the DNA sequence that occur due to errors in DNA replication.

  • Types of Mutations:

    • Spontaneous: Due to the insertion of an unstable base into the DNA sequence. Missense mutations involve replacing one type of amino acid with another. Nonsense mutations occur when an amino acid-encoding codon is changed to a stop codon.

    • Induced: Result from exposure to mutagens (chemicals or radiation) that cause mutations; e.g., Dravet Syndrome (genetic epilepsy).

Protection Against Mutation

  • DNA Repair: The correction of mismatched nucleotides by repair enzymes helps to maintain genetic integrity.

  • Nature of Genetic Code: Since often 2 to 4 codons specify the same amino acid, mutations that change the third base of a codon may still produce the same amino acid, thus not affecting the protein's function.

  • Presence of Two Copies: When two copies of each chromosome exist, a mutation in one copy can often be compensated for by the second copy, which may maintain enough of the gene’s normal function to preserve health.