Cellular Metabolism Notes

Cellular Metabolism

Metabolic Reactions

• Metabolism: The sum of all chemical reactions in the body.
• Cellular Metabolism: The sum of all chemical reactions occurring in a cell. These reactions usually occur in pathways or cycles.
• Types of Metabolic Reactions:
  • Anabolism: Small molecules are built into larger ones, requiring energy (ATP).
  • Catabolism: Larger molecules are broken down into smaller ones, releasing energy.

Anabolism and Catabolism

Anabolism

• Provides materials for maintenance, cellular growth, and repair.
• Requires ATP, which is produced during catabolism.
• Example: Dehydration synthesis
  • Smaller molecules are bound together to form larger ones.
  • H_2O is produced in the process.
  • Used to produce polysaccharides, proteins, and triglycerides.

Catabolism

• Breaks down larger molecules into smaller ones.
• ATP is produced.
• Example: Hydrolysis
  • Used to decompose carbohydrates, proteins, and lipids.
  • Uses H_2O to split the substances.
  • Reverse of dehydration synthesis.

Control of Metabolic Reactions

• All cells perform both catabolic and anabolic reactions.
• Rates of catabolism and anabolism must be carefully controlled to balance energy release and utilization.
• Imbalances can damage or kill a cell.
• Different cell types conduct specialized metabolic processes.
• Enzymes: Control the rates of both catabolic and anabolic reactions and greatly increase reaction rates.

Enzyme Action

• Enzymes (protein catalysts):
  • Globular proteins that catalyze specific reactions.
  • Increase rates of chemical reactions.
  • Lower the activation energy necessary to start reactions.
  • Not consumed in the reaction, so they are used repeatedly.
  • Each enzyme is specific to a particular substrate.
  • Ability to recognize substrate depends on the shape of the active site of the enzyme.
  • Many enzymes are named after their substrate, with the suffix "-ase" (e.g., "lipase" breaks down lipids).

Enzymes and Metabolic Pathways

Metabolic Pathways

• Series of enzyme-controlled reactions leading to the formation of a product.
• Each new substrate is the product of the previous reaction.
• Each step of a pathway is catalyzed by a different enzyme.

Rate-Limiting Enzyme

• A regulatory enzyme that catalyzes one step of pathway typically sets the rate for the entire reaction sequence.
• The number of molecules of this enzyme is limited.
• Often the first enzyme in the reaction sequence.
• In some pathways, the end product inhibits the rate-limiting enzyme (negative feedback).

Factors That Alter Enzymes

Cofactor

• Non-protein substance that combines with the enzyme to activate it.
• Some help fold the active site into the proper conformation.
• Some help bind the enzyme to the substrate.
• Can be an ion, element, or small organic molecule (coenzyme).

Coenzyme

• Organic molecule that acts as a cofactor.
• Most are vitamins, which are essential organic molecules that humans must obtain from their diet.

Denaturation

• Inactivation of an enzyme (or any other protein) due to an irreversible change in its conformation.
• Results in the enzyme being unable to bind to the substrate.

Energy for Metabolic Reactions

• Energy: The capacity to change something or the ability to do work.
• Common forms of energy: Heat, light, sound, electrical energy, mechanical energy, and chemical energy.
• Energy cannot be created or destroyed, but it can be changed from one form to another.
• Cellular respiration: Process that transfers energy from molecules and makes it available for cellular use.
• Most metabolic reactions use chemical energy.

Release of Chemical Energy

• Many metabolic processes require chemical energy, which is stored in ATP.
• Energy is held in chemical bonds and released when bonds are broken.
• Oxidation releases energy from glucose and other molecules via the loss of hydrogen atoms and their electrons.
• In cells, enzymes lower the activation energy needed for oxidation in reactions of cellular respiration.
• Energy is transferred to ATP:
  • 40% is released as chemical energy.
  • 60% is released as heat, which maintains body temperature.

ATP Molecules

• ATP (Adenosine Triphosphate):
  • Molecule that carries energy in a form the cell can use.
  • Main energy-carrying molecule in the cell.
  • Energy from ATP breakdown is used for cellular work.
  • Composed of three portions:
    • Adenine
    • Ribose (a sugar)
    • Three phosphates in a chain
  • The second and third phosphates are attached by high-energy bonds; energy can be quickly transferred to other molecules.

Carbohydrate Storage

• Carbohydrate molecules from foods can:
  • Enter catabolic pathways for energy production.
  • Enter anabolic pathways for storage.
  • React to form some amino acids.
• Excess glucose can be converted into and stored as:
  • Glycogen: Most cells, but liver and muscle cells store the most.
  • Fat: For storage in adipose tissue.

DNA (Deoxyribonucleic Acid)

• Deoxyribonucleic acid (DNA):
  • The genetic material.
  • Molecule that stores information on its sequence of nucleotides, which instructs a cell how to synthesize certain proteins.
  • The proteins coded for on DNA function as:
    • Enzymes
    • Blood proteins
    • Structural proteins of muscle and connective tissue
    • Antibodies
    • Cell membrane components

Genetic Information

• Genetic information: Instructions to tell cells how to construct proteins, stored in DNA sequence.
• Gene: Sequence of DNA that contains information for making one protein.
• Genome: Complete set of genetic information in a cell.
• Exome: Small portion of the genome that codes for proteins.
• Gene Expression: Control of which proteins are produced in each cell type, in what amount, and under which circumstances.

Structure of DNA

• Double helix:
  • Double-stranded molecule consisting of two chains of nucleotides.
  • DNA resembles a ladder twisted into a spiral.
  • The backbone of each strand is a sugar-phosphate chain.
  • Bases from the two complementary strands are linked together by hydrogen bonds: C-G, A-T.
• Nucleotides: Building blocks of DNA, consisting of:
  • 5-carbon sugar, deoxyribose
  • A phosphate group
  • A nitrogenous base (adenine, cytosine, guanine, or thymine)

DNA and Chromosome Structure

• The two nucleotide chains of the double helix are antiparallel (point in opposite directions).
• Complementary Base Pairing: Bases pair only with specific partners (A-T and C-G).
• A and G are purines, and C and T are pyrimidines.
• A purine only binds to a specific pyrimidine.
• DNA wraps around histone proteins to give the double helix a compact form in chromatin and chromosomes.

Protein Synthesis

• A sequence of 3 nucleotides provides a template for complementary RNA.
• Each unit of 3 RNA nucleotides represents a genetic code.
• The sequence of bases in a gene determines the amino acid sequence in a polypeptide.
• Each sequence of 3 nucleotides either represents an amino acid or signals to start or stop protein synthesis.
• Protein synthesis involves the processes of transcription and translation.

Transcription

• DNA (deoxyribonucleic acid) stores the master copy of the genetic code and remains in the nucleus.
• Protein synthesis occurs in the cytoplasm.
• RNA (ribonucleic acid) copies and transfers information from DNA to the cytoplasm.
• Transcription: The process of copying a DNA sequence onto an RNA sequence.
• Messenger RNA (mRNA): The type of RNA that carries genetic code from DNA to the ribosome in the cytoplasm.
• RNA Polymerase: Enzyme that catalyzes the formation of mRNA from the proper strand of DNA.

Translation

• Each amino acid is specified by a sequence of 3 bases in DNA, called codons.
• Protein synthesis occurs in the cytoplasm.
• mRNA leaves the nucleus and binds to a ribosome to act as a template for protein synthesis.
• At the ribosome, the genetic code, carried by mRNA, is used to synthesize a protein.
• Translation: The process of converting the genetic code, carried by mRNA, into a sequence of amino acids that becomes a protein.

Translation Details

• Protein synthesis requires that amino acids are added to the growing polypeptide chain in the proper sequence.
• Transfer RNA (tRNA): Aligns amino acids during translation along the mRNA strand on the ribosome.
• tRNA binds to its amino acid, transports it to a ribosome, binds to the mRNA according to its sequence, and adds its amino acid to the growing polypeptide chain.
• Each tRNA contains a sequence of 3 nucleotide bases, the anticodon, which binds to the complementary codon on the mRNA strand.
• As the ribosome moves down mRNA, each tRNA brings in its amino acid to be added to the growing protein.

Codons and Translation

• There are 20 types of amino acids.
• There are 64 possible codons (3-base sequences) on mRNA.
• Most codons correspond to amino acids.
• 1 to 4 mRNA codons code for each amino acid.
• The Initiation codon, AUG, codes for Methionine and signals the start of a protein.
• 3 codons are Stop codons, signaling the end of a protein; these do not have corresponding tRNAs.
• For each mRNA codon coding for an amino acid, there is a corresponding tRNA anticodon.

Ribosomes and Translation

• Ribosomes:
  • Organelles composed of Ribosomal RNA (rRNA) and protein molecules.
  • Composed of 2 unequal subunits.
  • Binding of tRNA and mRNA occurs in association with a ribosome.
  • The ribosome moves down the mRNA molecule, bringing in tRNAs carrying the proper amino acid to add to the growing protein chain.
  • Amino acids are joined by peptide bonds.
  • When the ribosome reaches a “stop” codon, the protein is released.
  • Ribosomes, mRNA, and rRNA can be used repeatedly.

Protein Synthesis Steps

Transcription (In the Nucleus)

1. RNA polymerase binds to the DNA base sequence of a gene.
2. This enzyme unwinds and exposes part of the DNA molecule.
3. RNA polymerase moves along one strand of the exposed gene and catalyzes the synthesis of an mRNA, whose nucleotides are complementary to those of the strand of the gene.
4. When RNA polymerase reaches the end of the gene, the newly formed mRNA is released.
5. The DNA rewinds and closes the double helix.
6. The mRNA passes through a pore in the nuclear envelope and enters the cytoplasm.

Translation (In the Cytoplasm)

1. A ribosome binds to the mRNA near the codon at the beginning of the messenger strand.
2. A tRNA molecule that has the complementary anticodon brings its amino acid to the ribosome.
3. A second tRNA brings the next amino acid to the ribosome.
4. A peptide bond forms between the two amino acids, and the first tRNA is released.
5. This process repeats for each codon in the mRNA sequence as the ribosome moves along its length, forming a chain of amino acids.
6. The growing amino acid chain folds into the unique conformation of a functional protein.
7. The completed protein molecule is released. The mRNA, ribosome, and tRNA are recycled.