Chapter 17: Molecular Biology – Gene Expression and Regulation

Central Dogma of Molecular Biology

The Central Dogma of Molecular Biology describes the flow of genetic information within a biological system. It states that genetic information is transferred from DNA to RNA to protein.

• DNA is transcribed into RNA.

• RNA is translated into protein.

• This process is fundamental for gene expression and cellular function.

• Example: The gene for hemoglobin is transcribed and translated to produce the hemoglobin protein in red blood cells.

The Genetic Code

The Genetic Code is a set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins by living cells.

• Each set of three nucleotides (codon) in mRNA corresponds to a specific amino acid.

• The code is nearly universal among organisms.

• Example: The codon AUG codes for the amino acid methionine and also serves as the start codon for translation.

Transcription: Locations, Components, and Mechanisms

Transcription is the process by which a segment of DNA is copied into RNA by the enzyme RNA polymerase.

• RNA Polymerase II synthesizes mRNA in eukaryotes.

• Sigma factor (in prokaryotes) helps RNA polymerase recognize the promoter region.

• Promoter: DNA sequence where transcription begins.

• Preinitiation complex: Assembly of proteins required for transcription initiation.

• Example: The TATA box is a common promoter element in eukaryotic genes.

Processing of pre-mRNA into mRNA

After transcription, pre-mRNA undergoes several modifications to become mature mRNA.

• Spliceosome: Removes introns and joins exons.

• 5' Cap: Added to the 5' end for stability and initiation of translation.

• Poly-A tail: Added to the 3' end for stability and export from the nucleus.

• Example: Human beta-globin pre-mRNA is spliced to remove non-coding regions before translation.

Structure and Function of Ribosomes

Ribosomes are the molecular machines that synthesize proteins by translating mRNA.

• Composed of two subunits: small and large.

• Contain A (aminoacyl), P (peptidyl), and E (exit) sites for tRNA binding and movement.

• Example: Eukaryotic ribosomes are 80S (40S small, 60S large); prokaryotic ribosomes are 70S.

Template and Non-Template DNA Strands

During transcription, only one DNA strand is used as the template for RNA synthesis.

• Template strand: The DNA strand that is transcribed.

• Non-template (coding) strand: Has the same sequence as the RNA (except T is replaced by U).

• Directionality: Transcription proceeds 5' to 3'.

Types of RNA: mRNA, tRNA, rRNA

Cells use several types of RNA, each with distinct functions.

• mRNA (messenger RNA): Carries genetic information from DNA to ribosomes.

• tRNA (transfer RNA): Brings amino acids to the ribosome during translation.

• rRNA (ribosomal RNA): Structural and catalytic component of ribosomes.

• Example: tRNAPhe carries phenylalanine to the growing polypeptide chain.

Charging of tRNA

tRNA charging refers to the attachment of an amino acid to its corresponding tRNA by aminoacyl-tRNA synthetase.

• Ensures correct translation of the genetic code.

• Example: tRNAMet is charged with methionine for initiation of translation.

Translation: Initiation, Elongation, Termination

Translation is the process of synthesizing a polypeptide from mRNA.

• Initiation: Ribosome assembles at the start codon (AUG).

• Elongation: Amino acids are added one by one to the growing chain.

• Termination: Occurs when a stop codon is reached; the polypeptide is released.

• Example: The stop codons UAA, UAG, and UGA signal termination.

Disassembly of the Translation Complex

After translation is complete, the ribosome, mRNA, and tRNA dissociate.

• Release factors help disassemble the complex.

• Allows ribosomes to be reused for new rounds of translation.

Transcription and Translation Using the Genetic Code

DNA sequences are transcribed into mRNA and then translated into polypeptides using the genetic code.

• Transcription: DNA → mRNA

• Translation: mRNA → polypeptide

• Example: DNA sequence ATG-GAA-TTT is transcribed to mRNA AUG-GAA-UUU and translated to Met-Glu-Phe.

Chapters 8 and 9: Cellular Respiration and Metabolism

Overall Chemical Equation for Cellular Respiration

Cellular respiration is the process by which cells extract energy from glucose and other molecules.

• General equation:

• Glucose and oxygen are converted to carbon dioxide, water, and ATP.

Redox Reactions: Oxidation and Reduction

Redox reactions involve the transfer of electrons between molecules.

• Oxidation: Loss of electrons.

• Reduction: Gain of electrons.

• These reactions are essential for energy production in cells.

• Example: NAD+ is reduced to NADH during glycolysis.

ATP: Cellular Energy Currency

ATP (adenosine triphosphate) is the primary energy carrier in cells.

• Used for muscle contraction, active transport, biosynthesis, and more.

• Energy is released when ATP is hydrolyzed to ADP and inorganic phosphate.

• Equation:

Structure of Mitochondria

Mitochondria are double-membraned organelles where most cellular respiration occurs.

• Outer membrane: Smooth and protective.

• Inner membrane: Folded into cristae, contains enzymes for ATP production.

• Matrix: Contains enzymes for the Krebs cycle.

• Example: The electron transport chain is located in the inner mitochondrial membrane.

NAD+ and FAD: Electron Carriers

NAD+ and FAD are coenzymes that transport electrons during cellular respiration.

• NAD+ is reduced to NADH; FAD is reduced to FADH2.

• They donate electrons to the electron transport chain, driving ATP synthesis.

Stages of Cellular Respiration

Cellular respiration consists of several stages:

• Glycolysis: Occurs in the cytoplasm; glucose is split into two pyruvate molecules.

• Pyruvate Oxidation and Krebs Cycle: Occur in the mitochondrial matrix; pyruvate is converted to acetyl-CoA, which enters the Krebs cycle to produce NADH, FADH2, and ATP.

• Oxidative Phosphorylation: Occurs in the inner mitochondrial membrane; electron transport chain and chemiosmosis generate most ATP.

Fermentation: Alcohol vs. Lactic Acid

Fermentation allows cells to produce ATP without oxygen.

The main goal of fermentation is to regenerate NAD+ so glycolysis can continue in the absence of oxygen.

Metabolism of Carbohydrates, Fats, and Proteins

Cells can use carbohydrates, fats, and proteins as fuel for cellular respiration.

• Carbohydrates: Broken down into glucose for glycolysis.

• Fats: Converted to fatty acids and glycerol; fatty acids undergo beta-oxidation to form acetyl-CoA.

• Proteins: Deaminated and converted to intermediates of the Krebs cycle.

• Example: During fasting, the body uses fat stores for energy.