Gene Expression and Protein Synthesis Gene expression refers to the process by which information from a gene is used to synthesize a functional

Gene expression refers to the process by which information from a gene is used to synthesize a functional gene product, typically a protein.
Key phases:
  - Transcription
  - RNA processing
  - Translation

Transcription is the first step in the process of going from a gene to the corresponding protein.
- Occurs in the nucleus of eukaryotic cells.
- Involves the synthesis of pre-mRNA from the DNA template.
Enzyme: RNA polymerase
- Binds to the promoter region of a gene and unwinds the DNA strands to initiate transcription.
- Synthesizes pre-mRNA by adding complementary RNA nucleotides based on the DNA sequence.

Pre-mRNA is the initial transcript before it undergoes processing.
RNA processing includes:
  - 5' capping: Addition of a 7-methylguanylate cap.
  - Polyadenylation: Addition of a poly-A tail at the 3' end.
  - Splicing: Removal of introns and joining of exons, facilitated by spliceosomes.

Translation is the second step where the mRNA sequence is decoded to produce a protein.
- Occurs at ribosomes in the cytoplasm or on the rough endoplasmic reticulum.
mRNA serves as a template for the amino acid sequence, with transfer RNA (tRNA) transporting amino acids to the ribosome.

Proteins are polymers of amino acids that perform a variety of functions within living organisms.

Refers to the final “touch-ups” made to a newly translated protein.
- These modifications are critical for regulating protein function, localization, stability, and interactions within the cell.
- Modifications can vary based on factors such as cell type and developmental stage.

Folding: Typically guided by chaperone proteins to achieve the correct conformation.
Phosphorylation/Dephosphorylation: Addition/removal of phosphate groups which can activate or deactivate enzymes.
Glycosylation/Deglycosylation: Addition/removal of carbohydrate groups impacting protein stability and interaction.
Lipidation/Delipidation: Addition/removal of lipid molecules playing roles in membrane association and signaling.

Proteins have sorting signals that direct them to the correct cellular locations.
These signals can be intrinsic regions in the protein or a result of post-translational modifications.
Examples:
  - Nuclear Localization Signal: A short sequence of amino acids that directs proteins to the nucleus.
  - Signal Peptides: Direct proteins to the endoplasmic reticulum (ER) for synthesis into the ER.
  - Transit Peptides: Target proteins to chloroplasts or mitochondria.

Cellular respiration is the process by which cells convert sugars into ATP, the energy currency of cells.

$C_6H_{12}O_6 + 6O_2 <br>ightarrow 6CO_2 + 6H_2O + ext{energy}$
It encompasses several stages:
  1. Glycolysis
  2. Pyruvate oxidation
  3. Citric acid cycle
  4. Oxidative phosphorylation

The Sun
- Emits photons that are converted into electrical energy (electrons) by organisms.
- Ultimate source of energy for most life forms.
Photosynthesis
- Converts light and carbon dioxide into sugars, capturing sunlight's energy into chemical forms.
- Anabolic reactions that build organic molecules.
Cellular Respiration
- Metabolic reactions that break down food molecules to produce ATP.
- Catabolic reactions that involve breaking down substances for energy.

Photosynthesis drives energy flow, where low-energy electrons from water are elevated to high-energy levels by sunlight, and these high-energy electrons are used in the reduction of CO2 to yield carbohydrates (e.g., glucose). Oxygen is released in the process.
Cellular respiration involves the oxidation of glucose, where glucose and organic molecules are broken down, and high-energy electrons are removed and transferred to oxygen, releasing energy to form ATP and some energy is lost as heat.

Two primary methods of ATP formation:
1. Substrate-Level Phosphorylation
2. Oxidative Phosphorylation

Involves the direct addition of a phosphate group to ADP from a substrate molecule to produce ATP.
Enzyme catalyzes this transfer.

ATP synthesis driven by electron transport chains where NADH and FADH2 donate electrons, leading to the creation of a proton gradient that powers ATP synthase to generate ATP.
‘Oxidative’ component refers to the oxidation of electron carriers, facilitating the phosphorylation of ADP to produce ATP.

Oxidation
- Loss of electrons.
- When a substrate loses electrons, it is said to be oxidized, and energy is typically released.
Reduction
- Gain of electrons.
- When a substrate gains electrons, it is reduced, and energy is typically absorbed.
Redox Reactions
- Coupled reactions where oxidation and reduction occur simultaneously, as one molecule donates electrons (is oxidized) while another accepts electrons (is reduced).

In a typical redox reaction, a donor (A) transfers its electron to an acceptor (B):
$A <br>ightarrow B$
A loses an electron (oxidized), and B gains it (reduced).

LEO says GER:
- LEO (Lose Electrons = Oxidized)
- GER (Gain Electrons = Reduced)

Essential for energy production in aerobic organisms.
Oxidation of glucose leads to the production of acceptable energy forms (like ATP) while also producing by-products such as CO2 and H2O.