Enzymes in Biology

Definition: Biological molecules, typically proteins, that speed up chemical reactions in living organisms
Characteristics:
- Highly specific to a particular reaction or substrate
- Increase reaction rates without being consumed by the reaction
- Optimal pH and temperature for activity
- Inhibited or activated by various molecules
Types:
- Oxidoreductases (catalyze oxidation-reduction reactions)
- Transferases (catalyze transfer of groups between molecules)
- Hydrolases (catalyze hydrolysis reactions)
- Ligases (catalyze formation of new bonds)
- Isomerases (catalyze isomerization reactions)
Regulation:
- Allosteric regulation (conformational change in response to binding of inhibitor or activator)
- Feedback inhibition (end product of a pathway inhibits an enzyme earlier in the pathway)
- Covalent modification (phosphorylation, ubiquitination, etc.)

Definition: Series of enzyme-catalyzed reactions that convert a starting molecule into a product
Types:
- Catabolic pathways (break down molecules to release energy)
- Anabolic pathways (build molecules using energy)
- Amphibolic pathways (involved in both catabolism and anabolism)
Key pathways:
- Glycolysis (breakdown of glucose to pyruvate)
- Citric acid cycle (breakdown of acetyl-CoA to produce ATP, NADH, and FADH2)
- Pentose phosphate pathway (generate NADPH and pentoses)
- Fatty acid synthesis (build fatty acids from acetyl-CoA)
Regulation:
- Substrate inhibition (high concentrations of substrate inhibit enzyme activity)
- Product inhibition (high concentrations of product inhibit enzyme activity)
- Hormonal regulation (insulin, glucagon, etc.)

Primary structure: Sequence of amino acids in a protein
Secondary structure: Local folded structures, such as alpha helices and beta sheets
Tertiary structure: Overall 3D shape of a protein
Quaternary structure: Interaction between multiple polypeptide chains
Types of bonds:
- Hydrogen bonds (between amino acids and water)
- Ionic bonds (between charged amino acids)
- Disulfide bonds (between cysteine residues)
- Peptide bonds (between amino acids)

Semiconservative replication: Each new DNA molecule contains one old strand (template) and one new strand
Steps:
1. Initiation: Binding of helicase to origin of replication, unwinding of DNA
2. Unwinding: Separation of DNA strands, binding of primers
3. Synthesis: Addition of nucleotides to template strands, proofreading and editing
4. Elongation: Continuous synthesis of new DNA strands
5. Termination: Completion of DNA replication, ligation of Okazaki fragments
Enzymes involved:
- Helicase (unwinds DNA)
- Primase (synthesizes primers)
- Polymerase (synthesizes new DNA strands)
- Ligase (joins Okazaki fragments)

Definition: Process by which cells respond to stimuli, such as hormones, growth factors, or neurotransmitters
Types of signaling:
- Autocrine signaling: Signaling within a cell
- Paracrine signaling: Signaling between nearby cells
- Endocrine signaling: Signaling between distant cells
Signal transduction pathways:
- Receptor tyrosine kinases: Activate downstream signaling pathways
- G-protein coupled receptors: Activate G-proteins, which activate downstream signaling pathways
- Ligand-gated ion channels: Directly open or close ion channels
Second messengers:
- Cyclic AMP (cAMP): Activates protein kinase A
- Inositol triphosphate (IP3): Releases calcium from intracellular stores
- Diacylglycerol (DAG): Activates protein kinase C

Enzymes are biological molecules, typically proteins, that speed up chemical reactions in living organisms
They are highly specific to a particular reaction or substrate
Enzymes increase reaction rates without being consumed by the reaction
They have an optimal pH and temperature for activity
Enzymes can be inhibited or activated by various molecules

Allosteric regulation involves a conformational change in response to binding of an inhibitor or activator
Feedback inhibition occurs when the end product of a pathway inhibits an enzyme earlier in the pathway
Covalent modification involves phosphorylation, ubiquitination, etc.

Metabolic pathways are series of enzyme-catalyzed reactions that convert a starting molecule into a product
Catabolic pathways break down molecules to release energy
Anabolic pathways build molecules using energy
Amphibolic pathways are involved in both catabolism and anabolism

Substrate inhibition occurs when high concentrations of substrate inhibit enzyme activity
Product inhibition occurs when high concentrations of product inhibit enzyme activity
Hormonal regulation involves insulin, glucagon, etc.

The primary structure is the sequence of amino acids in a protein
The secondary structure consists of local folded structures, such as alpha helices and beta sheets
The tertiary structure is the overall 3D shape of a protein
The quaternary structure is the interaction between multiple polypeptide chains
Types of bonds include hydrogen bonds, ionic bonds, disulfide bonds, and peptide bonds

DNA replication is semiconservative, meaning each new DNA molecule contains one old strand and one new strand
The process involves initiation, unwinding, synthesis, elongation, and termination
Enzymes involved in DNA replication include helicase, primase, polymerase, and ligase

Cell signaling is the process by which cells respond to stimuli, such as hormones, growth factors, or neurotransmitters
Types of signaling include autocrine, paracrine, and endocrine signaling
Signal transduction pathways involve receptor tyrosine kinases, G-protein coupled receptors, and ligand-gated ion channels
Second messengers include cAMP, IP3, and DAG