Unit 1 Biochemistry PDF

## Unit 1 - Biochemistry ### Functional groups - Atom / group of atoms that give molecules specific physical & chemical properties. - Hydroxyl (OH) - Polar - Amino (NH2) - Polar - Carbonyl (O) - Polar - Sulfhydryl (SH) - Polar - Carboxyl (O-OH) - Polar - Phosphate (PO4) - Polar -...

## Unit 1 - Biochemistry ### Functional groups - Atom / group of atoms that give molecules specific physical & chemical properties. - Hydroxyl (OH) - Polar - Amino (NH2) - Polar - Carbonyl (O) - Polar - Sulfhydryl (SH) - Polar - Carboxyl (O-OH) - Polar - Phosphate (PO4) - Polar - Methyl (CH3) - Non-polar ### Carbohydrates - Contain many hydroxyls → polar - Easily accessible energy storage - Monomers bond together with a glycosidic linkage to form a polysaccharide. - Alpha linkage = bulkier (helical) - Structure - Glycogen & Starch - Beta linkage = - Cellulose #### Glycogen - Flat structure - From alpha glucose - Short term animal energy storage - Many branches (fast to break down) #### Starch - From alpha glucose - Short term plant energy storage - Fewer branches (slower to break down) #### Cellulose - From beta glucose - Plant structural support - Long straight chains, H⁺ bonded to H⁺ ### Lipids - Fats - Phospholipids - Steroids - Wax #### Isomer - Compound with the same molecular formula but with different structures. - Structure / shape dictates function - Biological Reactions - Reactions that take place between functional groups. - Ethers (between 2 hydroxyls) - Dehydration = rxn where H2O is removed. - Synthesis - To produce a bigger molecule - Hydrolysis = rxn where H2O is added to make smaller molecules. - Ester Linkages → hydroxyl + carboxyl - Phosphate Ester → hydroxyl + phosphate - Peptide Linkage → carboxyl + amino - Ester = common in lipids - Phosphate = common in lipids + nucleic acids - Peptide = common in protein. #### Phospholipids - Composed of C, H & O - Energy rich (many bonds) + long term energy storage. - Contain minimal carboxyl & hydroxyl ∴ non-polar and hydrophobic - Provide cushioning / insulation #### Fats (Triglycerides) - Contain glycerol and fatty acids. - Fatty acids = long C-H chain (14-22) with a carboxyl group - The longer the less soluble. - Saturated - no double bonds - Straight C-H chain (unhealthy) - Solid at room temp. - Unsaturated - one or more double bonds - Not much H ions - Liquid at room temp - 2 types - cis, trans - Cis - very bulky - Liquid at room temp - Trans - pack together well - Very unhealthy. #### Phospholipids - Contain glycerol, two fatty acids, and phosphate group. - Amphipathic (hydrophilic and hydrophobic). - In H2O, form a lipid bilayer. ### Steroids - Hydrophobic molecules composed of 4-linked carbon rings. - Important biological functions: - Cell membrane - Sex hormones ### Waxes - Long chains of FAs linked to OH groups or carbon rings. - Hydrophobic - used as waterproof protection. ### Proteins - Made up of aa monomers bonded together with peptide bonds to make a polypeptide. - Proteins are made up of 14 polypeptides. - Polypeptides fold into 3D shape that gives its function. #### Levels of protein structure - **Primary structure (1°)** - aa - aa - aa - aa - Order of amino acids. - **Secondary structures (2°)** - Coiling or folding due to polarity of C-N backbone. - Alpha Helix (coiling) - Beta pleated sheets (folding) - **Tertiary structures (3°)** - R groups interact creating folds in protein chains. - **Quaternary structure (4°)** - Various polypeptides can join together. #### Denaturation - Changes in pH, temp, ion, etc. can disrupt and change proteins’ shape, disrupting function. #### Cell membrane - Sterols - Cholesterol - Hydrophobic - Helps maintain fluidity when temp changes. - Polar phosphate head (non-polar hydrophobic tails) - Saturated - Unsaturated ## Unit 2 - Metabolism ### ATP + Redox Rxns - **Exergonic** = rxns that overall release energy - **Endergonic** = rxns that overall absorb energy. - **Biological Pathway** = Rxn 1 (energy coupled rxn ) Rxn 2 - **ATP** = Adenine triphosphate - The molecule used to store free chemical energy inside cells. - Ribose - 3 phosphates (Adenosine) - **Phosphorylation** = the attachment of a phosphate group to a molecule. - Can be converted to: - Chemical energy - Mechanical energy - Heat - Transport across cell membrane. #### Oxidation - reduction (Redox) - Oxidation is loss of e- (OIL) - Reduction is gain of e- (RIG) ### Cellular Respiration - C6H12O6 + 6O2 → 6CO2 + 6H2O ### Photosynthesis - 6CO2 + 6H2O → C6H12O6 + 6O2 ### Aerobic Respiration - 1 glucose → 36-38 ATP - Glycolysis: 1 glucose → 2 pyruvate - 2 ATP - 2 NADH - Could shuttle across but could also have a cost. ### Glycolysis - **Hexokinase** - Glucose + ATP → Glucose 6-phosphate + H+ - **Phosphoglucose Isomerase** - Glucose 6-phosphate → Fructose 6-phosphate - **Phosphofructokinase** - Fructose 6-phosphate + ATP → Fructose 1,6-biphosphate + ADP + H+ - **Aldolase** - Fructose 1,6-biphosphate → Dihydroxyacetone phosphate + Glyceraldehyde 3-phosphate - **Triose phosphate Isomerase** - Dihydroxyacetone phosphate → Glyceraldehyde 3-phosphate - **Glyceraldehyde 3-phosphate dehydrogenase** - G3P + NAD⁺ + Pi → 1,3-biphospoglycerate + NADH + H⁺ - **Phosphoglycerate Kinase** - 1,3-bisphosphoglycerate → 3-phosphoglycerate + ATP - **Phosphoglycerate mutase** - 3-phosphoglycerate → 2-phosphoglycerate - **Enolase** - 2-phosphoglycerate → Phosphoenolpyruvate (PEP) + H2O - **Pyruvate Kinase** - PEP + ADP + H+ → Pyruvate + ATP #### Substrate level phosphorylation = process of making ATP by adding (P) to ADP - Steps 6-10 x 2 (because 2 G3Ps) #### Transport shuttles 1. **Glycerol 3-phosphate shuttle** - Energy is lost. Produces 36 - ATP - NADH → (redox) → Substrate redox → FAD⁺ → 2e⁺ + H⁺ → FADH (carries less ATP) 2. **Malate-asparatate shuttle** - Energy not lost. Produces 38 ATP - NADH → (redox) → Substrate redox → NAD⁺ → 2e⁻ + H⁺→ NAD⁺ (no cost) ### Pyruvate oxidation 1. The carboxyl end is removed as CO2 (decarboxylation) 2. Pyruvate is oxidized into acetate; while NAD⁺ is reduced to NADH + H⁺ 3. A coenzyme - A is attached to acetate, formin acetyl-CoA. ### Citric acid cycle 1. Acetyl - CoA + oxaloacetate → citrate - Citrate synthase 2. Citrate → isocitrate - Aconitase 3. Isocitrate + NAD⁺ → α-ketoglutarate + NADH + CO2 - Isocitrate dehydrogenase (redox) 4. α-ketoglutarate + NAD⁺ → Succinyl-CoA + NADH + CO2 - α-ketoglutarate dehydrogenase (redox) 5. Succinyl-CoA + GDP → succinate + GTP - Succinyl-CoA synthetase 6. Succinate + FAD⁺ → fumarate + FADH2 - Succinate dehydrogenase (redox) 7. Fumarate + H2O → Malate - Fumarase 8. Malate + NAD⁺ → oxaloacetate + NADH - Malate dehydrogenase (redox) #### Oxidative phosphorylation = the process of making ATP through transport of H⁺ - Proton/electrochemical gradient = difference in [H⁺] from one side to another. - Contributor to [H⁺] gradient 1. Proton Pumps 2. H2O formation (lessens) ### Electron transport chain process 1. **Complex I (NADH reductase)** - NADH is oxidized to NAD⁺; e⁻ are donated to complex I. - During this transfer, H⁺ (protons) are pumped from matrix to intermembrane space. 2. **Complex II (succinate dehydrogenase)** - FADH2 is oxidized to FAD⁺ and lost e⁻ go to complex II. - Does not pump protons. 3. **Coenzyme Q** - Acts as a shuttle to complex III. - Carries e⁻ from Complex I and II. 4. **Complex III (cytochrome c1)** - e⁻ pass from complex I and II (redox centers) - Protons pumped to intermembrane space (low EN → high EN). 5. **Cytochrome c** - Acts as shuttle to move e⁻ from complex III to complex IV. 6. **Complex IV** - e⁻ transferred to O2 (final e acceptor). - O2 + H⁺ + e⁻ forms water. 7. **ATP synthase** - Proton gradient drives ATP synthase since H⁺ flow back into matrix and energy is used to make ATP (ADP + Pi) - Process = Oxidative phosphorylation ### Alternate pathways - **Glycolysis** (triglyceride (G3P)) - Pyruvate - Acetyl-CoA - Citric acid cycle - Fatty acids (acetyl CoA) - **Amino (2C)** - can go in anywhere depending on R-group - **Beta-oxidation** = process of chemically breaking down fatty acids into 2 acetyl-CoA. - **Deamination** = process in which the amino (NH2) group is removed. ## Unit 3 - Molecular Genetics ### DNA structure & organization - **DNA** - Deoxyribose sugar - Phosphate group - Nitrogenous base - Adenine (A) - purine - Guanine (G) - purine - Cytosine (C) - pyrimidine - Thymine (T) - pyrimidine - Uracil (U) - pyrimidine - **Structure** - DNA’s nitrogenous bases held by hydrogen bonds. - DNA strands run antiparallel (opposite directions) - 5’ - 3’ - 3’ - 5’ - Thymine forms 2 hydrogen bonds with adenine (T = A) - Cytosine forms 3 hydrogen bonds with guanine (C = G) - **Organization** - DNA length is wrapped around histones to form a nucleosome. - Nucleosome coils into chromatin fibres. - Chromatin fibres form chromosomes. ### Gene to protein - **Intron** = non-coding regions (Prokaryotes x, Eukaryotes v) - **Exon** = coding regions (Prokaryotes & Eukaryotes v) - **mRNA** = “messenger” RNA - Carries code for proteins from DNA. - Carries codons - **tRNA** = “transfer” RNA - Matches codon with its anticodon. - **rRNA** = ribosomal RNA - Works with proteins to form ribosomes. ### DNA Replication - DNA replication begins at the replication origin = a specific sequence (helicase binds to). - This forms a replication bubble and helicase disrupts H-bonds, unzipping DNA. - This forms a replication fork. - SSB proteins attach to sugar phosphate to prevent reannealing. Gyrase also makes cuts to prevent coiling and release tension. - **Leading strand** = reads 3’ - 5’ - RNA primase places RNA primers which provides a 3’ end for DNA poly III. - Nucleotide triphosphates go through hydrolysis and dehydration synthesis to build DNA. - **Lagging strand** = reads 5’ - 3’ - RNA primase places RNA primer - DNA polymerase I replaces RNA with DNA. - Ligase fills empty spaces by ligation. - DNA polymerase II proofreads and fixes mistakes. - **Semiconservative replication** = two parent strands have new strand. ### Characteristics of the code - **Continuous** - **Has a reading frame** - If deletion or insertion occurs, the reading frame shifts. - **Redundant** - 64 codons for 20 amino acids - Prevents drastic effects w wobble position. - **Universal** - Same codon, same aa for all species. ### Transcription - RNA polymerase initiates transcription by scanning non-coding DNA strand. - It finds the promoter sequence and starts opening DNA strands. - Prokaryotes - TATAAT Box - RNA poly - Eukaryotes - TATA Box - RNA Poly - Reads 3’ - 5’ copies 5’ - 3’; stops at terminator sequence. - Eukaryote → pre-mRNA - Must be processed further before leaving nucleus. - Addition of a poly-A Tail: Add adenines to 3’ end. - Prevent degradation of mRNA by RNA enzymes in cytoplasm. - Add G-cap to 5’ end: Add 7 guanines to 5’ end - Acts as recognition site for ribosomes. - Spliceosomes: - Made of snRNPs (small ribonucleic proteins) that cut out introns. - Alternative splicing = different splicing patterns = different polypeptides. - *Now is mature RNA* ### Lac Operon - *Promoter* - *Operator* - Genes that code for breakdown of lactose - *Repressor protein attaches and blocks RNA poly, lac operon* - *Lactose present changes shape of active site repressor protein* - *Effector molecule* - Transcription - *Lac operon* ### Translation - **Initiation** - 5’ end & cap is recognized: - Small ribosome subunit binds to mRNA. - Initiator aa-tRNA (Met) binds. - Large ribosome subunit binds with initiator aa-tRNA in P-site. - Always starts with AUG codon. - **Elongation** - New aa-tRNA brings next aa to A-site. - Ribosomes form a peptide bond between two aa’s to form a polypeptide. - Ribosome moves over one codon. - tRNA in P-site → E- site (exit) - aa-tRNA in A-site → P-site - **Termination** - Translation stops at a stop codon. - Release factor protein helps ribosome subunits fall of mRNA. - Polypeptide chain is releaded. - **Protein modification** - Some aa’s may be glycosylated (sugar added) or phosphorylated (phosphate added). - Enzymes may cleave/cut at specific places. - Folding occurs. ### Binding sites: - A-site = holds incoming aa-tRNA’s - P-site = holds aa-tRNA growing chain - E-site = where tRNAs exit. ## Unit 4 - Homeostasis ### Nervous system - **Central nervous system** - Brain - Spinal cord - **Peripheral Nervous system** - Sensory pathways - Afferent system (into CNS!) - Motor pathways - Efferent system (out of CNS!) #### Action potential - Ion potential = produced when graded potential reaches threshold potential, which is reached and caused by voltage gated channels. A change in membrane potential difference. - Hyperpolarized (-90mV) - Resting potential (-70 mV) - Stimulus - Threshold potential (-50mV) - Na⁺ channels open - Depolarization (40 mV) - Na⁺ channels close - K⁺ channels open - Repolarization - All or none events! - Entire process continues down axon till axon terminal. #### Peripheral nervous system - **Somatic nervous system** - Skeletal muscles - Voluntary! - **Autonomic nervous system** - Smooth muscles & glands - Involuntary! - **Sympathetic nervous system** - Fight or flight - **Parasympathetic nervous system** - Relaxation ### Feedback loops - **Negative** - Normal conditions - Changed and process stops - Change occurs - Corrects change - **Positive** - Normal conditions - Change increases - End point reached - Change occurs - Processes amplify change - **Sensor** = tissue/organ that detects change. - **Integrator** = the control centre that compares existing and ideal conditions. - **Effector** = the system that brings the system to its optimal state. ## Unit 5 - Hormones ### Thyroid hormone - Produced by thyroid gland - To produce thyroid hormones, iodine is necessary. - Hormones: - Thyroxine (T4) - Most cells - Triiodothyronine (T3) - Increases metabolic rate and is essential for body growth. - Hypothalamus → TRH (thyroid releasing hormone). - Anterior Pituitary → TSH (thyroid stimulating hormone). - Thyroid Gland - T3 - T4 ### Anti-diuretic hormone (ADH) - Released by the posterior pituitary. - Acts in the kidney → Increases blood volume and pressure by increasing H2O absorption in nephron. - Hypothalamus → ADH releasing hormone. - Posterior Pituitary → ADH - Collecting duct → opens aquaporins - Reabsorption of H2O - Less urinary output - ADH helps regulate blood pressure. - It helps the body retain water by acting on the collecting duct in the kidney. ### Reproductive hormones - **Estrogen** - Stimulates puberty. - Development of secondary sexual characteristics. - **Progesterone** - Prepares and maintains uterus for pregnancy - Growth and development of embryo. ## Female reproductive system - Hypothalamus → GnRH - Anterior Pituitary → FSH and LH - Growing follicle - Estrogen - Ovulation - Corpus luteum - Some estrogen, lots of progesterone - ↑ Estrogen and progesterone inhibit FSH and LH. ## Male reproductive system - Hypothalamus → GnRH - Anterior Pituitary → LH and FSH - Leydig cells → testosterone - Sertoli cells → spermatogenesis - Inhibin ### Pituitary glands - Located below the brain - Has 2 major lobes: - Anterior - Posterior - Produces hormones that control most of the other endocrine glands. - Posterior Pituitary - Anti-diuretic hormone (ADH) - Oxytocin.