Osmosis, Tonicity, pH and Monosaccharides

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Water

• Osmosis involves water moving from a less concentrated (hypotonic) area to a more concentrated (hypertonic) area.
• Diffusion is the movement of a solute from an area of high concentration to an area of low concentration.
• Osmolarity can be hypo-, iso-, or hyperosmolar. Osmolarity (Osm) = i . [M]
• Effective osmolarity, osmotic pressure, or tonicity can be hypo-, iso-, or hypertonic. π= σ. ί. [M].RT
• [M] represents molarity, with molar concentration measured per 1000ml of solution.
• σ is the reflection coefficient, indicating cell membrane permeability, where 0 means permeable and 1 means impermeable.
• i is the Van't Hoff factor, referring to the number of dissociated ions.
• pH + pOH = 14
• pH = -log[H+]
• pOH = -log[OH-]
• %p/v indicates the weight (in grams) of solute per 100ml of solution volume.

Monosaccharides

• The simplest monosaccharides are trioses: glyceraldehyde and dihydroxyacetone.
• Monosaccharides are reducing sugars with optical isomerism, except for dihydroxyacetones.
• They possess either ketone or aldehyde groups, differentiated by the Fehling test.
• Sugars belong to the D series.
• Glucides include polyhydroxyketones and polyhydroxyaldehydes, with many -OH groups, except for deoxyribose.
• Monosaccharides are reducing substances in an alkaline medium.
• If the -OH group of the asymmetric carbon (4 different ligands) in a monosaccharide is above the plane when cyclized, it's the β form; if below, it's the α form.
• The existence of an asymmetric carbon allows for two spatial arrangements of substituents (non-superimposable mirror images), creating spatial isomers or stereoisomers called enantiomers.
• Enantiomers involve a change in all -OH groups, such as D-glucose and L-idose.
• Diastereoisomers involve a change in some -OH groups, such as D-mannose and L-idose.
• Epimers, a type of diastereoisomer, involve a change in one -OH group, such as D-glucose and D-mannose.

Disaccharides

• Formed by joining monosaccharides through O-glycosidic bonds; they are reducing if the hemiacetalic carbon (anomeric carbon) is free.
• Examples include α-maltose (glucose + glucose), α-lactose (glucose + galactose), and sucrose (glucose + fructose).
• β-cellobiose (monomer of cellulose, glucose + glucose in β1→4 linkage)

Polysaccharides

• Homopolysaccharides serve as reserve materials like starch and glycogen and as structural components like cellulose and chitin (monomer: N-acetylglucosamine).
• Starch, a nutrient reserve in plants, is composed of two different glucans:
• Amilose: helical chain with α(1→4) linkages.
• Amilopectin: larger than amylose, distinguished by α(1→6) branch points and α(1→4) linkages.
• Glycogen, a storage polysaccharide in animals, primarily in the liver and muscles, has α(1→4) linkages and is highly branched α(1→6), similar to amilopectin, providing more points for enzymatic action.
• Cellulose: a glucan with structural roles in plants, is a wall component with β(1→4) linkages.

Lipids

• Small molecules classified as saponifiable (containing saturated or unsaturated fatty acids) or non-saponifiable (lacking fatty acids).
• Fats: lipids containing saturated fatty acids, are solid at room temperature, and of animal origin.
• Oils: lipids containing unsaturated fatty acids, are liquid at room temperature, and of vegetable origin.
• Fatty acids, monoglycerides, and diglycerides form micelles in water.
• Natural unsaturated fatty acids typically have cis configurations.
• Fatty acid + alcohol = ester (esterification reaction)
• Fatty acid + base = soap (saponification reaction), forming amphipathic compounds.
• Essential fatty acids: linoleic and linolenic acids.
• Semi-essential fatty acid: arachidonic acid.
• Melting point of fatty acids:
• More double bonds lead to a lower melting point.
• Longer chains lead to a higher melting point.
• Description of saturated and unsaturated fatty acids:
• (16:0) indicates a 16-carbon chain with zero unsaturation, representing a saturated fatty acid.
• (16:1 Δ^9) indicates the double bond is located at position 9 from the -COOH end.
• (16:1ω9) shows the unsaturation at the 7th carbon from the terminal end (numbered from the end opposite the –COOH group).
• Example of a monounsaturated fatty acid: CH3-(CH2)7-CH=CH-(CH2)7-COOH
• (16:2 Δ^9,12) indicates two unsaturations starting from the 9th carbon and then every 3rd carbon, where unsaturations are located on carbon 9 and carbon 12
• CH3-CH2-CH2-CH=CH-CH2-CH=CH-CH2-CH2-CH2-CH2-CH2-CH2-CH2-COOH

Saponifiable Lipids

• Neutral and hydrophobic.
• Triglycerides: glycerol + long-chain fatty acids, function in energy storage and thermal insulation, forming LIPID DROPLETS.
• Waxes: long-chain alcohol + fatty acid, act in energy reserve and protection.
• Polar and amphipathic, forming bilayers.

Polar Lipids

• Components of the plasma membrane and form BICAPAS.
• Phospholipids: Glicerofosfolipides (saturated fatty acids and unsaturated + glycerol + PO43- + polar group, eg: phosphatidylcholine) Esfingofosfolípidos (fatty acids + esfingol + PO43- + polar group, eg: sphingomyelin).

Glycolipids

• Esfingoglucolípidos (differs from the sphingophospholipid for not having the PO43 group, eg: cerebroside and gangliosides)

Insaponifiable Lipids

• Do not contain fatty acids.
• Steroids: Cholesterol (amphipathic and component of plasma membrane) and cholesterol derivatives (vitamin D, sex hormones and cortisol, and bile salts).
• Eicosanoids: derived from arachidonic acid (20: 4): prostaglandins, thromboxanes and leukotrienes
• Isoprenoids: derivatives of isoprene 5C: ubiquinone (component of memb. plasma), dolichol (component of plasma membrane and RER membrane) and vitamins A, E and K.

Amino Acids

• L-amino acids. AAs
• Polar amino acids are typically located in the protein's exterior because they interact with water.
• Cysteine (Cys) is the only protein AA able to form disulfide bridges.
• Protein amino acids are all characterized by an α-carboxyl and α-amino group.
• Glycine (Gly) is the only AA that does not have a chiral (asymmetric) carbon.
• Classified according to their -R group

Amino Acids: Nonpolar

• Only contain -CH; glycine (Gly), alanine (Ala), valine (Val), and leucine (Leu).

Amino Acids: Neutral Polar

• Only contain -CH + -OH, -SH, -CONH2); serine (Ser) and cysteine (Cys).

Amino Acids: Basic Polar

• Positive; -CH + -NH2): lysine (Lys), histidine (His), and arginine (Arg).

Amino Acids: Acidic Polar

• Negative; -CH + -COOH): aspartate (Asp) and glutamate (Glu).

Amino Acids and pH

• Amino acids exist in different ionic states depending on pH levels:
• At low pH, the amino acid is positively charged, with both the amino and carboxyl groups protonated.
• At neutral pH, the amino acid exists as a zwitterion, with a neutral charge due to the protonated amino group and deprotonated carboxyl group.
• At high pH, the amino acid is negatively charged, with the amino group neutral and the carboxyl group deprotonated.

Peptide Bonds

• Peptide bonds are covalent linkages between the –COOH group of one amino acid and the –NH2 group of another, forming a polypeptide chain.

Proteins

• Native conformation: The most energetically favorable and biologically active state for a protein.
• Stabilization: Primarily through numerous weak non-covalent interactions within the molecule and with the surrounding water. These include electrostatic forces, hydrogen bonds, Van der Waals forces, and hydrophobic interactions.
• Disulfide Bonds: The only covalent bonds that stabilize protein conformation, forming through the oxidation of two cysteine (Cys) side chains, and are mainly found in proteins outside the cytosol because the cytosol is a reducing environment.
• Hydrophobic interactions occur between nonpolar R groups in proteins.
• Amino acids link to form proteins via peptide bonds.

Protein Structure

• Primary structure: sequence of amino acids, determining the protein's function, stabilized by peptide bonds.
• Secondary Structure: Spatial arrangement of primary structure, maintained by hydrogen bonds, including:
• Alpha-helix: Primary structure coils helically.
• Beta-sheet: Polypeptide chain arranges in a zigzag pattern; hydrogen bonds form between CO and NH groups.
• Tertiary Structure: Overall spatial arrangement of secondary structure, stabilized by R group interactions (hydrogen bonds, electrostatic attractions, hydrophobic attractions, disulfide bridges, Van Der Waals forces).
• Quaternary structure: Arrangement of multiple polypeptide chains (identical or not) with tertiary structure, linked through weak non-covalent bonds or occasional covalent disulfide bonds.

Protein Composition and Shape

• Composition:
• Simple Proteins (holoproteins): composed only of amino acids or their derivatives.
• Conjugated Proteins (heteroproteins): contain amino acids plus other substances such as lipoproteins, glycoproteins, phosphoproteins, hemoproteins, flavoproteins, or metalloproteins.
• Shape:
• Fibrous proteins: insoluble in water.
• Globular Proteins: soluble in water or polar solutions.

Bioenergetics

• ΔG: Gibbs Free Energy, under cellular conditions.
• ΔG = 0: Reaction at equilibrium.
• ΔG < 0: Spontaneous reaction (exergonic).
• ΔG > 0: Non-spontaneous reaction (endergonic).
• ΔG° < 0: Spontaneous reaction under standard conditions (1 atm, 25°C or 298K, pH=0). Reversibility can only be determined concerning ΔG° ~ 0.
• ΔG°' < 0: Spontaneous reaction under biochemical standard conditions (1 atm, 25°C or 298K, pH=7).

Enzymatic Kinetics

• To proceed, reactant molecules must reach an activated state (R#).
• Graph parameters: Activated state (R#), Activation Energy (Ea), and ΔG of the reaction.
• A lower Ea (Activation Energy) results in a faster reaction, indicating enzyme catalysis.
• Enzymes reduce Ea by interacting with reactants (substrates) to form an enzyme-substrate complex that has less activation energy than the substrate alone.
• The active site is a specific region where the enzyme binds to the substrate.
• In the enzyme-substrate complex, the enzyme’s active site must complement the substrate.
• The rate of an enzymatically catalyzed reaction depends on:
• Substrate concentration: Reaction velocity decreases with limiting substrate.
• Enzyme concentration: Changes in enzyme concentration affect Vmax, but not KM.
• pH variation: High pH changes decrease Vmax.
• Temperature modification: Enzymes are inactivated at both low and high temperatures, reducing Vmax.
• Inhibitors:
• Competitive inhibitors: increase KM but do not change Vmax.
• Non-competitive inhibitors: do not change KM but reduce Vmax.
• Kinetic parameters:
• Vmax: Registered when all active sites are occupied.
• KM: Substrate concentration at half of Vmax, with a lower KM indicating higher affinity.

Intermediate Metabolism

• Each reaction is catalyzed enzymatically.
• Metabolic pathways are linear, branched, or cyclic.
• Regulatory enzymes can modify their conformation through ligand binding, altering catalytic activities.
• Covalent Modification: conformational change via covalent ligand attachment to specific amino-acid residues, mainly phosphorylation or acetylation (serine or tryptophan residues).
• Allosteric Enzymes: contain another site (allosteric) besides the active site, to which modulators bind through weak interactions.
• Ligand binding to the allosteric site causes a conformational change that increases or decreases enzyme activity.
• A positive allosteric modulator (activator) increases enzymatic activity
• A negative allosteric modulator (inhibitor) decreases activity.
• Allosteric enzymes also function in negative feedback, where the ligand bound to the enzyme is the final product of the pathway (the modulator).
• Excess production of E sends signals to enzyme E1 (allosteric) to halt the metabolic pathway, preventing overproduction of E

Genetic Mechanisms Introduction to Nucleotides

• Bases of Nucleic acids
• Linked by phosphodiester bonds to form nucleic acids
• Formed by a phosphate group linked to a sugar (aldopentose) via phosphoester bond linked to a nitrogenous base (adenine, guanine, cytosine, thymine or uracil) by a N-glycosidic bond
• Adenine forms a double hydrogen bond with thymine or uracil (A=T or A=U) and cytosine forms a triple bond with guanine (C=G)
• Chargaff's rule: A + G = T + C
• Adenine and Guanine are purine bases formed by two rings and Thymine, Cytosine and Uracil are pyrimidine based formed by one ring. Ribonucleic Acids

Flow of Information and Replication

• DNA → Transcription → RNA → Translation → Protein
• Replication model is semi-conservative (each daughter molecule has one original strand); it occurs in a series of steps involving enzymes

General Steps of Replication

• The DNA double helix is unwound & hydrogen bonds are broken (using topoisomerase and helicase respectively)
• Each separated strand acts as a template for new strand (A with T; C with G bases pair under ADNpol3)
• Phosphodiester bonds form between phosphates and sugars of adjacent nucleotide
• Two new DNA molecules are formed, twisting into a double helix using hydrogen bonds Origin of replication:
• The point at which replication begins that moves sequentially to form y-shaped structures called replication forks
• Prokaryotes = 1 origin
• Eukaryotes = multiple origins Replication exhibits: directionality (both strands synthesized in both directions by origins), sequentiality (new strands lengthen progressively via sequential addition of nucleotides) & discontinuity
• Replication always occurs in 5'→3' direction (the 3’-OH end acts as the point of elongation for primase and also the point at which ADNpol3 begins working)

Enzymes Involved in Replication:

• Topoisomerases & SSB proteins work to relieve tension from the double helix after the origin is located
• Helicase works break H bonds between nitrogenous bases of paired nucleotides
• Primase (or RNA primer) polymerizes the 3’-OH end so ADNpol III can work, marking the chain’s beginning

ADN Polymerases

• New chains attach nucleotides in a complementary manner over the template, synthesizing the sugar-phosphate backbone of the daughter chain:
• Prokaryotes (E. coli): ADNpol I: fills gaps, repairs & eliminates the ADN primer found in Okazaki fragments ADNpol II & III: Adds bases to both strands in a 5'→3' direction & require a 3’-OH end
• Eukaryotes: 5 polymerases, with a and b mainly for replication, and d, e, and g being exonucleases that proofread (correcting by substituting mismatched bases via 3'→5' activity)
• *ADN fragments are mixed with RNA because ADNpol III can’t work in a 3'→5' direction: Las ADN polymerases possess nucleases with exonuclease 3'→5' (ADNpol I, II y III) and exonuclease 5'→3' only ADN pol I ADNs ligase: unites ADN fragments (without touching) after the ADNpol I removes RNAS that were in the lagging chain by exonuclease action 5'→3'

ADN Replication Damage

• Depurination (loss of purines (apurinic site/AP))
• Deamination (cytosine passes to U, A to hipoxantina, guanine to zantine (no impact on timina)
• Pyrimidine dimers TT, CC, TC
• Correction
• ADN glycosylase breaks the N-glycosidic bond & releases the wrong base, acting as AP endonuclease @ the AP site to open the chain for phosphodiesterase activity to remove the nucleotide sans base ADNpol and ligase then polymerize and reunite the chain (repair by BASE and nucleotide EXCISION)

Telomeres/Telomerase

• Telomeres = specialized nucleoprotein structures @ chromosome extremities composed of areas of non-coding and highly repetitive ADN that provide structural stability to chromosomes for cell division
• Telomerase = enzyme that synthesizes telomeric ADN, controlling telomere synthesis via TRANSCRIPTASA INVERSA that synthesizes ADN from a template of RNA It’s a ribonucleoprotein whose molecule contains an AAUCCC segment able to insert lose TTAGGG fragments

Genetic Mechanism - Eukaryotic Transcription

• Step 1 = Initiation: RNA polymerase binds to ADN and initiates separation of its strands in collaboration with cofactors
• Step 2 = Elongation; RNA polymerase desenrolls and re-enrolls the ADN strand + maintains separation + catalyzes the addition of new nucleotides + may restart its synthesis to prevent deterrance
• Step 3 = maturation/termination:

General Translation

• Addition of CAP5' = nucleotide of guanine is added to the 5' end for stability (cotranscriptional) to maintain stability and facilite ribosome access
• Addition of COLA of poly-A 3 ' a long sequence of poliadenylate is added. Prevents ARNm degradation
• Splicing removes introns and joins exons to form ARNm used to synthesize proteins

General Translation

• Synthesis of a protein molecule, which determines the primary structure ARNm moves to ribosomes in cytoplasm (AAs needed in this process are available the ARNt)
• ARNt → ANTICODON (5'→3′): bases complementary to the CODONES of the ARNm (5'→3')
• RIbosomes are 70S (major subunit 50S & minor 30S) in prokaryotes and 80S (60S major + 40S minor) subunits in eukaryotes that help translate the code from the ADN in form of messenger RNAs
  • Subunits have site P*where major binds with peptidic union
  • • 3 Sitios (EPA): E (exit), A (aminoacil) and P (peptidil) Iniciation Elongation -Termiantion

Translation Steps

• Pre-initiation AAs activate by transferase aminoacil ARNt Enzyme Amino acid + ATP - aminoacil ARNt syntesis → Aminoacil-AMP + PPi Aminoacil-AMP + PPI → Aminoacil-ARNt + AMP + PPi

General Membrane Transports: Plasmatics

Semi-permeable membrane formed by lipids which are maintained via noncovalent unions Lower sizes and higher hydrophobicity mean greater diffusion w/i the bicapa Water-soluble ions may not get through the bilipid layer and instead require an transport protein system

• Mosiac fluid model- lipids and proteins displace fluidly in all directions (rotations/lateral mvt, flexions)
• Bicapa contains composed of asymmetricaly distributed lipids, proteins, and glucids
  • In layers: negative internal m.l. and exteranl positive m.l Externa consists of: esfingmielina, fosfatidilcolina, colesterol and glycolipidis Interna: fosfatidiletanolamina, fosfatidilinositol and fosfatidilserina

Variables Influencing Membranes

Ác. Unsaturated fats Low cholesterol High temperatures Shortened hydrocarbon tails

Protein Classifications and Carbhydrates

Classified as integral proteins (tranmembrane protein atraviesa total or partly la bicapa) or periferical (can also bind both integrales as well as lipids (weak unions)

• Carbohydrate contain glucids and covalent link between proteins and lipids to form glycolipids ( gangliosides w/ oligosacarids linking with ceramida) form a glucocálix ythat protects mechanically or physically, atracs cations + H2O from medium , intervenes on recognician and adshesión celular