Water Chemistry and Characteristics

Water Chemistry

• Each water molecule consists of two hydrogen atoms and one oxygen atom
• Oxygen has high electronegativity, leading to unequal electron sharing in water molecules
• Oxygen is slightly negative and attracts the slightly positive hydrogen atoms of nearby molecules

Water Characteristics

• Water molecules stick together due to hydrogen bonds, creating cohesion and surface tension, seen in 'like' molecules (water <-> water)
• Water sticks to charged surfaces through adhesion, for example, water adhering to vessel walls, causing capillary action
• High specific heat, which is hard to change the temperature, requires significant energy to separate water molecules
• Water resists temperature changes when heat is absorbed or lost
• Large bodies of water are able to absorb and store significant amounts of heat
• Water's polarity enables it to dissolve many substances
• Polar charges of water allow other polar charged molecules to dissolve quickly
• Solutions are liquids with homogeneous mixtures
• Solvents dissolve other substances
• Solutes are substances that dissolves in solvents
• Polar substances dissolve polar substances
• Polar substances will not dissolve non polar substances
• Hydrophilic substances are water-loving, polar, and include ions, sugar, salt, and blood
• Hydrophobic substances repels water, non polar, and include oils, lipids, and cell membranes
• Water molecules can form up to 4 bonds

Polarity and Bonding

• In polar bonds, electrons are shared unequally
• Polar molecule results in electrical charge at opposite poles
• In nonpolar bonds, electrons are shared equally, examples are O2 and N2
• Covalent bonds involves the sharing of electrons
• Ionic Bonds involves metal and nonmetal atoms, where two ions bond via giving or taking electrons
• Compounds held together by ionic bonds are called salts
• Hydrogen bonds arises when the hydrogen of a polar covalent molecule bonds to electron of another polar covalent molecules
• Intramolecular forces are forces within a molecule that keep the molecule together
• Intermolecular forces involves attractions between different molecules using H-bonds, covalent and ionic bonds
• Van Der Waals interactions involves slight, constantly moving attractions between atoms and molecules close together, the weakest and quickest attraction

Chemical Context of Life

• The elements of life (CHONPS) are carbon, hydrogen, oxygen, and nitrogen that makes up 96%
• Phosphorus, sulfur, calcium, potassium and trace elements makes up the remaining 4%
• Carbon is one of the most important element
• Carbon has 4 valence electrons, tetravalence, and can form 4 covalent bonds
• Carbon forms single, double, or triple covalent bonds
• Carbon can also form macromolecules
• Isomers are molecules with same molecular formula but different atom arrangement
• Different structures results in different properties and functions
• Isotopes represents the different number of neutrons, different weight, and different radioactive particles that are given off in radioactive waves like PET scans
• Potential energy defines how much energy is stored, and in human bodies, ATP turns into ADP
• Buffers maintain pH levels -- Bicarbonate (HCO3) keeps is blood around 7.4
• Isomers shares the same element but are mirrored, and so are different molecules

Functional Groups of Organic Compounds

• Behavior of organic molecules depends on functional groups
• Amino groups are polar and hydrophilic, and are weak bases
• Carboxyl groups are polar and hydrophilic
• Carbonyl groups are weak acids and polar and hydrophilic
• Hydroxyl groups are polar and hydrophilic
• Phosphate groups are polar and hydrophilic
• Sulfhydryl groups are polar and hydrophilic
• Hydroxyl group is OH
• Carbonyl group is C double bonded to O
• Carboxyl group is C double bonded to O to OH, acidic
• Amino group is N bonded with 2 Hs
• Sulfhydryl group helps you stabilize protein structure
• Phosphate group is PO4.

Four Classes of Organic Compounds

• Macromolecules consists of polymers

Carbohydrates

• Carbohydrates are used by cells for energy and as structural materials
• Carbohydrates are classified into 3 groups: monosaccharides, disaccharides, and polysaccharides
• Monosaccharides, a simple sugar, consists of a single sugar molecule, such as glucose or fructose
• Glucose is important because it used in cellular respiration, providing energy for cells
• Sugars have the formula (CH2O)n where n = 3 to 8. Glucose has the formula C6H12O6
• Sugars may have same formula, but different arrangement as certain atoms drastically changes chemistry of molecule
• Disaccharides consists of 2 monosaccharides joined by a glycosidic linkage
• Sucrose consists of glucose and fructose, common table sugar
• Lactose, consists of glucose and galactose, is sugar in milk
• Maltose contains glucose and glucose
• Disaccharides are formed by losing a water molecule in a dehydration reaction
• Polysaccharides consists of a series of connected monosaccharides that are polymers
• Starches are polymers with of alpha-glucose monomers and energy storage molecules in plants
• Glycogen are polymers of branched alpha-glucose molecules that stores energy storage molecule in plants
• Cellulose consists of polymers of beta-glucose molecules that is a structural molecule in plant cell walls, the major component of wood
• Chitin is similar to cellulose, representing with structural molecule in exoskeleton of insects, spiders, and shellfish
• Alpha-glucose stars versus beta-glucose in cellulose creates dramatic chemical changes
• Bonds in starch are easily broken down (digested) by humans and animals
• Beta-glycosidic linkage in cellulose can only be broken down by specialized organisms like bacteria in termite and cow guts

Lipids

• Lipids are used by cells as long-term energy stores and as building blocks
• Lipids have hydrocarbon tail of CH2's that is nonpolar and repellant to water
• Lipids are hydrophobic and insoluble in water
• Lipids are nonpolar
• Lipids have three major groups of triglycerides, phospholipids, and steroids
• Triglycerides includes fats, oils, and waxes
• Triglycerides consist of a glycerol molecule and 3 fatty acids, (- CH chains w/carboxyl group)
• Glycerol backbone and fatty acids are connected by dehydration synthesis
• Can provide 2x energy than carbohydrates
• Can vary by the number of carbons in fatty acid chains and placement of bonds.
• Saturated fatty acids will have contain only single bonds between carbons which means they were "saturated" by hydrogens
• Saturated fatty acid remains solid animal fats and are "bad fats" which may implicate to heart disease and atherosclerosis
• Unsaturated fatty acids have one or more double bonds between carbons and thus fewer hydrogens and results in plant oils that are liquid and better for human consumption
• Phospholipids contain glycerol molecule+ 2 fatty acids + phosphate group (-PO32-)
• Fatty acid "tails” are nonpolar and hydrophobic with a phosphate "head" that is polar and hydrophilic
• Amphipathic molecules contains both hydrophilic and hydrophobic regions
• Bilayered structures provide structural foundations of cell membranes
• Steroids are comprised of backbones of four linked carbon rings
• Examples includes cholesterol, a component of cell membranes and the sex hormones testosterone and estrogen

Proteins

• Proteins comprised of chains of amino acids, called polypeptides
• Bonds between amino acids are known as peptide bonds through dehydration synthesis
• Each amino acid has a central carbon bonded to an amino group and a carboxyl group and a hydrogen and an R (“remainder”) group that varies among amino acids
• Proteins differ by number and arrangement of 20 different amino acids
• There are four levels of protein structure:Primary, Secondary, Tertiary, Quaternary
• Primary protein structure describes the order of amino acids
• Secondary protein creates a 3-D arrangement caused by hydrogen bonding produces alpha helix or beta-pleated sheets, forming fibrous proteins
• Tertiary protein structure produces shaped caused by interactions among R groups, for example, hydrogen bonding and disulfide bonds, Cystine, that dominates globular proteins
• Quaternary protein structure describes a protein assembled from 2 or more polypeptides, for example, globular protein hemoglobin has 4 polypeptide chains
• Proteins group depending on their function based on the following functions: structural, storage, transport, defensive, and enzyme
• Structural proteins are keratin in the hair and collagen in connective tissues
• Storage proteins are caseins in milk
• Transport proteins are in membranes of cells; and contains O2-carrying hemoglobin in blood
• Defensive proteins are antibodies that protection against foreign bodies
• Enzymes regulates the rate of chemical reactions

Nucleic Acids

• Nucleic acids stores genetic information of a cell in molecules of DNA
• DNA is a polymer of nucleotides
• Nucleotides of consists of a nitrogen base, a 5-C sugar called deoxyribose, and a phosphate group
• DNA is a double helix, two strands run antiparallel and are paired by hydrogen bonds between bases, bases are T paired with A, and G paired with C
• RNA differs in its sugar is ribose and base T is replaced by U, pairs with A and is single-stranded
• ATP (adenosine triphosphate) is a common source of activation energy for metabolic reactions
• Important DNA discoveries from Franklin using X-ray crystallography to capture the images of DNA, and Watson & Crick who discovered the double helix structure

Chemical Reactions in Metabolic Processes

• Hydrolysis breaks down compounds by adding H2O
• Dehydration synthesis joins 2 compounds by releasing H2O as a product
• Endergonic reaction requires an input of energy to occur
• Exergonic reaction gives off energy as a product
• Redox refers to reaction that transfers electrons, such as along the electron transport chain of the mitochondria during cellular respiration
• Chemical reactions occurring in biological systems are called metabolism and breaks down into catabolism, the breakdown of substances and anabolism, the synthesis or new formation of new substances

Enzymes

• Enzymes are globular proteins that act as catalysts or activators for metabolic reactions
• Catalysts speed up reactions by lowering the activation energy needed for the reaction to take place
• Substrates are the substances that enzymes targets to acts on
• Enzymes are substrate-specific and selectively interacts with specific substrate
• Shape or quaternary structures of an enzyme provides specificity
• Active site of enzyme is specific for substrate to fit it shape
• Binds to substrate induces active site of enzyme to change shape
• Enzymes remains unchanged and find and react with another substrate so it only needs a small amount of enzyme
• Efficiency of enzyme depends on temperature and pH
• Each enzyme each enzyme has it own optimal temperature and pHs
• Enzymes denature and lose the 3-D shape at non-optimal temperatures and pH
• Standard suffix for enzyme name is -ase
• Effectiveness of enzymes depends on: Temperature, pH, concentration of the substrate, and concentration of the enzyme
• Competitive Inhibition involves a substance that mimics the substrate and binds to the active site and physically blocks the substrate from attaching, overcome with large amount of substrate
• Noncompetitive Inhibition involves a substance that binds to a site other than the active site of the enzyme, causing a change in the shape of the active site so no longer interacts with the substrate

The pH Scale

• The pH scale indicates how acidic or basic a solution is
• The pH scale ranges from 0 to 14 with neutrality at 7, acidic numbers from 0–7 and basic ranges from 7 – 14
• The pH scale is logarithmic scale so a pH of 3 is 10 times more acidic than a pH of 4
• Chemical reactions in humans primarily functions around a neutral pH

Mathematical Routines

• Null hypothesis is the hypothesis that a researcher tries to disprove, reject, or nullify
• Alternative hypothesis starts at H₁ and then continue listing as many as are necessary for the experiment
• A measure of how spread out the data is from the mean Low standard deviation means closer to the mean High standard deviation means farther from the mean, known as spread out
• Standard Error of the Mean (SEM or SE) uses to the determine precision of and confidence in the mean value
• Formula calculates measured value, sum, mean, standard deviation, and degrees of freedom

Cell Structure and Function

• Ribosomes consists of RNA and proteins
• Ribosomes helps synthesizing proteins with large and small subunits
• Messenger (mRNA) RNA is transcribes from DNA and carries message to cytoplasm where ribosomes translate it into a polypeptide
• Transfer (tRNA) RNA carries specific amino acid to the correct position on the Ribosome using its anticodon
• Ribosomal (rRNA) RNA joins with proteins to make ribosomes where translation occurs to make a protein
• All life forms have ribosomes
• Rough endoplasmic reticulum includes series of connected flattened sacs, part of a continuous membrane organelle within the cytoplasm of eukaryotic cells and plays a central role in the transport of proteins made on its ribosomes
• Rough ER allows protein production, folding, quality control and dispatch of some proteins
• Software ER acts a network of membranes called cisternae held together by the cytosk that helps with synthesizing lipids, phospholipids in plasma membrane and steroids
• ERs helps maintain cell shape by interacting with cytoplasmic matrix, which Transports materials through vesicles
• Golgi apparatus are central intracellular membrane-bound organelles that traffic, process, and sorts newly synthesized membrane and secretory proteins and lipids and also packages proteins into vesicles for transportation
• Mitochondria makes up inner membrane folds to increases surface area allows the production of lots of ATP very quickly and Krebs cycle takes place in cellular respiration
• Carbon atoms enables to form valence around valence bonds with other atoms while all living things contains this form
• Primary component of macromolecules, including proteins, lipids, nucleic acids, carbohydrates
• Lysosomes are sphere shaped sacs filled with hydrolytic enzymes that break down biomolecules
• Membranes surrounding lysosomes separate components from the rest of the cell with proton pumps maintaining an acidic interior for digestion for using enzymes, breaking down organelles, and releasing enzymes into cytosol to start apoptosis
• Vacuoles membrane bound organelles that is generally small and circular, and central in plant cells that maintain water balance, constant osmotic pressure,
• Vacuoles provide space and the turgor pressure needed to push on cell walls
• Chloroplasts are large organelles that are bounded by double membrane, called chloroplast that also makes compartments with thylakoid sacs
• Chloroplasts has Photosystems containing chlorophyll and electron transport for light independent reactions
• Thylakoid membranes contains photosynthetic systems and collect more light
• Cellular Respiration is process how cells derive energy from glucose. Outputs include carbon dioxide, water, and energy (atp)
• Takes place in the cytoplasm and mitochondria of each cell of the body 3 stages: glycolysis, Krebs cycle, electron transport chain
• Glycolysis series of enzyme-catalyzed reactions extracts energy from glucose by splitting it into 2 three-carbon molecules Does Not require oxygen and many anaerobic organisms
• Krebs cycle series of biochemical reaction release energy stored in nutrients through oxidation to nutrients
• Results in 4 ATP, 10 NADH, 2 FADH2
• Electron transport chain collection of proteins bound to the inner mitochondrial membrane and organic molecules pass through series and energy by ATP-synthase
• Photosynthesis light energy into sugar
• Driven by light energy, glucose used, results water, carbon dioxide, oxygen absorbed
• Surface Area to Volume Ratio: biological system obtains resources or eliminate waste
• Increase in volume results in SA decrease, more cells are needed in SA increase
• Plasma membrane structure consists of hydrophobic, hydrophilic regions, embedded proteins, cholesterol
• Plasma membranes separates internal cell from environment
• Cell are permeable to membrane using transmembrane proteins
• Cell wall composition of bacteria are comprised of thick continuous peptidoglyca

Passive Transport

• Passive transport moves molecules without energy
• Diffusion, molecules or ions reach equilibrium
• Osmosis, diffusion of water from higher concentration

Active Transport

• Active transport is from high concentration. Utilizes ATP and energy. Endocytosis occurs as membrane pinches and brings molecule. Exocytosis is fusion of secretory vesicles.
• Sodium potassium pumps is for moving potassium ions into cell where potassium levels and moving sodium ion outside to fluid
• Facilitated diffusion increases transfer by channel and carrier proteins
• Osmosis maintains constant water, using hypertonic, hypotonic and isotonic systems. Water moves to MORE solute.

Osmosis and Cell Activity

• Hypotonic: solute is LESS, thus when water diffuses, it expands the cell
• Hypertonic: solute is MORE and shrink by outside diffusion
• Water Potential depends on solute in a water's ability to flow
• Membrane and bound organelles helps cells compartmentalize. Endosymbiosis led to organelles from prokaryotes
• All cell communications use direct contact through gap junctions or surface membrane of specialized regions in specialized reactions, proteins

Unit 3 Cellular Energetics

• Enzyme structure includes active site interacts with with substrate molecules. Made of amino acid, shapes of substrates have compatible chargers. Bonded at active site orients for product
• Activation energy is lowers by enzymes to make reactions happen fast
• Denaturation: Modification of the 3D shape of a protein, eliminating ability to catalyze reactions

Enzyme Inhibitors

• Inhibitors slow the substrate and block, alter shape
• Competeive binding at active
• Noncomplettive altering locations away increases speed, frequency, collisions in heat
• 1st Law, 2nd Law: thermodynamics. Enerrgy conservation and increase with heat

Reactions

• Catabolic Reactions. Complex molecules are broken down, hydrolyisis in nature
• Anabolic Reactions are going from small to large, uses dehydration Energy constant by coupled cellular processes for greater yield

Photosynthesis

• PS Evolution: The process happened to bacteria and other organisms who use autotrophs Heterotrophs eat organic molecules such as animals and humans Photosynthesis converts light energy to energy that is food
• Chloroplasts absorbs in plants with pores
• Photosynthesis takes carbon dioxide, water by radiant energy to release glucose and oxygen
• Light reactions: Convert solar energy to chemical energy of ATP and NADPH.
• Light- energy for short wavelengths and vision for detectable by the eye
• absorb violet-blue. red light, Chlorophyll used