Chapter 2 Pp
- 1. Chapter 2 Matter – anything that occupies space and has mass, matter includes solids, liquids, and gases. All forms of matter are made of one or more fundamental substances called elements. Elements can not be broken down to substances that have different properties. Common Elements – H, C, N, and O – 95% of human body Atom – smallest unit of matter that is unique to an element. Subatomic particles include: protons, neutrons & electrons. Protons and neutrons make up the atom’s core or nucleus. The electrons are outside of the nucleus. Protons have a (+) charge, neutrons are neutral, and electrons have a (-) charge and are attracted to the nucleus. Chemistry Comes Alive
- 3. Periodic Table of the Elements
- 4. Atomic Number – number of protons in its nucleus and is written as subscript to the left of its atomic symbol Mass Number – sum of the masses of its protons and neutrons (the mass of the electrons is so small it is ignored) Number of Protons = atomic number Number of Electrons = equal to the atomic number Number of Neutrons = mass number minus atomic number Isotopes – same atomic number but vary in their mass numbers
- 5. Chemical Bonds Each electron shell can hold a specific number of electrons Shell 1 – can hold 2 electrons Shell 2 – can hold 8 electrons Shell 3 – can hold 18 electrons When atoms form bonds, the important electrons are those in the outer level. Chemically inert (Noble gases) – outer level is filled to capacity or contains 8 electrons Chemically reactive – outer level contains < 8 electrons The number of electrons that can participate in bonding is limited to 8 electrons. Valence Shell – octet rule – rule of eights
- 8. Ionic Bonds – when an atom loses or gains one or more electrons, it becomes positively or negatively charged – an ION. A positive ion is called a CATION and a negative ion is called an ANION. Sodium (Na) has 11 e, only one in the outer shell, so it tends to be an electron DONOR. Chlorine (Cl) has 17 e, and its outer shell has 7 e, so it tends to be an electron ACCEPTOR. When a Na atom and a Cl atom come together, an electron is transferred from the Na atom to the Cl atom. Now both have 8 e in their outer shell.
- 9. Covalent Bond – when two atoms share one or more pairs of electrons this called a covalent bond. E.g., H has 1 e in the outer shell so it can accept 1 more e. A H atom can share with another H atom. Because they share the electron pair, each atom has a completed outer shell. H—H or H 2.
- 10. Oxygen – oxygen has 6 electrons in the outer shell, so atoms share 2 electrons to make a total of 8 electrons. Thus a double covalent bond. Nitrogen – nitrogen has 5 electrons in the outer shell so atoms share 3 electrons to make a total of 8 electrons. Thus, a triple covalent bond.
- 11. Types of Covalent Bonding There are two types of covalent bonding. Non-polar Covalent Bond – electrons are shared equally. E.g., CH 4 Methane Gas; C has 6 protons and H has 4 protons; equal attraction of the electrons. Nonpolar substances are hydrophobic (water fearing). Polar Covalent Bond – electrons are shared unequally , so there is a slight difference in charge. E.g., H 2 O Water; H has 2 protons and O has 8 protons; O attracts the electrons to a greater extent than H, so O is slightly (-) and H is slightly (+). In general, small atoms with 6 or 7 valence shell electrons, such as O, N, and Cl, are electrohungry and attract electrons very strongly. Polar substances are hydrophilic (water loving).
- 12. Hydrogen Bonding Hydrogen bonds form when a hydrogen atom, already covalently linked to one electronegative atom (usually nitrogen or oxygen), is attracted by another electron-hungry atom, and forms a “bridge” between them. Hydrogen bonds are too weak to bind atoms together to form molecules.
- 13. Comparison of Ionic, Polar Covalent, and Nonpolar Covalent Bonds
- 14. Chemical Reactions Most chemical reactions exhibit one of three major patterns: Synthesis (Anabolic) – A + B > AB Example: Glucose + Fructose > Sucrose Decomposition (Catabolic) – AB > A + B Example: Protein > Amino Acid + Amino Acid Exchange Reactions – AB + C > AC + B Example: ATP + Glucose > Glucose-phosphate + ADP Oxidation-Reduction (Redox) Reactions – are decomposition reactions and a special type of exchange reaction because electrons are exchanged between the reactants
- 15. Oxidation-Reduction Reactions Oxidation – the reactant losing the electrons is referred to as the electron donor and is said to be oxidized. Reduction – the reactant taking up the transferred electrons is called the electron acceptor and is said to become reduced. Redox reactions occur when ionic compounds are formed. E.g., NaCl – Na is oxidized and Cl is reduced E.g., Cellular Respiration………… C 6 H 12 O 6 + 6O 2 > 6CO 2 + 6H 2 O + ATP Glucose + Oxygen > Carbon Dioxide + Water + Energy Glucose is oxidized to carbon dioxide (loses H atoms) and oxygen is reduced to water (accepts H atoms)
- 16. Chemical Reactions Exergonic Reactions – release energy; reactions yield products that have less energy than the initial reactants but provide energy for other uses. Endergonic Reactions – energy absorbing; reactions contain more potential energy in their chemical bonds than did the reactants. Factors Influencing the Rate of Chemical Reactions Temperature – reactions proceed quicker at higher temperatures Particle Size – smaller particles quicker reaction Concentration – high concentration Catalysts - enzymes
- 17. Biochemistry Inorganic Compounds Water High heat capacity – absorbs and releases large amounts of heat before changing in temp. itself High heat of vaporization – liquid to a gas; requires that large amounts of heat be absorbed to break the H bonds that hold water molecules Polar solvent properties – Universal solvent Reactivity – Decomposition reactions = Hydrolysis; Synthesis reactions = Dehydration synthesis Cushioning
- 18. Characteristics of Water High Surface Tension – hydrogen bonding
- 19. Salts – an ionic compound containing cations other than H + and anions other than the hydroxyl ion (OH - ). When salts are dissolved in water, they dissociate into their component ions. E.g., NaCl + water > Na + and Cl - . All ions are electrolytes, substances that conduct an electrical current in solution ACIDS and BASES Acids – a substance that releases hydrogen ions (H + ) and anions when dissolved in water; they are called proton donors; HCL H + Cl - ; H 2 CO 3 - HCO 3 - + H + Bases – a substance that releases hydroxyl ions (OH - ) and cations when dissolved in water; they are called proton acceptors; NaOH Na + + OH -
- 20. pH: Acid-Base Concentration The more H + ions in a solution, the more acidic the solution is. The more OH - ions, the more basic or alkaline the solution is. pH units measure the concentration of H + ions. The pH scale runs from 0 – 14 and is logarithmic, i.e., each successive change of one pH unit represents a tenfold change in H + concentration.
- 21. Buffers Homeostasis of acid-base balance is carefully regulated by the kidneys and lungs and by chemical systems called BUFFERS. Buffers help prevent large shifts of pH in the body fluids Strong Acids – acids that dissociate completely and irreversibly in water and they can change the pH of a solution. E.g., HCl; 100 HCl molecules + 1 ml water > 100 H+ and 100 Cl- Weak Acids – acids that do not completely dissociate. E.g., H 2 CO 3 ; 100 H 2 CO 3 + 1 ml water > 90 H 2 CO 3 + 10 H + + 10 HCO 3 Strong Bases – bases that dissociate easily in water and quickly tie up H + Weak Bases – bases that do not dissociate easily in water and accepts relatively few protons
- 22. Carbohydrates Sugars, starches, glycogen and cellulose (plant) C, H, O – 1 C atom for each water molecule, hence carbohydrates (= watered carbon) Monosaccharides - 3-7 C atoms (e.g., glucose, fructose, galactose) Disaccharides – 2 monosaccharides > disaccharide + 1 H 2 0 C 6 H 12 O 6 + C 6 H 12 O 6 C 12 H 22 O 11 + H 2 0 Glucose + Fructose Sucrose + water (e.g., sucrose, lactose and maltose) Polysaccharides – 10’s & 100’s of monosaccharides joined through dehydration synthesis reactions (e.g., glycogen)
- 24. Carbohydrates
- 25. Lipids Lipids – C, H, O – amount of oxygen in lipids is usually less than that in carbohydrates, so there are fewer covalent bonds. Most lipids are insoluble in polar solvents such as water = hydrophobic Triglycerides, phospholipids, steroids, vit. A, E, & K Important for efficient transport in blood (since hydrophobic) lipids combine with proteins to form water-soluble lipoproteins Triglycerides – solid (FAT) and liquid (OILS) at room temperature; 2X energy per gram as C and P; store triglycerides in fat cells (adipose tissue = adipocytes) Building blocks – Glycerol (3 C atoms) and Fatty Acids ( 2 FA)
- 26. Neutral Fats Saturated Fats single covalent bond; each carbon bonds to the maximum number of hydrogen atoms; thus each fatty acid is SATURATED with hydrogen atoms tend to be solid at room temperature (Animal Tissues) and cocoa butter, palm oil and coconut oil Monounsaturated Fats Fats contain fatty acids with 1 double covalent bond between 2 C atoms and thus are not completely saturated with H atoms, e.g., olive oil, peanut oil Polyunsaturated Fats contain more than 1 double covalent bond between fatty acid carbons; e.g., corn oil, sunflower oil, soybean oil
- 28. Phospholipids Modified triglycerides; glycerol backbone (3 C) and 2 fatty acids + phosphate group The phosphorus-containing group gives phospholipids their distinctive chemical properties…the hydrocarbon tail is nonpolar and only interacts with nonpolar molecules….the phosphate head is polar and attracts other polar or charged particles – molecules that have both polar and nonpolar regions are said to be amphipathic.
- 29. Steroids flat molecules made of four interlocking hydrocarbon rings e.g., cholesterol, found in cell membranes and is the raw material for vit. D, steroid hormones and bile salts ; sex hormones Eicosanoids lipids derived from a 20 C fatty acid found in all cell membranes ; Prostaglandins – important in blood clotting, inflammation and labor contractions
- 30. Proteins Amino acids – building blocks of proteins; 20 different amino acids; bonded together by peptide bonds (covalent); dipeptide (2 AA); tripeptide (3 AA); polypeptide (10 AA or more) and polypeptides with 50 or more AA are called proteins. Proteins are more complex and a have a larger range of functions than either carbohydrates or lipids Structural proteins – cellular building materials; e.g., actin & myosin Functional (physiological) – e.g., enzymes (speed up biochemical reactions by increasing the frequency of collisions, lowering the activation energy and properly orienting the colliding molecules)
- 32. Structural Levels of Proteins Primary – linear sequence of AA composing the polypeptide chain Secondary – twist or bend upon themselves to form a more complex structure ; alpha or beta Tertiary – 3d shape of a polypeptide chain; unique for each protein Quaternary – describes the arrangement of the individual polypeptide chains and how they bond
- 33. Proteins (Enzymes) Most are globular proteins that act as biological catalysts Holoenzymes consist of an apoenzyme (protein) and a cofactor (usually an ion) Enzymes are chemically specific Frequently named for the type of reaction they catalyze Enzyme names usually end in -ase Lower activation energy Enzyme binds with substrate Product is formed at a lower activation energy Product is released
- 34. Enzyme Action Active site Amino acids Enzyme (E) Enzyme-substrate complex (E-S) Internal rearrangements leading to catalysis Dipeptide product (P) Free enzyme (E) Substrates (S) Peptide bond H 2 O +
- 35. Protein Denaturation In hostile environments (temperature, pH) lose shape (secondary, tertiary and quaternary) When a protein is subjected to extremes (e.g., pH drops or temperature rises above normal) the protein will unfold and lose their specific 3d structure. The protein is said to have been DENATURED. In some cases, process is reversible. In extreme cases, the protein is said to have been irreversibly denatured. Example: egg (albumin is a protein that makes up the “white” of the egg)….uncooked the white is actually clear when you cook the egg (temperature rises above normal) the albumin is denatured (changes the color and the structural arrangement of the protein)
- 36. Nucleic Acids organic molecules that contain C, H, O, N, and P DNA – deoxyribonucleic acid (A,T,C,G); Deoxyribose sugar; found in the nucleus; double-stranded RNA – ribonucleic acid (A,U,C,G); Ribose sugar; found outside of the nucleus; single-stranded; mRNA, tRNA, rRNA Basic units or building blocks of nucleic acids are called NUCLEOTIDES Nucleotides include: Nitrogenous Base – Adenine (A), Thymine (T), Cytosine ( C), Guanine (G), Uracil (U) Pentose sugar – deoxyribose or ribose Phosphate group
- 37. DNA Molecule
- 38. DNA Molecule
- 39. Adenosine triphosphate (ATP) – adenine-containing RNA nucleotide which have 2 additional phosphate groups ATP
- 40. How ATP drives cellular work