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Chapter 2 Matter: is anything that has mass and occupies space Matter is composed of atoms Being able to understand the structure of atoms is required to understand the nature of biological molecules Atomic Number: is the number of protons, the number of protons is equal to the number of electrons. Every atom of a particular element has the same number of protons. Element: is any substance that cannot be broken down to any other substance by ordinary chemical means. Atomic Mass: is the addition of protons and neutrons Mass: is the amount of a substance and is the same on every planet. Weight: is the force gravity exerts on a substance Electrons: are negatively charged particles located in orbitals surrounding the nucleus Ions: are charged particles that can either be a cation or anion. Cation: more protons than electrons and gives a positive charge. Anion: more electrons than protons in and gives a negative charge. Isotopes: are atoms of a single element with different numbers of neutrons. Example is carbon which has three c12, c13, and c14 Radioactive isotopes: are unstable and emit radiation as the nucleus breaks up. Half life: is the amount of time it takes for the number of atoms of a sample to decay. Elements can dictate the chemical nature of an atom. Valence orbital: is the outermost orbital that contains electrons and is key to how an atom reacts and its chemical behavior. Electrons occupy energy levels named K, L, M, and N where each level contains sublevels called orbitals. Orbitals are the area around a nucleus where electrons can be found. No orbital can contain more that two electrons. K is the lowest energy level and has only one orbital, L is the second energy level and has 4 orbitals and can contain a total of 8 electrons Noble gasses have their outer shell completely filled by electrons and are the most stable and least reactive elements. Electrons have potential energy the farther away they are from the nucleus. Highest energy level to lowest is N, M, L, and the lowest being K which has the least potential energy. Orbitals only tell us where an electron's relative location would be. Valence electrons are electrons in the outermost shell Periodic table displaces elements according to valence electrons. The most stable/nonreactive elements are those that have all eight valence electrons filled. Octet rule means that atoms try to completely fill their outermost energy levels. Most important elements in the body are Hydrogen, Carbon, Nitrogen, Oxygen, Potassium, Sodium, Calcium, Magnesium, Phosphorus, Sulfur, Iron and Chloride. There are 90 natural elements on the periodic table, only 12 are found in large amounts for animals. 4 elements make up 96.3% of the body and those are, carbon, hydrogen, oxygen and nitrogen. Some trace elements are also important. For the octet rule if the outer shell is filled the atom is nonreactive. If it is not filled it is reactive. If an atom wants to fill its shell it must ethier lose or gain an electron. Molecules: are groups of atoms that are held together in a stable association. Compounds: are molecules that contain more than one element. Atoms in molecules and compounds are held together by chemical bonds. Bonds in order from strongest to weakest: Covalent bond: sharing of electron pairs, strongest bond. It is formed when atoms share 2 or more valence electrons. Its strength is dependent on how many electrons are shared between atoms. Ionic bond: is the attraction of oppositely charged ions. An example is Na+Cl- and this is because Na loses an electron to become Na+ and Cl gains an electron to become Cl-. The become attracted to each other to form Na+Cl-. Hydrogen bond: sharing of a hydrogen atom. Hydrophobic interaction: is the forcing of hydrophobic portions of molecules together in the presence of polar substances. Van der waals attraction: Weak attractions between atoms due to oppositely polarized electron clouds. Weakest bond> Electronegativity: an atom's affinity for electrons Differences in electronegativity dictate how atoms are distributed in covalent bonds. Bigger differences in electronegativity leads to a more polar bond. Nonpolar bonds result in an equal sharing of electrons. Polar bonds result in an unequal sharing of electrons. Chemical reactions are the breaking or formation of chemical bonds, this leads to atoms shifting from one molecule to another without changing the number or identity of atoms. Reactants are original molecules before chemical reaction. Products are molecules resulting from a reaction. Chemical reactions are influenced by temperature, concentration of reactants and products and by the presence of catalysts. Many reactions can be reversed. Life is dependent on water because of its most important ability which is hydrogen bonding. Hydrogen bonds is the chemical association between partially negative o atoms and the partially positive H atoms of two water molecules. Hydrogen bonding occurs with O, N, and H of many compounds. Polarity of water: within a water molecule the bonds between oxygen and hydrogen are highly polar. oxygen is more electronegative than hydrogen so partial charges begin to develop. Cohesion: water molecules stick to other water molecules by hydrogen bonding. Cohesion at the surface of liquid water causes surface tension allowing very light objects to stand on top of it. Adhesion: water molecules stick to other polar molecules. Properties of water: Cohesion:hydrogen bonds hold water together. High specific heat: hydrogen bonds absorb heat when they break and release heat when they form, helping minimize temperature changes. High heat vaporization: many hydrogen bonds must break for water to evaporate. Lower density of ice: water molecules in an ice crystal are spaced relatively apart because of hydrogen bonding Solubility: polar molecules are attracted to ions and polar compounds, making these compounds soluble. Some of the other properties of water are that polar compounds that dissolve in water are hydrophilic which means they are water loving molecules. Nonpolar molecules that cannot dissolve in water are called hydrophobic molecules, water fearing molecules. Water causes hydrophobic molecules to form together in certain shapes or into layers like with water and oil. Ph scale measures if a substance is basic or acidic. Most biological reactions take place between Ph 6.5 and 8.0, this is called the physiological pH range, this range is also known for being fairly neutral. Acids are any substance that dissociates into H+ ions when exposed to water thereby lowering Ph, Bases are any substance that takes in H+ ions therefore increasing ph. Strong acids dissociate completely in water Weak acids partially dissociate in water.(example of this is carbonic acid h2co3 becomes a bicarbonate ion HCO3- in water. Buffers are substances that resist changes in ph. Composed usually of a weak acid and a salt, which release hydrogen ions when a base is added and absorb hydrogen ions when an acid is added. Its main goal is to keep ph relatively constant. Chapter 3 Carbon is the framework for biological molecules and is bonded to C, O, N, P or H It can form up to four covalent bonds, and bonded to itself and hydrogen can form nonpolar hydrocarbons. Nonpolar hydrocarbons bonded with other atoms form many biomolecules. Functional groups are specific molecular groups that bond to carbon hydrogen cores. Each group has unique chemical properties. The properties of each function group are retained to wherever they are bonded to and influence the behavior of the entire molecule. Primary functional groups Hydroxyl: found in carbohydrates, proteins, nucleic acids, and lipids/ Carbonyl: found in carbohydrates and nucleic acids. Carboxyl: found in proteins and lipids. Amino: found in proteins. Sulfhydryl: found in proteins. Phosphate: found in nucleic acids. Methyl: found in proteins and nucleic acids. Isomers: are molecules with the same molecular or empirical formula but different form. Structural isomers: differ in structure of carbon skeleton Stereoisomers: differ in how groups are attached to each other. Enantiomers are subcategories that have four unique groups attached and are mirror image molecules. Polymers are macromolecules that are made up of smaller units called monomers. carbohydrates, nucleic acids and proteins are all polymers. Macromolecules are made through dehydration and broken through hydrolysis. Dehydration synthesis reaction is when two smaller molecules come together to form a bigger molecule by removing a water molecule. Hydrolysis reaction is the opposite of dehydration reaction and breaks a larger molecule into smaller ones by the addition of a water molecule. Carbohydrates: Monosaccharides: are simple sugars and derivatives with 3-9 carbon atoms. disaccharide/oligosaccharides: are compounds that are formed by linking several monosaccharides together. Polysaccharides: polymers formed from multiple monosaccharide units. Glycan is the generic term for polysaccharides and oligosaccharides. Diverse functions of carbohydrates include metabolism, storage, generation of energy. Molecular recognition for the immune system, cellular protection for bacterial and plant cell walls, cell adhesion through glycoproteins, biological lubrication, and maintenance of biological structures through chitin and cellulose. disaccharides : two monosaccharides linked together by dehydration synthesis, used for sugar transport or energy. Examples are sucrose, lactose and maltose. Polysaccharides: are long chains of monosaccharides that are linked through dehydration synthesis, serve as energy storage( plants use starch, animals use glycogen) and can serve as structural support as well(plants use cellulose, arthropods use chitin. Nucleic acids are formed by nucleotide monomers which contain a sugar, phosphate and nitrogenous base. Sugar is deoxyribose in dna and ribose in rna. Nitrogenous bases include purines:(adenine and guanine) And pyrimidines:thymine (only in Dna), cytosine and uracil (only in Rna). Nucleotides are connected by phosphodiester bonds. Deoxyribonucleic acid also known as DNA contains information/instructions for protein synthesis. They are a sequence of bases. DNA comes in a double helix, two polynucleotide strands connected by hydrogen bonds using base pairing rules. Base pairing rules A with T in Dna , or A with U in Rna C with G. Chargaff’s rules Dna varies from species to species. Different tissues from the same species have the same DNA DNA does not change with age or environment All species contain A with T, G with C and A+G=T+C Ribonucleic Acid or RNA is similar to DNA except with nucleotides RNA contains ribose instead of deoxyribose. RNA is single helix and use information from DNA to specify sequence of amino acids in proteins. Adenosine triphosphate(ATP): Primary energy currency of the cell. Nicotinamide adenine dinucleotide or (NAD+) and flavin adenine dinucleotide or (FAD) are electron carriers of many cell reactions. Proteins or polypeptides are polymers of amino acids. 20 amino acids are used to build proteins using dna code. Amino Acid structure is composed of a central carbon atom, amino group(NH2), carboxyl group(COOH), single hydrogen and R group of variable structure. The twenty amino acids: Non Polar: Nonaromatic: alanine, valine, isoleucine, glycine, leucine. Aromatic: phenylalanine, tryptophan. Special function: proline, methionine. Polar uncharged: Nonaromatic: serline, threonine, asparagine, glutamine Aromatic: tyrosine. Special function: Cysteine Charged: Nonaromatic: glutamic acid, arginine, aspartic acid, lysine. Aromatic: histidine. Peptide bonds: are amino acids joined by a dehydration reaction Peptides: carbonyl oxygen has a partially negative charge and the amide nitrogen a partial positive charge, setting up a small electric dipole( a bond where the ends have opposite charges). Almost all peptide bonds in proteins occur in this trans configuration. Rotation of N to C and C to C can be described by dihedral angles on a model R groups can give special character to the protein. Some synthetic peptides have special useful traits. There are four levels of protein structure Primary protein structure is the sequence of amino acids Secondary structure is the interaction of groups in the peptide backbone. Tertiary structure is the final folded shape of a globular or fibrous protein consisting of a single polypeptide chain, it is stabilized by Hydrogen bonding, disulfide bridges ionic bonding and hydrophobic interactions. Quaternary structure is an arrangement of two or more individual, tertiary structures and polypeptide chains. The alpha helix can have two orientations and have an electric charge, transmitted through intrachain hydrogen bonding. Left handed alpha helices have not been observed in proteins. Several segments of a polypeptide can arrange into beta sheets, these segments can be nearby or far apart or be a different chain. The three dimensional arrangement of a protein is its tertiary structure, because of this proteins are classified as either globular or fibrous, fibrous proteins arrange in long strands or sheets. Globular proteins are very compact compared to fibrous proteins. The quaternary structure of proteins associates several subunits that can function together(hemoglobin) or independently such as in catalysis and regulation. Additional protein structural characteristics are motifs which are a folding pattern that involve two or more elements of a secondary structure and their connection. Another is domains that are functional units within a larger structure that perform functions like catalysis and regulation. Proteins can be classified based on motifs Proteostasis pathways: are the active form of a protein and are called native , misfolded proteins are called prions and cause diseases and other disorders. Chaperones proteins help proteins fold correctly, in cystic fibrosis, proteins fail to fold correctly Denaturation occurs by change in ph chemicals, such as guanidine and heat. Lipids are groups of molecules such as fats, oils, waxes, steroids, terpenes and some vitamins that are insoluble in water. Fats (triglycerides) have there fatty acids esterified with glycerol. If the fatty acids in the fat are saturated the fat will be solid. If it has unsaturated fatty acids it will be oily. The lipids include plant terpenes, cholesterol, steroid hormones, and prostaglandins. phospholipids are made up of a glycerol, 2 fatty acids and a phosphate. They are amphiphilic(like soap and emulsifiers) with a polar head that is hydrophilic and a nonpolar tail that is hydrophobic. Chapter 4 Cell theory: Robert hooke in 1665 was the first to observe cells using a microscope. Mathias Schleiden in 1838 and Theodor Schwann in 1839 proposed the cell theory that in modern form says: Organisms are composed of one or more cells where the processes of heredity and metabolism occurs within. Cells are the smallest living things and the basic unit of an organism\ Cells only arise from division of a previous cell. Cell size is limited, most cells are round and small due to a reliance on diffusion of substances in and out of a cell. Rate of diffusion is affected by surface area, temperature, concentration gradient, and distance. An organism of many small round cells has an advantage over an organism composed of fewer, larger, round cells. As a round cell’s size increases, its volume increases much more rapidly than its surface are and diffusion is slower. Although most cells are small and round some large cells adapt by having more than one nucleus(muscle) for genetic information to spread, or being skinny(neurons) to facilitate diffusion. Very few cells are visible to the naked eye. Most cells are less than 50 um in diameter. Resolution is the minimum distance two points can be apart and still be distinguished as two separate points. For the naked eye it has to be 100 um to be able to be distinguished by the human eye. Two main types of microscopes are light microscopes that use visible light and two magnifying lenses, they are limited to resolution using wavelengths of light, can can resolve structures that are 200 nm apart. Electron microscopes use a beam of electrons, resolve structures that are .2 nm apart. Electron microscopes transmit electrons through material, scanning electron microscopes beam electrons onto the specimen surface. Except for vertebrate eggs that can be seen with the naked eye most cells are microscopic with the cell membranes being only 5 nm thick. All cells have basic structural similarities being that they have a nucleus where DNA is stored, cytoplasm which is semifluid cell matrix and cytosol. Ribosomes which synthesize proteins and plasma membrane which is a phospholipid bilayer with transport and receptor proteins. Prokaryotic cells are the the simplest organism, they have a wall and membrane covering the cytoplasm Two domains of prokaryotes, bacteria with peptidoglycan which is susceptible to antibiotics, and archaea with walls made of sugars and proteins. Prokaryotic cells lack a membrane bound nucleus and cell shape is influenced by cytoskeleton. Prokaryotic cells have ribosomes. Some prokaryotes contain organelles with specific functions. An example of this are magnetosomes that are found in magnetotactic bacteria which helps them navigate using the earth's magnetic field. Bacterial microcompartments: are cellular compartments bounded by a semipermeable shell, they are 40 to 400 nm in diameter and their functions include to isolate specific metabolic processes and for storage. Cytoskeletons in prokaryotes possess molecules related to actin and tubulin that help influence the shape of the cell wall. The strength and shape of the cell is determined by the cell wall.