Ap Biology: Topic 1- The Chemistry Of Life

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Matter

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is anything that takes up space and has mass

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Element

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a substance that cannot be broken down to other substances by chemical reactions EX: gold, copper, carbon, and oxygen

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Compound

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a substance consisting of two or more elements combined in a fixed ratio. EX: water(H20) and table salt (Na-Cl)

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make up 96% of living matter. About 25 of the 92 natural elements are known to essential to life.

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C (carbon), H(hydrogen), O(oxygen) and N(nitrogen)

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Trace Elements

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elements required by an organism in only minute quantities (e.g., iron and iodine)

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Atoms

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the smallest unit of an element that still retains the property of the element. Atoms are made up of neutrons, protons, and electrons.

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Protons

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positively charged particles. They are found in the nucleus and determine the element.

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Electrons

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negatively charged particles that are found in the electron shells around the nucleus. They determine the chemical properties and reactivity of elements.

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Neutrons

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No charge, found in nucleus. Number can vary in the same element, resulting in isotopes. EX: 12C and 14C; both have 6 protons but 12C has 6 neutrons while 14C has 8 Neutrons.

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Atomic Number

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is the number of protons an element can possesses. Unique to every element.

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Mass number

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an element is the sum of its protons and neutrons.

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Chemical bonds

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interactions between the valence electrons of different atoms. Atoms are held together by chemical bonds to form molecules.

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Covalent bonds

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occurs when valence electrons are shared by two atoms.

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Non-polar Covalent Bonds

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occurs when the electrons are being shared equally between two atoms. EX: O=O, H-H

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Polar Covalent Bonds

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one atom has a greater electronegativity than the other, resulting is an unequal sharing of electrons.

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Ionic Bonds

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two atoms attract valence electrons so unequally that the more electronegative atoms steals the electron away from the less electronegative atom.

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Ion

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the resulting charged atom or molecule

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Hydrogen Bonds

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relatively weak bonds that form between the positively charged hydrogen atom of one molecule and the strongly electronegative oxygen or nitrogen of another molecule.

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Van der Waals interactions

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very weal, transient connections that are the result of asymmetrical distribution of electrons with in a molecule.

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Structure of Water

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made up of 1 atom of oxygen and two atoms of hydrogen, bonded to form a molecule

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Polarity of Water

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The end bearing the oxygen has a slightly negative charge, the end bearing the hydrogen atoms has a slightly positive charge.

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Hydrogen Bonds of Water

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Form between water molecules. negative oxygen from one water molecule is attracted to the slightly positive hydrogen end of another water molecule.

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What is the maximum number of hydrogen bonds a water molecule can make at a time?

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4

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Cohesion

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the linking of like molecules, reason for surface tension.

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Adhesion

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Clinging of one substance of another. EX: water droplets adhering to a glass windshield.

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Transpiration

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the movement of water molecules up the very thing xylem tubes and their evaporation from the stomates in plant.

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Specific Heat

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amount of heat required to raise or lower the temperature of a substance by 1 degree Celsius.

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Specific Heat of water

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water changes less when a given amount of heat is lost of absorbed. The reason oceans can support plant and animal life.

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Insulation of Bodies of water by floating Ice

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Water is lees dense as a solid than a liquid. Ice floats. This keeps large bodies of water from freezing solid and therefore moderates temperature.

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Water as a solvent

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It is an important solvent. Many things dissolve in water.

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Solvent

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the things a substance dissolves in.

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Solute

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The substance that is being dissolved.

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Solution

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A solute and a solvent together.

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Hydrophilic

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substances that are water-soluble. (ionic compounds, polar molecules (e.g., sugars), and some proteins.

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Hydrophobic

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Substances that are non polar and do not dissolve in water. (Oils)

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Transpiration

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the movement of water molecules up the very thing xylem tubes and their evaporation from the stomates in plant.

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Specific Heat

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amount of heat required to raise or lower the temperature of a substance by 1 degree Celsius.

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Specific Heat of water

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water changes less when a given amount of heat is lost of absorbed. The reason oceans can support plant and animal life.

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Insulation of Bodies of water by floating Ice

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Water is lees dense as a solid than a liquid. Ice floats. This keeps large bodies of water from freezing solid and therefore moderates temperature.

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Water as a solvent

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It is an important solvent. Many things dissolve in water.

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Solvent

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the things a substance dissolves in.

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Solute

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The substance that is being dissolved.

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Solution

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A solute and a solvent together.

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Hydrophilic

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substances that are water-soluble. (ionic compounds, polar molecules (e.g., sugars), and some proteins.

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Hydrophobic

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Substances that are non polar and do not dissolve in water. (Oils)

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pH scale

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runs between 0-14 and measures the relative acidity and alkalinity of aqueous solutions.

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Acids

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excess of H+ ions and a pH below 7.0

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Bases

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excess of OH- ions and pH above 7.0

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Water's pH

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pure water is neutral, It's pH is 7. H+=OH-

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Buffers

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substances that minimize changes in pH. They accept H+ from solutions when they are excess and donate H+ when they are depleted.

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Carbonic Acid (H2CO3)

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important buffer in living systems. It moderated pH changes in blood plasma and the ocean.

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Why is carbon unparalleled in its ability to form molecules that are large, complex and diverse?

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1) it has 4 valence electrons.
2) It can form up to 4 covalent bonds.
3) These can be single, double, or triple covalent bonds.
4) It can form large molecules
5) These molecules can be chains, ring shaped, or branched.

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Isomers

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molecules that have the same molecular formula but differ in their arrangement of these atoms. These differences can result in molecules that very different in their biological activities.

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Functional groups

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are attached to the carbon skeleton have diverse properties. The behavior of organic molecules is dependent on the identity of their functional groups.

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Common functional groups

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Hydroxyl, Carboxyl, Carbonyl, Amino, Phosphate, Sulfhydryl.

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Hydroxyl Functional Group

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OH, Alcohols such as ethanol, methanol; helps dissolve molecules such as sugars.

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Carboxyl Functional Group

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COOH, Carboxylic acids such as fatty acids and sugars; acidic properties because it tends to ionize source of H+ ions.

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Amino Functional Group

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NH2 Amines such as amino acids

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Phosphate Functional Group

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Organic phosphates, including ATP, DNA, and phospholipids.

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Sulfhydryl Functional Group

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The group is found in some amino acids; forms disulfide bridges in proteins.

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Polymers

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long chains molecules of repeating subunits called monomers.

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Monomers

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chain together to created polymers.

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Condensation or dehydration reactions

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create polymers from monomers. Two monomers are joined by removing one molecule of water.

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Hydrolysis

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occurs when water is added to to split large molecules. The reverse of dehydration synthesis.

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Carbohydrates

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include simple sugars and polymers such as starch . All carbohydrates exist in a ratio of 1carbon: 2 hydrogen: 1 oxygen of CH2O

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Mono-saccharides

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are the monomers of carbohydrates. EX: glucose (C6H12O6) and ribose (C5H10O5)

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Polysaccharides

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are polymers of mono-saccharides. EX: starch, cellulose, and glycogen.

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Energy Storage Polysaccharides

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Starch- storage polysaccharide found in plants
Glycogen- storage polysaccharide found in animals, Vertebrate muscle, and liver cell.

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Structural Support Polysaccharides

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Cellulose- major component of plant cell walls.
Chitin- Found in exoskeleton of arthropods, such as lobsters and insects and cell walls of fungi.

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Lipids

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Hydrophobic, are not polymers, are assembled from a variety of components, examples include waxes, oils, fats, and steroids.

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Fats or triglycerides

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made up of a glycerol molecule and three fatty acid molecules

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Fatty acids

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include hydrocarbon chain of variable lengthens. These chains are non-polar and therefore hydrophobic.

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Saturated fatty acids

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no double bonds between carbons
tend to pack solidly at room temperature
are linked to cardiovascular disease
are commonly produced by animals
EX: butter and lard

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Unsaturated fatty acids

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have some carbon double bonds; this results in kinks
tend to be liquid at room temperature
are commonly produced by plants
EX: corn oil and olive oil

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Functions of Lipids

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Energy storage: fat store twice as many calories/gram as carbohydrates
Protection of vital organs and insulation. In humans and other mammals fat is stored in adipose cells.

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Phospholipids

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make up cell membranes. They have a glycerol backbone(head), which is hydrophilic; two fatty acid tails, which are hydrophobic. are a bi-layer to make the cell membrane.

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Steroids

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made up of four rings that are fused together.

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Cholesterol

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a steroid that is a common component of cell membranes

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The two Steroid hormones are?

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Estrogen and Testosterone

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Proteins

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polymers made up of amino acid monomers

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Amino Acids

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contain a central carbon bonded to a carboxyl group, an amino group, a hydrogen atom, and a R group (variable group or side chain)

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Peptide bonds

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link amino acids. They are formed by dehydration synthesis. the function of a protein depends on the order and number of amino acids.

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Four levels of protein structure

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Primary, Secondary, Tertiary, and Quaternary

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Primary Structure of Proteins

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the unique sequence in which amino acids are joined.

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Secondary Structure of Proteins

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refers to one of two three-dimensional shapes are the result of hydrogen bonding.
Alpha helix- a coiled shape
Beta Pleated sheet- an accordion shape

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Tertiary Structure of a Protein

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the complex globular shape, due to interactions between R groups. Globular proteins such as enzymes are held in position by these R group interactions.

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Quaternary Structure of a Protein

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the association of 2 or more polypeptide chains into one large protein. Hemoglobin is a globular protein with quaternary structure, it is composed of 4 chains.

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Protein Shape

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It is crucial to protein function. If it doesn't fold correctly its function is changed. it can be a amino acid substitution as seen in sickle cell disease.

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Chaperonins

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Assist in proper folding of proteins within cells.. They provide an isolating environment in which a polypeptide may attain final conformation.

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Denaturation

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proteins denature when it loses its shape and ability to function due to heat, a change in pH, or some other disturbance.

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DNA and RNA

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Deoxyribonucleic acid and ribosenucleic acid
They are polymers of nucleotides

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Nucleotides

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made up of three parts
Nitrogenous base (Adenine, Thymine, Cytosine, guanine, and uracil)
Pentose (5 carbon sugar) deoxyribose in DNA or ribose in RNA.
Phosphate group