AP Bio - Unit 1

What are the major elements in biological molecules?

Carbon, hydrogen, nitrogen, oxygen, sulfur and phosphorus

Atomic Number

number of protons

Atomic Weight/Mass Number

average of isotopes

Covalent bonding

Bond between two nonmetal atoms sharing electrons; More common than ionic bonds and found in carbon-based organic molecules; polar covalent bonds unequally share electrons and nonpolar covalent bonds equally share electrons

Ionic bonding

Bond between metal (cation) and no metal (anion); known as salts and have a net zero charge; certain salts are called electrolytes, necessary for nerve impulse condition, muscle contractions, and water balance.

What is an organic compound?

A molecule that contains carbon (excluding carbon dioxide) and are bound to hydrogen; may also contain oxygen, nitrogen, etc

What are functional groups:

Groups of atoms that occur within molecules and confer specific chemical properties to those molecules; found in the carbon “backbone” of macromolecules; different groups contribute to different chemical properties; can be hydrophilic or hydrophobic depending on their charge or polarity

Hydroxyl (OH-) Properties

Polar

Sulfhydryl (SH)

Polar

Methyl (CH3)

Nonpolar, hydrophobic

Carboxyl (COOH)

Hydrophilic, charged, ionizes to release H+; acidic

Carbonyl (C=O)

Hydrophilic, polar

Amino (NH2)

Charged, accepts H+ to form NH3+, basic

Phosphate (PO4)

Charged, ionizes to release H+, basic

Structure of Water

The nucleus of oxygen has a greater force of attraction than the nucleus of hydrogen, making the shared electrons closer to oxygen; since the electron pairs are shared unequally, the bonds are considered polar covalent.

Polarity (Properties of Water)

Results in the unequal sharing of electrons; creates slightly positive charge on hydrogen and slightly negative charge on oxygen; allows other water molecules to created h-bonds due to the opposite charges.

Cohesion

Water molecules are attached to each other due to h- bonds; allows for surface tension; cohesion and surface tension allow denser items to “float” on top of water

Adhesion

the attraction between water molecules and other molecules. can sometimes be stronger than water cohesive forces when water is exposed to charged surfaces

Density (Properties of Water)

Vaires on the states of matter; when water is frozen, the molecule form a crystalline structure upheld by h-bonds; the lower density of ice is due to the orientation of the h-bonds; molecules push further apart compared to liquid water

Solvency (Properties of Water)

Polarity of water allows ions and polar molecules to readily dissolve in it; referred to as universal solvent; ions from ionic compounds will individually react with polar regions and break their ionic bonds (a.k.a dissociation)

Sphere of hydration (Properties of Water)

formed when the charges associated with these molecules form h-bonds with water, surrounding the particle with water molecules; keeps the particles separated in the water

Latent Heat of Vaporization (Properties of Water)

Heat of vap is the amount of energy required to change one gram of a liquid substance to a gas; water has a high heat of vap; h-bonds are significatly stronger to other liquids, making it harder for water to vaporize; KE is released as h-bonds break during boiling point; energy is used up, cooling the environment

Specific Heat Capacity (Properties of Water)

the amount of heat one gram of substance must absorb or lose to change it’s temp by one degree Celcius; for water, it’s one calorie; water has highest specific heat capacity of any liquid; water takes longer to heat and cool

What elements are in carbohydrates?

Carbon, oxygen, hydrogen

Monomers

Combine with each other using covalent bonds to form polymers; release water molecules in dehydration synthesis to make polymers

Polymers

Covalently bonded monomers

Function of carbohydrates

Provide energy to the body through glucose, a monomer and component of starch; ratio of C:H:O is 1:2:1; components of carbon + water; classified as mono-, di-, and polysaccharides

Monosaccharides

Simple sugars; # of carbons often range from 3-7; suffix of “-ose”; an aldehyde group signifies an aldose; a ketone group signifies a ketose; also known as trioses, pentoses, and/or hexoses

Glucose

Energy is released during cellular respiration to help make ATP; glucose is used to energize plants; excess glucose is stored as starch and used by humans & animals.

Disaccharides

Two monosaccharides bonded through the process of dehydration synthesis; hydroxyl group of 1 monosaccharide reacts with the H+ of the other monosaccharide forming a covalent bond known as a glycosidic bond (alpha or beta); e.g. lactose, maltose, and sucrose

Polysaccharides

Long chains of monosaccharides linked by glycosidic bonds (branched or unbranched); starch, glycogen, cellulose, and chitin are all polysaccharides

Starch

created when plants store excess glucose in their roots and seeds; consumed by humans and broken down by enzymes to create maltose and glucose; made of glucose monomers joined by alpha 1-4 and alpha 1-6 glycosidic bonds

Amylose

starch formed by unbranched chains of glucose monomers (alpha 1-4)

Amylopectin

starch formed by a branched polysaccharide (alpha 1-6 at the branch points)

Cellulose

cell wall of plants; made of glucose monomers linked by beta 1-4 glycosidic bonds

Glycogen

stored the form of glucose in humans and other vertebrates, stored in liver and muscle cells; when blood glucose decreases, glycogen is broken down to release glucose (glycogenolysis)

Chitin

a nitrogen-containing polysaccharide and made of repeating units of N-acetyl-beta-d-glucosamine (a modified sugar); main component of fungal cell walls

Dehydration Synthesis

“to put together while loosing water”; A reaction where water molecules are released as a byproduct of monomers, becoming polymers; hydrogen covalently bonds with hydroxyl to create water; catalyzed by enzymes

Hydrolysis

“to split with water”; polymers are broken down into monomers through the use of a water molecule; polymer breaks into two parts: one gains an H+, and the other gains hydroxyl from the split of a water molecule; catalyzed by enzymes; process releases energy

Lipids

nonpolar in nature due to their hydrocarbons that have mostly no polar C-C or C-H bonds; cells store long-term energy in the form of fat; provide insulation from the environment for plants and animals; building blocks for hormones; include fats, waxes, phospholipids, and steroids

Fatty Acids

made of long chains of hydrocarbons to which a carboxyl group is attached; number of carbons in a fatty acid range from 4-36; in a fat molecules (glycerol + fatty acids), fatty acids are attached to three carbons of the glycerol molecule with an Easter bond through an oxygen atom, water molecules are then released

Saturated Fats

Two hydrocarbon chains linked by a single bond; saturated by H; number of hydrogens attached to carbons is maximized; solid at room temp.

Unsaturated fats

Two hydrocarbon chains linked by a double bond, creating a kink; number of hydrogens bonded to carbons is minimized; liquid at room temp. (oils)

Triglycerides

Made of one glycerol attached to 3 fatty acids through ester bonds; stores extra energy in animals; made and broken down through parts of the glucose catabolism pathways

Structure of Phospholipids

hydrophilic head contains a phosphate group and glycerol backbone; hydrophobic tails contain an unsaturated fatty acid and a saturated fatty acid; composed of fatty acid chains attached to glycerol or sphingosine backbone; phosphate group attached to the diacylglycerol is modified by an alcohol

Function of Phospholipids

major constituents of the plasma membrane (outer layer of all living cells); amphipathic molecules (hydrophobic & hydrophilic)

Waxes

Made up of long fatty acid chains esterified to long-chain alcohols; hydrophobic

Steroids

Fused ring structure; hydrophobic and insoluble in water; four linked carbon rings, which usually have a short tail or an hydroxyl group

Cholesterol

Most common steroid; made in the liver and is a precursor to steroid hormones such as testosterone and estradiol, vitamin D, and bile salt; found in the plasma membrane and phospholipid bilayer

LDL Cholesterol

“low-density lipoproteins”; a.k.a. “bad” cholesterol; causes heart disease

HDL Cholesterol

“high-density lipoproteins”; a.k.a. “good” cholesterol; lowers risk of heart disease because cholesterol in the blood is taken to the liver

Function of Proteins

polymer of amino acids; different structures of proteins allow for different functions such as: structural, regulatory, contractile, or protective

What are the three things that can denature proteins?

change in temp, pH, or exposure to chemical solutions

Essential amino acids

Isoleucine, leucine, lysine, methionine, phenylalanine, tryptophan, valine, histidine, threonine, arginine

Dipeptide

The combination of two amino acids through a peptide bond; soluble in water

Polypeptide

Amino aid chains; has an “N” (amino) terminal on one end and a “C” (carbonyl) terminal on the other; polymer of amino acids

Primary Structure - Proteins

sequence of amino acids in a polypeptide chain change in nucleotide sequence of the gene’s coding region could add a different amino acid, causing different protein structure and function; determined by sequence of DNA bases

Secondary Structure - Proteins

local folding of the polypeptide in some regions of the protein; most common are alpha helix and beta-pleated sheet structure (both held by h-bonds)

Alpha Helix - Secondary Structure of Protein

structure has h-bonds between the oxygen atoms in the carbonyl group in 1 amino acid and another amino acid that is 4 amino acids down the chain; helix turn has 3.6 amino acid residues; r group follows from helix chain

Beta-Pleated Sheet - Secondary Structure of Protein

“pleats” are formed by h-bonding between H+ and O- in the backbone of the polypeptide chain; R groups are attached to carbon and are below & above folds; folds are parallel and antiparallel

Tertiary Structure - Proteins

3D structure for a polypeptide; structure is created by the interactions between R groups; R group counteracts the h-bonds (like charges repel each other); during folding, the hydrophobic R groups of non polar amino acids are on the interior of protein, which the hydrophobic ones are outside; cysteine side chains interact to form disulfide linkages with oxygen (only covalent bonding in protein folding); structure includes most enzymes and globular proteins

Quaternary Structure - Proteins

formed from several polypeptides and the interactions of the subunits; weaker interactions stabilize overall structure; not all proteins have this structure

Digestive Enzymes

includes amylase, lipase, pepsin, and trypsin; helps in digestion of food by catabolizing nutrients into monomeric units

Contractile Enzymes

includes acting and myosin, controls muscle contractions

Transport Enzymes

includes hemoglobin & albumin, carry substances in the blood or lymph throughout the body

Defense Enzymes

includes immunoglobulins, protects the bodyin from foreign pathogens

Hormonal Enzymes

includes insulin and thyroxine, coordinates the activity of different body systems

Structural Enzymes

includes acting, tubulin, and keratin; constructs different structures (e.g. cytoskeleton)

Storage Enzymes

includes leyume storage proteins and egg white (albumin); provides nourishment in early development of the embryo and the seedling

Nucleic Acids

carry genetic blueprint of a cell and carry instructions for the functioning of the cell; DNA dictates the structure of mRNA in transcription, while RNA controls protein structure in translation

Nucleotide Structure

phosphate group, pentose sugar (either ribose or deoxyribose), and nitrogenous base; elements are carbon, hydrogen, oxygen, nitrogen and phosphate

Nitrogenous bases

bases are organic molecules and contain carbon & nitrogen and an amino group that can bond with an extra H+ ion (more basic)

Base Pairs - DNA & RNA

DNA contains the nucleotides adenine, guanine, cytosine, and thymine; RNA has adenine, guanine, cytosine, and uracil; adenine & guanine are purines and have two C-N rings, while cytosine, thymine, and uracil are pyrimidines and have one C-N ring; base pairs for DNA are A-T, G-C

DNA Structure, Function, & Location

double-helix structure; sugar & phosphate are on the outside, creating the backbone; nitrogenous bases are stacked on the inside, bound by h-bonds; controls all of the cellular activities by turning genes “on/off”; found in the nucleus (eukaryotes), chloroplast, and mitochondria

RNA Structure, Function, & Location

single-stranded; made of ribonucleotides linked by phosphodiester bonds; controls protein synthesis; mRNA acts as an intermediary for DNA to communicate with the rest of the cell; in the cytoplasm, leaves the nucleus

tRNA

carries the correct amino acid to the site of protein synthesis

mRNA

acts as a messenger between DNA and the cell

rRNA

a major constituent of ribosomes on which mRNA binds; ensures proper alignment of mRNA and ribosomes