mastering biology chapter 3

hydrocarbon

an organic compound containing only C and H

isomer

compounds with the same molecular formula but different 3D structures

structural isomer

differs in covalent bonds between atoms

geometric isomer

differs in the arrangement of atoms around a double bond

enantiomer (stereoisomer)

molecules that are mirror images of each other

carbon chain (skeleton)

-varies in length
-varies in number & location of double bonds
-can be branched/unbranched
-can be arranged in rings

functional group

-atoms attached to a carbon skeleton involved in chemical reactions
-determines the characteristics of a molecule
-compounds that contain them are usually hydrophilic

hydroxyl group

-O bonded to H
-needs to be bonded w/ a carbon skeleton

alcohol

organic compound that contains a hydroxyl group (i.e. ethanol)

carbonyl group

-C double bonded to O
-can be located within or at the end of a carbon skeleton
-works w/ carboxyl groups to make sugars

aldehyde

organic compound in which the carbonyl group is attached at the end of a carbon chain

ketone

organic compound in which the carbonyl group is attached to a carbon atom within the carbon chain

carboxyl group

-C double bonded to O and single bonded to a hydroxyl
-acts as an acid by donating H+
-found in all proteins

carboxylic acid

organic compound that contains a carboxyl group

amino group

-N bonded to two H atoms
-acts as a base by picking up H+ from a solution to become ionized (NH3+)
-found in all proteins

amine

compound containing an amino group

amino acid

-Organic compounds containing a central C bonded to an H atom, amino group, carboxyl group, and R group
-R-group that projects from the backbone makes each amino acid unique
-Building blocks of proteins

phosphate group

-P doubled bonded to O single bonded to 3 O atoms
-acts as an acid, losing H+

phosphate

-organic compound containing phosphate groups
-involved in energy transfers (ATP)

sulfhydryl group

-S bonded to H
-groups can react & form a crosslink that stabilizes the structure of many proteins

thiol

organic compound that contains a sulfhydryl group

methyl group

-C bonded to 3 H atoms
-hydrophobic
-nonpolar

methylated compounds

-organic compound that contains a methyl group
-component of DNA that affects gene expression

monomer

subunit that serves as a building block of polymers

polymer

-many monomers linked together by covalent bonds
-caused by dehydration

dehydration synthesis (condensation reaction/polymerization)

-covalently bonding monomers to form a polymer through the removal of H2O (H and OH)
-energy can be stored when the bonds are formed

hydrolysis

-chemical reaction in which bonds between molecules in a polymer are broken down by the addition of H2O to form monomers (H and OH)
-energy is released when the bonds are broken

macromolecule (organic compound)

-giant molecule (polymer) formed by the joining of smaller molecules (monomers) through dehydration
-contains carbon

nucleic acids

-contains C, H, O, N, P
-polymer made of nucleotide monomers
-sequence of nucleotides carries information

DNA

-Polymer that stores hereditary information
-Single molecule contains 2 polynucleotides
-Double helix formed by the twisting of 2 complimentary strands of nucleotides
-Backbone consists of alternating sugars and phosphates
-Strands are held together by hydrogen bonds between pairs of nitrogenous bases

nitrogenous base pairs

-adenine w/ thymine (uracil in RNA)
-cytosine w/ guanine

RNA

-Polymer that synthesizes proteins
-Consists of a single-stranded polypeptide
-Contains ribose
-Uracil instead of thymine
-Copied from a DNA molecule
-Shorter than DNA

nucleotide

-building block of DNA/RNA
-consists of a five-carbon sugar (deoxyribose/ribose), nitrogenous base, and a phosphate group

polynucleotide

-polymer of nucleotide monomers
-backbone consists of alternating sugars and phosphates
-bases are attached to the sugars

gene

-String of nucleotides
-Sequence of nucleotides determine the primary sequence of amino acids of the produced protein
-Contains the information necessary to build protein/molecule of RNA
-Carries information that is then translated into the amino acid sequence of proteins

chromosome

-long DNA molecule with part of or all of the genes
-genes are separated by junk DNA

genome

complete collection of an organism's chromosomes and the genes within them

carbohydrates

-contains C, H, and O in a 1:2:1 ratio
-used as fuel for cellular work (form of immediate energy)
-form of glucose
-hydrophilic

membrane carbohydrates

-Marks the cell's identity
-Controls the cell's activities
-Protein made by other cells can bind to them

glucose

-Monosaccharide that serves as a building block for many polysaccharides
-Oxidation in cellular respiration is a source of ATP
-Carbon skeleton can be used to build many organic molecules

glycosidic bond

covalent bond that joins a carbohydrate w/ another group

monosaccharide

-monomer of carbohydrates
-simple sugar
-similar 1:2:1 ratio
-contain numerous hydroxyl groups and a carbonyl group
-carbon skeletons range from 3 to 7 C's

polysaccharide

-long chains of sugars
-monosaccharides joined together via dehydration
-act as identification tags on cell membranes

lactose

-disaccharide (sugar) consisting of glucose and galactose

sucrose

-disaccharide consisting of glucose and fructose
-circulates in plant sap
-obtained from sugar cane and sugar beets to form table sugar

maltose

-disaccharide consisting of 2 glucose
-produced by the digestion of starch in a sprouting seed/intestine of an animal

cellulose (fiber)

-polysaccharide that composes plant cell walls
-provides structural support
-most abundant organic compound
-indigestible without the help of bacteria

chitin

polysaccharide that provides structural support in animal cells

starch

-polysaccharide found in the chloroplast
-stores energy
-made of glucose

glycogen

-polysaccharide that stores energy in animal cells by linking sugar molecules with insoluble grains
-found in muscles & liver

lipids

-contains C, H, and O
-3 fatty acids joined to 1 glycerol
-stores energy between C and H bonds
-hydrophobic

plaque

lipid-containing deposit in a blood vessel

triglyceride (fat molecule)

-Glycerol bound w/ 3 fatty aids
-Varies in the length of hydrocarbon tails (4 to 26 C's)
-Varies in the number and location of double bonds (0 to 4)
-Stores energy in spherical droplets
-Contains more energy per gram than any other biological fuel

ester bond (ester linkage)

joins fatty acid tails to a glycerol backbone

glycerol

-consists of three carbons
-each carbon is bonded to a hydroxyl and H

phospholipid

-glycerol bound to 2 fatty acid tails and phosphate group
-forms cell membrane
-hydrophobic fatty acid tails face inward, mingling together
-hydrophilic heads face outward, exposed to aqueous solutions on both sides of the membrane

steroid

-lipid consisting of 4 fused rings
-differ in what is attached to the rings
-act as chemical messengers

anabolic steroid

-steroids used to stimulate muscle growth
-can prevent bone growth
-synthetic variants of testosterone

cholesterol

-Steroid that is an important component of animal cell membranes
-Acts as a precursor molecule for the synthesis of other steroids
-Ratio to other membrane lipids impacts the ability of the cell & substances that are allowed to cross the membrane

vitamin D

steroid that aids in calcium & phosphate metabolism

estradiol

steroid female sex hormone produced by the ovaries

testosterone

steroid male sex hormone produced by the testes

wax

-dense, waterproof lipids
-saves water in plants and animals by coating their surfaces

cuticle

waxy outercoating of plants

lipoprotein

-Lipid bound to proteins/phospholipids
-Phospholipids & proteins line the surface (they have parts that are compatible with water)
-Fats and steroids occupy the interior
-Helps lipids move through the body

fatty acid

-Consists of a carboxyl group and long hydrocarbon chain
-Tails contain only nonpolar (C-H) bonds
-Hydrophobic

unsaturated fatty acid

-Contains at least one double bond (kink) in their hydrocarbon chain
-Reduced number of H's
-Usually found in vegetable oils
-Liquid at room temperature
-Stimulates the breakdown and secretion of cholesterol.

saturated fatty acid

-Contain only single bonds in their hydrocarbon chains
-2 to 3 H's on each C
-Found in animal fats
-Solid at room temperature
-Impede the excretion of cholesterol
-Stimulate cholesterol synthesis in the liver

kink

-Formed by double bonds
-Prevents fatty acids from packing tightly
-Keeps them liquid at room temperature

trans fat

-unsaturated fat formed during hydrogenation of saturated fat
-contain fewer double bonds
-linked to health risks (i.e. heart attacks)

hydrogenation

process of adding hydrogen to double bonds

proteins

-contains C, H, O, N, sometimes S
-polymer of amino acids
-made from varying combinations of 20 amino acids
-consists of one or more polypeptides folded into a specific structure

primary structure

-Linear string of amino acids that forms the backbone of the polypeptide chain
-Determined by genetic info

secondary structure

-Local patterns or folds of a polypeptide chain between amino & carboxyl groups
-Caused by interactions between R-groups

alpha helix

coiling of polypeptides

beta-pleated sheet

folding of polypeptides

tertiary structure

-Overall globular (3D) shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain
-Hydrophobic R-groups cluster in the center
-Positively/negatively charged R-groups can form ionic bonds
-Polar R-groups can form hydrogen bonds
-Sulfur-containing R-groups can form covalent bonds

quaternary structure

-2 or more individual polypeptide subunits
-not present in all proteins

denaturation

-the unraveling of a protein, losing its structure and function
-the separation of 2 strands of DNA
-caused by changes in pH, salt concentration, or temperature

transport proteins

-embedded in cell membranes
-moves sugar molecules & other nutrients to cells
-carries molecules from place to place

structural proteins

-Shape cells
-Anchor cell parts
-Bind cells together, making organized units

signal proteins

-Hormonal proteins that coordinate an organism’s activities by acting as signals between cells
-Bind to receptor proteins that can then relay messages in a cell

sensory proteins

-proteins that detect environmental changes (i.e. light)
-respond by emitting or producing signals that call for a response

storage protein

-proteins that stockpile building components in cells that can be used to make other proteins
-storage proteins in seeds provide raw materials used by the developing plant

contractile protein (motor proteins)

-Protein that move parts of the cell
-Works together in muscle cells to move a whole animal

gene regulatory protein

-Protein that bind to DNA in specific locations
-Control whether or not genes will be read
-Allows cells to become specialized for different functions & respond to changes in their surroundings

antibody

defensive proteins of the immune system that bind to pathogenic invaders, marking the foreign objects for destruction

enzyme

-Organic protein that changes the rate of a chemical reaction without being consumed by it
-Catalyze and regulate chemical reactions
-Only work on specific substrates
-Lower activation energy
-Reusable

active site

binding site between an enzyme and its substrate

lock and key hypothesis

the active site of an enzyme is specifically shaped to fit only 1 specific substrate.

lactase

enzyme that only works on the substrate lactose

peptide bond

-covalent bond between an amino group of one subunit w/ a carboxyl group of another subunit
-formed by dehydration

disulfide bridge (bond)

-covalent bond between S atoms of 2 cysteine amino acids
-stabilizes structure of proteins

covalent bond

formed by the equal sharing of outer-shell electrons

ionic bond

-formed by the transfer of electrons
-1 atom loses an electron to form a positive ion & the other atom gains an electron to form a negative ion
-held together by charge differences

hydrogen bond

-formed by the attraction between H+ of one water molecule & O- atom of another water molecule
-holds water molecules together
-form, break, and reform with great frequency because they are weak

polar bond

-formed by the unequal sharing of electrons
-one atom is positively charged and the other is negatively charged

nonpolar bond

-formed by the equal sharing of electrons
-no charge separation

cohesion

-sticking together of 2 like molecules (H2O)
-caused by the attraction of opposite charges (polarity)

adhesion

-sticking together of 2 unlike molecules (H2O & another substance)
-caused by the attraction of opposite charges (polarity)