Ap Bio Unit Chemistry of Life Terms

Disaccharide

A double sugar, consisting of two monosaccharides joined by dehydration synthesis.

Monosaccharide

A single sugar molecule such as glucose or fructose, the simplest type of sugar.

Polysaccharide

Carbohydrates that are made up of more than two monosaccharides.

Glycosidic Linkage

A covalent bond formed between two monosaccharides by a dehydration reaction. Also its a bond that forms between a monosaccharide and another molecule (like another monosaccharide).

Starch

A storage polysaccharide in plants consisting entirely of glucose.

Cellulose

A substance (made of sugars) that is common in the cell walls of many organisms.

Lipid Examples

Fatty acids, fats, saturated fats, unsaturated fats, steroids, phospholipids, cholesterol, triglycerides. 

Unsaturated Fat

A lipid made from fatty acids that have at least one double bond between carbon atoms.

Saturated Fat

A lipid made from fatty acids that have no double bonds between carbon atoms. 

Steroid

Lipid molecule with four fused carbon rings. 

Polyunsaturated vs Monounsaturated Fat

Polyunsaturated contains 2 or more double bonds whereas Monounsaturated contains 1 double bond. Type of unsaturated fat.

Tans Fat

Hydrogenated unsaturated fat which is extremely unhealthy as they raise cholesterol levels. They are trans isomers of unsaturated fatty acids.

Cis isomer

Bent. The hydrogen atoms are on the same side of the double bond. This bend keeps the molecules from packing tightly → liquid at room temp (like olive oil). Only applicable to unsaturated fats not saturated fats as saturated fats cannot have the hydrogens on the same side at every double bond site. 

Trans isomer

Straight. The hydrogen atoms are on opposite sides of the double bond. The molecule becomes more linear, like saturated fat → solid at room temp (like margarine). Only applicable to unsaturated fats not saturated fats as saturated fats cannot have the alternative hydrogens at the double bond sites. 

Phospholipid

A lipid that contains phosphorus and that is a structural component in cell membranes.

Nucleotide

Monomer of nucleic acids made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base. 

Nucleic Acid Examples

DNA, RNA, (ATP and ADP are modified nucleic acids).

Protein Examples

Amino acids, primary, secondary, tertiary, quaternary structures, collagen, hemoglobin, enzymes.

Triglyceride

A lipid made of three fatty acid molecules and one glycerol molecule.

Amino Acid Examples

Glutamine, proline, cysteine, and lycine to name a few.

Primary Structure of a Protein

Sequence of amino acids. Covalent peptide bonds between amino and carboxyl groups. Once these bonds form there is an amino and carbonyl group present. 

Secondary Structure of a Protein

Protein structure is formed by folding and twisting of amino acid chain. Hydrogen bonds between amino and carbonyl groups. Forms alpha helix and beta pleated sheets.

Tertiary Structure of a Protein

Protein structure is formed when the twists and folds of the secondary structure fold again to from a larger 3D structure. Bonds between the R groups of each amino acid. Bond types are Hydrogen Bonds, Hydrophobic Interactions, Ionic Bonds, and Disulfide Bridge. Still bonding within 1 polypeptide. 

Quaternary Structure of a Protein

Protein structure is a protein consisting of more than one folded amino acid chain. Bonding between 2 or more polypeptides. Bonds are also between the R groups of different polypeptide chains rather than the same chain as in tertiary structures. Bond types are Hydrogen Bonds, Hydrophobic Interactions, Ionic Bonds, and Disulfide Bridge.

Disulfide Bridge

The covalent bond between two sulfur atoms (-S—S-) linking two molecules or remote parts of the same molecule.

Hydrogen Bonds

Very weak bonds; occurs when a hydrogen atom in one molecule is attracted to the electrostatic atom in another molecule.

Nucleic Acid

Kind of macromolecule that stores, transfers, and expresses genetic information.

Carbon, Hydrogen, Oxygen, Phosphorus, Nitrogen (CHOPN)

Elements that make up a nucleic acid.

Atoms in Nucleic Acids

C, H, O, N, P

Elements in Proteins

C, H, O, N, S (sometimes)

Elements in Carbohydrates

C, H, O

Elements in Lipids

C, H, O, P (sometimes)

Functional Groups in Carbohydrates

Hydroxyl, Carbonyl.

Functional Groups in Proteins

Amino, Carboxyl (turns into carbonyl after dehydration synthesis to form a chain of amino acids), R Groups.  

Functional Groups in Lipids

Hydroxyl, Carboxyl, Phosophate (for phospholipids), Methyl (at the end of hydrocarbon tails of fatty acids), Carbonyl (in some lipids). 

Functional Groups in Nucleic Acids

Phosphate, Hydroxyl, Carbonyl, Amino

Double helix

Term used to describe the arrangement of a DNA strand.

RNA

Ribonucleic acid; a polymer of nucleotides that transfers genetic information.

How RNA differs from DNA

The sugar in RNA is ribose; Uracil bonds with Adenine; RNA is single-stranded.

Amino acid

Building block (monomer) of proteins, composed of an amino group and a carboxyl group, a hydrogen atom, and an R-group.

Structure of an amino acid

A carboxyl group, an amino group, a central Carbon, a Hydrogen, and an R-group.

Peptide Bond

Covalent bond formed between amino acids.

Polypeptide Chain

A long line of amino acids bonded together by peptide bonds.

R-group

Stands for the rest of the compound, different for each kind of amino acid, giving the amino acid its properties.

Properties the R-group may give the Amino Acid

Hydrophilic or hydrophobic, polar or nonpolar, acidic or basic.

Four Levels of a proteins structure

Primary structure, secondary structure, tertiary structure, quaternary structure.

How do Hydrophobic R-groups Behave

Move together to the interior of a protein, away from water.

Carbon, Hydrogen, Oxygen (CHO)

Elements that makeup both Carbohydrates and Lipids

Fatty Acid

Building block of a triglyceride made of a hydrocarbon chain and a carboxyl group at one end.

Glycerol

A carbon alcohol that is hydrophilic. E shape. Can form up to 3 ester bonds with 3 fatty acids. Can also bond with a phosphate group.

Functions of Lipids

Long-term energy storage, insulation, part of the cell membrane, chemical messenger, waterproofing.

Phospholipid

Lipid made of two hydrocarbon chains, glycerol, and a phosphate group.

Hydrophobic tail

Another name for the hydrocarbon chain in a phospholipid.

Hydrophillic head

Another name for the phosphate group in a phospholipid.

-ose

Suffix carbohydrates usually end in (gluc-ose, fruct-ose).

Examples of Carbohydrate Mono, Di, and Polysaccharides.

Monosaccharides: Glucose, Fructose, Galactose

Disaccharides: Sucrose, Lactose, Maltose

Polysaccharides: Starch, Glycogen, Cellulose, Chitin

Macromolecules

Large organic molecules

Hydrocarbons

Carbon and hydrogen atoms that are covalently bonded that make them stable and nonpolar. 

Nonpolar 

Not soluble in water.

Polar

Soluble in water.

Dehydration Synthesis

Reaction that links monomer molecules together, releasing a molecule of water for each bond formed

Hydrolysis

The process of adding a water molecule to break a polymer into monomers.

Charge of the oxygen atom in a water molecule

slightly negative

Charge of the hydrogen atoms in a water molecule

slightly positive

Hydrophilic vs Hydrophobic

Hydrophilic: Term for substances that dissolve in water. Water loving.

Hydrophobic: Term for substances that do not dissolve in water.

High Specific Heat

Property of water in which water changes temperature very slowly with changes in heat due to hydrogen bonding.

Evaporative cooling

Water carries the heat it absorbs away in sweat due to its high specific heat.

The reason ice floats in liquid water

Less dense as a solid; hydrogen bonds form crystalline structure that keeps the water molecules separate.

Cohesion

The attraction of like substances; water molecules are attracted to other water molecules; this is due to the hydrogen bonding between water molecules.

-H bonding between H2O creates it (sticky)
-allows for the movement of water against gravity
-high surface tension

Adhesion

The attraction of unlike molecules; water molecules are attracted to other polar surfaces.

-H2O molecules form H bonds with other substances
~capillary action
~meniscus
~water climbs up fiber

Polar vs Nonpolar Covalent Bond

Polar Covalent Bonds: Bond that forms when electrons are shared unequally; like that between the oxygen atom and hydrogen atoms in a water molecule

Nonpolar Covalent Bonds: Bond that forms when electrons are shared equally.

Water

-polar molecule
-polar colvalent bonds
-oxygen end is partial negative and the hydrogens have a partially positive end
-cohesive

Cohesion

-H bonding between H2O creates it (sticky)
-allows for the movement of water against gravity
-high surface tension
-water moves up a tree by transpiration (helped by ____)

Adhesion

-H2O molecules form H bonds with other substances
~capillary action
~meniscus
~water climbs up fiber

Evaporative cooling

-organisms use to regulate their temperature
-ex: sweating
-water evaporates through a surface, cooling occurs

Isomers

-molecules with the same molecular formula but different structures
-different chemical properties
-different biological functions

Structural vs Geometric Isomers

Structural Isomers: differ in covalent arrangement of atoms.

Geometric Isomers: same covalent relationships by different spatial arrangements.

Cholesterol

-important cell component
-animal cell membranes
-helps keep membrane fluid, flexible and mobile
-precursor of all other steroids
~including vertebrate sex hormones
-high levels in blood may contribute to cardiovascular disease

Proteins

-most structurally and functionally diverse group
-function: involved in almost everything
~enzymes (pepsin, DNA polymerase)
~structure (keratin, collagen)
~carriers and transport (hemoglobin, aquaporin)
~cell communication (signals and receptors)
~defense (antibodies)
~movement (actin and myosin)
~storage (bean seed)
-structure:
~monomer amino acids
~polymer polypeptide
-can be one or more polypeptide chains folded and bonded together
-large and complex molecules
-complex 3D shape

Amino acids

-structure: central carbon (alpha carbon)
-amino group
-carboxyl group (acid)
-R group (side chain)
~variable group
~different for each
~confers unique chemical properties
-physical and chemical properties based on R groups attached

Lipids

-functions: long term energy storage and concentrated energy, cushions organs, and insulates body
-not a true polymer and not large enough to be a macromolecule
-big molecules made up of smaller subunits
-not a continuous chain
-all mix poorly in water (hydrophobic)
-include waxes, pigments, fats, pils, phospholipids, and steroids
-structure: a glycerol (3 Carbons) and a fatty acid chain

Carbohydrates

-composed of C, H, O
-function: energy, raw materials, energy storage, and structural storage
-monomer: sugars

Denaturation

-although proteins fold as they are made, under certain conditions, these proteins will not fold properly
-can be caused by heat, change in pH, change in solution, or salinity
-will be inactive
-some proteins will be able to regain their original structure by removing the elements

Purines

-double ring N base
-adenine (A) and guanine (G)

Pyrimidines

-single ring N base
-cytosine (C), thymine (T), uracil (U)

Nitrogenous Bases in DNA

Adenine, Thymine, Cytosine, Guanine

Nitrogenous Bases in RNA

Adenine, Guanine, Cytosine, Uracil

Phosphodiester Bond

-new base added to sugar of previous base
-polymer grows in one direction

-covalent bond that links the phosphate backbone of nucleic acids

Metabolism

-the totality of an organism's chemical reactions
-each reaction will follow a pathway
-what manages the material being used and formed and the energy needed for the changes

Metabolic pathway

-a specific molecule is altered resulting in a product (needs enzymes in order to be changed)

Catabolism

-breaking down of complex molecules to simpler compounds
-releases energy
-known as hydrolysis or digestion

Anabolism

-uses energy in order to form bonds/ molecules
-go through biosynthetic pathways
-dehydration synthesis

ATP

Adenosine triphosphate (ATP) = adenosine (organic molecule) + three phosphate groups. When one phosphate is removed by a reaction with water. ATP to ADP + inorganic phosphate.

Types of Proteins

Enzymatic Proteins: Accelerate chemical reactions (act as catalysts).

Defensive Proteins: Protect the body against disease.

Storage Proteins: Store amino acids or other substances for later use.

Transport Proteins: Move substances across membranes or through the bloodstream.

Hormonal Proteins: Coordinate organismal activities via signaling.

Receptor Proteins: Receive and transmit chemical signals.

Contractile and Motor Proteins: Enable movement.

Structural Proteins: Provide mechanical support.

Antiparallel

DNA consists of 2 strands, each one being the opposite of the other. One strand is 3 prime to 5 prime whereas another is 5 prime to 3 prime. Their bases compliment one another.

Base Pairing: Adenine binds with…

Thymine

Base Pairing: Guanine binds with…

Cytosine