[AP Bio] Unit 1.4-1.6: Properties, Structures, and Functions of the 4 Macromolecules of Life

Chapter 3.1-3.6

How many covalent bonds can carbon make?

4 covalent bonds

Covalent Bond

a chemical bond that involves the sharing of electrons to form electron pairs between atoms

Valence

the number of covalent bonds an atom can form

What are the 4 main atoms in organic molecules?

Carbon, Hydrogen, Oxygen, Nitrogen

What provides the structure for most organic molecules?

Carbon Chains

Hydrocarbon

an organic molecule consisting of only carbon and hydrogen atoms; serves as the underlying framework for most complex organic molecules

• Not prevalent in most living organisms, but are often found in a cell’s organic molecules

• Can undergo reactions that can release large amounts of energy

Isomers

one of two or more compounds that have the same number of atoms of the same elements but different structures, and hence different properties

What are the 3 types of isomers?

1. Structural Isomers

2. Cis-Trans Isomers/Geometric Isomers

3. Enantiomers

Structural Isomers

one of two or more compounds that have the same molecular formula but differ in the covalent arrangements of their atoms

Cis-Trans Isomers

one of two or more compounds that have the same molecular formula and covalent bonds between atoms but differ in their spatial arrangements due to the inflexibility of double bonds

• Single bonds allow atoms to rotate freely around the bond axis, but this doesn’t occur with double bonds

Enantiomers

one of two compounds that are mirror images of each other and that differ in shape due to the presence of an asymmetric carbon

• Kind of like left-handed and right-handed versions of the same molecule

• Important in the pharmaceutical industry because the two enantiomers of a drug may not be equally effective, or have very different effects

Functional Groups

a specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and involved in chemical reactions

Hydroxyl Groups

• Consists of one oxygen atom with a single covalent bond to a hydrogen atom

  • Compound Name: Alcohol (ends in -ol)

Carbonyl Groups

Consists of one carbon atom with a double covalent bond to an oxygen atom

Compound Names:

• Ketone: if the carbonyl group is within a skeleton

• Aldehyde: if the carbonyl group is at the end of a skeleton

Carboxyl Groups

Consists of a carbonyl and hydroxyl group attached to the same carbon atom

• Compound Names: Carboxylic Acid/Organic Acid

Amino Groups

Bonds to alpha carbon in amino acid along with carboxyl group, a hydrogen atom, and an R group (variable side chain)

• Compound Name: Amine

Sulfhydryl Groups

Consists of sulfur atom with a single covalent bond to a hydrogen atom—hydrophilic and can increase solubility of organic compounds in water

• Compound Name: Thiol

Phosphate Groups

Consists of phosphorus atom bonded to 4 oxygen atoms

• Compound Name: Organic Phosphate

Methyl Groups

Consists of one carbon atom bonded to 3 hydrogen atoms—not reactive; serves as a “tag” on biological molecules

• Compound Name: Methylated Compound

ATP (Adenosine Triphosphate)

an adenine-containing nucleoside triphosphate that releases free energy when its phosphate bonds are hydrolyzed, with the energy used to drive endergonic reactions in cells

• Consists of the organic molecule, adenosine attached to a string of three phosphate groups

• ATP can turn into ADP (adenosine diphosphate) when reacting with water

Polymer

a long molecule consisting of many similar or identical monomers linked together by covalent bonds

Monomer

the subunit that serves as the building block of a polymer

Polymerization

the chemical process in cells where monomers are joined together to make polymers

• Enzymes (specialized macromolecules—usually proteins) facilitate these processes and speed up chemical reactions

Condensation Reaction

a reaction in which two molecules are covalently bonded to each other, with the loss of a small molecule

Dehydration Reaction

specifically when a water molecule is lost during a condensation reaction

Hydrolysis

a chemical reaction that breaks bonds between two molecules by the addition of water; functions in the disassembly of polymers to monomers

• Essentially a reverse of the dehydration reaction

Carbohydrates

consists of sugar (monosaccharide) or one of its dimers (disaccharides) or polymers (polysaccharides)

Monosaccharide

the simplest carbohydrate, active alone or serving as a monomer for disaccharides and polysaccharides

• Also known as simple sugars

• Glucose (C₆H₁₂O₆) is the most common monosaccharide, and consists of a carbonyl group and multiple hydroxyl groups

Disaccharide

a double sugar, consisting of two monosaccharides joined by a glycosidic linkage formed by a dehydration reaction

• Sucrose is the most prevalent disaccharide, as it is commonly known as table sugar, with its two monomers being glucose and fructose

Glycosidic Linkage

a covalent bond formed between two monosaccharides by a dehydration reaction

Polysaccharide

a polymer of many monosaccharides, formed by dehydration reactions

• Polysaccharides are macromolecules with a few hundred to a few thousand monosaccharides

• Can serve as storage material or building material for cells, determined by its sugar monomers and location of glycosidic linkages

Starch

a storage polysaccharide in plants, consisting entirely of glucose monomers joined by glycosidic linkages

• Synthesis of starch allows plants to stockpile surplus glucose, and can be withdrawn through hydrolysis, breaking the bonds of the glucose monomers

Glycogen

an extensively branched glucose storage polysaccharide found in the liver and muscle of animals; the animal equivalent of starch

• Stored fuel can’t sustain an animal for more than a day unless they’re replenished by eating

Cellulose

a structural polysaccharide of plant cell walls, consisting of glucose monomers joined by β glycosidic linkages

• There are two different ring structures for glucose, called alpha (α) and beta (β)

Chitin

a structural polysaccharide, consisting of amino sugar monomers, found in many fungal cell walls and in the exoskeletons of all arthropods

• Similar to cellulose

Lipids

any of a group of large biological molecules, including fats, phospholipids, and steroids, that mix poorly, if at all, with water

• Lipids consist of mainly nonpolar bonds, and since water is polar, they don’t mesh well

Fats (Triglycerides)

a lipid consisting of three fatty acids linked to one glycerol molecule

Fatty Acids

carboxylic acid with a long carbon chain, varying in length and number/location of double bonds

• Carbon at one end of the fatty acid is connected to a carboxyl group, giving it the name of a “fatty acid”

• Fatty acids in a fat can be the same, or all entirely different

Saturated Fatty Acid

a fatty acid in which all carbons in the hydrocarbon tail are connected by single bonds, meaning that the maximum number of hydrogen atoms possible are attached to the carbon skeleton

Unsaturated Fatty Acid

a type of fatty acid characterized by the presence of one or more double bonds in their hydrocarbon chains, lessening the amount of hydrogen atoms that are present in the carbon skeleton

What state of matter do saturated fats typically come in at room temperature?

Solid (butter, lard) — straight shape

• More flexible due to their lack of double bonds, allowing them to stack more compactly

What state of matter do unsaturated fats typically come in at room temperature?

Liquid (olive oil, cod liver oil) — bent shape

• The location of cis double bonds prevent the molecules from packing close together enough to solidify at room temperature

What is a fat’s major function?

Energy storage—a gram of fat stores twice as much energy as a gram of a polysaccharide

Phospholipid

a lipid made up of glycerol joined to two fatty acids and a phosphate group and consists of a polar head and two nonpolar fatty acid tails

Steroid

a type of lipid characterized by a carbon skeleton consisting of four fused rings with various chemical groups attached

• Consists of ZERO fatty acids

Cholesterol

steroid that forms an essential component of animal cell membranes and acts as a precursor molecule for the synthesis of other biologically important steroids

Catalyst

a chemical agent that selectively increases the rate of a reaction without being consumed by the reaction

How many amino acids exist?

There are only 20 amino acids in existence

• Bonds together through peptide bonds and makes polypeptides

Peptide Bond

a covalent bond between the carboxyl group on one amino acid and the amino group on another, formed by a dehydration reaction (removal of a water molecule to bond)

Protein

a biologically functional molecule made up of one or more polypeptides folded and coiled into a specific three-dimensional structure

Polypeptide

a polymer of many amino acids linked together by peptide bonds

Amino Acid

an organic molecule possessing both a carboxyl and an amino group. Amino acids serve as the monomers of polypeptides

What are the 4 groups attached to the “central carbon” of an amino acid?

1. Amino Group (NH2)

2. Carboxyl Group (COOH)

3. Hydrogen Atom (H)

4. R Group

   • The variable portion of an amino acid that affects its role in a polypeptide due to its properties

Polypeptide Backbone

the repeating sequence of atoms in a polypeptide chain, formed by linking amino acids through peptide bonds

• Shown as N-C-C in diagrams—also sometimes called the NCC backbone

Globular Proteins

proteins that have a roughly spherical shape

Fibrous Proteins

a type of protein characterized by their elongated, fiber-like structures, shaped like long strands or cables

What are the 4 levels of protein structure?

1. Primary Structure

2. Secondary Structure

3. Tertiary Structure

4. Quaternary Structure (only for some proteins)

What does a primary protein structure look like?

linear chain of amino acids

• Dictates a protein’s secondary and tertiary structure, ultimately determining its function, due to the chemical nature of the backbone and R groups

What are the 2 shapes of a secondary protein structure?

alpha helix & beta sheet

• Alpha Helix (α): a coiled structure resembling a spiral staircase, where the coils are held together by hydrogen bonds between nearby amino acids

  • Provides elasticity + strength to the protein

• Beta Sheet (β): resembles a folded paper fan, where strands of the polypeptide chain lie side by side, connected by hydrogen bonds

  • Can be parallel/unparallel

  • Contributes to stability of protein

What affects the 3D tertiary structure of a protein?

Hydrophobic Interaction: where amino acids with nonpolar (hydrophobic) side chains/R groups end up in clusters in the middle of the protein

• This leaves hydrogen bonds between polar side chains & ionic bonds between positively and/or negatively charged side chains to help stabilize the structure

What makes up the quaternary structure of a protein?

consists of two or more polypeptides, or in other words, more proteins coming together (some proteins only)

• Multiple polypeptide chains are referred to as subunits

Denaturation

process in which a protein loses its native shape due to the disruption of weak chemical bonds and interactions, thereby becoming biologically inactive

When does denaturation occur?

Under extreme (noncellular) conditions of:

• pH

• Salt Concentration

• Temperature

What are the 2 types of nucleic acids?

DNA (Deoxyribonucleic Acid) & RNA (Ribonucleic Acid)

What are the 4 nitrogenous bases in DNA?

1. Adenine (A)

2. Thymine (T)

3. Cytosine (C)

4. Guanine (G)

What are the 4 nitrogenous bases in RNA?

1. Adenine (A)

2. Uracil (U)

3. Cytosine (C)

4. Guanine (G)

What nitrogenous base is different between DNA & RNA?

Thymine (in DNA) & Uracil (in RNA)

Messenger RNA (mRNA)

acts as a messenger that carries genetic information from DNA to the ribosome, where proteins are synthesized

• An mRNA molecule interacts with the cell’s protein-synthesizing machinery to direct the production of a polypeptide

Nucleotide

the building block of a nucleic acid, consisting of a five-carbon sugar (pentose) covalently bonded to a nitrogenous base and one to three phosphate groups

Nucleoside

the portion of a nucleotide without any phosphate groups

• Adding 1 to 3 phosphate groups to the 5’ carbon of the pentose in the nucleoside will make a nucleotide

Polynucleotides

a polymer consisting of many nucleotide monomers in a chain which can be nucleotides of DNA or RNA

What are the 2 families of Nitrogenous Bases?

Pyrimidines & Purines

Pyrimidines

one of the two types of nitrogenous bases found in nucleotides, characterized by a six-membered ring

• Cytosine (C), Thymine (T), and Uracil (U)

Purines

one of the two types of nitrogenous bases found in nucleotides, characterized by a six-membered ring fused to a five-membered ring

• Adenine (A) and Guanine (G)

Deoxyribose

the sugar component of DNA nucleotides, having one fewer hydroxyl group than ribose

Ribose

the sugar component of RNA nucleotides

Phosphodiester Linkage

phosphate group that covalently links the sugars of two nucleotides

Double Helix

the form of native DNA, referring to its two adjacent antiparallel polynucleotide strands wound around an imaginary axis into a spiral shape

• Sugar-Phosphate Backbone is on the outside of the helix, with nitrogenous bases being on the inside of the helix

Antiparallel

refers to the arrangement of the sugar-phosphate backbones in a DNA double helix (they run in opposite 5' to 3' directions)

What are the 4 macromolecules of life?

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic Acids