BSC2010 Exam 1 Study Guide

Atomic structure & molecule interaction

Atoms are made of protons, neutrons, and electrons; valence electrons determine bonding; atoms form bonds to fill valence shells; electrons are shared (covalent) or transferred (ionic)

Atom structure

Nucleus contains protons and neutrons; electrons are in orbitals grouped into electron shells; each orbital holds 2 electrons; valence shell is the outermost shell and determines bonding

Valence shell

Outermost electron shell containing valence electrons that participate in chemical bonding

Valence electrons

Electrons in the valence shell that determine how atoms interact and bond

Covalent bond

Bond formed when atoms share electrons to become more stable

Nonpolar covalent bond

Covalent bond where electrons are shared equally (ex: C-H bond)

Polar covalent bond

Covalent bond where electrons are shared unequally due to electronegativity differences creating partial charges (ex: water)

Electronegativity

Strength at which an atom pulls shared electrons toward itself

Ionic bond

Bond formed when electrons are transferred between atoms creating ions that attract each other

Ion

Atom or molecule that carries a charge

Cation

Positively charged ion formed by losing electrons

Anion

Negatively charged ion formed by gaining electrons

Water polarity

Water has bent shape and polar covalent bonds giving it overall polarity

Hydrogen bond

Weak attraction between partial charges of polar molecules (important in water)

Water as a solvent

Water dissolves polar and charged substances because it forms hydrogen bonds

Solvent

Substance that dissolves other substances

Solute

Substance dissolved in a solvent

Solution

Mixture formed when solute is dissolved in solvent

Hydrophilic

Substances that interact well with water because they are polar or charged

Hydrophobic

Substances that do not dissolve in water because they are nonpolar

Cohesion

Attraction between like molecules (water molecules stick together)

Adhesion

Attraction between unlike molecules (water sticks to other surfaces)

Surface tension

Cohesive force at the surface of water that makes it resist stretching

Water expands when frozen

Ice is less dense than liquid water because water forms an open crystal structure when solid

Specific heat

Amount of heat required to raise 1 gram of a substance by 1°C

High specific heat of water

Water resists temperature change and stabilizes environments

Heat of vaporization

Energy required to change 1 gram of liquid into gas

High heat of vaporization

Sweating cools organisms because evaporation removes heat

Water dissociation

Water dissociates into H+ and OH- ions

Hydronium ion

H3O+ formed when a proton associates with water

Acid

Substance that increases proton (H+) concentration

Base

Substance that decreases proton (H+) concentration

pH

Measure of hydrogen ion concentration (pH = -log[H+])

Buffer

Substance that minimizes changes in pH to maintain homeostasis

Condensation (dehydration) reaction

Reaction that removes water to form bonds between monomers

Hydrolysis

Reaction that adds water to break bonds between monomers

Amino acid

Monomer of proteins containing amino group, carboxyl group, hydrogen, and R group

Amino group

Functional group (NH3+) found in amino acids

Carboxyl group

Functional group (COO-) found in amino acids

R group (side chain)

Variable group that determines amino acid properties such as hydrophobic or hydrophilic

Peptide bond

C-N covalent bond linking amino acids formed through condensation

Peptide

Chain of fewer than 50 amino acids

Polypeptide

Chain of more than 50 amino acids

Protein

Fully folded functional polypeptide

Primary structure

Unique amino acid sequence of a protein

Importance of primary structure

Determines higher protein structure; one amino acid change can alter function

Secondary structure

Folding pattern caused by hydrogen bonding in the backbone

Alpha helix

Type of secondary structure formed by hydrogen bonds

Beta pleated sheet

Type of secondary structure formed by hydrogen bonds

Tertiary structure

3D folding caused by interactions between R groups

Hydrophobic interaction (proteins)

Water forces nonpolar R groups inward which helps protein fold

Van der Waals interactions

Weak interactions that help stabilize tertiary structure

Disulfide bond

Covalent bond formed between sulfhydryl (SH) side chains

Ionic bonding (proteins)

Attraction between charged side chains that stabilizes tertiary structure

Quaternary structure

Structure formed when 2+ polypeptide subunits interact

Dimer

Protein made of 2 polypeptide subunits

Homodimer

Dimer made of two identical subunits

Heterodimer

Dimer made of two different subunits

Protein folding

Process where protein forms functional shape due to chemical interactions

Denaturation

Unfolding of a protein that causes loss of function

Molecular chaperone

Protein that assists folding by blocking incorrect interactions

Prion

Infectious misfolded protein that can cause other proteins to misfold

Protein function depends on shape

Folding creates active and binding sites; if shape changes function is lost

Enzyme

Protein catalyst that speeds up chemical reactions

Substrate

Reactant molecule an enzyme binds to

Active site

Region of enzyme where substrates bind

Why proteins are good catalysts

Enzymes bind substrates and orient them correctly making reactions more likely

Protein functions

Catalysis, structural support, movement, signaling, transport, defense

Carbohydrate

Molecule important for energy storage, structural support, and cell identity

Monosaccharide

Simple sugar and building block of carbohydrates

Oligosaccharide

Short chain of monosaccharides

Polysaccharide

Large carbohydrate polymer made of many monosaccharides

Aldose

Monosaccharide with carbonyl group at the end

Ketose

Monosaccharide with carbonyl group in the middle

Triose

Monosaccharide with 3 carbon atoms

Pentose

Monosaccharide with 5 carbon atoms

Hexose

Monosaccharide with 6 carbon atoms

Monosaccharide structural variation

Differ by carbon number, carbonyl location, and arrangement of hydroxyl groups

Ring form of monosaccharides

Monosaccharides commonly form rings in aqueous solutions

Glycosidic linkage

Bond linking monosaccharides formed through condensation between hydroxyl groups

Alpha glycosidic linkage

Linkage common in energy storage polysaccharides

Beta glycosidic linkage

Linkage common in structural polysaccharides

Starch

Plant energy storage polysaccharide made of alpha glucose

Amylose

Unbranched starch with only alpha 1,4 glycosidic linkages

Amylopectin

Branched starch with some alpha 1,6 glycosidic linkages

Glycogen

Highly branched energy storage polysaccharide in animals (branches every ~10 monomers)

Cellulose

Structural polysaccharide in plant cell walls with beta 1,4 glycosidic linkages

Cellulose structure

Every other glucose is flipped creating linear strands with hydrogen bonding between strands

Chitin

Structural polysaccharide in fungi cell walls and exoskeletons made of NAG

NAG

N-acetylglucosamine monomer that makes up chitin

Peptidoglycan

Structural polysaccharide in bacterial cell walls with beta 1,4 glycosidic linkages and amino acid chains

Storage polysaccharides

Starch and glycogen; alpha linkages allow easier breakdown for energy

Structural polysaccharides

Cellulose, chitin, peptidoglycan; beta linkages create strong fibers

Carbohydrates in cellular identity

Carbs on cell surfaces form glycoproteins and glycolipids used in recognition and signaling

Glycoprotein

Protein with carbohydrate attached used for cell recognition

Glycolipid

Lipid with carbohydrate attached used for cell recognition

Why alpha linkages store energy

Alpha linkages are easier to break down so glucose is released quickly

Why beta linkages provide structure

Beta linkages form linear chains that hydrogen bond into strong fibers

Lipid

Carbon-containing compound insoluble in water due to many C-C and C-H bonds

Hydrocarbon

Molecule made only of carbon and hydrogen; nonpolar and hydrophobic