Exam 1: Biology 1113

Chapters 2-9

Theory of Chemical Evolution

The theory that the formation of increasingly complex carbon-containing substances culminate in a molecule that could replicate itself

Atom

the smallest identifiable unit of matter

Types of atoms found in most matter in organisms

Hydrogen (H), Carbon (C), Nitrogen (N), and Oxygen (O)

Solvent

Any liquid in which one or more solids or gases can dissolve

Solution

A liquid containing one or more dissolved solids or gases in a homogeneous mixture.

Properties of Water

Efficient Solvent, Adhesion, Cohesion, and Surface Tension

Why is water an effective solvent?

The polar nature of water molecules

Hydrophilic

Substances that interact with water

Hydrophobic

Substances that do no interact with water

van der Waals interactions

The stabilization by weak electrical attractions of hydrophobic molecules that are close to each other

London Dispersion Forces

Type of van der Waals interaction; the interaction of minute partial charges in two nonpolar molecules once they are extremely close to each other

Cohesion

The attraction between like moleculesW

Why is water cohesive?

Hydrogen bonds

Adhesion

The interaction of a liquid and a solid surface

What surfaces does water adhere to?

Any surface that have any polar or charged components

Surface tension

the cohesive force caused by attraction between the molecules at the surface of a liquid

Consequence of Surface Tension

Water resists any force that increases its surface area

Density of Water

Denser as a liquid than a solid

Specific heat

the amount of energy required to raise the temperature of 1 gram of a substance by 1 degree Celsius

Why does water have a high specific heat?

Hydrogen bonds must be broken before heat can be transferred to the water molecules

Heat of vaporization

The energy required to change 1 gram of water from a liquid to gas

The chemical reaction between water molecules

Dissociation

Chemical equilibrium

The state where the forward and reverse reactions proceed at the same rate; the quantities of reactants and products remain constant.

Homeostasis

The relatively stable chemical and physical conditions in an organism’s cells, tissues, and organs

Buffers

Compounds that minimize changes in pH

What are most buffers?

Weak acids

Solute

Substance dissolved in a solvent

Endothermic reaction

A reaction that absorbs thermal energy from the system

Exothermic system

A reaction that releases thermal energy from the system

Energy

The capacity to do work or supply heat

Potential energy

Stored energy

Chemical energy

A molecule’s potential to form stronger bonds

Kinetic energy

Energy of motion

Thermal energy

The kinetic energy of molecular motion

Temperature

A measure of how much thermal energy its molecules possess

Heat

The transfer of energy

First Law of Thermodynamics

Conservation of energy; energy cannot be created or destroyed, but transferred and transformed

The heart of chemical evolution

Energy transformation

What makes a reaction spontaneous?

If the products have a lower potential energy than the reactants

Entropy

The amount of disorder in a system

Second Law of Thermodynamics

All spontaneous reactions always increase entropy of the system and environment

Organic compounds

Molecules that contain carbon bonded to other elements

Functional groups

A small group of atoms bonded together in a precise configuration and exhibit particular chemical properties that it imparts to any organic molecule in which it occurs

Types of Functional Groups

H-, N-, O, P-, and S-containing groups

Amino and carboxyl functional groups

Functional groups that tend to attract or release a hydrogen ion when in solution

Amino groups

Functional group that acts like a base

Carboxyl groups

Functional group that acts like an acid

Functional groups in Amino Acids

Amino and carboxyl groups

Type of bonding amino and carboxyl groups form

Hydrogen Bonds

Carbonyl groups

Functional groups that is the site of reactions that link molecules into larger, more complex organic compunds

Hydroxyl groups

Functional group that acts like a weak acid

Why are molecules with hydroxyl group usually soluble in water?

Hydroxyl groups are polar; form hydrogen bonds

Phosphate groups

Functional groups that carry a negative charge on two of their oxygen atoms

What happens when a phosphate group is transferred?

The change in charge affects the structure of recipient molecule

What is stored in bonded phosphate groups?

Chemical energy

Sulfhydryl groups

Functional group that consists of a sulfur atom bonded to a hydrogen atom

What type of bond can sulfhydryl groups form?

Disulfide bonds

Macromolecules

Larger molecules made up of smaller molecular subunits joined together

Monomer

A molecular subunit used to build a macromolecule

Polymer

The structure formed when a large number of monomers bond together

Polymerization

The process of linking monomers together

Condensation (dehydration) reaction

The linking of monomers into a polymer with the result of a water molecule being formed.

Hydrolysis reaction

The breaking of polymers apart by adding a water molecule

Amino acids

A small organic molecule with a central carbon atom bonded to an amino group, a carboxyl group, a hydrogen atom, and a side chain (R-group)

Effects of charges on functional groups

Help amino acids stay in solution to interact with other amino acids and other solutes and affect the amino acid’s chemical reactivity

R-group

The part of the amino acid structure that make each of the 20 different amino acids unique

Peptide bond

The linking of amino acids through a C-N covalent bond that results from a condensation reaction

What affects the solubility of amino acids?

The polarity and charge of the R-groups

Polar and electrically charged R-groups in water

Hydrophilic; interact readily with water and dissolve easily in water

Nonpolar R-groups or highly electronegative atoms in water

Hydrophobic; do not interact with water and tend to coalesce in aqueous solution

Types of amino acid groups

Charged, uncharged polar, and nonpolar

Key points of a Peptide-bonded backbone

R-group orientation, Directionality, and Flexibility

R-group orientation

Property that allows the side chains of a residue that extend out of the backbone that make it possible to interact with other residues and water

Directionality

Property that allow for the determining of the start and end of a residue sequence with N-terminus and C-terminus

N-terminus

Start of residue sequence; Free amino group (-NH₃⁺)

C-terminus

End of residue sequence; Free carboxyl group

Flexibility

Property that allow single bonds around peptide bonds to rotate

Oligopeptide

A polymer that has fewer than 50 amino acids

Polypeptides

A polymer that contains 50 or more amino acids

Protein

Any chain of amino acid residuesP

Primary Structure of a Protein

The unique sequence of amino acids

Why is the primary structure of a protein fundamental?

The primary structure determines the function

Secondary Structure of a Protein

The interactions between functional groups in the peptide-bonded backbone

What type of bonding happens between sections of peptide-backbone?

Hydrogen bonding between C=O and N-H groups

Possible structures of DNA

Alpha-helix and beta-pleated sheet

Tertiary Structure of Protein

The distinctive three-dimensional shape of proteins from the interactions between residues that are brought together as the backbone bends and folds

Types of interactions involving R-groups

Hydrogen bonding, Hydrophobic interactions, van der Waals interactions, Covalent bonding

and Ionic bonding

Ionic bonding in R-groups

Bonding formed between groups that have full and opposing charges

Covalent bonding in R-groups

Bonding formed between side chains of two cysteines through a reaction between sulfhydryl groups

van der Waals interactions in R-groups

Interactions that force nonpolar side chains close to one another by hydrophobic interactions

Hydrogen bonding in R-groups

Hydrogen bonding between polar side chains and opposite partial charges either on the peptide backbone or other R-groups

Hydrophobic interactions in R-groups

Interaction that forces hydrophobic side chains to gather due to being surrounded by hydrophilic polar side chains

What does the tertiary structure depend on?

The primary and secondary structure

Quaternary structure

The combination of polypeptides

Macromolecular machines

Complexes of multiple proteins that assemble to carry out a particular function

What is crucial to a protein’s function?

Folding

Molecular chaperones

Special proteins that can facilitate the folding of proteins

Prions

A protein particle that can induce proteins to fold into infectious, disease-causing agents

Functions of Proteins

Catalysis, Structure, Movement, Signaling, Transport, and Defense

Catalysis with Proteins

Speeds up chemical reactions