Chapter 2.1-2.6: The Molecules of Life - Chemistry

why is there chemistry in biology class?

biology studies living things - all living things are made up of chemicals

- chemistry helps us understand at the cellular and molecular level

matter

anything and everything that takes up space

elements

substances that cannot be chemically broken down - contain only one kind of atom

atoms

the basic unit of matter

atomic number

# of protons (elements defined by them)

atomic mass

# of protons + neutrons

isotopes

atoms of the same element that have different # of neutrons (proton # stays the same)

ions

atoms with the same # of protons and neutrons are neutral

- some chemical processes result in the loss or gain of electrons

if an atom gains or loses an electron,...

then it can carry a charge

neutral

6 protons

6 neutrons

6 electrons

negatively charged

5 protons

6 neutrons

6 electrons

positively charged

6 protons

6 neutrons

5 electrons

shells

represent energy levels or electron clouds surrounding the atomic nucleus

orbitals

describe the most probable regions where electrons can be found within a given shell (max # is 2)

periodic table

elements in the same row have the same # and types of orbitals

- to the right, the atomic # increases

chemical bonds

atoms combine via chemical bonds to form molecules

valence electrons

an electron in the outer shell of an atom, which can participate in the formation of a chemical bond

covalent bonds

a chemical bond formed by a shared pair of electrons holding two different atoms together

electronegativity

the property of an atom (in a given chemical element) to attract shred electrons

- as positive protons increase, electrons are held more closely to nucleus

polar covalent bonds

electrons are not equally shared between 2 atoms

- results in partial negative charges on the oxygen and partial positive charges on the hydrogen

nonpolar covalent bonds

form when atoms share electrons equally

- same electronegativity

if an atom gains or loses an electron,...

then it can carry a charge

ionic bonds

a chemical bond in which two ions with opposite charges associate with each other due to their difference in electronegativity

hydrogen bond

forms between two water molecules when the partial positive charge of a hydrogen atom is attracted to the partial negative charge of an oxygen atom

- in liquid water, H-bonds break and reform

cohesion

the attraction between molecules

adhesion

the attraction between molecules and a surface

what is water's unusual property?

water is less dense when solid

solvent

a liquid capable of dissolving a substance

solute

a dissolved substance

solution

the mixture of solute and solvent

hydrophilic

"water loving"; describes a class of molecules with which water can undergo hydrogen bonding

hydrophobic

"water fearing"; describes a class of molecules poorly able to undergo hydrogen bonding with water

pH

a measure of the concentration of hydrogen ions (H+) in a solution

- ranges from 0 to 14

- a measurement of the concentration of protons in a solution

- pH in most cells is approximately 7 and is tightly regulated because most chemical reactions can be carried out only in a narrow pH range

acids

higher concentration of hydrogen ions (H+) and a pH closer to 0 (less than 7)

bases

lower concentration of hydrogen ions (H+) and a pH closer to 14 (greater than 7)

neutral

when the concentrations of protons (H+) and hydroxide ions (OH-) are equal

properties of water

1. polar (regions of partial positive and partial negative charges)

2. cohesive (hydrogen bonding between water molecules)

3. adhesive (hydrogen bonding between water and other molecules)

4. high surface tension (extensive hydrogen bonding on the surface of liquid water)

5. less dense as a solid than liquid (open, crystalline structure of solid water)

6. high specific heat (extensive hydrogen bonding of liquid water)

7. good solvent (hydrogen bonding with other polar molecules)

cohesion via hydrogen bonding

the tendency of water molecules to stick to one another

top four elements in humans

1. carbon

2. oxygen

3. hydrogen

4. nitrogen

(excluding water)

organic molecules

molecules containing carbon

tetrahedron

CH4: because of the shape of the orbitals, the carbon atom lies at the center of a three-dimensional structure, and the four molecular orbitals point toward the four corners of this structure

isomers

same chemical formula, different arrangements of atoms (structure)

4 types of complex organic macromolecules

carbohydrates, proteins, lipids, nucleic acids

proteins

provide structural support and act as catalysts to facilitate chemical reactions

nucleic acids

encode and transmit genetic information

carbohydrates

provide structural support for many organisms and a source of energy

lipids

make up cell membranes, store energy, and are important in cell communication

polymers

chain of repeating units (monomers) that are connected through covalent bonds

amino acids

an organic molecule containing a central carbon atom attached to a carboxyl group, an amino group, a hydrogen atom, and a side chain

- the building blocks (monomers) of proteins (polymers)

nucleotides

a constituent of nucleic acids, consisting of a 5-carbon sugar, a nitrogen-containing base, and one or more phosphate groups

monosaccharides

a simple sugar (monomer of carbohydrate)

polysaccharides

a polymer of simple sugars

- provide long-term energy storage or structural support

polypeptide

proteins are also called this

- linked amino acids form this

nucleotides are composed of three components:

1. 5-carbon sugar (ribose or deoxyribose)

2. a base containing nitrogen

3. one or more phosphate groups

peptide bond

amino acids are joined through a covalent bond called this

- when they are formed, the carboxyl group releases an oxygen tomorrow, and the nitrogen loses two hydrogen atoms (forms water molecules)

pyrimidine bases

cytosine (C), thymine (T), uracil (U)

purine bases

guanine (G) and adenine (A)

phosphodiester bond

joins two nucleotides together

- bond is formed between the phosphate group of each nucleotide and the 3'-OH of the last nucleotide

complimentary base pairings

A-T

G-C

types of sugars

1. monosaccharides

2. disaccharides

3. polysaccharides

4. complex carbohydrates

monosaccharide

contains one sugar molecule

- often a subunit, or monomer of more complex sugars

disaccharide

contains two bonded monosaccharides

- usually linked via glycosidic linkages (bonds)

complex carbohydrates

long, braided chains of monosaccharide monomers

lipids: properties & structure

- do not mix well with water (all hydrophobic)

- not made of repeating monomers

- fatty acids are a type of lipid with long chains of carbon with a carboxyl group at the end

* saturated (single bond) or unsaturated bond (no van der waals forces

--> different structure based on the presence of C-C double bonds

van der waals forces

a slight attraction that develops between the oppositely charged regions of nearby molecules

- sometimes fatty acids line up next to each other (can be very stable in the cell)

- hydrocarbon chains in fatty acids have non-polar covalent bonds

- electrons are moving around the atoms in fatty acids, creating short-lived regions with slight negative charges --> these are attracted to slight positive regions in another atom

* these forces are weaker than hydrogen bonds, but many act together to stabilize molecules --> the length of hydrocarbon chains increases these forces

melting point

the kinks in the fatty acids are caused by unsaturated carbons that have double bonds between them

- this reduces tightness between the molecules, causing a lower melting point

why is animal fat solid at room temperature?

animal fats are saturated (able to stack tightly)

- without double bonds causing kinks in the structure, animal fats can stack closely together and are stabilized by more van der waals interactions than unsaturated fats

Miller-Urey experiment

subsequent testing has shown that the building blocks of life can form macromolecules