Biology

fall semester 2026

why is chemistry necessary in biology

it provides the molecular foundations of life

determines comp, structure, function, interactions of bio molecules

defines chem rxn that provide energy, support, communation, and maintain life process

covalent bonds

atoms chemically combined in fixed numbers/ratios to form molecules of living and non-living matter

compounds

molecules whos component atoms are different (two or more atoms)

essential vs. trace elements

essential are those that an organism needs to live a healthy life and reproduce (20-25%) of natural elements

trace elements required in minute quantities

deficiency of essential elements

disrupts specific cellular processes, leading to characteristic physiological disorders

radioactive isotopes

undergo spontaneous nuclear decay, emitting particles and energy

used for medical diagnosis and fossil aging

radiation emitted can be detected and act as natural clocks

electrons and energy

electrons within an atom differ in the amount of stored (potential) energy they posess

the amount of energy determines where an electron is located around the nucleus

higher-energy electrons are generally farther from the nucleus

electron shells

energy levels

each has a characteristic amount of energy

orbitals

regions where electrons are most likely to be found within a shell

valence shell

outermost shell

atoms are most stable when the valence shell is full

if incomplete, the atom tends to gain/lose/share to become stable

covalent bonds

when atoms share a pair of valence electrons

strongest bond

nonpolar vs polar covalent bond

non polar the atoms share equally

polar one atom is more electronegative, not equal

electronegativity

the ability of an atom to attract electrons

ionic bonds

the electrical attraction between oppositely charged ions formed by electron transfer

ion formation

electron transfer creates oppositely charged ions ( cations and anions )

ionic bond formation

the + and - ions attract each other through electrostatic attraction

hydrogen bonds

when a hydrogen atom covalently bound to an electronegative atom (oxygen, nitrogen) interacts with an electronegative atom of another molecule

in living cells, the electronegative partners are usually oxygen or nitrogen atoms

where do hydrogen bonds form

between molecules with polar covalent bonds, where partially positive hydrogen is attracted to partially negative atoms in another molecule

van der waalls interactions

relatively weak electrical forces that attract molecules to one another

exist between virtually all atoms/molecules

stabilizes the shape of large molecules like proteins

molecule’s shape

determined by orientation of chemical bonds, which is determined by valence electrons

important for its function because of complementary molecular shapes with other bio molec

similar shapes = similar functions

water makes up ____ percent of a cell’s composition

70-95%

what does a water molecule contain

two hydrogen atoms covalently bonded to an oxygen

these covalent bonds are polar because oxygen is more electronegative than hydrogen

what are the poles of water molecule

because electrons are not shared equally:

partial negative pole near oxygen

partial positive pole near hydrogen

hydrogen bonds in water molecule

form between the slightly positive H of one water molecule and the slightly negative O of another water molecule

a water molecule can form up to ___ hydrogen bonds, and what are they?

four

two through its H atoms and two through the two lone pairs of electrons on its oxygen

four emergent properties of water

1. cohesive and adhesive (sticks to itself and others)

2. ability to moderate temperature

3. expansion upon freezing

4. versatility as a solvent

liquid water’s hydrogen bonds

constantly break and reform, allowing molecules to move closer together, increasing density

ice hydrogen bonds

form a stable, open crystal structure that keeps water molecules farther apart, reducing density

water vapor hydrogen bonds

mostly broken, allowing molecules to move independently and spread far apart, resulting in lowest density

water cohesion

hydrogen bonds holding water molecules together

creates strong interactions between water molecules, allowing water to maintain a continuous structure and resist derformation

adhesion

attraction between different substances

how does cohesion and adhesion help

the transport of water against gravity in plants

surface tension

resistance of the water surface to breaking, caused by cohesion between water molecules through hydrogen bonds

specific heat capacity

the amount of heat (joules) that must be absorbed or lost to change the temperature of a gram of a substance of 1 degree C

water has a high, so it cools and heats up more slowly than most substances

why does water have a high specific heat capacity

because of the large number of hydrogen bonds between water molecules

why is water a good temperature buffer

oceans can absorb or release a large amount of heat with only a slight change in its own temperature

density of ice vs water? why important?

the hydrogen bonds are stabilized so that the average distance between water molecules is less than in liquid water

this means ice is less dense than water and therefore floats on top of it

if it sunk, all bodies of water would eventually freeze solid, life would be impossible

water reaches its greatest density at

4 degrees C

water is the _____ of life , why?

solvent

due to its polarity, large variety of molecules can be dissolved

hydrophillic molecules

can be dissolved in water

form hydrogen bonds or ion-dipole interactions with water that allow them to

hydration shell

a sphere of water molecules that surrounds each ion of an ionic compound when dissolved in water

pH

a logarithmic measure of the concentration of hydrogen ions in a solution

negative logarithimic scale, meaning a higher pH means a lower H+ concentration

acidic/neutral/basic pH

acidic: less than 7 pH, high concentration of H+

neutral: 7, equal H+ and OH-

basic: higher than 7, low H+

pH of pure water

a hydrogen atom in a hydrogen bond between water molecules can shift from one molecule to the other

the hydrogen atom leaves its electron behind, and is transfered as a proton, or a hydrogen ion

the molecule with the extra proton is now a hydronium ion (H+)

the molecule who lost the proton is now a hydroxide ion

dynamic equillibrium

which water molecules disassociate at the same rate in which they are being formed

buffers

substances that minimize changes in the concentration of H or OH in a solution or in a living cell

acid-base pair

in buffers that can exchange protons

why does carbon dominate life (6)

1. small enough to form strong covalent bonds

2. large enough to bond with many different atoms

3. tetravalent, allowing four simultaneous covalent bonds

4. stable enough to preserve complex structures

5. reactive enough for metabolism

6. compatible with liquid water

structure-function relationship

1. different molecular shapes

2. different chemical properties

3. diffferent biological functions

4. greater biological comeplexity

hydrocarbons

molecules composed of only carbon and hydrogen

four ways the carbon skeleton can vary in hydrocarbons

1. length ( number of carbon atoms in the chain)

2. double bond position

3. branching (side chains attached to main carbon chain)

4. presence of rings (carbon atoms joined in a ring structure)

isomers

molecules with the same molecular formula but different molecular structures

different chem and bio properties s

structural isomers

have the same molecular formula but different structural formulas because their atoms a

cis-trans isomers

same molecular formula, same structural formula (connectivity of atoms), different spatial arrangement (configuration) of atoms

differ in the three dimensional arrangement of functional groups due to restricted rotation around a double bond

functional groups are arranged on the same side (cis) or on the opposite side (trans)

enantiomers

differ in the three-dimensional arrangement of functional groups caused by chirality (an asymmetric carbon)

produces mirror image molecules

same formula and connectiveity

all amino acids except glycine….

have a L and D enantiomer

only the L form is used in biological system

differences between two enantiomers

if a drug may have different effects

structure-function relationship

functional groups

determine chemical properties and bio activity

specific arrangement of atoms that confer unique properties to molecules and are often involved in chemical rxn

seven functional groups most important for life

1. hydroxyl

2. carbonyl

3. carboxyl

4. amino

5. sulfhydryl

6. phosphate

7. methyl

4 classes of biological macromolecules

protein, libids, carbs, nuleic acids

polymer

long molecule consisting of many similar building blocks

monomer

small building block molecules that make up polymers

dehydration reactions

how polymers are synthesized

water is a product of the rxn

hydrolysis reaction

how polymers are dissassembled

the reverse of dehydration rxn

monosaccharides

simplest carbs

disaccharide

linking only two monosaccharides together

polysaccharide

function: fuel and structural materal

structure: long chains of monosaccharides linked together

both determined by monosaccharide composition and glycosidic linkage positions

naming, structure, and formula of monosaccharides

multiples of CH2O (ratio of 1:2:1)

simple sugars end in -ose, named based of the number of carbons

can exist in a linear or ring form, all have a C=O bond when in linear form

classification of monosaccharides

aldoses - contain aldehyde group

ketoses- contains a ketone group

gluce vs galactose vs fructose

glucose is the primary cellular fuel

galactose and fructose are converted to glucose before most cells use them

glycosidic linkage

the covalent bond linking disaccharide

glucose, galactose, and fructose can be combined to form…

maltose, lactose, and sucrose

for specific biological functions, such as transport storage or nutrition

alpha vs beta glycosidic bond

differ in the orientation of the glycosidic bond at the anormeric carbon

anormeric carbon

carbon of the carbonyl group (aldehyde or ketone) in the linear form

starch

a polymer of glucose

used by plants to store glucose

the simplest form: amylose

glycogen

a polymer of glucose, and is used by animals to store glucose

cellulose

polymer of glucose, used by plants to make strong cell walls

how can cellulose, starch, and glycogen have such different properties?

glycosidic linkages

microfibrils

straight cellulose polymers that can H-bond with each other

parellel cellulose molecules which form strong building materials for plants

lipids

not polymers, but are all hydrophobic

3 major types of lipids

1. triacylycerols (ex fats and oils)

2. phospholipids (ex cell membranes)

3. steriods (ex sex hormones)

triacylglycerols

neutral fats

energy storage, insulation, and protection of internal organs

three fatty acid chains attached to a glycerol

glycerol

a three carbon alcohol (three hydroxyl groups)

fatty acids

a hydrocarbon with a carboxyl group at the end

vary in length and the number and location of double C=C bonds

ester linkage

how a fatty acid connects to a glycerol

saturated fatty acids

no C=C double bonds

unsaturared fatty acids and 2 types

one or more C=C double bonds

monounsaturated: 1 double bond

polyunsatured: 2 or more double bonds

triacylglyerols

containing mostly satured fatty acids

usually solid at room temperature (eg butter)

straight hydrocarbon chains pack tightly together

omega-3 fatty acids

unsaturated fatty acids that are not synthesized in human body

must be supplied in diet

how can we compare energy in macromolecules

by meauring how much energy is stored in 1g of each

phospholipid molecules

major constituent of cell membranes and cell signaling

2 fatty acid chains

1 glycerol molecule

1 phosphate molecule

amphipathic phospholipids

having both hydrophobic and hydrophillic parts of the molecule

when placed in water, phospholipids….

self-assemble into a phospholipid bilayer

shield their hydrophobic tails from water

steroids

constituents of cell membranes (e,g) cholesterol

components of vitamins and hormones

structure: made from sterol, four carbon rings composed of 20 covalently bonded C atoms

proteins

highly diverse, workhorses of most cellular functions

polypeptides made of amino acids subunits

enzymes

act as catalysts, increasing the rate of chemical rxns

structural proteins

provide structural support and shape to tissues, such as collagen

motility proteins

drive muscle contraction and cell movement

regulatory proteins

control and coordinate cell functions

transport proteins

move substances in and out cells