FREE AP Biology Unit 1 Study Guide
- Kaylyn Kim
- Aug 25, 2025
- 15 min read
PRE-KNOWLEDGE
Atom: the smallest unit of matter
Contains:
protons (+ charge)
neutrons (0 charge)
electrons (- charge)
Note: electrons are of a much smaller size than protons or neutrons. Neutrons are slightly bigger than protons.
Element: a substance made up of only one type of atom
In a periodic table, it is expressed with:
Atomic number: expresses the number of protons that an element contains (remains the same ALL the time)
Chemical Symbol (abbreviation of the first two letters or Latin root name)
Element Name
Atomic weight
NOTE: Even when the number of neutrons or electrons changes, the number of protons is always consistent within the same element.
Isotope: a version of an element that contains a different number of neutrons
Ion: a group of atoms that has a charge
Anion: an ion with a negative net charge → more electrons than protons
Cation: an ion with a positive net charge → more protons than electrons
Chemical Bonds:
[Kaylyn's Analogy: BULLY IS TAKING UR FOOD]
Ionic Bond: a bond between oppositely charged ions
One atom gives up its electron to give to another atom
Essentially, everyone wants to maintain their perfect octet structure, and the different elements are doing what is most CONVENIENT and EFFICIENT to them to
[Kaylyn's Analogy: SHARING IS CARING]
Covalent Bond: a chemical bond formed when electrons are SHARED between two atoms
Molecule: a group of 2 or more atoms that are COVALENTLY bonded together
Chemical: a substance with a definite composition → able to determine all of its properties and characteristics
Compound: a substance of 2 or more different elements that have been chemically joined
Valence Electrons: electrons on the outer shell of the atom
Polar: molecule has unequal charge
Non-Polar: molecule has evenly spread charge
TOPIC 1.1 - All about water
Water’s Characteristics
1 electronegative oxygen atom (it likes to hog electrons) and 2 hydrogen atoms that want to get rid of one valence electron to complete a set
The oxygen molecule and the hydrogen molecules are connected by COVALENT BONDS (bonds where multiple molecules share electrons)
The different water molecules are connected by HYDROGEN BONDS (bonds that form because of the slight polarity of water molecules)
There is a partial NEGATIVE charge at the oxygen, a partial POSITIVE charge at the hydrogens - this causes the negative ends to be attracted to the positive ends (and vice versa)
Hydrophillic molecules LOVE water, hydrophobic molecules DO NOT (oils and fats)
Water’s Properties
Cohesion: all water molecules move with each other
The reason for water having a high surface tension (the little bubble cover you see on top of the water’s surface)
High Surface Tension: resistance of water’s surface to rupture when placed under tension (like a bug or a paper clip)
Reasoning: the water molecules on the surface of the water have no molecules pulling them from above, so ****they are more attracted to each other (COHESION) than the AIR.
The surface contracts to the smallest possible surface area as a result of this attraction
ex) water droplets, insects gliding on water
High Heat Capacity
heat capacity: the amount of heat needed for 1 gram of water to increase by 1°C
If the heat capacity is high, it means that it needs lots of heat for water to increase → makes the overall temperature of an environment or organism very stable, won’t constantly change because of some extra heat → MINIMIZES TEMP VARIATIOn
High heat of vaporization
heat of vaporization: the amount of energy needed to change 1 gram of liquid water to its gas form at a constant temp.
if the heat of vaporization is high, it means it needs a lot of energy to change from liquid to gas → to regulate temperature and avoid overheating
Adhesion: water’s ability to stick to other surfaces
responsible for most of capillary action and transpiration
transpiration: the process by which evaporation + cohesion + adhesion pulls up water in plants
ex) water can travel up the xylem in trees
UNIVERSAL SOLVENT: able to dissolve POLAR molecules quickly
Reasoning: a water molecule has a slight polarity, which is why it can form ionic bonds (bonds that take another’s electrons) with other polar molecules
ex) mix salt in water
Density as a solid
GAS: water molecules are spread apart
LIQUID: water molecules are close together → hydrogen bonds are easily broken apart
SOLID: water molecules form a crystal structure → hydrogen bonds are stable
Because the density of ice is LESS than the density of liquid water, it allows aquatic life to survive during the winter because the lake will freeze from TOP-BOTTOM, instead of BOTTOM-UP.
This is also the reason why ice floats (a substance floats of it is less dense than other components in the mixture)
CAPILLARY ACTION and MENISCUS
Capillary action: Cohesion + Adhesion in action
attraction between water molecules (cohesion) enables the water molecules to move as a group
The surface tension allows the surface to be intact
attraction between water and container (adhesion) enables the water to go up
RESULT: a concave meniscus
examples)
dip a paper towel in water and the water climbs up the towel
roots carry water from the soil to the plant
tear ducts carry tears to the eye
Difference between covalent vs. hydrogen bonds
Covalent bonds are WITHIN one water molecule (between the oxygen and 2 hydrogens)
Hydrogen bonds exist with different water molecules (as the partially positive ends connect with the partially negative ends)
TOPIC 1.2 - ELEMENTS OF LIFE
The only elements you need to know: CHONPS
Carbon - central element
Hydrogen - used in energy exchange (NAD+, NADH in cellular respiration), used to create energy gradients, standard for acidity/alkalinity (acids vs. bases)
Nitrogen - nitrogen cycle
Oxygen - photosynthesis + cellular respiration
Phosphorus - in ATP
Sulfur
4 Macromolecules’ Elemental Composition
Nucleic Acids: Nitrogen, oxygen, carbon, phosphorus, hydrogen [CHONP]
Proteins: Nitrogen, oxygen, carbon, hydrogen, sulfur [CHONS]
Carbohydrates: Oxygen, carbon, hydrogen [CHO]
Lipids: Oxygen, carbon, hydrogen, phosphorus [CHO (P)]
TOPIC 1.3
Monomer: a building block for polymers
Polymer: a large molecule made of repeating subunits (monomers) → with specific 3D shapes and functions
Like a LEGO CASTLE!
Dehydration synthesis - ENZYMES combining monomers to create polymers
also called “condensation reaction”
Dehydration: because water is the waste product of the reaction
Synthesis: because we are combining two molecules into one
ENZYMES run this reaction
enzymes pull a hydroxyl group off of one monomer and pull a hydrogen out of the other monomer → AKA creates H20 and pulls it out
This creates a COVALENT BOND between the two molecules to SHARE ELECTRONS
Hydrolysis - ENZYMES breaking down polymers into monomers
Reactions that end with “lyse” have to do with breaking down something
Enzymes insert a water molecule between the two monomer components and this breaks the bond that held the two monomers together
Functional Group: a group of atoms that provide a particular function or characteristic when it is present in another molecule
Hydroxyl [OH]: Polar, hydrophilic
Carbonyl [C=O]: Polar, hydrophilic → increases solubility (ability to dissolve in a solvent) of water
Carboxyl [COOH]: Polar, hydrophilic
acidic → likes to donate their hydrogen ions (H+) → becomes COO-
essential in amino acids
Amine group [NH2]: Polar, hydrophilic
Basic → wants to gain another hydrogen ion
essential in amino acids
Phosphate group [PO43-]: polar, hydrophilic
acidic → wants to lose hydrogen ions
Key for energy exchange in ATP (adenosine triphosphate) → addition or removal of phosphate is used to store or release energy
phosphorylation/dphosphorylation
Sulfhydryl group [SH]: polar, hydrophilic
likes to form bonds with other sulfhydryl molecules → this forms a disulfide bridge, which is important in protein structure and folding
Methyl group [CH3]: nonpolar and hydrophobic
DNA methylation → methyl group is used to turn off genes
appears in phospholipid tails
Acetyl: used to activate DNA (opp of methyl)
NOTE: ALL macromolecules are composed of monomers that have already gone through dehydration synthesis to form those large, complex molecules.
TOPIC 1.4
Macromolecule: a large, organic molecule
4 Different types of macromolecules/biomolecules: carbohydrates, lipids, proteins, nucleic acids
Lipid: hydrophobic → phospholipid bilyaer
Nucleic Acid: DNA and RNA
Carbohydrate: ends with “—ose”
Protein: peptide bonds
4 Major Macromolecules’ Characteristics
Carbohydrates
NOTE: all carbohydrates end with “—ose”
Name analysis
Carbo: 6 carbons
Hydrate: same ratio of oxygen: hydrogen as the ratio of oxygen: hydrogen in water (1 oxygen: 2 hydrogens)
Alternative name: Saccharide = Greek word for sweet 🍭 because glucose tastes sweet
What does it contain?
one carbon atom to one water molecule
[MONOMER OF CARBOHYDRATES] Monosaccharides: “one sugar”
Function) energy source and building blocks for more complex sugar structures
The most common form → exactly one carbon atom for each H20 molecule (with around 3-7 carbon atoms in total)
Most oxygen atoms are found in hydroxyl form (OH), one is part of a carbonyl (C=O) group
They can be in RING-shaped form or LINEAR chain → alpha (opposite sides) and beta form (same side)
Named based on # of carbons
Trioses (3 carbons)
Pentoses (5 carbons)
Hexoses (6 carbons)
ISOMER: having the same chemical formula, but different atom configuration
Glucose (6-carbon sugar)
Galactose: sugar found in milk - a stereoisomer of glucose (atoms are bonded in the same order, but different 3D organization)
Fructose: sugar found in fruit - a structural isomer of glucose and galactose (atoms are bonded in a different order)
Disaccharides: two monosaccharides join together through dehydration synthesis (release a water molecule and form a covalent bond known as GLYCOSIDIC LINKAGE)
Function) energy transfer
Examples:
Lactose (the sugar in milk) combination of glucose and galactose
Lactase: the enzyme that hydrolyzes lactose into monosaccharides → which mammals create when they are still drinking their mother’s milk because they need to be able to digest the milk. However, when you are an adult, most mammals don’t produce lactase because they don’t need to drink milk anymore.
Yet, because some human groups had access to milk products even when they were adults, this created groups that were able to have lactase persistence (continuing to produce lactase even through adulthood).
Maltose (malt sugar) - two glucose molecules
Sucrose (table sugar) - glucose and fructose
Polysaccharides: a long chain of monosaccharides linked by glycosidic bonds
Function) energy storage and structure
Examples of energy storage)
Starch - a stored form of sugar in plants
a combination of two polysaccharides - amylose and amylopectin
amylose: chains of glucose monomers
amylopectin: mostly glucose monomers
[DIGESTING CELLULOSE] Most animals cannot break down (hydrolyze) the bonds connecting the glucose monomers in cellulose (because we don’t have the enzymes that will actually use it for energy). A few animals (termites or ruminants) have symbiotic relationships with microorganisms that can convert cellulose into glucose.
On the other hand, starch has different bonds, which is why humans can digest it more easily.
Glycogen - storm form of sugars in HUMANS and other VERTEBRATES
A polymer of glucose monomers
Stored in liver and muscle cells
When blood glucose levels decrease, glycogen is broken down through hydrolysis
Examples of structure
Cellulose - the substance that cell walls are made up of
glucose monomers by 1-4 glycosidic bonds
Beta glycosidic linkages → cannot be digested by humans
[DIGESTING CELLULOSE] Most animals cannot break down (hydrolyze) the bonds connecting the glucose monomers in cellulose (because we don’t have the enzymes that will actually use it for energy). A few animals (termites or ruminants) have symbiotic relationships with microorganisms that can convert cellulose into glucose.
On the other hand, starch has different bonds, which is why humans can digest them more easily.
Hydrophilic → wants to go outside
Adenine and guanine are two-ringed → purine
Cytosine and thymine are single-ringed → primidine
partial - charge at nitrogen, partial + charge at hydrogen
partial - charge at oxygen, partial + charge at hydrogen
So, this forms a hydrogen bond
Get rid of the methyl group from thymine to make uracil
Why uracil? → evolution theory that it came before thymine (which is like an upgraded version LOL)
Chitin - the substance for the exoskeleton of insects
resembles cellulose, made up of glucose and nitrogen
Lipids
Need to be WHOLLY or PARTLY nonpolar (hydrophobic)
Note composed of REPEATING monomers → they have monomers though…
Functions
Fats/Oils: energy storage
Waxes: waterproofing
Phospholipid: membrane formation
Steroid: signaling hormones
Phospholipid
Hydrophobic/nonpolar tail
Hydrophillic/polar head
Head and tail connected by glycerol
When they are in water, the heads interact with water and the tails avoid water
Names: triglycerides (fats/oils), triacylglycerol
Fatty acid
Fatty: bc the carbon chain is hydrophobic
Acid: bc there is a carboxyl group (that is acidic)
Glycerol: 3 carbon chain, each with an OH group → sugar alcohol (because it has a hydroxyl group)
3 Acyl groups: a carbonyl group that is bonded to another chain
Bond between these two through dehydration synthesis → forms covalent bonds together also releasing 3 water molecules
Saturated fats
no double bonds between carbons
“saturating the fat with as many hydrogens as possible”
solid at room temperature → relatively dense
ex) butter
Unsaturated fats
not as many hydrogens as possible
keeps the molecules from being dense → typically liquid at room temperature
Monounsaturated fat → only 1 double bond between carbons
Polyunsaturated fat → multiple double bonds between carbons
Trans fats: “unhealthy”
“cis configuration”
“trans configuration” → not found in nature, where you saturate the unsaturated fats with more hydrogen but not enough to be a saturated fat, trans bonds
TOPIC 1.5
CENTRAL DOGMA: the process of creating proteins goes from DNA to RNA to protein
DNA replication, transcription, translation
DNA REPLICATION
Location:
Eukaryotic cell → nucleus
Prokaryotic cell → not in nucleus
When: before cell division (mitosis/meiosis) → interphase
Players: many enzymes that ends in “ase” → speed up reactions
Helicase: unzipping enzyme → breaks the hydrogen bonds that holds the bases together
DNA Polymerase: replicates the DNA molecules
Primase: tells the DNA polymerase where to start working by creating the primer (made up of RNA)
Ligase: glues the DNA fragments together
Process
Starts at the Origin → helicase unwinds the DNA
the SSB (single-stranded binding proteins) keep the two strands separated
the topoisomerase prevents the DNA from supercoiling
Primase creates the RNA primers on both strands
DNA polymerase builds the new strands in the 5’ to 3’ direction [leading strand]. Hence, the 3’ to 5’ direction has to constantly try and keep up with the unwinding. This strand is called the lagging strand, where primers have to keep being placed.
Fragments = “OKAZAKI fragments”
The ligase seals the gaps between the okazaki fragments
Semi-conservative: each copy contains one original strand and one new strand
TRANSCRIPTION → change one form of something into another form
Location: nucleus
Process
DNA is unzipped by the RNA polymerase at the promoter (the marker that indicates where the RNA polymerase should attach to the DNA strand)
The RNA polymerase “reads” the DNA’s bases and creates complementary pairs. [This time, thymine is replaced with uracil. Everything else stays the same].
DNA - 3 prime to 5 prime
Messenger RNA - 5 prime to 3 prime direction
This forms an mRNA (messenger RNA) strand, which is then sent out of the nucleus and into the cytoplasm.
TRANSLATION → translating RNA nucleotides into chain of amino acids
Location: cytoplasm/ribosome
Process
The tRNA strands reads the mRNA’s bases in threes. Certain tRNA strands bind to the mRNA if they are complementary.
Transfer RNA strands are just floating in the cytoplasm; they have an amino acid attached to them)
One comes and leaves an amino acid behind, another tRNA comes and leaves an amino acid behind, etc. → a long chain of amino acids
Continues until the stop codon indicates that the polypeptide (chain of long amino acids) is complete
MORE BACKGROUND INFO
What is an acid vs. a base?
Essentially, solutions are classified as acid/base based on their hydrogen ion concentration relative to pure water
Acid: a cation
contains a high concentration of hydrogen ions (H+), greater than pure water → wants to increase the concentration of H+ in a solution by donating one of its hydrogen atoms
pH lower than 7 → acidic
Base: an anion
contains a low concentration of hydrogen ions, less than pure water → wants to decrease the concentration of H+ in a solution by providing a molecule that removes hydrogen ions
pH above 7 → basic (alkaline)
pH: the hydrogen ion concentration in a solution
0-14 (nothing lower or higher)
Neutral pH: 7 (the pH of water)
What is deprotonation vs. protonation?
Deprotonation: removal of H+
Protonation: addition of H+
How do you number carbon?
Note: the numbering for the carbon always pertains to the SUGAR portion of the nucleotide
for DNA: either 5’ to 3’ OR 3’ to 5’
Sugar of DNA has carbons → the carbons on the sugar are numbered right AFTER the oxygen in a CLOCKWISE direction
→ 5’ to 3’
→ 3’ to 5’
Proteins: macromolecules made out of amino acids
Amino acids: monomers of proteins
Involved in the translation process to create proteins to serve different functions to survive
20 common amino acids
Name Analysis
Amino: it contains an AMINE functional group
Acid: it contains a carboxyl functional group → carboxyl is acidic (wants to donate its protons)
ALL amino acids have an alpha carbon (central carbon) that has a covalent bond with:
1) Amine group
2) Carboxyl group
3) 1 hydrogen atom
4) R group - can be polar, non-polar, acidic, basic, etc.
The difference is in the 4th covalent bond with a side chain → AKA called R GROUPS
These side chains determine the behavior/shape of the proteins (how they fold, interact with the environment, etc.)
No polarity → Hydrophobic → want to enter inside of the protein
Polarity → Hydrophilic → want to be outside of the protein
How do the amino acids connect? → through peptide bonds
Dipeptide: the smallest chain, a molecule with 2 amino acids connected by 1 peptide bond
Polypeptide: chains of amino acids → can eventually become a protein or a part of a protein
Primary Str: a sequence of the polypeptide (chain of amino acids connected by peptide bonds, created by ribosomes during translation/protein synthesis)
Linear chain
Secondary Str: interactions involving the polypeptide’s backbone
in 3D form
interactions between carbonyl groups and amino groups → through dehydration synthesis, they form hydrogen bonds and they create a particular shape
Two common forms
alpha helix → corkscrew shape
beta-pleated sheets → if the parts of the polypeptide chain is parallel or antiparallel
Tertiary Str: interactions between amino acid side chains (R groups)
The overall shape is determined by the R group in the amino acids (aka the SIDE CHAINS)
The R group determines the characteristics of the amino acids, so this also determines the folding/shape of the protein
New ingredients)
Hydrogen bonds
Ionic bonds
Covalent bonds
Hydrophobic clustering
If the R group is hydrophobic, that amino acid will try to get away from water by going inside
Hydrophilic → wants to go outside
Adenine and guanine are two-ring → purine
Cytosine and thymine are single-ringed → primidine
partial - charge at nitrogen, partial + charge at hydrogen
partial - charge at oxygen, partial + charge at hydrogen
So, this forms a hydrogen bond
Get rid of the methyl group from thymine to make uracil
Why uracil? → evolution theory that it came before thymine (which is like an upgraded version LOL)
Quaternary Structure: interactions between multiple folded tertiary polypeptides
TOPIC 1.6
Nucleic acids: macromolecules made out of nucleotides
DNA: genetic material found in living organisms → MOLECULE OF HEREDITY
Location:
Eukaryotes → nucleus
Prokaryotes → nucleoid (special cell region)
NAME
Deoxyribonucleic acid → It is a nucleic acid because it is found in the nucleus of eukaryotes
Deoxyribose → comes from the deoxyribose sugar
Deoxyribose sugar is 5-carbon sugar that, typically, takes on a pentagonal/ring-like structure
Acid → considered an acid because each nucleotide contains a phosphate group
What is a nucleotide?
Basic building block of nucleic acid
Contains 1 sugar group, 1 phosphate group, 1 nitrogenous base
Nitrogenous base pairs (adenine, thymine, guanine, cytosine)
Adenine and guanine are two-ring → purines
Cytosine and thymine are single-ringed → primidine
partial - charge at nitrogen, partial + charge at hydrogen
partial - charge at oxygen, partial + charge at hydrogen
So, this forms a hydrogen bond
Get rid of the methyl group from thymine to make uracil
Why uracil? → evolution theory that it came before thymine (which is like an upgraded version LOL)
A phosphate group (makes it an acid)
A sugar group (deoxyribose sugar)
Connected to other nucleotides
Note: the nitrogenous bases are connected via HYDROGEN BONDS
Nitrogen wants to gather hydrogen protons because it is electron-negative.
Nitrogen is electronegative, so when nitrogen bonds with a hydrogen
partial - charge at nitrogen, partial + charge at hydrogen
partial - charge at oxygen, partial + charge at hydrogen
So, this forms a hydrogen bond
Get rid of the methyl group from thymine to make uracil
Why uracil? → evolution theory that it came before thymine (which is like an upgraded version LOL)
Oxygen is also electronegative
partial - charge at oxygen, partial + charge at hydrogen
So, this forms a hydrogen bond
Get rid of the methyl group from thymine to make uracil
Why uracil? → evolution theory that it came before thymine (which is like an upgraded version LOL)
Note: the phosphate and sugar groups are connected by phosphodiester linkages
What does DNA contain?
Chains of nucleotides
What is the DNA structure?
Double helix structure - like a twisted ladder with rungs consisting of the nucleotide/nitrogenous bases, the backbone consists of the sugar and phosphate
The two strands are considered complementary because they match perfectly with each other and form a helix together
Anti-parallel structure of DNA
The direction of the deoxyribose sugars is different for left and right ladders
Count the carbons after the oxygen in a clockwise direction
Left side: 5’ to 3’ direction
Right side: 3’ to 5’ direction
RNA
Properties
Single-stranded
Ribose, a nitrogenous base, and a phosphate group
Functions
Some viruses use RNA as their “genetic material”
Information transfer
It can act as an enzyme to catalyze reactions
ATP is RNA’s monomer
What is the RNA structure?
Just add a hydroxyl group to all of the deoxyribose sugars on the left-hand side only because RNA tends to be SINGLE-STRANDED
The nitrogenous bases are slightly different, but JUST LIKE DNA, they all have NUCLEOTIDES [nitrogen-containing ring (nitrogenous base), a five-carbon sugar, and at least one phosphate group)
Adenine, guanine, cytosine, and uracil (in place of thymine)
Get rid of the methyl group from thymine to make uracil
Why uracil? → evolution theory that it came before thymine (which is like an upgraded version LOL)
Different types of RNA
Messenger RNA (mRNA) - serves as a messenger between DNA and ribosomes by being a copy of a strand of DNA
Then, the ribosome reads the mRNA’s nucleotides in groups of three (called CODONS) to create a complementary strand.
Ribosomal RNA (rRNA) - helps mRNA bind in the right spot at the ribosome so that its nucleotides can be read, and also helps create bonds that link amino acids
Transfer RNA (tRNA) “CARRIERS” - involved in protein synthesis, for bringing the amino acids to the ribosome for protein synthesis
NUCLEOTIDES
Nitrogenous bases
Adenine and guanine - purines (structures contain two fused carbon-nitrogen rings)
Cytosine and thymine - pyrimidines (a single carbon-nitrogen ring)
Sugars (slightly different for DNA and RNA): both 5-carbon sugars
Deoxyribose: "deoxy" = lacking one oxygen
Ribose: has an oxygen atom
Phosphate
In DNA and RNA, each nucleotide has one phosphate group
POLYNUCLEOTIDE CHAINS
Has directionality → two ends go in different directions
DNA goes from 5’ to 3’
When a new nucleotide is attached through the sugar ends, the bond is called a phosphodiester linkage
EXTRA VOCAB
Amphiphatic molecules: having both polar and nonpolar regions
Amphi = both kinds on both sides
Able to interact with both hydrophilic and hydrophobic molecules
Adenine and thymine = purines, connected by 2 hydrogen bonds
Cytosine and guanine = pyrimidine, connected by 3 hydrogen bonds → more stable, harder to break
NOTE: Every unlabeled vertex implies that there is a CARBON ATOM
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