Chapter 3: The Chemical Building Blocks of Life 

Miranda Bognar 

Period 5A 

Quizlet Unit 1- ​https://quizlet.com/6287696/ap-bio-unit-1-test-study-guide-flash-cards/ 

Carbon: The Framework of Biological Molecules 

1. Functional groups account for differences in molecular properties 

a. Hydrocarbons are nonpolar because of the even distribution of 

bonds through carbon and hydrogen atoms.  

b. Most cells contain other atoms that have different 

electronegativity. This causes the molecules to have a partial 
negative and positive charge. This means that they are polar. 

c. Some​ functional groups​ include acidic carboxyl, phosphate, basic 

amino. These can hydrogen bond 

2. Isomers have the same molecular formulas but different structures 

a. Isomers​ are molecules that have the same atomic formula but 
consist of different structural arrangements. (ex. glucose and 
fructose)  

b. A difference in structure are called​ ​structural isomers​ (Glucose + 

fructose) 

c. Stereoisomers​ ​have the same carbon skeleton but the difference 

is how groups are arranged. The subcategory is called 
enantiomers​. These are mirror images of each other. Mirrored 
 molecules are called ​chiral molecules​. This happens when carbon 
is bound to four different molecules¨. 

d. Chiral compounds have an effect of polarized light. This has them 

rotate to the right (​dextro,D​) or to the left (​levo,L​).  

3. Biological macromolecules include carbohydrates nucleic acids, 

proteins, and lipids​-table 3.1 ☆ pg. 37 

a. Polymers​ are long molecules that are made by ¨linking together¨ 

many small ​monomers​.  

b. Carbohydrates​ are polymers made of ring shaped sugars/​Nucleic 

acids​ are ¨polymers of nucleotides¨/​Amino acids ​are polymers of 
proteins/​Lipids​ are macromolecules (don't follower 
monomer-polymer relation) that link fatty acids to 
glycerol-Theses are formed by a ​dehydration reaction.​ Breaking 
them down is a reaction called ​hydrolysis reaction 

i. The dehydration reaction​-or condensation 

1. Removing -OH and H (same thing as taking H2O) is 

the process of creating a covalent bond between two 
monomers. This is the reaction that is used when 
joining nucleotides during DNA synthesis, or glucose 
joining together to make starch, or linking fatty acids 
to glycerol in lipids.  

2. Every subunit added to a macromolecule is removing 

one water molecule. Substance must be held close 
together so that the right chemical bonds will be 
¨stressed and broken¨-​catalysis  
 ii. The hydrolysis reaction 

1. This reaction is the ​reversal​ of the dehydration 

reaction.  

2. This happens by adding water molecules. H is added 

to one subunit and OH is added to another. This breaks 
the covalent bond. (eating a potato) 

Lesson 3.2 

Carbohydrates- ​Loose groups of molecules that have carbon, 

hydrogen, oxygen in ​molar ratios​ (1:2:1) (CH2O)x where ¨x¨ is the number 
of carbon atoms 

★ Because of the many C-H bonds that release energy when 

oxidation-​losing electrons ​occurs, this makes them good for 
energy storage. 

Monosaccharides ​-(simple sugars) ​are the simplest carbohydrates 

★ simple sugars have at least 3 carbon atoms but the ones that play 
a ¨central role in energy storage¨ have 6 (ex. C6H12O6) 
★ 6 Carbon sugars can be in a straight line but almost always form 
rings 
★ Glucose-​ most important monosaccharide for energy storage (7 
energy storing C-H bonds) 
■ Glucose can be in 2 forms: Alpha and beta 
Fructose-​ structural isomer that differs in the position of the carbonyl 
carbon (C--H) from the ring 

Galactose-​ stereoisomers that differs in the position of OH and H groups 

from the ring 

Humans and animals don't do this! 

★ Plants have the glucose converted into transport form before 

being moved. 
★ These transport forms of sugars are usually made by linking 2 
monosaccharides to form a ​disaccharide- ​2 monosaccharides 
linked 
○ Enzymes cant break down the bonding holding the 2 
monosaccharide subunits. The disaccharide aids in that  
 ○ There are different transport forms depending on what 
monosaccharides are linked (ex. Glucose + fructos[structural 
isomer] = disaccharide -> sucrose) 
■ Sucrose​ is used by most plants to transport glucose and 
the main sugar we eat (sugarcane) 
■ Glucose + galactose (stereoisomer) = disaccharide -> 
Lactose (is an energy source) 
● People who have lactose intolerance can't break it 
back down into 2 monosaccharides.  

Polysaccharides-​ ​Longer polymers made up of monosaccharides that 

joined through dehydration 

Starch- a storage polysaccharide has all of alpha-glucose molecules 

linked in long chains. Insoluble (amyloses- simplest 
starch)(amylopectin-more complicated variant of amylose) 

- Pectins are branched polysaccharides (short amylose branched 

consist of 20 to 30 glucose subunits) 
- Glycogen- insoluble polysaccharide with branched amylose 
chains. Much longer chain length and more branches 

Cellulose- Structural polysaccharide with beta-glucose molecules 

linked in long chains. Huge part in the plant cell walls 

- For glucose to link, they need to be the same form (Alpha or beta) 
- Unbranched beta-linked chains make tough fibers 
 - Starch-hydrolyzing enzymes cannot break the bond between 2 
beta-glucose units because they only recognise alpha-linkages 
- Because of its ability to not be broken down by most animals, 
its worlds as well as a biological structural material. 
(excluding cows) 

Chitin- structural material found in arthropods and many fungi 

- Polymer of N-acetylglucosamine (substituted version of glucose) 

- When cross linked by proteins it creates tough surface 
material that can be used as a hard exoskeleton to insects 
and crustaceans. 
- Not many organisms can digest chitin but many have chitinase 
enzyme to protect against fun 

------------------------------- 

Lesson 3.3 

The biochemical activity depends on the making of a large number of 

proteins, each with a specific sequence 

2 varieties of Nucleic Acids 

- Deoxyribonucleic acid (DNA) 

- Ribonucleic acid (RNA) 

DNA-​holds the genetic information 

 - 2 chains wrapped around each other in a long linear molecule in 
eukaryotes (Helix)(double chain- double helix) 
- Circular molecule in most prokaryotes 

RNA​-short lived copies of DNA used to direct protein synthesis during 

gene expression. 

- Nucleic acid macromolecules are templates for producing exact 

copies of themselves. This allows genetic information to be 
preserved during cell division and reproduction of organisms 

Messenger RNA (mRNA) 

Transcribed single stranded copies of part of the DNA. 

- Blueprints specifying the amino acid sequences of proteins 

Ribosomal RNA (rRNA) 

RNA is part of the ribosome in the form of ribosomal RNA 

Transfer RNA (tRNA) 

Carried amino acids 

Nucleotides-​ subunits of nucleic acids. Can form polymers by joining 

phosphate of one nucleotide to a hydroxyl group of the sugar of another 
nucleotide by dehydration.  

3 components of nucleotides 

- Pentose (5 carbon sugar) 

 - A phosphate  
- An organic nitrogenous base 

5 types of nitrogenous bases 

- Double ring molecule called ​purines- adenine (A) (DNA & RNA) 
- Double ring molecule called purines- guanine (G) (DNA & RNA) 
- Single ring molecule called pyrimidines- cytosine ¨C¨ (DNA & RNA) 
- Single ring molecule called pyrimidines- thymine (T) (DNA) 
- SIngle ring molecule called pyrimidines- uracil (U) (RNA) 

^all attracted to other pair with a hydrogen bond 

● Bases that participate in base pairing are ​complementary ​to each 

other 

Adenosine Triphosphate (ATP) 

¨Energy currency of the cell¨ 

- A cell uses ATP as energy for many reasons. (ex. Chemical 

reactions, power transportation across membranes, power 
movement of cells) 

Nicotinamide adenine dinucleotide (NAD+) 

- Carries high energy electron from oxidized molecules and gives 

them to ATP producing pathways  

Flavin adenine dinucleotide (FAD) 

 - Acts as a soluble electron carrier (can be reversibly oxidized and 
reduced) 

Phosphodiester bond​- linking 2 sugars through phosphate (chain of 

nucleotides) and are polar 

Nucleic acid​- chain of 5 carbon sugars linked together by 

phosphodiester bond with a nitrogenous base protruding from each 
sugar 

Eukaryotic organisms​: THe DNA is more complexed with protein to form 

structures we call chromosomes. This makes a higher order structure 
that affects the function of DNA  

RNA vs DNA 

- Ribose sugars 
- Uracil 
- Single stranded (transciped/copied from DNA) 

Lesson 3.4 

Proteins are the most diverse macromolecule (chemically + 

functionally) 

☆table 3.2-good reference☆ 

Enzyme catalysis​-facilitate specific chemical reactions 

★ Enzymes are three dimensional globular proteins that fit perfectly 

on the molecules ¨they act on¨ 
○ This facilitates chemical reactions but stressing a particular 
chemical bond 

Defense-​ use their shapes to recognize foreign microbes and cancer 

cells (globular proteins) 

★ Form the body's endocrine and immune systems 

Transport-​ moving small molecules + ions (variety of globular proteins) 

★ Ex. hemoglobin transports oxygen to the blood. Composed of 2 

alpha-globin chains and 2 beta-globin peptide chains 
★ Ex. membrane transport proteins help move ion and molecules 
across the membrane 

Support-​ protein fibers play structural roles 

★ Ex. keratin in hair, fibrin in blood clots,  

★ collagen forms matrix of skin, ligaments, tendons, and bones 
making it the most abundant protein in a vertebrates body 

Motion 

★ Muscles contract with sliding motion of (2 kinds of protein 

filaments) actin and myosin 
 ★ Contractile proteins helps in a cell's cytoskeleton and moving 
materials in the cell 

Regulation 

★ Genes are ¨turned on and off¨ all throughout development 

Storage 

★ Calcium + iron are stored in the body by binding as ions to storage 

proteins 

Proteins are linear polymers made up of 20 different amino acids 

Amino acids​- Subunit structure where proteins are produced 

consisting of the carboxyl group, and amino group, a hydrogen, 
and side group (R group)--only the side group different from one 
amino acid to another 

★ R group determines the chemistry of amino acids, hydrogen bonds 

■ The 20 common amino acid group are grouped into 5 
chemical class based on their R group 
1. Nonpolar amino acids (ex. Leucine)(R group=CH2 or CH3) 
2. Polar uncharged amino acids (ex. threonine)(R=O2 ro OH) 
 3. Charged amino acids (ex.glutamic acid)(R=acids of bases-that 
can ionize) 
4. Aromatic amino acids (ex.phenylalanine)(R=carbon ring w/ 
alternating single and double bonds-nonpolar) 
5. Amino acids w/ special functions + unique prop.  

A different amino acid changes the shape of the protein because 

of the difference in side groups. 

(ex.methionine-first amino acid in a chain,proline-causes kinks in 

chains, cysteine-links chains together) 

D-amino acids: rare 

L-amino acids: found in proteins 

When an amino acid is ionized it has a + amino group and a - carboxyl 

group. These undergo dehydration to form a covalent bond, then linking 
the 2 amino acids together which is called ​peptide bond 

- The lack of rotation from the peptide bonds determines the 

structural character  

Polypeptide-​ a protein is made of one or more unbranched chains and 

these chains are called polypeptide chains. These also have amino 
acids linked onto their structure by peptide bonds. 

● All internal amino acids are nonpolar because of the hydrophobic 

nature of the nonpolar molecules. This pushed the nonpolar 
 portions of the amino acid chain into the protein interior. This has 
the proteins of the surface (minus a few) 

Primary​ ​structure-​ amino acid sequence of a protein 

Secondary​ ​structure-​ hydrogen bonding between carbonyl group and 

amino group from primary structure 

(Cylindrical) ​Alpha helix​- polypeptide chain is wound into a spiral bc of 

interactions between amino and carboxyl groups in the peptide 
backbone. 

(Planar)​ Beta sheet​- polypeptide folds into itself 

Tertiary structure​-folded shape protein bc of hydrophobic interactions 

with water, ionic + covalent bonding between side chains of different 
amino acids 

- Many small proteins can be fully unfolded (​denatured)​ but will 

refold 
- Larger proteins tend to form insoluble clumps when denatured 
- Stabilized by hydrogen bonding between r groups with different 
amino acids, electrostatic attraction between r groups with 
opposite charges, & hydrophobic exclusion of nonpolar r groups. 
- Stability of a protein is greatly influenced by how well the 
interior fits together. 

Quaternary structure​-more than one polypeptide chain, each with its 

own tertiary structure; individuals called subunits 
 - When 2 or more polypeptide chains form a function protein, the 
individual chains are called subunits of the protein 
- In proteins made of subunits, when they come in contact with each 
other, they are nonpolar and help transmit info  

Motifs-​ a substructure in proteins that allows functions 

- Beta-alpha-beta motif created a fold at the core of the nucleotide 

binding sites ← common protein 
- Helix-turn-helix has 2 alpha helices separated by a bend ← very 
important bc its used to bind proteins to the DNA double helix 

Domains-​ part of proteins that binds DNA 

- Functional units within a larger structure (substructure within 

tertiary structure) 
- Proteins made up of many domains 
- Help with folding into proper shape 

Chaperone proteins​- class of enzymes that help proteins fold properly + 

help misfolded proteins 

- Escherichia coli- essential protein GroE chaperonin 

- Flexible 
- Improper folding of proteins can cause disease 
- Ex. cystic fibrosis 

Denaturation​-a change in nature that has causes a protein to change 

shape, or unfold completely 
 - Can happen when pH, temperature, or ionic conventions changes 
- Usually proteins that do this are inactive 
- When environment is reestablished, a small protein could suddenly 
refold into its natural shape (​renaturation)​  
- Larger proteins can result refold 

Dissociation- reversible separation of protein subunits from a 

quaternary structure without changing the tertiary structure. (dissolving 
of ionic compounds in water) 

Lesson 3.5 

Lipids-​ nonpolar, hydrophobic organic molecule that is insoluble in 

water (polar) but does dissolve in nonpolar organic solvents (including 
fats, oils, waxes, steroids, phospholipids, and carotenoids) 

- Cannot fold because of many C-H bonds 

- When placed in water, lipids cluster together 
- Made up of fatty acids + glycerol 
- Fatty acids- long chain hydrocarbons with COOH at one end 
- Most fats contain 40 carbon atoms making them better 
at storing energy 
- Glycerol- 3 carbon polyalcohol (3 OH groups) 

(triacylglycerol) ​Triglyceride-​ Individual fat molecule made of a glycerol 

and 3 fatty acids 
 - The many C-H bonds of fats form long term energy storage 

Saturated fat​-All internal carbon atoms in a fatty acid chain are 

bonded to 2 hydrogen atoms (has max. 
Hydrogen atoms poss.) 

Unsaturated-​ 1 or more fatty acids don't have 

the max. Number of hydrogen attached to their 
carbons 

Monounsaturated-​ fatty acids with 1 double bond 

Polyunsaturated-​ fatty acids with more than 1 double bond 

between carbons  

- Low melting point because of chains 

bending at double bonds 
● double bonds cant rotate so this affects the 
melting point 

Terpenes-​ long chain lipids 

- Important pigments (ex. Chlorophyll, rubber) 

Steroids-​ made of 4 carbon rings 

Prostaglandins- group of 20 lipids that are modified fatty acids with 2 

nonpolar tails attached to a 5 carbon ring 

- Act as ¨local chemical messengers¨ in vertebrate tissues 

 When an organism consumes excess carbohydrates, it is 
converted to starch, glycogen, or fats saved for future use 

Phospholipids- like a triglyceride but with phosphate relapsing one 

of the fatty acids. Has 3 subgroups (polar head, 2 long nonpolar 
tails) 

1. Glycerol-​ 3 carbon alcohol with each carbon having a 

hydroxyl group. Forms backbone of phospholipid molecule 
2. Fatty​ ​acids-​ Long chains of CH2 with COOH as tail. 2 fatty 
acids are attached to the glycerol backbone  
3. Phosphate​ ​group​ (PO4)- attached to one end of a glycerol + 
organic molecule linked to it (ex. Choline, ethanolamine, or 
amino acid serine 

Micelles-​ In water, lipid molecules nonpolar tails move away from the 
water creating a spherical micelles that have the tails facing inward