## Scientific Inquiry

Two types: discovery science, hypothesis-based science.

- A **null hypothesis** predicts that an intervention in an experiment will have no

effect.
- The **alternative hypothesis** predicts that the intervention will have an
effect.

## Elements of Life

**Matter** is made up of elements.

An **element** (单质) is a substance that cannot be broken down to other substances

by chemical reactions.

A **compound** (化合物) is a substance consisting of two or more elements in a fixed

ratio.

A compound has characteristics different from those of its elements.

<aside>
ℹ️

Carbon is the backbone of organic molecules. Carbon, hydrogen, oxygen, and nitrogen
account for approximately 96% of the total mass of human cells.

</aside>

<aside>
ℹ️

The four major classes of organic molecules are **proteins, nucleic acids,
carbohydrates**, and **lipids**.

</aside>

Proteins are made of amino acids. Nucleic acids are made of nucleotides.
Carbohydrates are made of monosaccharides.

- Carbohydrates: C H O
- Lipids: C H O P
- Proteins: C H O N S
- Nucleic acids: C H O N P

Chemical reactions start from reactants, make and break chemical bonds, and result
in products.

Carbon’s electron configuration allows it to form four covalent bonds.

- A **covalent bond** is the sharing of a pair of valence electrons by two atoms.

- Single covalent bond = single bond; double covalent bond = double bond.
- **Ionic bonds**.
- Covalent and ionic bonds are **strong bonds** between molecules.

Common functional groups:

- $\ce{-OH}$: Hydroxyl group

- $\ce{>C=O}$: Carbonyl group
- $\ce{-COOH}$: Carboxyl group
- $\ce{-NH2}$: Amino group
- $\ce{-SH}$: Sulfhydryl group
- $\ce{-OPO3^{2-}}$: Phosphate group
- $\ce{-CH3}$: Methyl group

Common prefixes:

- macro- mono- poly-

- di- tri- tetra- pent- hex-
- saccharide: sugar
- oligo-: several
- de-: absent
- ose: sugar
- in: protein
- lysis: breakage
- philic: like
- phobic: dislike
- mer: unit

## Structure of Water and Hydrogen Bonding

**Weak chemical bonds**, including **hydrogen bonds**, are also important in

organisms.

- A **hydrogen bond** forms when a hydrogen atom covalently bonded to one

electronegative atom is also attracted to another electronegative atom.

The water molecule is a **polar molecule**.


- In **polar molecules**, the centers of the positive and negative charges are
different.
- Because water is a polar molecule, the positively-charged locations attract the
negatively-charged locations, resulting in hydrogen bonds.
- **Electronegativity** is the ability for the proton in an atom to pull.

The properties of water result from its polarity and hydrogen bonding. Four of
water’s properties that facilitate an environment for life:

- **Cohesion and adhesion.**

- **Cohesion** is the tendency for water molecules to stick to **other water
molecules**.
- **Adhesion** is the tendency for water to stick to **other polar or charged
substances**—for example, between water and plant cell walls.
- For example, droplets. Water droplets are round because of cohesion. Adhesion
allows water to cling to solid surfaces.
- **Surface tension** is a measure of how hard it is to break the surface of a
liquid—related to **cohesion**.
- **Capillary action** is related to both adhesion and cohesion, but more so
adhesion.


- **Ability to moderate temperature.**

- Water can absorb or release a large amount of heat with only a slight change
in its own temperature—that is, it has a high **specific heat**.
- A higher temperature breaks water’s hydrogen bonds first, and only then
increases the molecule movement speed. Therefore, the high specific heat is
attributed to hydrogen bonds.
- **Floating of ice on liquid water.**
- Ice floats in liquid water because hydrogen bonds in ice are more “ordered,”
making ice less dense.
- **High solvency.**
- A **solution** is a liquid that is a homogeneous mixture of substances. A
**solvent** is the dissolving agent of a solution. The **solute** is the substance
that is dissolved. An **aqueous solution** is one in which water is the solvent.
- A **hydrophilic** substance is one that has an affinity for water. A
**hydrophobic** substance is one that does not have an affinity for water.

## Molecules and Macromolecules

Macromolecules are polymers, built from monomers.

The four major classes of large biological molecules are **proteins, nucleic acids,
carbohydrates**, and **lipids**.

- Lipid is a special case: it’s not a macromolecule, because it’s not made of
monomers.
- Proteins, nucleic acids, and carbohydrates are **polymers** made from
**monomers**.

**Dehydration** (aka. dehydration synthesis) ****connects multiple monomers to

become a polymer.

- One end loses $\ce{H}$. One end loses $\ce{-OH}$. A new covalent bond is formed.
This is known as **polymerization**.

**Hydrolysis** adds a water molecule across a covalent bond to break large

molecules into smaller ones.

### Carbohydrates

Carbohydrates are $\ce{(CH2O)_n}$. They are sources of energy and components of

cell walls.

The simplest carbohydrates are **monosaccharides**. **Polysaccharides**.

Though often drawn as linear skeletons, sugars may form rings in aqueous solutions.

Common monosaccharides include:

- Ribose 核糖 (5 carbons)
- Deoxyribose 脱氧核糖 (5 carbons)
- The second carbon on deoxyribose connects to $\ce{H}$. Ribose: $\ce{-OH}$.
- Glucose 葡萄糖 (6 carbons)
- Glactose 半乳糖 (6 carbons)
- Fructose 果糖 (6 carbons)

A **disaccharide** is formed when a dehydration reaction joins two monosaccharides.

This forms a covalent bond known as a **glycosidic linkage**.

Common polysaccharides include the following. These are all made of glucose but
structured differently.

- Starch 淀粉—only in plants

- Glycogen 糖原—only in animals
- Cellulose/fiber 纤维素
- Chitin 几丁质—mostly in exoskeletons of arthropods

### Lipids

**Lipids** are defined by the property of being **hydrophobic**, as they consist

mostly of hydrocarbons, which form nonpolar covalent bonds.

Lipids are not polymers.

Important lipids: **fats**, **phospholipids**, and **steroids** 固醇.

- Fats are made from **glycerol** 甘油 and **fatty acids** 脂肪酸. In a fat, three fatty
acids are joined to glycerol, creating a **triacylglycerol** 甘油三酯, or triglyceride.
- **Saturated fatty acids** have the maximum number of hydrogen atoms possible
and no double bonds.


- **Unsaturated fatty acids** have double bonds.


- A diet rich in saturated fats may contribute to cardiovascular disease.

Unsaturated fats are typically liquid, and saturated fats solid.
- In a phospholipid, two fatty acids and a phosphate group are attached to
glycerol.
- The phosphate group is hydrophilic. The fatty acid is hydrophobic. This
creates a phospholipid bilayer.
- Steroids always have four rings.
- **Cholesterol** is a component in animal cell membranes.

### Nucleic Acids

There are two types of nucleic acids: **deoxyribonucleic acid** and **ribonucleic
acid**.

Nucleic acids are polymers and are also known as **polynucleotides**. They are made
of **nucleotides**.

Each nucleotide consists of a **nitrogenous base**, a pentose sugar, and a

**phosphate group**. Specifically, **nucleoside** is nitrogenous base + sugar, and
nucleotide is nucleoside + phosphate group.

There are two types of nitrogenous bases: **pyrimidines 嘧啶** and **purines 嘌呤**.

- Pyrimidines: cytosine, thymine, and uracil

- Purines: adenine and guanine
- A, G, C, and T are in DNAs. A, G, C, and U are in RNAs.

**DNAs**

In DNAs, A pair with T, C pair with G. They are paired with **hydrogen bonds**. A
and T pair with two hydrogen bonds, C and G pair with three hydrogen bonds.

Otherwise, each nucleotide vertically connects to each other with a

**phosphodiester bond** 磷酸二酯键.

DNA strands have a 5’-phosphate group at one end and a 3’-hydroxyl group at the
other end.

DNA forms a double helix, where the two backbones run in opposite 5’ to 3’
directions from each other, an arrangement known as **antiparallel**.

### Proteins

Functions of protein:

- Selective acceleration of chemical reaction

- Coordination of an organism activities
- Movement
- Protection against disease
- Transportation of substances
- Respond to chemical stimuli (information)

Proteins are formed of **amino acids**. The R group (side chain) determines the
property of an amino acid.


The R group of an amino acid can be categorized by three possible chemical

properties: **hydrophobic and nonpolar**, **hydrophilic and polar**, or **ionic**.

Amino acids are connected by **peptide bonds** 肽键 ($\ce{CO-NH}$) to form proteins.

Two amino acids connect to create a dipeptide 二肽. Proteins are one or multiple
polypeptides.

Proteins are folded into 3D shapes that determine their functions.

- Proteins are directional. The N terminus has a dangling amino group. The C
terminus has a dangling carboxyl group.
- The **primary structure** of a protein is its amino acid sequence. This structure
determines how a protein folds.
- The **secondary structure** of proteins refer to the local folding that forms
from interactions between atoms of the polypeptide backbone of the amino acid
chain. **The “polypeptide backbone” refers to the amino acid sequence without R
groups.** There are two common types: $\alpha$ helices and $\beta$ pleated sheets.


- The **tertiary structure** is determined by interactions between R groups. For

example, strong covalent bonds called **disulfide bridges** 二硫键 may reinforce the
protein’s structure.
- The **quaternary structure** arises from interactions between multiple
polypeptides. Not all proteins have quaternary structure—only those with multiple
polypeptides.

**Function is determined by shape**. ****This sentence shall be answered when

relevant.