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Jan 3, 2026

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13 pages

AP Biology Unit 1 Comprehensive Notes

Layna

@layna_r2

Ready to dive into the world of biological molecules? This... Show more

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Structure of Water and Hydrogen Bonding

Water is far more than just H₂O—it's the molecule that makes life possible! Water forms when oxygen (which is highly electronegative) shares electrons unequally with two hydrogen atoms through covalent bonds, creating a polar molecule with partially positive and negative regions.

This polarity allows water molecules to form hydrogen bonds with each other (cohesion) or with other charged molecules (adhesion). These weak but important interactions give water special properties that life depends on. Water's cohesive nature creates surface tension, where molecules at the surface form stronger bonds with each other than with the air above.

Water's structure creates several emergent properties that support life, including its ability to dissolve many substances (high solvency). These properties aren't just chemical curiosities—they're absolutely essential for biological processes to function.

Quick Tip: Remember that water's structure leads to its function! The unequal electron sharing creates polarity, which enables hydrogen bonding, which then creates water's special properties that make life possible.

Elements of Life

Living systems are energy-hungry! They require constant energy input to grow, reproduce, and maintain organization. This follows the law of conservation of energy—energy can't be created or destroyed, only transformed. Living organisms primarily use energy stored in chemical bonds to power life processes.

Besides energy, living systems need a steady exchange of matter with their environment. Carbon is the superstar element used to build all major biological molecules. It forms the backbone of carbohydrates, proteins, nucleic acids, and lipids. Other crucial elements include nitrogen (for proteins and nucleic acids), hydrogen, oxygen, and phosphorus.

Carbon's special ability to form carbon skeletons by bonding with other carbon atoms makes it uniquely suited for building complex biological molecules. These carbon-containing structures can form chains, branches, and rings—creating an amazing variety of molecules with different functions.

Remember This: Carbon is like the building block of life because it can form stable bonds with up to four other atoms, allowing for incredibly complex and diverse biological molecules!

Introduction to Biological Macromolecules

Think of biological molecules as LEGO structures—small pieces connect to build something amazing! Monomers are the building blocks that join together to form polymers (large macromolecules). Each type of biological molecule has specific monomers: monosaccharides for carbohydrates, amino acids for proteins, nucleotides for nucleic acids, and fatty acids/glycerol for lipids.

The process of joining monomers is called dehydration synthesis. During this reaction, an -OH group from one monomer and an -H from another are removed (forming water as a byproduct), and a covalent bond forms between the monomers. This is how cells build complex molecules from simpler parts.

The reverse process, hydrolysis, breaks polymers back down into monomers. Water is split into H+ and OH- components, which attach to the separated monomers. This is how your digestive system breaks down food into usable components.

Chemistry Connection: "Dehydration" synthesis literally means "removing water" to build something, while "hydrolysis" means "splitting with water" to break something down. These opposite reactions allow cells to both build and recycle complex molecules!

Creating and Breaking Biological Molecules

Creating carbohydrates is like snapping together building blocks! During dehydration synthesis, one carbohydrate monomer loses an -OH group while another loses just the -H from its -OH group. A covalent bond forms between them, and the removed -H and -OH combine to form water (H₂O).

Proteins form through a similar process, but with amino acids as the building blocks. Each amino acid has an amine group (NH₂) at one end and a carboxyl group (COOH) at the other. During synthesis, the -OH from one amino acid's carboxyl group and an -H from another amino acid's amino group are removed, forming water and creating a bond between the amino acids.

Breaking proteins down happens through hydrolysis, the opposite of dehydration synthesis. Water molecules are split, with the -H attaching to one amino acid and the -OH to the other, breaking the bond between them. This returns the protein to its individual amino acid monomers.

Real-Life Connection: Your digestive system performs hydrolysis constantly! When you eat protein-rich foods like chicken or beans, your body breaks down the proteins into amino acids through hydrolysis reactions so you can use them to build your own proteins.

Properties of Biological Molecules

In biology, structure determines function at every level of organization. Change the structure, and you'll change how something works—this principle applies from simple molecules to complex organisms.

Nucleic acids (like DNA and RNA) are information-storing polymers made of nucleotide monomers. Each nucleotide has three main parts: a five-carbon sugar, a phosphate group, and a nitrogen base. The sequence of these nucleotides encodes biological information—like the instructions for building proteins!

While both DNA and RNA store information, they have important structural differences. DNA nucleotides contain deoxyribose sugar, while RNA has ribose sugar. DNA uses the bases adenine (A), guanine (G), cytosine (C), and thymine (T), while RNA replaces thymine with uracil (U). These small differences lead to very different roles in the cell.

Big Idea Alert: The ability of nucleic acids to store information in their sequence is what allows for genetic inheritance! The specific order of bases in DNA is like a code that can be passed from parent to child, storing instructions for building and operating a living organism.

Proteins: Structure and Function

Proteins are incredibly versatile molecules that do most of the work in your cells! They begin as amino acids, which have directionality with an amino (NH₂) end and a carboxyl (COOH) end. When linked together, these amino acids form a polypeptide chain—the primary structure of a protein.

What makes amino acids unique is their R-group—a variable "side chain" attached to the central carbon. R-groups can be hydrophobic $water-fearing$ , hydrophilic $water-loving$ , or ionic (charged). The sequence and types of R-groups determine how the protein will fold and function.

Different proteins have different sequences of amino acids, creating endless possibilities for protein structure and function. Two proteins with just a slightly different sequence of amino acids can have completely different shapes and functions—that's why protein sequence matters so much!

Think About It: Imagine if you changed just one letter in a sentence—it could completely change the meaning! Similarly, changing just one amino acid in a protein can sometimes dramatically alter its function, which is what happens in some genetic diseases.

Carbohydrates and Lipids

Carbohydrates and lipids might seem less glamorous than proteins and nucleic acids, but they're just as essential! Complex carbohydrates are made of monosaccharide monomers, with their specific structures determining their properties and functions—like whether they provide quick energy or structural support.

Lipids don't follow the typical polymer structure but are made of subunits like fatty acids and glycerol. The saturation of fatty acids (how many hydrogen atoms they carry) affects their structure and function. Saturated fatty acids pack tightly together, while unsaturated ones have kinks from double bonds that prevent tight packing.

Phospholipids are specialized lipids with both hydrophilic $water-loving$ and hydrophobic $water-fearing$ regions, making them perfect for forming cell membranes. These membranes also contain proteins that can interact with both the watery environments inside and outside the cell and the hydrophobic interior of the membrane.

Practical Application: The next time you see "saturated fat" or "unsaturated fat" on a food label, you'll know the difference! Saturated fats (like butter) tend to be solid at room temperature because their fatty acids pack together tightly, while unsaturated fats (like olive oil) are usually liquid because their kinked structure prevents tight packing.

Structure and Function of Nucleic Acids

Nucleic acids have a specific directionality that's crucial to how they work. Each nucleotide has a sugar with a 3' hydroxyl group and a 5' phosphate group, giving the entire molecule a 5'-to-3' direction. In DNA, two strands run in opposite (antiparallel) directions, forming the famous double helix.

The two strands of DNA are held together by hydrogen bonds between complementary base pairs: adenine pairs with thymine (using 2 hydrogen bonds), and guanine pairs with cytosine (using 3 hydrogen bonds). These specific pairings are essential for DNA replication and protein synthesis.

The sequence of nucleotides in DNA and RNA encodes biological information—it's like a genetic language! Any change to this sequence can alter the encoded information, potentially changing how an organism develops or functions.

Visualization Tip: Think of DNA as a twisted ladder. The sugar-phosphate backbones form the sides of the ladder, while the base pairs form the rungs. The ladder always has a top (5') and bottom (3') end, with the two sides running in opposite directions.

Nucleic Acid Synthesis and Protein Structure

During nucleic acid synthesis, new nucleotides can only be added to the 3' end of a growing strand. This directional growth is a fundamental rule of DNA replication and RNA synthesis. The process uses covalent bonds to connect free nucleotides to the growing chain.

Proteins also have directionality, with an amino terminus and a carboxyl terminus. Amino acids are connected through peptide bonds, forming a linear chain. This sequence of amino acids represents the primary structure of a protein and determines how it will fold into its functional form.

Changes in the nucleotide sequence can alter the encoded information, which may affect the amino acid sequence in proteins. This relationship between nucleic acid sequence and protein structure is the basis of the central dogma of molecular biology—DNA makes RNA makes protein.

Cool Fact: Your DNA contains about 3 billion nucleotides, and if you stretched out the DNA from just one of your cells, it would be about 6 feet (2 meters) long! Your body has trillions of cells, so all your DNA stretched out would reach to the sun and back multiple times.

Protein Structure and Carbohydrate Directionality

Proteins don't just remain as linear chains—they fold into complex 3D structures! There are four levels of protein structure: primary (the amino acid sequence), secondary (local folding into alpha helices and beta sheets), tertiary (the overall 3D shape), and quaternary (when multiple protein chains interact).

These folding patterns aren't random—they're determined by the properties of the amino acid R-groups and are stabilized by various bonds and interactions. The final shape minimizes free energy and creates a functional protein.

Carbohydrates also show how small structural changes can create big functional differences. For example, the simple switch between alpha and beta linkages between glucose molecules creates either starch (digestible by humans) or cellulose (indigestible by humans but provides structural support in plants).

Make the Connection: Next time you eat bread or pasta (starch) and vegetables (containing cellulose), remember that both are made of the exact same glucose molecules—just connected differently! This tiny structural difference is why you can digest one but not the other.

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AP Biology

•

195

•

Jan 3, 2026

•

13 pages

AP Biology Unit 1 Comprehensive Notes

Layna

@layna_r2

Make the Connection: Next time you eat bread or pasta (starch) and vegetables (containing cellulose), remember that both are made of the exact same glucose molecules—just connected differently! This tiny structural difference is why you can digest one but not the other.