Biochemistry Basics Made Simple: Water, pH Scale, and the Four Biological Macromolecules
- Mr. Substrate
- 4 days ago
- 14 min read
Updated: 3 days ago
Biochemistry doesn’t have to feel overwhelming, not when you break it down the right way.
In this post, we’re diving into the essential biological molecules that every high school biology or intro bio student should understand: water, the pH scale, and the four major macromolecules — carbohydrates, lipids, proteins, and nucleic acids.
These aren’t just vocabulary words, they’re the foundations of life. Everything your body does, from digesting food to making hormones to copying DNA, depends on the structure and function of these molecules. So if you’ve ever felt lost trying to memorize the difference between saturated and unsaturated fats, or wondered how a tiny nucleotide can store the entire genetic code… you’re in the right place.
Let’s break down the science clearly and visually and if you need a cheat sheet, I’ve got you covered with a free Biochemistry Basics Summary Sheet at the end of the post!
💧Structure of Water: The Molecule That Makes Life Possible
Water may seem simple, but its structure is the reason life on Earth can exist the way it does. In this section, we’ll break down the shape, bonding, and unique properties of water — all of which play a critical role in biology.
The Shape and Polarity of a Water Molecule
A water molecule (H₂O) forms when one oxygen atom shares electrons with two hydrogen atoms, creating polar covalent bonds. These bonds are arranged at an angle of 104.5°, giving water its distinctive bent shape.
This shape creates a separation of charge — oxygen becomes slightly negative (δ⁻), and hydrogen slightly positive (δ⁺) — making water a polar molecule.
Hydrogen Bonds: Small but Mighty
Because of its polarity, water molecules can attract one another. The slightly positive hydrogen of one molecule is drawn to the slightly negative oxygen of another. This attraction is called a hydrogen bond.
While individual hydrogen bonds are weak compared to covalent or ionic bonds, many of them working together create a strong network. These hydrogen bonds give water many of its unique and vital properties.
Properties of Water That Support Life
High Specific Heat Capacity
Water resists changes in temperature. This is because its hydrogen bonds absorb heat energy without quickly breaking. As a result, water heats up and cools down slowly, helping organisms maintain a stable internal environment and protecting ecosystems from temperature fluctuations.
High Heat of Vaporization
When water evaporates (e.g., when we sweat), it takes a lot of energy with it — that’s water’s high heat of vaporization in action. This makes water an efficient cooling system for the body and helps regulate climate in coastal areas.
Water as a Powerful Solvent
Thanks to its polarity, water dissolves many substances — especially other polar or charged ones. This is why water is often called the “universal solvent.”
When ionic compounds like NaCl (table salt) dissolve in water, the positive and negative ions separate and interact with the ends of water molecules. This process is essential for chemical reactions in cells, where ions and polar molecules must move freely.
Hydrophilic molecules: attracted to water (e.g., sugars, salts)
Hydrophobic molecules: repel water (e.g., oils, fats)
Cohesion, Adhesion & Surface Tension
Water molecules stick together (cohesion) and also cling to other polar surfaces (adhesion). These properties explain:
How water travels up plant stems (via capillary action)
How blood flows through vessels in animals
Why water forms droplets or why insects can “walk” on water (surface tension)
At the surface, water molecules cling tightly together due to hydrogen bonding, creating a flexible “skin” at the water’s surface — strong enough to support small organisms.
Ice Floats: A Life-Saving Quirk of Water
Most substances become denser when they freeze — but not water. As water cools below 4°C, hydrogen bonds lock molecules into a rigid structure that’s less dense than liquid water. That’s why ice floats.
Floating ice insulates the water below, allowing aquatic life to survive in cold climates. If ice sank, entire lakes and oceans could freeze solid from the bottom up — devastating ecosystems.
🧪 Understanding the pH Scale: Acids, Bases, and Buffers
In biology, maintaining a stable pH isn’t just a preference — it’s essential for life. From enzyme function to blood chemistry, even a small change in pH can cause serious issues. Let’s explore how acids and bases work, how the pH scale helps us measure them, and how living systems stay balanced using buffers.
Water Ionizes to Form Ions
When water molecules split apart (a process called ionization), they release equal amounts of:
Hydrogen ions (H⁺) — also called protons
Hydroxide ions (OH⁻)
This balance of H⁺ and OH⁻ is the foundation for understanding acidity and alkalinity.
What Makes a Solution Acidic?
Acids are substances that increase the concentration of H⁺ ions when they dissolve in water. The more fully an acid releases hydrogen ions, the stronger the acid.
Examples of acidic substances:
Lemon juice
Vinegar
Coffee
Tomatoes
For instance, hydrochloric acid (HCl) is a strong acid — it dissociates almost completely in water, releasing a large number of H⁺ ions. This sharp increase in H⁺ makes the solution highly acidic.
What Makes a Solution Basic?
Bases are substances that either:
Take up H⁺ ions from a solution, or
Release OH⁻ ions into the solution
When a base like sodium hydroxide (NaOH) dissolves in water, it dissociates to release OH⁻ ions, which then neutralize H⁺ ions.
Examples of basic substances:
Ammonia
Milk of magnesia
Soaps and detergents
The fewer H⁺ ions in a solution (and the more OH⁻), the more alkaline or basic it becomes.
The pH Scale Explained
The pH scale is used to measure how acidic or basic a solution is. It ranges from 0 to 14, and is based on the concentration of H⁺ ions in a solution.
pH Value | Meaning |
0–6 | Acidic (High H⁺) |
7 | Neutral (H⁺ = OH⁻) |
8–14 | Basic/Alkaline (Low H⁺, High OH⁻) |
Biological systems are extremely sensitive to pH changes. For example, the pH of human blood must stay near 7.4. Even small deviations can lead to serious health issues.
Buffers: The Body’s pH Balancers
To prevent harmful pH swings, living organisms use buffers — special chemicals that can either absorb excess H⁺ or OH⁻ ions.
In your body, buffers play a key role in regulating blood pH. If your blood drops to pH 7.0, it can lead to acidosis. If it rises to pH 7.8, alkalosis can occur. Both conditions are dangerous and can be life-threatening.
Buffers help by:
Taking up extra H⁺ ions if the solution becomes too acidic
Absorbing excess OH⁻ ions if it becomes too basic
Even many commercial products, like shampoos and deodorants, are buffered to protect your skin and make them safer to use.
🔬 Biological Macromolecules: The Building Blocks of Life
All living things are made up of four major types of organic molecules, also known as biomolecules:
👉 Carbohydrates, Lipids, Proteins, and Nucleic Acids.
These molecules are essential for life, and they’re all organic, meaning they contain both carbon and hydrogen atoms. What makes them so versatile and vital? The answer lies in carbon’s unique bonding abilities.
Why Carbon Is the Backbone of Life
Carbon atoms are small but mighty. Each carbon atom has four electrons in its outer shell, which means it can form up to four covalent bonds with other atoms — including carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur. These are the elements that make up most of your body.
This ability allows carbon to form:
Straight chains
Branched chains
Rings
That’s why carbon can be used to build a huge variety of molecular structures — from simple sugars to complex proteins and DNA strands.
Monomers and Polymers
Many biomolecules are macromolecules, meaning they’re large molecules made up of smaller repeating units.
The smaller building blocks are called monomers
When monomers link together, they form polymers
Here’s how that looks for each macromolecule class:
Macromolecule | Monomer | Polymer |
Carbohydrates | Monosaccharides | Polysaccharides |
Proteins | Amino acids | Polypeptides |
Nucleic Acids | Nucleotides | DNA or RNA strands |
Lipids | Glycerol + Fatty Acids | (Not true polymers) |
Unlike the others, lipids aren’t true polymers — they’re made of two different subunits (glycerol and fatty acids), not repeating monomers.
How Macromolecules Are Built and Broken Down
Condensation (Dehydration) Reactions
To build macromolecules, cells use condensation reactions — also called dehydration synthesis.
In this process:
An -OH (hydroxyl) group is removed from one monomer
An -H (hydrogen) is removed from another
The monomers bond, and a water molecule is released
This is how your body links sugars, amino acids, or nucleotides to create the large molecules it needs.
Hydrolysis Reactions
To break these molecules down again, cells use the reverse process: hydrolysis.
In this reaction:
A water molecule is added
An -OH group joins one piece
An -H joins the other
The bond is broken
Hydrolysis allows your body to digest food and release energy or building blocks for new structures.
Bonus Fact: These reactions don’t just happen on their own. Your cells use enzymes to speed them up — acting like molecular scissors or glue, depending on the job.
🍞 Carbohydrates: Fuel and Structure for Life
Carbohydrates are one of the most important macromolecules in biology. Not only do they provide a quick source of energy for living organisms, but some carbohydrates also serve important structural roles in cells and tissues.
Most carbohydrates follow a 1:2:1 ratio of carbon to hydrogen to oxygen (CH₂O), which is why the word literally means carbon + water.
What Are Carbohydrates Made Of?
Carbohydrates can exist as:
Monosaccharides (single sugar units)
Disaccharides (two sugars linked together)
Polysaccharides (long chains of sugars)
These sugars are made up of carbon, hydrogen, and oxygen, and they’re hydrophilic — meaning they dissolve easily in water thanks to their many hydroxyl (-OH) groups.
Monosaccharides: Simple Sugars
Monosaccharides are the simplest type of carbohydrate — single sugar molecules that serve as building blocks for larger carbohydrates.
Glucose (C₆H₁₂O₆) is the most important monosaccharide — it’s the primary energy source for nearly all organisms.
Other common monosaccharides include:
Fructose (fruit sugar)
Galactose (milk sugar)
Ribose and Deoxyribose, which are found in RNA and DNA, respectively
These molecules typically contain 3 to 7 carbon atoms, and are categorized as:
Pentoses (5-carbon sugars)
Hexoses (6-carbon sugars)
Because of their solubility and small size, monosaccharides move easily through the bloodstream or plant sap.
Disaccharides: Double Sugars
Disaccharides are formed when two monosaccharides bond during a dehydration reaction, which removes a water molecule.
Common examples include:
Sucrose (glucose + fructose): table sugar, transported in plants
Lactose (glucose + galactose): found in milk
Maltose (glucose + glucose): used in brewing and digestion
Some people are lactose intolerant, meaning they lack the enzyme lactase needed to digest lactose — a great example of how enzyme function ties into carbohydrate metabolism.
Polysaccharides: Complex Carbohydrates
Polysaccharides are long chains of monosaccharides (usually glucose), and they fall into two main roles:
Energy Storage:
Starch: how plants store glucose (e.g., in potatoes or grains)
Can be unbranched (amylose) or branched (amylopectin)
Glycogen: how animals (including humans) store glucose, especially in the liver and muscles
Highly branched for faster breakdown when energy is needed
Controlled by hormones like insulin
These storage molecules are insoluble in water and too large to pass through membranes, making them ideal for long-term storage without disrupting cell function.
Structural Polysaccharides
Some polysaccharides aren’t for energy — they provide support and structure instead:
Cellulose: found in plant cell walls
The most abundant organic molecule on Earth
Indigestible by humans, but serves as fiber in our diet
Chitin: found in fungal cell walls and the exoskeletons of insects, crabs, and lobsters
Has antibacterial and antiviral properties
Used in medicine (e.g., wound dressings), cosmetics, and agriculture
Peptidoglycan: found in the cell walls of bacteria
Contains a sugar backbone plus short amino acid chains for extra rigidity
🧈 Lipids: Long-Term Energy, Cell Membranes, and More
Lipids are a diverse group of organic molecules that don’t dissolve in water. That’s because most lipids are made of nonpolar hydrocarbon chains — meaning their electrons are evenly shared and they can’t form hydrogen bonds with water. This hydrophobic nature is key to their role in energy storage, insulation, and building cell membranes.
Let’s explore the major types of lipids: triglycerides, phospholipids, steroids, and waxes.
Triglycerides: Fats and Oils for Long-Term Energy
Triglycerides are the lipids we commonly refer to as fats and oils. They’re made up of:
One glycerol molecule (a 3-carbon compound with hydroxyl groups)
Three fatty acids, which are long hydrocarbon chains ending in a -COOH (carboxyl group)
These molecules are formed through a dehydration reaction and broken down by hydrolysis, just like other macromolecules.
Saturated vs. Unsaturated Fats:
Saturated fatty acids have no double bonds — they’re “full” of hydrogen and pack tightly. Solid at room temp (e.g., butter).
Unsaturated fatty acids have one or more double bonds, creating kinks that prevent tight packing. Liquid at room temp (e.g., olive oil).
Some unsaturated fats exist in a trans configuration (trans fats), which affects how they behave in the body and has been linked to health concerns.
Why Fat Is Efficient for Energy Storage:
Fat contains more energy-rich C-H bonds than carbohydrates
Fat takes up less space — no water is stored with fat droplets
Animals like birds and mammals use fat for insulation and fuel, especially in cold environments or during migration
Phospholipids: The Foundation of Cell Membranes
Phospholipids are modified triglycerides — they still contain glycerol and two fatty acids, but the third fatty acid is replaced by a polar phosphate group.
This structure gives phospholipids:
A hydrophilic head (attracted to water)
Hydrophobic tails (repelled by water)
In water, phospholipids spontaneously form a bilayer, with heads facing outward and tails tucked inside — like a molecular sandwich. This bilayer makes up the plasma membrane that surrounds all cells and internal organelles.
Thanks to their shape and chemistry, phospholipids are critical for cell structure and function. They also keep membranes fluid and selectively permeable, allowing cells to control what enters and exits.
Steroids: Hormones and Membrane Stability
Steroids are lipids with a completely different structure — they have four fused carbon rings rather than long chains.
Key examples include:
Cholesterol: stabilizes animal cell membranes and serves as a precursor for other steroids
Testosterone and Estrogen: sex hormones that regulate reproduction and development
Even though testosterone and estrogen have similar core structures, their functional groups give them very different effects on the body.
⚠️ Note: While cholesterol is essential, excess cholesterol can build up in blood vessels, contributing to high blood pressure and heart disease. That’s why balance is key.
Waxes: Protection and Waterproofing
Waxes are formed when long-chain fatty acids bond with alcohols. They’re:
Solid at room temperature
Water-resistant
Highly stable
Waxes are found:
In plants: forming a cuticle that prevents water loss
In animals: for skin, fur, and feather maintenance
In humans: as earwax, which protects the ear canal from dirt, bacteria, and insects
In bees: as beeswax, used to build honeycomb cells
🧬Proteins: Structure, Function, and Folding
Proteins are often described as the workhorses of the cell — and for good reason. They make up nearly half the dry weight of your cells and carry out almost every essential task in the body. From building tissue to defending against infection, no other macromolecule matches the diversity of roles proteins play.
But what gives proteins this versatility? It all comes down to their structure — which is determined by the unique sequence and chemical properties of their building blocks: amino acids.
What Are Proteins Made Of?
Proteins are polymers made of amino acids, linked together by peptide bonds. Each amino acid contains:
An amino group (-NH₂)
A carboxyl group (-COOH)
An R group (also called a side chain) that varies between amino acids
There are 20 different amino acids, each with a different R group. Some are hydrophilic (water-attracting), others are hydrophobic (water-repelling). Some can form ionic bonds, while others — like cysteine — can form strong disulfide bonds (-S-S-).
These variations in chemistry affect how the amino acids interact with each other — and therefore, how the protein folds and functions.
How Are Proteins Built?
Proteins form when amino acids link through dehydration reactions, forming peptide bonds. A short chain of amino acids is called a peptide, and a long chain is called a polypeptide.
Once the polypeptide folds into a specific shape, it becomes a functional protein.
The Four Levels of Protein Structure
Protein function depends entirely on structure — and proteins can have up to four levels of organization:
1️⃣ Primary Structure:
The linear sequence of amino acids
Like letters in a word, changing even one amino acid can change the entire protein
2️⃣ Secondary Structure:
Local folding into alpha helices or beta pleated sheets
Caused by hydrogen bonding between nearby backbone atoms
3️⃣ Tertiary Structure:
The overall 3D shape of a single polypeptide
Held together by hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges
Most enzymes and globular proteins have this structure
4️⃣ Quaternary Structure:
Some proteins are made of more than one polypeptide chain
Example: Hemoglobin, which has four subunits
If any level of structure is disrupted, the protein can become nonfunctional.
Denaturation: When Proteins Lose Their Shape
Proteins need the right temperature and pH to maintain their shape. High heat or changes in pH can cause a protein to denature — meaning it unravels and loses function. If too many proteins denature, cells can’t survive.
Protein Folding and Disease
Protein folding is a high-stakes process. Specialized helper proteins, called chaperones, assist in folding new proteins correctly and can even help fix misfolded ones.
When folding goes wrong:
Diseases like cystic fibrosis and Alzheimer’s can result
A group of fatal brain disorders called TSEs (e.g., mad cow disease) are now believed to be caused by prions — misfolded proteins that trigger other proteins to misfold
The Many Roles of Proteins in the Body
Proteins are incredibly versatile. Here are just a few of their vital roles:
Function | Example |
Metabolism | Enzymes speed up reactions (e.g., amylase) |
Support | Keratin (hair/nails), Collagen (tendons/skin) |
Transport | Hemoglobin carries oxygen; membrane proteins regulate entry/exit |
Defense | Antibodies fight infection |
Regulation | Hormones like insulin and growth hormone |
Motion | Actin and myosin allow muscle contraction |
Wherever life is happening in the body, proteins are involved.
🧬 Nucleic Acids: The Instructions for Life
Every cell in your body contains a detailed instruction manual — and that manual is written in nucleic acids.
Nucleic acids are large biological molecules that store and transmit genetic information, control how cells behave, and direct the production of proteins. The two main types are:
DNA (Deoxyribonucleic Acid)
RNA (Ribonucleic Acid)
What Are Nucleic Acids Made Of?
Like proteins and carbohydrates, nucleic acids are polymers, made up of repeating monomers called nucleotides.
Each nucleotide contains:
A 5-carbon sugar (ribose or deoxyribose)
A phosphate group
A nitrogenous base
There are two types of nitrogenous bases:
Purines (double-ring): Adenine (A) and Guanine (G)
Pyrimidines (single-ring): Cytosine (C), Thymine (T), and Uracil (U)
📌 DNA uses A, T, C, G
📌 RNA uses A, U, C, G (U replaces T)
DNA: Long-Term Storage of Genetic Information
DNA contains the instructions for making proteins and for copying itself. Its structure is a double helix — two strands twisted around each other, with hydrogen bonds between complementary base pairs:
A pairs with T
G pairs with C
This complementary base pairing ensures that DNA can be accurately replicated — a critical process for cell division and heredity.
RNA: The Messenger and Helper
RNA plays many roles in helping the cell carry out instructions stored in DNA.
Key types of RNA include:
mRNA (messenger RNA): Carries the genetic code from DNA to the ribosome
tRNA (transfer RNA): Helps match the correct amino acids during protein synthesis
rRNA (ribosomal RNA): Forms part of the ribosome and catalyzes peptide bond formation
RNA is usually single-stranded, and it can fold into complex shapes to carry out its functions.
ATP: The Energy Currency of the Cell
Not all nucleotides are used to build DNA or RNA. One very important nucleotide is ATP (Adenosine Triphosphate).
ATP consists of:
Adenine (a nitrogen base)
Ribose (a sugar)
Three phosphate groups
Those last two phosphate bonds are high-energy. When the final phosphate group is removed through hydrolysis, energy is released — and the molecule becomes ADP (Adenosine Diphosphate).
Cells use this released energy to power:
Enzyme reactions
Muscle contractions
Nerve signals
Macromolecule synthesis
Cell division
Just like you spend money for goods and services, cells “spend” ATP to do work — that’s why ATP is known as the energy currency of the cell.
Ready to Review It All in One Place?
You’ve just walked through the full breakdown of water, acids and bases, carbohydrates, lipids, proteins, and nucleic acids — and how they all come together to form the chemistry of life.
To help you review faster and study smarter, I created a colorful, student-friendly Biochemistry Basics Summary Sheet. It’s perfect for:
Visual learners
Exam prep
Quick concept checks
Teaching in class or tutoring
👇 Download your free summary sheet below:
and keep it as your go-to guide for all things macromolecules!
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