AP Biology: Unit 1

What is the basic structure of water?

Two hydrogen atoms bonded to an oxygen atom in an upside down V formation by a covalent bond

Why is water a polar molecule?

Oxygen is more electronegative than hydrogen, causing an unequal sharing of electrons which gives hydrogen a slightly positive charge and Oxygen a slightly negative charge.

How does water form hydrogen bonds?

The partially negative oxygen atom in one water molecule is attracted to the partially positive hydrogen atom in another, forming weak hydrogen bonds between water molecules.

 Compare adhesion and cohesion. 

Cohesion is waters ability to bond to itself, while adhesion is its ability to bond to other polar molecules.

Describe water’s specific heat. Why is this important?

Water has a high specific heat, meaning it can absorb a lot of heat before its temperature changes. This is important because it helps regulate temperature in organisms and environments.

Why is water considered the ultimate solvent?

Water is considered the ultimate solvent because of its polarity, allowing it to dissolve a wide range of substances, especially ionic compounds and polar molecules.

What are some of carbon’s fundamental characteristics?

Carbon can form four covalent bonds, allowing it to build complex molecules. It can form single, double, or triple bonds and can bond to a variety of atoms, including hydrogen, oxygen, nitrogen, and other carbon atoms.

Why is Carbon found in all living organisms?

Carbon is versatile in forming stable bonds with many elements, making it the backbone of biological molecules like proteins, carbohydrates, and nucleic acids.

What types of bonds do carbon atoms often form with other atoms? Explain why.

Carbon often forms covalent bonds (single, double, or triple) with other atoms because it has four electrons in its outer shell, allowing it to share electrons to achieve a stable configuration.

Dehydration Synthesis

An enzyme removes a hydroxyl group from one molecules and a hydrogen atom from another. A covalent bond forms between the molecules, and water also forms. This is how macromolecules are made.

Hydrolysis

An enzyme attaches a hydroxyl group and a hydrogen atom (both from water) at the cleavage site. Breaks down macromolecules.

Hydroxyl Group

 (-OH), found in carbohydrates and nucleic acids

Carbonyl Group

 (C=O), found in Carbs and lipids

Carboxyl

 (-COOH), Found in proteins and fatty acids

Amine

(-NH₂), Found in amino acids

Phosphate

(-PO₄³⁻), Found in nucleic acids and phospholipids

Methyl

(-CH₃): Found in Lipids and amino acids

A. Carbohydrates

- Monomer Name: Monosaccharides (e.g., glucose, fructose)

- Function: Provide energy, store energy, and provide structural support in cells.

- Example: Glucose (C₆H₁₂O₆), used as a primary energy source in cellular respiration.

- Composition: Carbon (C), Hydrogen (H), and Oxygen (O) in a general ratio of 1:2:1 (C₆H₁₂O₆).

B. Lipids

- Monomer Name: Fatty acids and glycerol (though lipids don't have a single repeating monomer like proteins or carbohydrates).

- Function: Store long-term energy, make up cell membranes, and act as signaling molecules.

- Example: Triglycerides (fats and oils), made of three fatty acids and one glycerol.

- Composition: Primarily Carbon (C), Hydrogen (H), and Oxygen (O), but in a much lower oxygen ratio than carbohydrates.

C. Proteins

- Monomer Name: Amino acids (e.g., leucine, glycine)

- Function: Serve as enzymes, structural components, transport molecules, and in cellular communication.

- Example: Hemoglobin, which transports oxygen in the blood.

- Composition: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), and sometimes Sulfur (S).

D. Nucleic Acids

- Monomer Name: Nucleotides (e.g., adenine, thymine, cytosine, guanine for DNA; adenine, uracil, cytosine, guanine for RNA)

- Function: Store and transfer genetic information, guide protein synthesis.

- Example: DNA (Deoxyribonucleic acid), which stores genetic instructions for the development and functioning of living organisms.

- Composition: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), and Phosphorus (P).

Simple Carbohydrate

 Monosaccharides (e.g., glucose) are single sugar molecules.

 Polysaccharides

(e.g., starch) consist of long chains of monosaccharides.

What are the main components of a carbohydrate?

Carbon, hydrogen, and oxygen in a 1:2:1 ratio

What are lipids composed of?

Lipids are composed primarily of carbon, hydrogen, and oxygen, with a higher proportion of carbon and hydrogen compared to oxygen.

Saturated Fats

No double bonds between carbon atoms; solid at room temperature

Unsaturated Fats

One or more double bonds; liquid at room temperature.

What are the basic components of a protein?

Proteins are made of amino acids, which have an amino group, carboxyl group, hydrogen atom, and an R group attached to a central carbon atom.

Primary

The linear sequence of amino acids.

Secondary

 Local folding patterns like alpha helices and beta sheets due to hydrogen bonds.

Tertiary

 The overall 3D structure of a single polypeptide chain (protein) formed by interactions between side chains.

Quarternary

The arrangement of multiple polypeptide chains into a functional protein.

How do enzymes work?

Enzymes lower the activation energy needed for a reaction, speeding up the reaction by providing an alternative reaction pathway.

Describe the trends observed in the enzyme graph to the right. Why does the line with an enzyme level off?

An enzyme speeds up a chemical reaction. The graph levels off because once the substrate runs out the enzyme has nothing else to react with.

 How could you speed up an enzyme-catalyzed reaction? Slow down? 

Speed Up: Increase temperature (up to a point), increase substrate concentration.

Slow Down: Lower temperature, add inhibitors.

What causes enzymes to become denatured?

High temperatures, extreme pH levels, or chemical inhibitors can denature enzymes, causing them to lose their shape and function.

DNA

Double-stranded, contains deoxyribose, uses thymine. Contains the instructions (genes) for making proteins and is transcribed into mRNA.

RNA

Single-stranded, contains ribose, uses uracil. mRNA carries the instructions from DNA to the ribosome, where tRNA helps assemble the correct amino acids into a protein.

Hershey and Chase

Proved DNA is the genetic material.

Avery and MacLeod

 Identified DNA as the substance responsible for transformation in bacteria.

Watson and Crick

Developed the double helix model of DNA.

Rosalind Franklin and Maurice Wilkins

Provided key X-ray diffraction data for the DNA structure.

Peptide Bonds

Covalent bonds that link amino acids together, forming the primary structure (sequence) of the protein.

Hydrogen Bonds

 Stabilize secondary structures (like alpha helices and beta sheets) by forming between polar groups within the protein.

Ionic Bonds

Form between oppositely charged side chains, helping stabilize the protein’s 3D (tertiary) structure.

 Structure of Proteins Affect on Regulation of Enzyme Activity

 The shape of an enzyme controls how well it works. If its structure changes, it may not bind to its target (substrate) properly, stopping or slowing down the reaction. Enzymes can be regulated by molecules that change their shape and either block or enhance their activity.

Protein structures effect on Cell Signaling

Proteins involved in cell communication need a specific shape to bind to signaling molecules. If their shape changes, they may not work correctly, disrupting signals between cells. The correct structure allows proteins to fit with their signaling partners and transmit signals properly.

Phospholipids

- Structure: Have a water-loving head and water-hating tails, forming two layers.

- Function: Act as a barrier that controls what goes in and out of the cell.

Proteins

- Structure: Found inside or on the membrane.

- Function: Help move things in and out of the cell, receive signals, and communicate with other cells.

Cholesterol

- Structure: Sits between the phospholipids.

- Function: Keeps the membrane flexible and stable.

Composition of Proteins

Proteins are made of amino acids, which contain carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur. They are linked by peptide bonds.

Role of Proteins in Membrane Structure

Proteins are embedded in the cell membrane and help maintain its structure.

Some proteins act as channels or carriers to move substances in and out of the cell. Active transport proteins use energy to move molecules against their concentration gradient.