AP Biology Unit 1: Chemistry of Life Notes Pt. 1

Intro to Chemistry of Life

1) How do you define electronegativity based on what you have watched in the video?

- Electronegativity is the measure of the attraction of an atom for bonding electrons in molecules compared to that of other atoms. The higher the value, the more the atom wants the electron.

2) Is Hydrogen bonding an intra-molecular bonding or intermolecular one? How does hydrogen bonding form?

- Hydrogen bonding is an intramolecular force, as well as an intermolecular force. This means that there can be hydrogen bonding that impacts both atoms on a molecular level as well as hydrogen atoms of other molecules.

- Van Der Waals forces are formed by interactions between charged molecules. 

Water Molecule Properties

1- What creates the attractions between water molecules?

The attraction between water molecules is created due to the structure of the molecules and the hydrogen bonding that is caused by the attraction. They are organized randomly below the surface, but the surface is organized in a way that makes a smooth surface. All of the attraction is towards the center of the water droplet. This gives the surface of the water droplet tension so it seems to stick to itself. 

 2- Describe how hydrogen bonding is important to cohesion. Give an example of how cohesion and adhesion are important to living things. 

Hydrogen bonding is important to cohesion because it allows for water molecules to bond together, to make larger droplets that cause surface tension. With this surface tension, animals like water striders are able to survive comfortably on the water surface. Adhesion allows for the water molecules to bond with the xylem tube in plants to help it move up the plant so water is provided throughout the plant. 

3- Describe how hydrogen bonding is important to the fact that ice floats. Give an example of how this property helps sustain life. 

If a lake has ice, and the ice was denser than the water, it would sink to the bottom of the lake. Then the top layer would freeze, and this would repeat. Eventually, the whole lake would be frozen. Hardly any organisms would be able to survive these severe conditions. With ice having a less density than water, the organisms in the lake are able to survive the harsh winter.

4- Define cohesion and adhesion

- Cohesion is the property of water that allows it to stick to itself. 

- Adhesion is the property of water that allows it to stick to substances that are either objects or surfaces other than itself. 

Water as a Solvent

1-Define the following terms: Solution, solvent, solute, hydration shell and dissociation.

• Solution: A homogeneous mixture of solvent and solute

• Solvent: A substance that can dissolve other molecules and compounds (solutes)

• Solute: Molecules and compounds dissolved in a substance (solvent)

• Hydration shell: A three dimensional sphere of water molecules formed to break ions 

• Dissociation: process where a compound or molecule breaks apart to form ions

2- Briefly describe the process of dissolving salt into water. (should not be less than 3 lines)

Salt molecules are dropped into the water. The water as a molecule uses its positively charged hydrogen to pull apart the chlorine ion. It also uses its negatively charged oxygen to pull apart the sodium. The water stays intact while the salt is dissociated into two ions. H is positive, O is negative, Na is positive, Cl is negative (Opposites attract)

3- What happens to ionic bonding of the salt and hydrogen bonding between water molecules?

Ionic bonding between the salts are dissociated and become ions. Hydrogen bonding also weakens since water molecules create hydration shells instead. 

Organic Molecule Worksheet 

1. What are the 3 main elements

   1. Carbon (C)

   2. Hydrogen (H)

   3. Oxygen (O)

2. What are the other elements

   1. Nitrogen (N)

   2. Sulfur (S)

   3. Phosphorus(P)

3. Diagram of Carbon

   1. Valence electrons

   2. 4 covalent bonds

4. Molecular vs Structural

   1. Molecular - Elements are listed with a subscript for number of corresponding elements.

   2. Structural - Model with location of each element, and each bond is represented.
      

Building an Organism Worksheet

1) Main source of energy for animals

1. Food

2) Main source of energy for plants

1. Carbon - atmosphere

2. Nitrogen and phosphorus - soil

3) Macromolecule components

1. Proteins

2. Nucleic Acids

3. Carbohydrates

4. Lipids

• Carbon and its importance: Carbon atoms allow for 4 covalent bonds to take place, which is the most any atom can offer. In these bonds, there is energy stored which is saved when the organism needs energy. In animals, energy is stored as glycogen, and in plants, energy is stored as starch. This energy is used for carbohydrates, proteins, lipids, and nucleic acids.

Carbohydrate Chemistry 

1. Major function of monosaccharides

   1. Provide energy for cell metabolism

   2. Join together to form carbohydrate macromolecules

2. Ribose vs glucose

   1. Ribose - pentose (5 carbon) monosaccharides

   2. Glucose - hexose (6 carbon) monosaccharides

3. Isomer definition and importance

   1. Isomers are compounds with the same chemical formula but different arrangement of atoms. They are important because each isomer has different properties.

Condensation and hydrolysis of sugars

1. Disaccharide sugars formed and broken down

   1. Formed: Condensation reactions - a water molecule is released (dehydration)

   2. Broken down: Hydrolysis reactions - a water molecules is added 

2. Name the reaction

   1. Condensation reactions (Disaccharide + Water)

   2. Hydrolysis reactions (Two monosaccharides)

3. Keep the center oxygen molecule out of both monosaccharide

Lipids

1. Main components of symbolic triglyceride

   1. Glycerol

   2. Ester bond

   3. Fatty acids

2. Why do lipids have high energy content?

   1. Triacylglycerols are highly concentrated stores of metabolic energy because they are reduced and anhydrous (without water). They are able to provide more than two times the amount of energy the same amount of carbohydrates can provide. The structure of triacylglycerols allows for the fatty acids to break apart from the glycerol through the simple process of hydrolysis. 

3. Fatty acids

   1. Saturated vs unsaturated fatty acids

      1. Saturated bonds only contain single bonds, so it has the maximum number of hydrogen atoms possible. This makes these bonds extremely straight. Unsaturated bonds contain single and double bonds, so it is not fully saturated with hydrogens. This causes the bonds to be bent. 

   2. Relate neutral fat to type of fatty acid present

      1. If a neutral fat contains double bonds, with the maximum amount of hydrogen then the melting point is lower. It is a liquid at room temperature.

4. Describe what happens 

   1. During the esterification (condensation) to produce a triglyceride

      1. Glycerol bonds with a fatty acid. This forms an ester bond and releases water. It is hydrolysis and results in lipids broken down.

   2. When a triglyceride is hydrolyzed

      1. Three water molecules are added to triglyceride to break down the ester bonds. This separates the triglyceride into glycerol and fatty acids. 

5. Biological role of lipids

   1. Source of energy

   2. Metabolism for energy, water, and CO2

   3. fuel of aerobic respiration

   4. Forms cellular membranes

   5. Waterproofing

   6. Shock absorption (cushioning)

   7. Insulation

Nucleic Acid DNA vs RNA

1. Nucleotides present

   1. DNA: Adenine, Thymine, Guanine, Cytosine

   2. RNA: Adenine, Uracil, Guanine, Cytosine

2. Sugars present

   1. DNA: Deoxyribose

   2. RNA: Ribose

3. Molecules only with tag

   1. DNA has thymine. H at carbon 2.

   2. RNA has uracil. OH is at carbon 2.

4. Number of Strands
   1. DNA is double stranded
   2. RNA is single stranded

Amino Acids

1. Structure and properties

   1. Each amino acid in protein is unique since they have different R groups. Although all amino acids contain an amine group and a carboxyl group, each amino acid has its own R group to distinguish them from others.

   2. The primary structure of a protein is a linear chain. They have peptide bonds to connect the amino acids, which are composed of an amine group, a carboxyl group, a carbon atom, a hydrogen atom, and an r group. 

   3. The primary structure is determined by the R group. It determines how the amino acid would interact with other amino acids and determine how the amino acid chain folds up into a functional protein. 

   4. The sequence and composition influences how a protein folds up since the R group determines how the amino acid is folded up. The R group is important since it gives the structure its unique traits. 

2. Peptide Bonds

   1. Amino acids are joined together by peptide bonds which are created between the carboxyl group of one amino acid and the amine group of another amino acid. 

   2. Peptide bonds are formed through condensation. This causes two amino acids to join and become a dipeptide, through the release of a water molecule.

   3. Bond between the carbon and nitrogen. 

   4. Di- and Polypeptides are broken down into amino acids with the presence of water. The water molecule provides a hydrogen and a hydroxyl group, forming two amino acids.

Protein Structure

1. Main feature in each structure

   1. Primary structure (amino acid sequence)

      1. Amino acids are linked by polypeptide bonds to form polypeptides.

   2. Secondary structure (α-helix or β-pleated sheet)

      1. Maintained through hydrogen bonds between neighboring CO and NH groups. Forms within a polypeptide from interaction between amino acids. 

   3. Tertiary structure (Folding of the 2° structure)

      1. Maintained by more distant interactions like disulfide bridges. It forms a three dimensional shape.

   4. Quaternary structure

      1. The arrangement and position of each subunit in a multiunit protein. Interactions between tertiary structure help maintain shape.

2. Proteins and how they can become functional structures

   1. Amino acids are linked through peptide bonds to form polypeptide chains. These chains are structurally maintained (an α-helix or β-pleated sheet) through the use of hydrogen bonds. These α-helix or β-pleated sheets interact through distant interactions, bending it in various places. Finally, when many tertiary structures interact, along with other proteins, it creates a three dimensional structure representing the arrangement and position of each subunit in a multiunit protein.

Protein Shape is Related to Function

1. Using the example of insulin, explain how interactions between R groups stabilize the protein's functional structure

   1. Interactions between R groups stabilize the functional structure for proteins, and in insulin, there are multiple quaternary structures. These structures are stabilized through disulfide bridges between amino acids. In the case of insulin, there is a disulfide bridge between neighboring cystines. This allows the insulin to properly function and stimulate glucose uptake by cells. 

2. Why do channel proteins often fold with non-polar R groups to the channel's exterior and polar R groups to its interior?

   1. Channel proteins often fold so that non-polar R groups (hydrophobic) are in the channel's exterior and polar R groups (hydrophilic) are its interior. This allows for hydrophilic molecules and ions to pass through the channel into the cell, through the membrane. 

3. Why does denaturation often result in the loss of protein functionality?

   1. Denaturation often results in the loss of protein functionality since the chemical bonds holding the protein together are broken. Since these bonds are broken, the protein can no longer hold its three dimensional shape. There are many reasons this occurs, like exposure to heat, and pH unbalance. 

4. Every amino acid has a R group attached to the central carbon. The R group which is also called the side chain provides the amino acid with specific characteristics. This includes the size, charge, and the pH of the amino acid. This will also eventually play a large role when the polypeptide chain is formed and the protein is folded up accordingly. 

Behaviors

1) Provide one example of taxis behavior and one example of kinesis behavior.

- Taxis: Pupil dilation when standing in a dark room and a flashlight is brought close to the eye.

- Kinesis: Wandering around a museum, without a sense of urgency and stopping and looking at paintings that catch your eye.

2) Describe what innate and learned behaviors are. Provide one example and explain the adaptive value of each of these two categories of behavior to an individual animal.

- Innate behavior: Blinking in reaction to eyes drying out. It is a behavior that is necessary for survival that people are born with. 

- Learned behavior: Avoiding to touch hot stoves. Though the reaction of touching a stove and it being hot is an innate behavior, learning from this and avoiding to touch a stove is a learned behavior. Learned behavior allows for the individual to understand their mistake and avoid it since it may hurt their survival chance.