BIO-249 Lecture Exam 2: Chemistry & Biomolecules

1. What are the three subatomic particles that make up an atom?

2. How are protons, neutrons, and electrons arranged in an atom?

3. What subatomic particles make up the nucleus of an atom?

4. What does it mean for an atom or molecule to be ‘electroneutral’?

1. Subatomic Particles

   1. Neutron: neutral charge

   2. Proton: positive charge

   3. Electron: negative charge

2. Arrangment

   • Nucleus: Neutron & proton

   • Electron cloud: electrons orbit the nucleus in orbitals

3. Electroneutral

   • Net charge of zero

In a sentence, define what a chemical element is. Name the four major elements that comprise the human body.

• Element: has a unique atomic number

• 4 Major Elements

  1. Carbon

  2. Hydrogen

  3. Oxygen

  4. Nitrogen

In a sentence or two, describe the octet rule for electrons

• The tendency of atoms to prefer to have eight electrons in the valence shell

• When atoms have fewer than eight electrons, they tend to react and form more stable compounds

• Atoms can lose or gain electron to acheive the octet rule

What is an ion, cation, and anion? Are these atoms electroneutral?

• Ion: charged atom

• Cation: positively charged ion

• Anion: negatively charged ion

• NONE of them are electroneutral

In a sentence or two, describe what a molecule is and what a chemical bond is.

• Molecule: two or more atoms bonded together by attractive forces

• Chemical bond: connects two or more atoms and formed when atoms donate OR share their electrons

• Ionic bond definition

• Covalent bond definition

• Ionic Bond: when electrons are DONATED or STOLEN hehehe

  • Metal and nonmetal atoms

• Covalent Bond: when electrons are SHARED between atoms

  • nonmetal atoms

• Polar molecule definition

• Nonpolar molecule definition

• Classify water’s polarity

• Polar Molecule: uneven share of electrons

• Nonpolar: even distribution of electrons

• Water is polar

  • electrons are MORE attracted to oxygen

Hydrogen bond definition

• Hydrogen Bonding: temporary bonds between polar MOLECULES

• Covalent & ionic bonds connect ATOMS, whereas hydrogen bonds connect MOLECULES

What happens to ionic compounds (e.g., Sodium Chloride) when mixed in water? What happens to polar molecules when mixed in water?

• Ionic compounds break up into individual ions

  • the hydrogen bonds are stronger than the ionic bonds, thus they break them apart

  • Lots of H₂O molecules surround the ions

• Polar molecules DISSOLVE in water/polar solvent

  • the covalent bonds are stronger than the hydrogen bonds, so the polar molecules will still stay in tact

  • The molecule WILL NOT be broken down into its individual atoms

If a molecule is polar, is it hydrophillic or hydrophobic?

Hydrophilic

Do polar and nonpolar molecules “mix well” in a water solution?

No, they separate into distinct layers due to their polarity

What is a chemical reaction, and what are the reactants and products of a chemical reaction?

• Chemical Reaction:

  • Interactions between different molecules or atoms

  • Creating OR destroying bonds

• Reactants: Molecules before a chemical reaction

• Products: molecules after a chemical reaction

What are the three basic types of chemical reactions (each described in a sentence)? Note: See lecture.

1. Decomposition: breaking a compound and its bond into individual atoms

   • Digestive processes (fats & proteins)

2. Synthesis: creating compound and forming new bonds

   • Building fuel sources (fat, muscle proteins, etc)

3. Displacement/exchange: redox reactions and acid/base reactions

• What are 2-3 factors that can change the rate of chemical reactions in the human body?

• Which of these two is more likely to change within the human body?

• Chemical Rate Factors

  • ALL are directly proportional to the rate

    1. Temperature

       • Fluxtuates

    2. Pressure

       • stays consistent

    3. Concentration

       • Constant changes in the body

• What is a solution?

• What is the solute and solvent of a solution?

• Solution

  • Contains a solvent and a solute

• Solute: the thing being dissolved

• Solvent: the dissolving agent

• In the lecture, what are the two ways we can describe the concentration of a solution?

• What is a mole?

• How do we define molarity?

• How is molarity expressed in units?

• Concentration

  1. Mass/volume

     • g/L OR mg/mL

  2. Molarity

     • moles/L or M

• Mole: an atomic mass in grams of a certain substance

  • 180 g of glucose = 1 mole of glucose

• Molarity: number of moles of solute per liter of solution

  • moles/L or M

• What are the basic definitions (1 sentence) of an acid and a base?

• When an acid dissolves in water, what does it release typically?

• When a base dissolves in water, what does it typically release?

• Acids: give off hydrogen ions

• Bases: remove hydrogen ions

  • produces hydroxide as well

• What is pH?

• What does it mean for a solution to have a low or high pH?

• pH: measure of how much hydrogen ions are in a solution

• Low pH

  • HIGH concentration of [H⁺]

  • acidic

• High pH

  • LOW concentration of [H⁺]

  • basic

• What is the range of a pH scale?

• What is considered a neutral pH?

• pH Range

  • 0-14

• Neutral pH: 7

• Why does pH have to be kept constant within the human body?

• What happens to proteins and cells when pH changes?

• Constant pH

  • Proteins will be denatured if the pH deviates from their normal range

• pH changes lead to protein denaturation

  • Protein loses shape & cannot function

• Describe what carbohydrates are in a sentence or two.

• What elements are they typically composed of?

• Are carbohydrates polar or nonpolar?

• In a sentence or two, describe the general function of carbohydrates.

• Carbohydrates: energy source for humans

  • formed from monosaccharides (simple sugars)

• Elements

  • Carbon, hydrogen, & oxygen

• ALL carbohydrates are POLAR → hydrophilic

What is a monosaccharide, disaccharide, and polysaccharide? Give example molecules for each type of carbohydrate.

• Monosaccharide: simplest unit of sugar

  • Fructose

  • Glucose

  • Galactose

• Disaccharide: two sugar molecules bonded by covalent bonds

  • Sucrose: glucose + fructose

  • Maltose: glucose + glucose

  • Lactose: galactose + glucose

• Polysaccharide: multiple monosaccharides bonded together

  • Chitin: in invertebrate animals

  • Glycogen: stored glucose molecule, found in the muscles & liver

  • Cellulose: plant cell walls

  • Starch: stored energy for plants

• Describe what lipids are in a sentence or two.

• Are lipids polar or nonpolar?

• Based on its atomic composition, how is it similar and different from carbohydrates?

• Lipids: fatty nonpolar, & hydrophobic compounds that serve as an energy source

• Lipids vs Carbohydrates

  • Similarities

    1. Chemical composition

       • Carbon, hydrogen, oxygen

    2. Energy source

  • Differences

    1. Lipids = nonpolar

    2. Lipids can be saturated or unsaturated (double bond)

For triglyceride, identify the glycerol part and what part is the fatty acid chain

• Triglyceride Function

  • Most common lipid form → used as a slow source of energy

• Glycerol

  • alcohol group acts as the backbone of triglycerides

• Fatty Acid Chain

  • long carbon skeleton with a carboxyl group at the end

Describe three representative lipids found in the body and their respective function

1. Triglycerides: slow source of energy

   • insulates the body & protects internal organs

2. Phospholipids: animal cell membrane that protects the cell from the external environment

3. Steroids: cell signaling

   • Ex: Cholesterol: fluidity in the animal cell membrane & precursor to hormones

• Describe what proteins are in a sentence or two

• What is the basic, repeating molecule that makes up proteins?

• What makes one amino acid unique from another amino acid?

• Protein Function

  • Defense, catalysts, transport, cellular communication, structural support, etc

• Amino Acids: building blocks of proteins

• R group

  1. differs with each amino acid

  2. Determines the unique characteristics of a particular amino acid → determines function

• What is a peptide bond?

• What is a chain of amino acids called?

• What is the specific name of the reaction that forms the peptide bond, and its chemical reaction (synthesis, decomposition, or exchange)?

• Peptide Bond

  • Amino group joins the carboxyl group via a dehydration rxn

  • Covalent bond that joins amino acids → forms a polypeptide

• Polypeptide: a chain of amino acids linked together by peptide bonds

• Synthesis/Dehydration Reaction

  • forms the peptide bond

Protein Structure Levels

1. Primary Structure: chain of amino acids

   • linear chain

2. Secondary Structure: pleated sheet/helix structure

   • amino acids folds onto itself

   • intermolecular forces (hydrogen bonds)

3. Tertiary Structure: specialized structure & shape → niche function

   • intermolecular interactions between R chains of the amino acids

     • hydrophobic interactions

     • hydrogen bonding b/w polar sides

     • disulfide bridges (covalent bonding)

4. Quaternary Structure: multiple polypeptide chains

   • megaproteins (hemoglobin and collagen)

• When a protein loses its shape, we say the protein has been _______.

• What two properties of water can change the shape of protein

• Denatured

• Water denaturing properties

  1. Temperature

  2. pH

• What are active/binding sites on proteins?

• What is a ligand for a protein?

• Ligand Binding Steps

• Active Sites: location where the protein accepts the ligand

• Ligand: signal molecule that initiates a cellular process by binding to the protein’s active site

• Ligand Process

  1. Ligand binds to the protein’s active site

  2. Protein changes its shape & transforms the ligand

  3. Protein reverts back to its normal shape & ligand unbinds & leaves

If the shape of the protein changes, how does it affect the function of the protein?

• Location of protein shape change determines the protein’s functionality

  • Active site: changes protein function

  • non-active site: no effect

Enzyme Function

• Selective accerlation of chemical reactions

• digestive enzymes catalyze the hydrolysis of bonds in food molecules

Protein Functions

1. Catalyst: accelerates a chemical reaction

   • substrate binds to the protein’s active site → transforms into products

2. Membrane Transporters & Receptors

   • Transporters

     • Channel proteins for water

     • Gated channels open/close in response to signals

   • Receptors

     • signal attaches to the protein → creates an internal signal for the cell to respond with

3. Signal Molecules: cellular response/communication

   1. Cell to cell

   2. Bloodstream

4. Binding Proteins: binds to nonpolar & hydrophobic substances (can’t be dissolved in water)

   • lipids

   • O₂ (Fe in red blood cells)

   • Lipoprotein: holds onto lots of fat

     • uses LDL to bind to fat

5. Defensive Proteins: immune system produces immunoglobulins/antibodies

   • immunoglobulins: glycoproteins produced by the plasma cells that detect pathogens

6. Regulatory Proteins: regulate gene expression

   • proteins inside the nucleus that bind to DNA to initiate or stop gene expression

7. Structural proteins: support (resilience & strength)

   • active sites aren’t used

   • microfilaments, intermediate filaments, microtubules, etc

• What are DNA and RNA and their function?

• What is the basic repeating molecule that makes up DNA and RNA?

• What are the four different nucleotides that make up DNA, and what are the four different nucleotides that make up RNA?

• DNA & RNA Function

  • Hold genetic information for our cells

  • RNA: single-stranded & contains uracil

• Nucleic Acids

  • monomer for DNA & DNA

  • Sugar (deoxyribose or ribose), phosphate group, & nitrogen base

• Nucleotides

  • DNA: G, C, T, A

  • RNA: G, C, U, A

What is ATP, and how is it different than ADP?

• ATP Function

  • Cellular energy currency

  • Remove a phosphate group to release energy

• ATP vs ADP

  • ATP → ADP: releasing/creating energy

  • ADP → ATP: spending energy