Questions and Answers
What is the chemical reaction that breaks down all the major macromolecules?
Hydrolysis
What is the strongest type of intermolecular bond?
Hydrogen bonds
Why is water a liquid at high temperatures?
Hydrogen bonding holds the water molecules closer together.
What is an amphipathic molecule? Give an example.
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What is a lipid?
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What are the 6 major groups of lipids?
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What is the structure of a tri-glyceride?
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What happens if you add water to an ester group in a tri-glyceride?
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What is important to know about the longer carbon chains in a tri-glyceride regarding water solubility?
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How soluble are shorter chain fatty acids?
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What is special about saturated fatty acids regarding their melting point?
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What is special about unsaturated fatty acids regarding their melting point?
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Explain the phospholipids structure.
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What regions are polar and nonpolar in a membrane?
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Explain glycolipids structure.
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What do steroids look like?
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How do lipids move through the blood despite being insoluble?
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What are the major classes of lipoproteins?
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What are proteins made up of?
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Describe amino acid structure.
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What are the basic amino acids?
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What are the acidic amino acids?
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What are the nonpolar amino acids?
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What is the primary structure of a protein?
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What is the secondary structure of a protein?
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What is the tertiary structure of a protein?
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What is the quaternary structure of a protein?
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What are the five forces that create tertiary structure?
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What levels of structure are disrupted during the denaturation process?
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What is the difference between a proteoglycan and a glycoprotein?
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What is the empirical formula for any carbohydrate?
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Describe the chemical structure of glucose.
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Where is glucose stored in alpha linkages?
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Who stores glucose with beta linkages?
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What molecule is added to glycogen, starch, and cellulose to break off individual glucose molecules?
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What are the four macromolecules?
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What are the three parts of a nucleotide?
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What molecule breaks up nucleic acids into nucleotides?
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What are some other important nucleotides?
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What are minerals?
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What are enzymes?
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What is activation energy?
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An enzyme is typically larger than the substrate.
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Where does a substrate attach to an enzyme?
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What are the two hypotheses of enzyme and substrate interactions?
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One enzyme is tailor-made for one reaction.
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What are saturation kinetics?
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What factors affect enzymatic reactions?
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How do cells regulate enzymes?
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What are the general types of enzyme inhibition?
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What is feedback inhibition?
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What are specific ways in which enzymes are inhibited?
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What is competitive inhibition?
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What is non-competitive inhibition?
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What is irreversible inhibition?
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What is respiration?
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Where does glycolysis take place?
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Does glycolysis require oxygen?
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Is glycolysis poisoned by oxygen?
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What is the net ATP produced by glycolysis?
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What happens to the NADHs at the end of glycolysis if oxygen is not present?
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If oxygen is present, what happens to the products of glycolysis?
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What is the energy cost of transporting one NADH into the mitochondria?
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How many ATPs does each NADH produce during the electron transport chain (ETC)?
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In the mitochondrial matrix, what happens to the pyruvates?
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What are the energetic products of the TCA cycle?
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Overall, aerobic respiration of a single glucose molecule results in a net of how many ATPs?
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What is the electron transport chain (ETC)?
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What is aerobic respiration?
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What is the final electron acceptor in the ETC?
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How are tri-glycerides burned for energy?
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How are proteins burned for energy?
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What is the rule of the ratio of gene to polypeptide?
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How many copies of a gene do prokaryotes have?
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For most genes, how many copies do eukaryotes have?
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What are the three main components of a nucleotide?
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What are the four nitrogenous bases?
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What are the four nucleosides?
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What is the difference between a nucleotide and a nucleoside?
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What are the purines?
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What are the pyrimidines?
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Which carbon is the PO4 group attached to?
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What kind of bond connects the PO4 group to the 3rd carbon on the pentose sugar of the nucleotide chain?
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In a phosphodiester bond, which numbered carbons are connected?
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How do the nitrogenous bases bond to each other?
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How many bonds are formed between A and T?
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How many bonds are formed between C and G?
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Why is replication semi-conservative?
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In what direction does replication occur?
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What enzyme separates the two strands of DNA?
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In what direction does DNA polymerase move?
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In what direction does DNA polymerase polymerize the complementary strand?
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In what direction does the replisome move?
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What is the replisome composed of?
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Which polymerase polymerizes the leading strand?
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Which polymerase polymerizes the lagging strand?
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What are Okazaki fragments?
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How does RNA differ from DNA?
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What are the types of RNA?
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Where is RNA synthesized?
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Study Notes
Hydrolysis and Macromolecules
- Hydrolysis is the chemical reaction responsible for breaking down major macromolecules into their smaller components.
Inter-molecular Bonds
- Hydrogen bonds are the strongest type of intermolecular bonds, while dipole-dipole and Van der Waals forces are weaker.
Water Characteristics
- Water remains a liquid at high temperatures due to hydrogen bonding, which keeps molecules closely packed.
Ampipathic Molecules
- Ampipathic molecules possess both hydrophobic and hydrophilic regions; example: Phospholipid (hydrophilic phosphate group and hydrophobic lipid tails).
Lipids
- Lipids are biological molecules characterized by low solubility in water, commonly referred to as fats.
Major Groups of Lipids
- Key classes of lipids include:
- Fatty acids
- Triglycerides
- Phospholipids
- Glycolipids
- Steroids
- Terpenes (e.g., pine oils, vitamin A).
Structure of Triglycerides
- Triglycerides consist of a glycerol backbone with three fatty acid chains linked via ester bonds.
Hydrolysis of Triglycerides
- Adding water to triglycerides hydrolyzes ester bonds, yielding glycerol and fatty acids, a reaction accelerated by lipases.
Solubility of Fatty Acids
- Longer carbon chains in triglycerides decrease water solubility due to less significant polar carboxylic groups.
Short vs. Long Chain Fatty Acids
- Short-chain fatty acids exhibit slight water solubility, while longer chains are significantly less soluble.
Saturated vs. Unsaturated Fatty Acids
- Saturated fatty acids contain solely single bonds, resulting in a straight chain and higher melting points due to stronger Van der Waals forces.
- Unsaturated fatty acids have one or more double bonds, yielding a lower melting point and potentially oily consistency at room temperature.
Phospholipids Structure
- Phospholipids have a glycerol backbone, with one carbon attached to a phosphate group and two fatty acid chains, forming a bilayer in cell membranes.
Membrane Regions
- In membranes, polar phosphate regions face outward (hydrophilic), while nonpolar fatty acid chains face inward (hydrophobic).
Glycolipids
- Glycolipids include a glycerol backbone with two fatty acid chains and a carbohydrate attached to one carbon.
Steroids
- Steroids are characterized by slightly amphipathic four-ring structures.
Lipid Transport in Blood
- Lipids are transported in the bloodstream via lipoproteins like HDL and LDL.
Classes of Lipoproteins
- Major lipoprotein classes include:
- Chylomicrons (largest)
- VLDLs (very low density)
- LDLs (low density)
- HDLs (high density and smallest).
Protein Composition
- Proteins consist of one or more polypeptide chains formed by amino acids.
Amino Acid Structure
- Amino acids comprise four components:
- Amino group (NH2)
- R group (20 possible variations)
- Carboxylic acid group (COOH)
- Hydrogen atom.
Basic and Acidic Amino Acids
- Basic amino acids: Histidine, Arginine, Lysine.
- Acidic amino acids: Aspartic acid, Glutamic acid.
Nonpolar Amino Acids
- Nonpolar amino acids include Phenylalanine, Leucine, Tryptophan, Methionine, Glycine, Isoleucine, Valine, Alanine, and Proline.
Protein Structures
- Primary structure: Sequence of amino acids and disulfide bond locations.
- Secondary structure: Includes alpha helices and beta sheets.
- Tertiary structure: 3D shape formed by folding.
- Quaternary structure: Assembly of multiple polypeptide chains.
Forces in Tertiary Structure
- Key forces creating tertiary structure include covalent bonds, disulfide bridges, hydrogen bonds, hydrophobic interactions, and Van der Waals forces.
Denaturation Effects
- Denaturation disrupts secondary through quaternary structures.
Glycoproteins vs. Proteoglycans
- Glycoproteins: Made mostly of protein; involved in cell signaling.
- Proteoglycans: Rich in carbohydrates; serve as structural components.
Carbohydrate Empirical Formula
- General empirical formula for carbohydrates is CH2O.
Glucose Structure
- Glucose is an aldehyde with four chiral centers, existing as a six-membered ring.
Glucose Storage
- Animals store glucose in glycogen (alpha linkages); plants store it in starch.
Cellulose Structure
- Plant cell walls contain cellulose, characterized by beta linkages.
Hydrolysis Reaction
- Water breaks glycosidic bonds in glycogen, starch, and cellulose, aided by enzymes like amylase.
Four Major Macromolecules
- The primary macromolecules are proteins, lipids, carbohydrates, and nucleic acids.
Nucleotide Composition
- Nucleotides consist of ribose sugar, a nitrogenous base, and a phosphate group.
Nucleic Acid Breakdown
- Nucleic acids are hydrolyzed to nucleotides using water and the aid of nucleases.
Important Nucleotides
- Key nucleotides include FADH, NADH, ATP, and cyclic AMP.
Mineral Functions
- Minerals are inorganic elements essential for:
- Establishing electrochemical gradients
- Acting as cofactors for proteins
- Forming bone matrix compounds.
Enzyme Characteristics
- Enzymes primarily consist of proteins that accelerate reactions by lowering activation energy.
Activation Energy Definition
- The energy required to break reactant bonds and transition into the product state.
Substrate Interaction
- Substrates bind to enzymes at the active site, which is typically larger than the substrate.
Enzyme Models
- Two hypothesized models for enzyme-substrate interaction:
- Lock and Key Model
- Induced Fit Model.
Enzyme Specificity
- Each enzyme is uniquely designed for a specific reaction, enhancing cellular control.
Saturation Kinetics
- Reaction rates increase with substrate availability until enzyme saturation is reached.
Enzyme Regulation Factors
- Enzyme activity is influenced by optimal temperature and pH levels.
Enzyme Regulation Methods
- Cells regulate enzyme function through:
- Inhibition mechanisms
- Production of inactive forms that activate when required.
Types of Enzyme Inhibition
- Inhibition classifications include feedback inhibition and chemical inhibition (e.g., poisons).
Competitive vs. Non-competitive Inhibition
- Competitive inhibition involves competing for the active site, while non-competitive inhibition modifies enzyme shape, reducing substrate affinity.
Irreversible Inhibition
- Irreversible inhibitors covalently bind to the active site, making it permanently inactive.
Respiration Definition
- Respiration encompasses energy-requiring metabolic stages.
Glycolysis Location
- Glycolysis occurs in the cytosol and does not require oxygen.
Glycolysis Products
- Net yield from glycolysis includes 2 ATP, 2 NADH, and 2 pyruvate molecules.
Anaerobic Fate of NADHs
- In the absence of oxygen, NADH is oxidized back to NAD+ via fermentation, yielding CO2 and either ethanol or lactic acid.
Aerobic Fate of Glycolysis Products
- In aerobic conditions, glycolysis products transition into the mitochondria.
Mitochondrial NADH Transport Cost
- Transporting each NADH into the mitochondria requires 1 ATP.
ATP Yield from NADH
- Each NADH generates 3 ATPs during the electron transport chain (ETC).
Pyruvate to Acetyl-CoA Conversion
- Pyruvates are converted to acetyl-CoA in the mitochondrial matrix, feeding into the TCA cycle.
TCA Cycle Products
- Energetic outputs from the TCA cycle include 1 ATP, 3 NADH, and 1 FADH.
Total ATP from Aerobic Respiration
- Aerobic respiration of one glucose molecule yields a total of 36 ATP.
Electron Transport Chain Overview
- The ETC consists of cytochrome proteins in the mitochondrial inner membrane that pass high-energy electrons, creating a proton gradient for ATP synthesis.
Final Electron Acceptor
- Oxygen serves as the final electron acceptor in the ETC.
Fatty Acid Metabolism
- Triglycerides are metabolized into fatty acids and glycerol; glycerol enters glycolysis, while fatty acids convert to acetyl-CoA in the mitochondria.
Protein Metabolism
- Amino acids enter metabolic pathways at varying points, depending on their specific structure.
Gene to Polypeptide Ratio
- Each gene typically results in the production of one polypeptide.
Gene Copies in Prokaryotes
- Prokaryotes generally possess one copy of each gene.
Gene Copies in Eukaryotes
- Eukaryotes generally have one copy of most genes, with some exceptions (e.g., tRNA and rRNA).
Nucleotide Composition Reiterated
- A nucleotide consists of a nitrogenous base, a pentose sugar, and a phosphate group.
Nitrogenous Bases and Nucleosides
- Four nitrogenous bases: Adenine, Thymine, Cytosine, Guanine.
- Four nucleosides: Adenosine, Cytidine, Guanosine
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