Organic Molecules, Protein Synthesis, and Cellular Respiration Study Guide

Introductory Review Questions

• Glycogen and Starch Properties: Glycogen and starch are storage molecules found in animals and plants, respectively.

• Cell Membrane Composition: The plasma membrane of cells is primarily composed of phospholipids.

• Amino Acid Identification: The general formula for an amino acid includes a central carbon ($C$), a hydrogen atom ($H$), an amino group ($NH_2$), a carboxyl group ($COOH$), and a variable side chain ($R$).

• DNA Stability: In the DNA double helix, complementary base pairs are held together by hydrogen bonds.

Carbohydrates (Glucides)

• General Characteristics:

  • Carbohydrates are organic matter also known as sugars or hydrates of carbon.

  • They serve as the main source of energy for cells.

  • Elemental composition includes Carbon ($C$), Hydrogen ($H$), and Oxygen ($O$), following the general formula $(CH_2O)_n$.

  • They are categorized into monosaccharides, disaccharides, and polysaccharides.

  • Many are macromolecules called polymers, which are molecules made of a large number of identical or similar structural units (monomers) linked by covalent bonds.

• Monosaccharides:

  • The molecular unit of all carbohydrates (a single monomer).

  • They contain a carbonyl group and are classified as an aldose or a ketose.

  • Classification by carbon count ($(CH_2O)_n$):

    • If $n = 3$: Trioses (e.g., glyceraldehyde, dihydroxyacetone).

    • If $n = 5$: Pentoses (e.g., ribose).

    • If $n = 6$: Hexoses (e.g., glucose, galactose, fructose).

  • Glucose: Formula is $C_6H_{12}O_6$. It has several isomers including galactose ($C_6H_{12}O_6$) and fructose ($C_6H_{12}O_6$).

  • Pentose Examples: Ribose ($C_5H_{10}O_5$) and Deoxyribose ($C_5H_{10}O_4$).

• Disaccharides:

  • Formed by the assembly of two monosaccharides through a covalent bond with the elimination of a water molecule ($H_2O$).

  • Maltose: Composed of glucose + glucose.

  • Sucrose (Saccharose): Composed of glucose + fructose.

• Polysaccharides:

  • Polymers of monosaccharides.

  • Starch: Composed of amylose and amylopectine.

  • Cellulose: A structural polysaccharide.

  • Glycogen: A highly branched chain of glucose molecules.

  • Other examples include inulin and agarose.

Lipids

• General Characteristics:

  • Organic matter serving as energy reserves and the main constituents of cell membranes.

  • Composed of $C$, $H$, $O$, and sometimes Phosphorous ($P$).

  • Insoluble in water (apolar).

  • Categories include fatty acids, triglycerides, phospholipids, and sterols.

• Concept of Polarity:

  • Electronegativity: The attraction an atom exerts on the electrons it shares in a covalent bond.

  • Polar Molecules: Regions with partial positive charges ($\text{pole } +$) and negative charges ($\text{pole } -$). These are soluble in water and often contain Oxygen ($O$) and Nitrogen ($N$).

  • Apolar Molecules: Shared electrons are distributed equitably (no partial charge), making them insoluble in water. These are mainly composed of Carbon ($C$) and Hydrogen ($H$).

• Fatty Acids:

  • Long chains of carbon atoms carrying hydrogen, with a carboxyl group ($-COOH$) at one end.

  • Saturated Fatty Acids: Examples include Palmitic acid (found in palm oil).

  • Unsaturated Fatty Acids: Examples include Oleic acid (found in olive oil).

• Triglycerides:

  • Produced by the reaction between one glycerol molecule and three fatty acid molecules.

  • The most abundant lipids; found as animal fats and vegetable oils.

  • Serve as energy storage and are stored in humans in adipocytes.

• Phospholipids:

  • Main constituents of cell membranes.

  • Structure: Glycerol skeleton + 2 fatty acids + another molecule linked to a phosphate group.

  • They are amphiphilic (containing both hydrophilic and hydrophobic parts).

• Steroids:

  • Composed of $C$, $O$, and $H$.

  • Carbons are joined to form four rings known as the sterol nucleus.

  • Cholesterol: A component of the plasma membrane (acting as a stabilizer) and a precursor to steroid hormones.

Proteins

• General Characteristics:

  • Organic matter and the primary building material for cellular structure and the body.

  • Involved in nearly all cellular functions.

• Functions of Proteins:

  • Structure: e.g., Actin.

  • Mobility/Movement: e.g., Myosin.

  • Metabolism: Enzymes.

  • Transport: e.g., Hemoglobin.

  • Regulation: e.g., Hormones.

  • Immunity: Antibodies.

  • Membrane Interactions: Receptors and membrane transporters.

  • DNA Organization: Histones (for compaction).

  • Gene Expression: Transcription factors.

• Amino Acids and Polypeptides:

  • Proteins are polymers composed of amino acids.

  • The nature of the side chain (Radical group $R$) determines the specificity of each amino acid.

  • Polypeptides differ by the nature, number, and sequence of amino acids.

  • A protein consists of one or more polypeptides (sometimes associated with other molecules or metal ions).

  • 20 Standard Amino Acids:

    • Non-polar: Valine, Isoleucine, Leucine, Methionine, Phenylalanine, Glycine, Alanine, Proline, Tryptophane.

    • Polar, Uncharged: Tyrosine, Serine, Threonine, Cysteine, Asparagine, Glutamine.

    • Polar, Positively Charged: Arginine, Lysine, Histidine.

    • Polar, Negatively Charged: Aspartic acid, Glutamic acid.

  • Essential Amino Acids Mnemonic: "Le Trs Lyrique Tristan Fait Vachement Mditer Iseult" corresponds to Leu, Thr, Lys, Trp, Phe, Val, Met, Ile.

• Peptide Bonds:

  • Formed between the carboxyl group of one amino acid and the amine group of another through the elimination of $H_2O$.

  • The resulting chain has an amine end ($N$-terminal) and a carboxyl end ($C$-terminal).

• Levels of Protein Organization:

  • Primary Structure: The linear sequence of amino acids in a polypeptide.

  • Secondary Structure: Repetitive patterns formed by folding or coiling, stabilized by hydrogen bonds (e.g., $\alpha$-helix or $\beta$-pleated sheet).

  • Tertiary Structure: The overall global shape (conformation) of a polypeptide, reinforced by interactions between $R$ groups (hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges).

  • Quaternary Structure: The relationship and arrangement of two or more polypeptide chains that compose a functional protein (e.g., transthyretin consists of four identical subunits).

Nucleic Acids

• General Concepts:

  • Gene: The unit of genetic information.

  • Genes are made of DNA (Deoxyribonucleic acid), which belongs to the class of compounds called nucleic acids.

  • Two types: DNA and RNA (Ribonucleic acid).

• DNA Functions:

  • Provides instructions for its own replication.

  • Directs RNA synthesis and controls protein synthesis.

  • Constitutes the genetic material inherited from parents.

  • Does not participate directly in the day-to-day operations of the cell.

• Structure of DNA and RNA:

  • Composed of monomers called nucleotides, which form polynucleotides.

  • Nucleotide Components:

    • Sugar (Pentose): Ribose (in RNA) or Deoxyribose (in DNA).

    • Phosphate group.

    • Nitrogenous base.

  • DNA Configuration: A double helix structure resembling a ladder.

    • Rails/Sides: Alternating deoxyribose and phosphate groups.

    • Rungs/Steps: Nitrogenous bases linked by hydrogen bonds.

  • Base Complementarity:

    • Adenine ($A$) pairs with Thymine ($T$) via 2 hydrogen bonds ($A-T$).

    • Cytosine ($C$) pairs with Guanine ($G$) via 3 hydrogen bonds ($C-G$).

  • The human genome consists of 46 DNA molecules.

  • The linear order of these four bases in a gene determines the primary structure (amino acid sequence) of a protein.

Protein Synthesis

• Central Dogma: The function of a gene is to dictate the production of a protein ("one gene, one polypeptide"). Gene expression consists of two main stages: transcription and translation.

• Transcription:

  • Definition: Synthesis of any type of RNA using a DNA template.

  • Location: Nucleus.

  • Key Elements: Precursor nucleotides, RNA polymerase, and the DNA template.

  • Three Steps:

    1. Initiation: RNA polymerase binds to a specific DNA sequence called a "Promoter" which marks the beginning of the gene. The two DNA strands unwind.

    2. Elongation: RNA polymerase adds RNA nucleotides in the $5' \rightarrow 3'$ direction following base complementarity. The DNA double helix reformats behind the enzyme, and the new RNA strand detaches.

    3. Termination: Transcription continues until the polymerase transcribes a sequence called a "Terminator." The enzyme then releases the RNA and detaches from the DNA.

• RNA Maturation (Eukaryotes):

  • Definition: Modification of pre-messenger RNA (pre-mRNA) into mRNA.

  • Location: Nucleus.

  • Segments:

    • Introns: Non-coding sequences that do not contribute to protein information.

    • Exons: Expressed sequences that contain information for protein synthesis.

  • Splicing: The process of removing introns and joining exons.

  • Additions: A $5'$ cap and a $3'$ poly-A tail are added to the mRNA.

• The Genetic Code:

  • Information is transferred from mRNA to protein through codons (triplets of bases).

  • There are Start codons (Methionine/AUG) and Stop codons (UAA, UAG, UGA).

• Translation:

  • Definition: The cell constructs a protein based on instruction in the mRNA.

  • Interpretation: Transfer RNA (tRNA) interprets the message.

  • tRNA Function: Transports amino acids from the cytosol to a ribosome. One end carries a specific amino acid, while the other end has an anticodon that binds to the complementary mRNA codon.

  • Ribosomes: Sites of translation with one mRNA binding site and three tRNA binding sites. They facilitate the pairing of tRNA anticodons with mRNA codons and add amino acids to the growing polypeptide chain.

  • Process Stages: Initiation, Elongation, and Termination.

Cellular Respiration and Metabolism

• Metabolic Locations:

  • Glycolysis occurs in the cytoplasm.

  • Aerobic cellular respiration occurs in the mitochondria.

  • Transcription occurs in the nucleus.

  • Translation occurs in the cytoplasm (at ribosomes).

• Mitochondria:

  • Sites of aerobic cellular respiration, a catabolic process using $O_2$ to extract energy from carbohydrates and lipids.

  • Transforms organic matter into mineral matter and provides energy to synthesize ATP.

  • The overall equation: $\text{Organic matter} + O_2 \rightarrow CO_2 + H_2O + ATP$.

• Stages of Respiration:

  1. Glycolysis:

     • Occurs in the cytosol.

     • Oxidizes glucose into two 3-carbon organic ions called pyruvate.

     • Produces 2 net ATP and 2 coenzymes (NADH).

  2. Pyruvate Oxidation and Krebs Cycle (Citric Acid Cycle):

     • Occurs in the mitochondrial matrix.

     • Oxidizes Acetyl-CoA derived from pyruvate.

     • Produces $CO_2$, 2 ATP, and high-energy coenzymes (NADH and $FADH_2$).

  3. Oxidative Phosphorylation:

     • Involves the electron transport chain and chemiosmosis.

     • Located in the inner mitochondrial membrane.

     • The majority of ATP is produced here.

     • Final Electron Acceptor: Dioxygen ($O_2$).

Questions & Discussion

• Question 1: Regarding glycogen and starch, which proposal is exact?

  • Correct Answer: D. Glycogen and starch are storage molecules found in animals and plants, respectively.

• Question 2: The plasma membrane of cells is mainly composed of…

  • Correct Answer: C. Phospholipids.

• Question 3: Identify the general formula (Amino Acid).

  • Answer: B. An amino acid.

• Question 4: DNA base pairs are held by…

  • Correct Answer: B. Hydrogen bonds.

• Question 5: Correct sequence for functional protein formation?

  • Correct Answer: C. Transcription - maturation of mRNA - translation - maturation of the protein.

• Question 6: Regarding the biological process (Transcription illustrated):

  • Options: A. Transcription. B. Occurs in the nucleus. C. Only in eukaryotes. D. Can occur in mitochondria. (Note: Transcription can occur in mitochondria for mitochondrial DNA).

• Question 7: Protein sequence MET-ARG-SER-VAL. Which DNA sequence could code for it?

  • Analysis: MET is ATG. Using the genetic code provided, SER and VAL sequences are verified against options.

• Question 8: Regarding metabolic locations, which is false?

  • Correct Answer: A. Glycolysis in the endoplasmic reticulum (False, it occurs in the cytoplasm).

• Question 9: Glycolysis is a pathway that…

  • Correct Answer: B. Oxidizes glucose.

• Question 10: Final electron acceptor in aerobic respiration?

  • Correct Answer: D. Dioxygen ($O_2$).