Chapter 1-7: Biology Lecture Review
Macromolecules and Nucleic Acids – Comprehensive Study Notes
Language and framing from the lecture:
Monosaccharide, Disaccharide, Polysaccharide: monosaccharide = one sugar; disaccharide = two sugars; polysaccharide = many sugars. Joined by glycosidic linkages.
Poly- means many; mer = part. Examples using the root poly include polygon, polypeptide, polysaccharide.
Amphipathic meaning having both hydrophilic and hydrophobic parts. Example: amphipathic phospholipid with a hydrophilic head and hydrophobic tail.
Metabolic carbon fate (weight loss scenario):
Question: when someone loses mass due to exercise, caloric deficit, etc., where does the mass go?
Intuition activity showed many guessed energy loss; the correct broad answer is that mass leaves primarily as breath (carbon in CO₂) with some contribution from urine and other waste, but the majority is exhaled as CO₂ derived from carbon-containing substrates.
Concrete point: the carbon in carbon dioxide is the fate of carbon from macromolecules as they are oxidized in metabolism (Krebs cycle and beyond).
Clarification: fat stores contain more energy in their chemical bonds than carbohydrate stores, so fat yields more energy per bond when oxidized, which relates to why fat is a large energy reservoir.
Takeaway: follow carbon through metabolism; it often exits as CO₂ in breath; this is the application of the Krebs cycle to macromolecule catabolism.
Dehydration vs. hydrolysis (water as a diagnostic):
Dehydration (condensation) reaction: two molecules join, releasing a molecule of water. Example: peptide bond formation between amino acids releases
ext{AminoAcid}1 + ext{AminoAcid}2
ightarrow ext{Dipeptide} + H_2O.Hydrolysis reaction: water is used to break a bond, splitting a molecule into two parts (e.g., breaking a polymer into monomers).
Context: these reactions apply across the four major macromolecule categories: carbohydrates, lipids, proteins, nucleic acids.
Carbohydrates
Definition and hierarchy:
Carbohydrates include sugars (monosaccharides) and their polymers (disaccharides, polysaccharides).
Monosaccharide: single sugar unit.
Disaccharide: two sugar units joined by a glycosidic linkage.
Polysaccharide: many sugar units joined by glycosidic linkages; roles include energy storage or structural support.
Key storage and structural examples:
Starch: storage polysaccharide in plants; primarily glucose monomers; stored as granules in plastids (chloroplasts).
Glycogen: storage polysaccharide in animals; stored in liver and muscles; hydrolysis releases glucose when energy is needed.
Cellulose: structural polysaccharide in plant cell walls; polymer of glucose, but with a beta(1→4) glycosidic linkage different from starch.
Enzymes digesting starch hydrolyze alpha-linkages; humans lack enzymes to digest cellulose beta-linkages, so cellulose is largely indigestible (insoluble fiber) but healthful for digestion; some microbes have cellulose-digesting enzymes.
Chitin: structural polysaccharide in arthropod exoskeletons; also used in surgical settings as threads due to its properties.
Glucose polymers and differences:
All three (starch, glycogen, cellulose) are polymers of glucose, but the glycosidic linkage pattern determines their properties and digestibility for humans.
Practical note:
Hydrophobic/hydrophilic distinction is more central to lipids, but glycosidic linkages and polymer architecture govern carbohydrate function.
Lipids
General properties:
Lipids are hydrophobic due to predominant C–H bonds (nonpolar covalent bonds) in hydrocarbons.
Major lipid classes: fats (triglycerides), phospholipids, steroids.
Phospholipids and membranes:
Amphipathic molecule: one part hydrophilic (polar head) and one part hydrophobic (nonpolar tail).
They assemble into a phospholipid bilayer, forming the fundamental structure of cell membranes.
The outside (polar head) is hydrophilic; the inside (tails) is hydrophobic.
The membrane incorporates proteins for transport and signaling.
Steroids:
Carbon skeleton with four fused rings.
Cholesterol is a membrane component in animals and is linked with heart disease in common beliefs; cholesterol influences membrane fluidity.
Proteins
Overview and significance:
Proteins account for more than 50% of the dry mass of cells.
Functions include:
Enzymatic catalysis (e.g., digestive enzymes like amylase in saliva).
Storage of nutrients (e.g., casein in milk; ovalbumin in egg white as amino acid source during development).
Hormonal signaling (e.g., insulin regulates blood glucose).
Movement (motor proteins; contraction via myosin; cilia/flagella motion).
Transport (channel proteins and carrier proteins in membranes).
Receptors and cell signaling.
Structural support and defense (collagen, keratin; antibodies).
Immune defense (antibodies binding pathogens).
Protein structure and terminology:
Proteins are polymers of amino acids linked by peptide bonds.
A single peptide bond forms between two amino acids via a dehydration/condensation reaction.
Primary structure: amino acid sequence.
Secondary structure: alpha helices and beta-pleated sheets; stabilized predominantly by hydrogen bonds in the peptide backbone.
Tertiary structure: three-dimensional folding of a single polypeptide; interactions include hydrogen bonds, hydrophobic interactions, van der Waals forces, ionic bonds, and disulfide bridges.
Quaternary structure: assembly of multiple polypeptide chains (subunits) into a functional protein.
Key bonds and interactions (illustrative):
Backbone peptide bonds link successive amino acids.
Hydrogen bonds stabilize secondary structures (between peptide backbones, not R groups).
Tertiary interactions include:
Hydrogen bonds between side chains.
Hydrophobic interactions/Van der Waals forces driving folding to bury hydrophobic residues.
Ionic bonds between charged side chains.
Disulfide bridges between cysteine residues.
Examples of quaternary structure:
Collagen: a fibrous protein with three polypeptide chains wound into a rope-like triple helix.
Hemoglobin: a globular protein composed of four polypeptide subunits (two alpha, two beta) functioning as an oxygen transporter.
Amino acids: properties and shorthand codes:
All amino acids share an amino group, a carboxyl group, an alpha carbon, and a side chain (R group).
20 standard amino acids; classification by R group:
Nonpolar (hydrophobic): side chains rich in carbons/hydrogens; e.g., often lack electronegative atoms. Example: tryptophan (Trp, W) and proline (Pro, P).
Polar (hydrophilic): side chains with electronegative atoms (O, N, S) that create partial charges; these interact with water.
Charged (hydrophilic): basic (positively charged) or acidic (negatively charged) side chains; interact with water.
Practical note: You do not need to memorize all R groups, but you should be able to classify an amino acid as hydrophobic (nonpolar) or hydrophilic (polar or charged) based on its side chain, and know common shorthand names (e.g., Pro/P; Trp/W).
Structure dictates function:
If a mutation alters the protein’s structure, it will likely alter its function.
This principle underpins analyses of genetic mutations and disease (e.g., how a single amino acid change can affect folding and activity).
Sickle cell disease (an explicit mutation example):
Caused by a mutation in the beta-globin gene: a charged amino acid glutamic acid (Glu, E) is replaced by valine (Val, V) in the beta chain (E→V).
This polar-to-nonpolar substitution introduces a hydrophobic patch on the exterior surface of the hemoglobin molecule.
Consequences: under stress/low oxygen, hemoglobin polymerizes, causing red blood cells to adopt a sickle shape, leading to capillary blockages, painful crises, and increased clearance (anemia).
Orientation note: Glu normally resides on the exterior, being hydrophilic; Val is hydrophobic and promotes abnormal interactions -> altered quaternary structure and function.
Nucleic Acids
Overview:
DNA and RNA are polymers of nucleotides (polynucleotides).
Nucleotide composition: a five-carbon sugar (pentose), a phosphate group, and a nitrogenous base.
Nucleoside = base + sugar; Nucleotide = nucleoside + phosphate.
DNA uses deoxyribose (2' carbon lacks an oxygen, hence “deoxy”); RNA uses ribose (has a 2' OH).
Base pairing and structure:
Complementary base pairing: A binds with T (in DNA); G binds with C. In RNA, A pairs with U instead of T.
The DNA double helix is stabilized by hydrogen bonds between complementary bases and by phosphodiester bonds forming the backbone.
Phosphodiester bond concept: backbone linkage between the phosphate of one nucleotide and the sugar of the next nucleotide; this bond stabilizes the strand.
Nucleotides in the cell:
In DNA, sugar is deoxyribose; in RNA, sugar is ribose.
The presence of an OH on the 2' carbon in RNA changes chemistry and reactivity relative to DNA.
Practical exercise (complementary base pairing): example walkthrough
Given a sample with counts (for DNA):
Cytosine C = 350,000
Guanine G = 6,000 (and thus G pairs with C, so C and G counts must match)
Steps:
Since C pairs with G, there must be an equal amount of G: G = 350,000.
Remaining nucleotides: 1,000,000 total - (C + G) = 1,000,000 - 700,000 = 300,000.
The remaining must be split equally between A and T: A = T = 150,000.
Resulting counts: C = 350,000; G = 350,000; A = 150,000; T = 150,000.
Nucleotides and bases, quick concepts:
A nucleotide's phosphate group is attached to the sugar; the base sits on the sugar.
In DNA, the sugar is deoxyribose; in RNA, ribose; the 2' position difference is a key structural distinction.
Quick True/False practice (from the lecture):
True: A nucleotide is comprised of a five-carbon sugar, a phosphate group, and a nitrogenous base.
False: The phosphate group does not bind to the base within a nucleotide; it binds to the sugar (the sugar-phosphate backbone).
True: In the DNA double helix, one strand can appear 5'→3' on one side and 3'→5' on the opposite strand (antiparallel orientation).
Conceptual activity to remember structure:
A hands-on demonstration was used to visualize the nucleotide: one hand represents the 5' phosphate, the other represents the 3' sugar; the base attaches to the sugar; phosphodiester bonds link consecutive nucleotides to form the backbone.
In a growing DNA strand, polymerization proceeds from the 5' end toward the 3' end (the new nucleotides are added to the 3' end).
To form a double-stranded DNA molecule, complementary bases on opposite strands pair (A with T, G with C) and the two strands run in opposite directions (antiparallel).
Transcription and translation (contextual link):
DNA is transcribed into mRNA in the nucleus; mRNA exits through nuclear pores; ribosomes translate mRNA into a polypeptide (protein).
The five-prime and three-prime ends play roles in mRNA regulation and protein synthesis; the first amino acid of a polypeptide is the N-terminus and the last is the C-terminus in proteins (analogous terminologies appear in protein discussion).
Key concepts tying macromolecules together
Carbon tracking across macromolecules:
Carbohydrates, lipids, proteins, and nucleic acids all contain carbon backbones; metabolic processes break down these polymers to yield energy and chemical building blocks, with carbon often exiting as CO₂ in respiration.
The Krebs cycle is a central hub: its activity explains how carbon from macromolecules ends up as CO₂ that’s exhaled.
Structure determines function across macromolecules:
Proteins are the primary example in the notes: their function is dictated by their three-dimensional structure, which in turn is dictated by amino acid sequence and interactions (hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions).
Mutations that alter amino acid properties (e.g., hydrophilic to hydrophobic) can dramatically alter structure and function (as seen in sickle cell disease).
Practical and ethical dimensions in biology education and medicine:
The lecture emphasizes that many people may not know certain details (e.g., the fate of carbon in metabolism) and that experts may disagree; nonetheless, correct understanding follows fundamental carbon-based logic.
In medicine, analyzing mutations (e.g., sickle cell) requires understanding how a single amino acid change alters protein folding and function, which has ethical and practical implications for diagnosis, prognosis, and treatment planning.
Quick reference: memory aids and orientation
Antiparallel DNA: one strand 5'→3', the other 3'→5'. The backbone is phosphodiester bonds between 5' phosphate and 3' sugar ends.
N-terminal vs C-terminal in proteins: N-terminus bears an amino group; C-terminus bears a carboxyl group.
Four levels of protein structure:
Primary: amino acid sequence.
Secondary: alpha helices and beta-pleated sheets; backbone hydrogen bonds stabilize.
Tertiary: R-group interactions; disulfide bridges; hydrophobic/hydrophilic distribution.
Quaternary: multiple polypeptides (e.g., collagen, hemoglobin).
Major macromolecule categories and key features:
Carbohydrates: monosaccharides, glycosidic linkages; starch/glycogen (storage) vs cellulose/chitin (structure).
Lipids: hydrophobic; phospholipids (amphipathic; bilayer membranes) and steroids (four-ring skeleton; cholesterol in membranes).
Proteins: diverse functions; enzymes; storage; hormonal; movement; immune; transport; receptors; structural.
Nucleic acids: DNA/RNA; nucleotides; base pairing rules; phosphodiester backbone; 5' and 3' ends; antiparallel arrangement.
Endnote
The lecture ends with a kinesthetic demonstration of nucleotide structure (5' phosphate, 3' sugar, base) and a memory cue for identifying the 5' and 3' ends within a double-stranded DNA context, followed by an emphasis on the importance of understanding orientation for transcription, replication, and mutation analysis.