Biomolecules Lecture Notes (Proteins, Carbohydrates, Lipids, Nucleic Acids)

Proteins

Primary structure: the sequence of amino acids and the order in which they're bonded; making or changing the order changes the primary structure
Secondary structure: the backbone of the polypeptide folds due to interactions within the backbone only; side chains (R groups) do not drive secondary structure
- Key interactions: hydrogen bonds between carbonyl oxygens and amide hydrogens along the backbone
- Visual cues: polar groups attracting to each other over time forming patterns like alpha helices or beta-pleated sheets
- Diagrammatic cue: dashed lines represent hydrogen bonds
Backbone vs side chains: secondary structure involves backbone interactions (carbonyls and amide hydrogens); side chains occur off the backbone and come into play at later levels
Tertiary structure: when side chains start to interact with each other, producing a highly diverse 3D shape
- Interactions can include: hydrogen bonds, ionic bonds, hydrophobic effects, and van der Waals forces
- Covalent disulfide bridges can form between two sulfhydryl groups, providing strong covalent stabilization
Quaternary structure: arrangement when multiple polypeptide chains interact (not formed in every protein)
Hydrogen bonds: play roles in both secondary and tertiary structures (backbone-backbone in secondary; side-chain interactions in tertiary)
Other stabilizing interactions in 3D structure: ionic bonds, hydrophobic effects, van der Waals forces, covalent disulfide bonds
Protein denaturation: proteins can lose their 3D structure under adverse conditions (too acidic, high ionic strength, or high temperature)
- Which force breaks last during denaturation? Disulfide bridges (covalent bonds) are most resistant; they break last because covalent bonds are the strongest
- Other forces can be disrupted earlier: hydrogen bonds, ionic bonds, and some hydrophobic interactions become weaker as temperature rises or the environment changes
Recap on level of structure: primary (amino acid sequence) → secondary (backbone hydrogen bonds forming helices/sheets) → tertiary (side-chain interactions) → quaternary (assembly of multiple chains)

Carbohydrates

General formula and ratio: carbohydrates are often represented by the formula where for every carbon atom there is a water molecule, i.e.
Cn(H2O)_n
Monomer: glucose is the most common monosaccharide for energy; a six-carbon sugar
- Glucose:
  ext{C}6 ext{H}{12} ext{O}_6
- Fructose: also a six-carbon sugar with the same formula but different bonding pattern
- For monosaccharides, the ratio holds: for every carbon, 2 hydrogens and 1 oxygen, i.e. the pattern Cn(H2O)_n
Conceptual view: carbohydrates are hydrated carbons
Monosaccharides vs polymers:
- Monosaccharide (one unit)
- Disaccharide (two linked monosaccharides) by a dehydration (glycosidic/sugar linkage) reaction
- Polysaccharide (many linked monosaccharides)
Dehydration synthesis (glycosidic bonds): linking two monosaccharides removes water
- Generic form:
  ext{Monomer} + ext{Monomer}
  ightarrow ext{Disaccharide} + ext{H}_2 ext{O}
Disaccharides: energy transporters (composed of two monosaccharides)
- Examples mentioned (familiar names): maltose, sucrose, lactose (milk sugar)
Polysaccharides: large polymers with two major functional roles
- Energy storage: starch (plants) and glycogen (animals)
- Structural support: cellulose (plants) and chitin (arthropod exoskeletons)
Structure-function relationships
- Branching vs unbranched affects function and accessibility to enzymes
- Starch and glycogen are branched to allow rapid energy release (more ends for enzymatic attack)
- Cellulose is unbranched (linear) and forms organized, rigid structures; hydrogen bonding between chains increases strength
Branching rationale in glucose polymers
- Branched polymers offer many entry points for enzymes to cleave glucose units simultaneously, enabling rapid energy release when needed
- Unbranched polymers like cellulose form tight, rigid structures, aiding structural support
Illustrative structures (general):
- Starch: branched polymer
- Glycogen: highly branched polymer in animals
- Cellulose: straight, unbranched polymer with strong inter-chain hydrogen bonding
Functional summary
- Carbohydrates provide energy (quick energy from monosaccharides; storage in polysaccharides) and structural support (cellulose in plants; chitin in arthropods)
Quick recap formulas and checks
- Monosaccharide verification example: a formula like ext{C}4 ext{H}6 ext{O}_2 does not fit the monosaccharide ratio (requires H=2C and O=C for each carbon)
Visuals noted in lecture
- Rings of glucose in cells are common; in textbooks, ring structures are often shown, but the predominant cellular form is the ring form

Lipids

General features: lipids are mostly nonpolar hydrocarbons; rich in carbon-hydrogen bonds; largely insoluble in water (hydrophobic)
Role: long-term energy storage in a compact form (more energy per unit mass than carbohydrates)
Three main types discussed: 1) Triglycerides (triacylglycerols) – energy storage fats
- Structure: one backbone (glycerol) and three fatty acid tails
- The backbone contains hydroxyl (–OH) groups; attachment to fatty acids occurs via dehydration synthesis (three times)
- The long hydrocarbon tails are the energy-rich portion
- Saturated vs unsaturated fatty acids affect packing and state at room temperature
  - Saturated: no double bonds; straight chains; pack tightly; solid at room temperature
  - Unsaturated: contain one or more double bonds; causes kinks; typically liquid at room temperature
  - Cis configuration: hydrogens on the same side causing a bend; trans configuration (engineered) keeps chains straighter; trans fats can be solid at room temperature
    2) Phospholipids – key components of cell membranes
- Amphipathic: one end is hydrophilic (polar head, phosphate group, negatively charged and highly polar), the other end is hydrophobic (two long fatty acid tails)
- Structure: glycerol backbone with two fatty acid tails and a phosphate-containing head group
- Behavior in water: tails avoid water and orient inward; heads face outward toward water, forming a bilayer spontaneously
- Result: a phospholipid bilayer forms that protects hydrophobic tails inside while exposing hydrophilic heads to water
  3) Steroids – a diverse, non-polymeric lipid class with four fused rings
- Four-ring structure (cycloalkane fused rings) that forms the backbone of steroids
- Includes cholesterol and steroid hormones (e.g., estrogen, testosterone)
- Structural and functional diversity arises from different functional groups attached to the fused-ring core
Phospholipids and membranes
- The bilayer arrangement arises spontaneously in aqueous environments due to amphipathic nature
- Role in membranes: build the fundamental barrier and interact with cholesterol to modulate fluidity and stability
Cholesterol and membrane interaction
- Cholesterol is a steroid-like molecule that integrates into phospholipid membranes and modulates properties
- It participates in membrane dynamics and is a precursor for steroid hormones
Practical takeaways
- When asked to identify lipids by appearance:
- A molecule with three long hydrocarbon tails and a glycerol backbone is a triglyceride (energy storage)
- A molecule with a polar head group and two nonpolar tails is a phospholipid (membrane component)
- A molecule with four fused rings and no polymer is a steroid (e.g., cholesterol, hormones)
Hydrophobic/hydrophilic considerations
- Lipids are generally hydrophobic due to nonpolar C–H and C–C bonds
- The cell membrane uses amphipathic phospholipids to create a stable barrier while allowing selective interactions with water and polar molecules

Nucleic Acids

Major types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)
- DNA: stores genetic information long-term
- RNA: expresses genetic information to synthesize proteins and perform other roles
Polymer and monomer
- Nucleic acids are polymers built from nucleotides
- Monomer: nucleotide, which contains three parts:
- Phosphate group (large, negatively charged)
- Five-carbon sugar (pentose)
  - DNA uses deoxyribose (missing one oxygen relative to ribose)
  - RNA uses ribose
- Nitrogenous base (contains nitrogen; carries genetic information)
Backbones and bases
- Backbone: alternating phosphate and sugar forming the phosphodiester-linked chain
- Bases hang off the sugar-phosphate backbone and encode genetic information
- Two strands (DNA) run in opposite directions (antiparallel) and are held together by hydrogen bonds between bases
Nitrogenous bases and their types
- Purines: two-ring structures (e.g., Adenine A and Guanine G)
- Pyrimidines: single-ring structures (e.g., Cytosine C, Thymine T in DNA, Uracil U in RNA)
- Base pairing (governs DNA double-helix width):
- Adenine pairs with Thymine (A–T) via two hydrogen bonds in DNA
- Guanine pairs with Cytosine (G–C) via three hydrogen bonds
- In RNA, Uracil pairs with Adenine (A–U)
- A mnemonic mentioned (not essential): Purines = A and G (AG); Pyrimidines = C, U/T (CUT)
- Another structural note: to keep width consistent, a purine pairs with a pyrimidine (one-ring with two-ring pairing)
Key bonds and formation
- Phosphodiester bonds: connect nucleotides in a chain; formed via dehydration synthesis
- A dehydration reaction joins the phosphate of one nucleotide to the sugar of the next
DNA vs RNA structure and function
- DNA: typically double-stranded; long-term storage of genetic information; uses deoxyribose sugar; bases are A, T, C, G
- RNA: typically single-stranded; used to express genetic information and perform cellular functions; uses ribose sugar; bases are A, U, C, G
Genetic code and expression
- The sequence of nitrogenous bases encodes genetic information (the alphabet A, C, G, T/U)
- The backbone (phosphate-sugar) is shared by all nucleic acids; the bases provide the information content
Terminology in context
- The bond linking nucleotides is called a phosphodiester bond
- The polymerization process of nucleic acids, like proteins and carbohydrates, proceeds via dehydration synthesis

Exam and study resources (lecture announcements and guidance)

Exam details
- Exam on Thursday; 40 multiple-choice questions; 50 minutes total
- Pencil requirement: bring a number 2 pencil; mechanical pencils acceptable
- Exam window in class is lenient, but timing will be enforced once the exam starts
Preparatory materials and activities
- Chapter 5 pre-reading due today; suggested to complete tonight or tomorrow as material on biological molecules features on the exam
- Practice resources: an additional practice quiz in the prep module on Canvas; a second case study available
- Case study timing: due next week (e.g., Tuesday); designed to reinforce topics like polarity and biological molecules
- Instructor resources: slides from exam review and a recording of the day’s explanation will be posted; the review aims to align with learning objectives
Study strategy and alignment to objectives
- Learning objectives are the best guide for exam prep; they specify what you should be able to do (e.g., predict forces influencing protein tertiary structure, identify which bonds are involved in a given scenario)
- Active study recommended: work through study guides, practice exams, dynamic study modules, and case studies rather than just reviewing slides
- Textbook summaries can be useful for alternative explanations but aren’t a substitute for active practice
Practice exam design and expectations
- Some questions will be straightforward (identifying elements or basic concepts), while others will require deeper structural understanding (e.g., determining which portion of a molecule is an amino acid or identifying the correct branching points in polysaccharides)
- Practice questions are designed to mirror learning objectives; some questions map directly to objectives, others will require application and synthesis
Quick recap of content emphasis for the exam
- For carbohydrates: composition, ratios, monomer/polymer types, glycosidic bonds, energy storage vs structure, and structure-function relationships
- For lipids: types (triglycerides, phospholipids, steroids), properties (saturated vs unsaturated; cis/trans), and membrane biology
- For proteins: levels of structure, bonding types, denaturation, and stability of disulfide bonds
- For nucleic acids: monomers, backbone, base types, DNA vs RNA, and phosphodiester bonds
Final guidance
- The best way to prepare is to actively work through the study questions and practice exams, then review summaries if needed
- If you’re unsure about any case study connections, use instructor availability (email discussions) for clarifications

Quick reference: key formulas and concepts (to memorize or recognize)

Carbohydrate general formula (per carbon):
Cn(H2O)_n
Glucose formula (common monosaccharide):
ext{C}6 ext{H}{12} ext{O}_6
Dehydration synthesis (generic):
ext{Monomer} + ext{Monomer}
ightarrow ext{Disaccharide} + ext{H}_2O
Phosphodiester bond (nucleic acids): dehydration-linked backbone with phosphate-sugar linkage
Lipid types and cues:
- Triglycerides: glycerol backbone + 3 fatty acids; energy storage
- Phospholipids: amphipathic; hydrophilic head, hydrophobic tails; membrane bilayer
- Steroids: four fused rings (e.g., cholesterol, sex hormones)
Cellular membrane intuition
- Hydrophobic tails face inward; hydrophilic heads face outward; bilayer forms spontaneously in water
Protein structure cues
- Primary: sequence of amino acids
- Secondary: backbone interactions (hydrogen bonds) forming helices/sheets
- Tertiary: side-chain interactions; diverse 3D shapes
- Quaternary: multiple chains interacting
Denaturation cues and force ranking
- Covalent disulfide bonds tend to withstand denaturation longer than hydrogen bonds or ionic interactions