Comprehensive study notes on hydrogen bonds, pH, fatty acids, proteins, triglycerides, and nucleotides
- Hydrogen bonds require a hydrogen atom attached to a highly electronegative atom (typically O, N, or F) that is attracted to another electronegative atom in a different molecule or a different part of the same molecule.
- Classic examples of hydrogen bonds:
- O–H···O (water–water, water–biomolecule)
- O–H···F (due to fluorine’s high electronegativity)
- Not a hydrogen bond: H–C interactions are not considered hydrogen bonds because carbon is only slightly electronegative relative to H and doesn’t provide the strong dipole needed for a hydrogen bond.
- Why this matters: Hydrogen bonding explains polarity and “like dissolves like” behavior, as well as many properties of water.
- Water’s special properties discussed:
- Cohesion: water molecules sticking to each other via hydrogen bonds (cohesive forces). Analogy: “co-parenting”—water molecules cooperate and stay together, enabling droplets and surface tension.
- Adhesion: water sticking to surfaces (e.g., a water droplet clinging to a window pane).
- Surface tension: arises from strong hydrogen bonding at the air–water interface; relatively strong but not as strong as covalent bonds.
- Hydrogen bonds are relatively hard to break because of the attraction between partial charges; this contributes to water’s high cohesion and high boiling point relative to other small molecules.
- In a hydrated salt scenario (e.g., water with NaCl): water forms hydrogen bonds with the water molecules and can hydrogen-bond to the ions or to the oxygen/hydrogen atoms of the system. Na+ is not an electronegative acceptor in the same sense; Cl− (and water’s H-bonds) participates in the network.
- Quick exercise described in the slide: counting hydrogen bonds in a water–salt picture. The presenter estimated around 15 hydrogen bonds (counting both water–water hydrogen bonds and water–ion interactions). The key point is: hydrogen bonds involve H attached to an electronegative atom and attracted to another electronegative atom; Na+ itself is not a hydrogen-bond donor/acceptor in this context.
- pH context introduced here ties into hydrogen ion (H⁺) dynamics and cellular homeostasis (next section): hydrogen ions (H⁺) and hydronium (H₃O⁺) are central to pH.
pH, acids, bases, and their practical implications
- pH stands for either Power of Hydrogen or Potential Hydrogen (two terms you might see). It measures hydrogen ion concentration; a key parameter in cellular homeostasis and solvent balance.
- Neutral pH is 7.0 (water at room temperature is near neutral). On the scale:
- pH < 7 is acidic
- pH > 7 is basic (alkaline)
- Range on the pH scale is typically 0–14 in aqueous solutions;
- 0 (very acidic) to 7 (neutral) to 14 (very basic)
- Acids and bases (simplified identification):
- Acids often have an H in the front when written in formulas (e.g., HCl, HNO₃).
- Bases often have an OH (or resemble hydroxide) in their formula (e.g., NaOH). Note: the exact naming can vary; the key idea is that acids donate H⁺, bases donate OH⁻ or accept H⁺.
- Water’s role and pH: the pH concept is tied to H⁺ (or hydronium, H₃O⁺) concentrations.
- Practical implications: changes in pH can alter proton/hydroxide gradients across membranes and influence cellular processes (e.g., ATP synthesis relies on proton gradients).
- If you have a solution with pH 3 and you want to raise the pH (make it less acidic), you add a base. If you want to lower the pH further (more acidic), you add an acid.
- Quick Q&A from the lecture:
- If pH = 3 and you want to raise the pH, you add a base.
- If you want to lower the pH (make more acidic), you add an acid.
- Examples linked to everyday substances (from the slide):
- Acids: lemon juice, orange juice, tomato juice, urine, stomach acid.
- Bases: soapy solutions (e.g., some detergents), baking soda solutions, etc.
- Important takeaways for exams:
- Neutral = 7; acidic goes down the scale; basic goes up the scale.
- Acids usually contain H at the start; bases commonly involve OH groups in their species.
- pH is a logarithmic scale; small changes represent large shifts in hydrogen ion concentration (not explicitly in the transcript but a foundational concept).
Fatty acids and triglycerides: saturated vs unsaturated
- Two main types of fatty acids to know: saturated and unsaturated.
- Saturated fatty acids:
- Contain only single bonds between carbon atoms (no C=C double bonds).
- Molecules are more linear and can pack tightly, leading to dense, solid fats at room temperature (e.g., butter).
- The linear arrangement allows close stacking in a solid form.
- Unsaturated fatty acids:
- Contain at least one C=C double bond (one or more).
- Double bonds introduce kinks (bends) in the hydrocarbon chain, preventing tight packing.
- This looser packing results in lower density and liquids at room temperature (e.g., olive oil).
- The concept of single vs double bonds (and occasional triple bonds, though fatty acids are commonly single or one or more double bonds):
- A single bond allows a straight, linear chain.
- A double bond introduces a bend/kink in the chain, reducing tight packing.
- A triple bond would introduce another kind of bonding but is not typical for fatty acids in biology.
- Example discussion from the slide:
- A triglyceride is shown with glycerol backbone and three fatty acids.
- The fatty acids in the shown triglyceride are saturated (shown with single bonds). If there were double bonds, you would draw those as double lines to indicate unsaturation.
- Practical examples mentioned:
- Olive oil is unsaturated (liquid at room temperature).
- Butter is saturated (solid at room temperature).
- Important structural components to know about triglycerides:
- Glycerol backbone (the three-carbon molecule with hydroxyl groups).
- Three fatty acids attached via ester bonds to the glycerol backbone.
- The general reaction is esterification: glycerol + 3 fatty acids → triglyceride + 3 H₂O (illustrative representation; see below for a compact equation).
- Quick compact representation (informative but simplified):
- Glycerol backbone: ext{Glycerol} = ext{HO-CH}2- ext{CH(OH)-CH}2 ext{OH}
- Triglyceride formation (ester bonds):
ext{Glycerol} + 3 ext{R-COOH}
ightarrow ext{Glycerol}-( ext{O-C(=O)-R})3 + 3 ext{H}2 ext{O}
- Takeaways for exams:
- Triglycerides consist of glycerol plus three fatty acids.
- Saturated fats have only single bonds; unsaturated fats have at least one double bond leading to kinks and lower packing density.
Building blocks of proteins: amino acids and peptide bonds
- Proteins are made from building blocks called amino acids (monomers).
- Amino acids general structure: ext{NH}_2- ext{CHR}- ext{COOH} where R is the side chain (the identifier group).
- Peptide bonds:
- Amino acids are linked together by peptide bonds, formed by a condensation reaction that removes water (a dehydration synthesis).
- In a peptide bond, the carboxyl carbon (C) of one amino acid links to the amide nitrogen (N) of the next amino acid, resulting in the backbone pattern …-N-C-C-N-C-C-…
- Condensation example (simplified):
ext{R}1{-} ext{COOH} + ext{NH}2{ ext{R}}2
ightarrow ext{R}1{-} ext{CO-NH- R}2 + ext{H}2 ext{O}
- Primary structure:
- The primary structure is a linear sequence of amino acids joined by peptide bonds.
- The speaker emphasized that the “N-terminus to C-terminus” orientation forms the peptide bonds; the order of amino acids determines the primary sequence.
- Secondary and tertiary structures arise from additional interactions (e.g., hydrogen bonds, disulfide bonds) that cause folding.
- Example from the lecture:
- A short chain with three amino acids shows two peptide bonds (connecting successive amino acids).
- The instructor noted that some students use the term “peptides” interchangeably with amino acids; scientifically, three amino acids connected form one oligopeptide chain of length three, with two peptide bonds between them.
- Important distinctions you may be asked about:
- Primary structure = linear sequence of amino acids.
- Secondary structure involves local folding (e.g., alpha helices, beta sheets) stabilized by hydrogen bonds (not deeply covered here).
- Tertiary structure involves overall 3D folding; disulfide bonds and other interactions contribute to the folding.
Nucleotides: components and properties
- Nucleotides are the building blocks of nucleic acids (DNA and RNA) and have three components:
- Nitrogenous base (e.g., adenine, thymine in DNA; adenine, cytosine, guanine; thymine is replaced by uracil in RNA).
- Pentose sugar (five-carbon sugar): ribose in RNA, deoxyribose in DNA.
- Phosphate group (the phosphate group is negatively charged in the backbone of DNA/RNA).
- The slide emphasizes the classic three components:
- Nitrogenous base
- Pentose sugar (five-carbon sugar)
- Phosphate group
- Charges and structure:
- The phosphate group contributes negative charge to the backbone in DNA/RNA (hence the negative charge of the nucleic acids).
- An example provided in the lecture mentions adenine as a nitrogenous base and notes the DNA context with thymine (A–T pairing and C–G pairing are the canonical base pairs in DNA; the lecture notes only briefly mention this, with a plan to cover pairing in more depth later).
- A note on the phosphate group terminology:
- The lecture text mentioned a phosphate group with three phosphates (which is accurate for ATP, a nucleotide in its energy-carrying form). In a standard single nucleotide, there is typically one phosphate group, while ATP contains three phosphate groups; this distinction is important for accurate exam answers.
- Quick recap:
- Nucleotide = Nitrogenous base + Pentose sugar + Phosphate group.
- DNA uses deoxyribose; RNA uses ribose; bases include adenine (A), thymine (T) in DNA, cytosine (C), guanine (G); thymine pairs with adenine, cytosine pairs with guanine in DNA.
Connections and rally points for exam readiness
- Core concepts to anchor your understanding:
- Hydrogen bonds: criteria (H attached to a highly electronegative atom; bond to another electronegative atom), and why they enable cohesive properties of water and interactions with biomolecules.
- Cohesion vs adhesion: how hydrogen bonding drives droplets, surface tension, and how water interacts with various surfaces and other molecules.
- pH and acids/bases: neutral pH 7, scale direction, and how adding acids or bases shifts pH; relationship to cellular processes and homeostasis.
- Fatty acids and triglycerides: saturation level affects geometry and physical state; implications for membranes, energy storage, and fluidity.
- Proteins: amino acids as building blocks; peptide bonds linking amino acids; primary structure as the linear sequence; later chapters cover higher-order protein folding.
- Nucleotides: three-part structure; backbone negative charge due to phosphate group; foundational to DNA/RNA structure and function.
- Real-world relevance and exam-style cues:
- Recognize hydrogen-bond donors/acceptors in biomolecules and predict interactions (e.g., water–biomolecule interactions, protein folding tendencies).
- Distinguish saturated vs unsaturated fatty acids and predict physical state at room temperature.
- Identify the components of triglycerides and nucleotides, and describe the bond types that assemble amino acids into proteins.
- Ethical/philosophical notes: not a focus of this lecture, but understanding molecular interactions helps appreciate why certain biological processes require precise conditions (pH, temperature, ionic strength) for life to function properly.
- Quick formula and notation reminders (for your quick reference):
- pH relationship to hydrogen ion concentration: pH = -\log_{10}[H^+].
- Neutral water condition: pH = 7. (at standard room temperature)
- Peptide bond formation (condensation):
ext{R}1{-} ext{COOH} + ext{H}2 ext{N-R}2
ightarrow ext{R}1{-} ext{CO-NH-R}2 + ext{H}2 ext{O}. - Triglyceride formation (simplified esterification):
ext{Glycerol} + 3 ext{R-COOH}
ightarrow ext{Glycerol}( ext{O-CO-R})3 + 3 ext{H}2 ext{O}. - Nucleotide components: base + sugar (pentose) + phosphate group; in DNA, bases include A, T, C, G and sugar is deoxyribose; in RNA, ribose and Uracil (U) replaces thymine (T).
