GL

Notes on Nucleic Acids, Proteins, and Lipids

Nucleic Acids: DNA and RNA

  • Types of nucleic acids discussed: DNA and RNA

  • DNA nucleotides contain: thymine, adenine, cytosine, guanine

  • RNA nucleotides contain: uracil replaces thymine; thymine is absent in RNA

  • Sugar moieties:

    • DNA uses deoxyribose (oxyribose) – described in the transcript as lacking one oxygen; standard biology notes: deoxyribose lacks the 2'-OH that ribose has

    • RNA uses ribose

  • Strand structure:

    • DNA is double-stranded; RNA is single-stranded

    • DNA is often described as forming a double helix; strands are antiparallel

  • Base pairing rules:

    • Thymine (T) pairs with Adenine (A)

    • Cytosine (C) pairs with Guanine (G)

    • In RNA, Uracil (U) pairs with Adenine (A) (no thymine in RNA)

  • Directionality of strands:

    • One strand runs 5'→3' and the other runs 3'→5' (antiparallel)

    • The 5' end is where the phosphate group is attached; the 3' end has the hydroxyl group on the sugar

  • Example: complementary strand pairing rules

    • If a strand has A, T, C, G in a given sequence, the complementary strand has T, A, G, C correspondingly

    • For a 3' TAC ACC TAG 5' strand, the complementary 5' ATG TGG ATC 3' strand is formed (A↔T, C↔G)

  • Practical identification questions from the transcript:

    • DNA is double-stranded and forms a double helix; DNA contains thymine; RNA contains uracil

    • The sugar in DNA is deoxyribose; the sugar in RNA is ribose

  • Functional context of DNA (gene expression):

    • DNA directs development by gene expression

    • Genes are transcribed into messenger RNA (mRNA) and then translated into proteins

    • DNA ultimately influences phenotype by directing the production of proteins

  • Visual reference mentioned: DNA’s role in development and gene expression

Proteins: Monomers, Bonds, and Structures

  • Proteins are composed of one or more polypeptides

  • Polypeptide definition: a long molecule made of repeating units called amino acids

  • Monomers for nucleic acids and proteins:

    • DNA and RNA monomers: nucleotides or mononucleotides

    • Proteins monomers: amino acids (there are 20 different amino acids)

  • Basic amino acid structure (central carbon alpha carbon):

    • Four groups attached to the α-carbon:

    • Carboxyl group: \ -COOH

    • Amino group: \ -NH2

    • Hydrogen atom: \ -H

    • R group (side chain): variable among amino acids

  • The 20 amino acids differ only in their R groups; the rest of the molecule (carboxyl, amino, hydrogen) is the same across all amino acids

  • Classification of amino acid side chains (as described in the transcript):

    • Hydrophilic (polar) side chains

    • Electrically charged side chains (positive or negative)

    • Nonpolar (hydrophobic) side chains

  • Amino acid count and memorization:

    • There are 20 amino acids used to build proteins; memorize the number, not every individual name or structure

  • Protein functions highlighted in the transcript:

    • Enzymes accelerate chemical reactions

    • Structural proteins (e.g., keratin, collagen)

    • Casein (protein in milk) as storage example; milk is white

    • Albumin (protein in blood/plasma; mentioned in eggs as a nutrient context)

    • Insulin (protein; hormone that regulates blood sugar)

    • Hemoglobin (protein that transports oxygen)

    • Actin and myosin (protein filaments responsible for muscle movement)

    • Antibodies (protein-based protection)

    • Receptors in nerve cells (protein function as receptors for stimuli)

  • General functions of carbohydrates, nucleic acids, and proteins (as context):

    • Carbohydrates: nutrients, structure, energy storage

    • Nucleic acids: store and transmit genetic information

    • Proteins: wide range of functions including catalysis, storage, transport, structure, signaling, defense

  • Essential vs nonessential amino acids (concept):

    • Essential amino acids must be obtained from the diet; nonessential can be synthesized by the body

  • Protein synthesis and bonds:

    • Peptide bond formation is a dehydration reaction between the carboxyl group of one amino acid and the amino group of the next amino acid

    • General reaction representation:

    • \text{AminoAcid}1{-}COOH + \text{H}2N{-}\text{AminoAcid}2 \rightarrow \text{AminoAcid}1{-}CO{-}NH{-}\text{AminoAcid}2 + \text{H}2\text{O}

    • Hydrolysis: water is added to break peptide bonds, yielding individual amino acids

  • Protein structure and levels of organization:

    • Primary structure: linear sequence of amino acids bonded by peptide bonds

    • Example: a polypeptide with around 125 amino acids; ends: amino (N) terminus and carboxyl (C) terminus

    • Secondary structure: local folding stabilized by hydrogen bonds

    • Two main forms:

      • Alpha (α) helix

      • Beta (β) pleated sheet

    • Stabilizing force: hydrogen bonds between backbone atoms

    • Tertiary structure: three-dimensional folding of a single polypeptide; multiple types of interactions stabilize the 3D shape

    • Stabilizing interactions: hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic (Van der Waals) interactions

    • Quaternary structure: assembly of multiple polypeptides into a functional protein

    • Some proteins consist of a single polypeptide (no quaternary structure)

    • Hemoglobin is a classic example involving multiple polypeptides (context in the transcript mentions four polypeptides in some proteins)

  • Concept of protein maturation/denaturation:

    • Denaturation: loss of native secondary and tertiary structure due to disruption of non-covalent interactions (hydrogen bonds, ionic bonds, hydrophobic interactions) and, in some cases, disulfide bridges

    • Denaturation does not necessarily break peptide bonds; the primary sequence may remain intact

    • pH and temperature extremes can denature enzymes/proteins (enzymes are proteins)

    • Normal blood pH range referenced: 7.35 \le \mathrm{pH} \le 7.45

    • Below 7.35 (acidic) or above 7.45 (basic/alkaline) denaturation risk increases; extreme conditions disrupt enzyme function

    • Denaturation outcomes in the transcript context:

    • Denatured proteins lose secondary/tertiary structure and become nonfunctional

    • Gelatin is discussed as an example in the transcript; heating can denature proteins; gelatin may be used to illustrate heat-related changes (the transcript suggests gelatin can be irreversibly denatured by heat, and boiling a egg denatures proteins)

  • Distinctions: denaturation vs hydrolysis

    • Denaturation: disruption of non-covalent interactions; no breakage of peptide bonds; polypeptide remains as a chain but loses structure

    • Hydrolysis (digestion): cleavage of peptide bonds; polypeptides are broken into individual amino acids

Lipids: Fats, Phospholipids, and Steroids

  • Lipids are not polymers; they are large, nonpolar molecules with little to no affinity for water

  • Major lipid types discussed:

    • Fats (triglycerides)

    • Phospholipids

    • Steroids (cholesterol as an example)

  • Fat structure:

    • A fat molecule (triacylglycerol) consists of one glycerol backbone and three fatty acids

    • Chemical formula concept:

    • Glycerol backbone: \text{Glycerol} with three fatty acids attached via ester bonds

    • Not a repeating polymer like carbohydrates, nucleic acids, or proteins

  • Fatty acids: saturated vs unsaturated

    • Saturated fatty acids: no double bonds; carbon chain is linear; pack tightly; typically solid at room temperature

    • Unsaturated fatty acids: contain one or more double bonds; introduces a bend/kink; packs loosely; typically liquid at room temperature

  • Examples described in the transcript:

    • Saturated fat examples (solid at room temperature): butter, bacon grease (lard)

    • Unsaturated fats (liquid at room temperature): most vegetable oils (e.g., canola, peanut, olive, sesame, sunflower oils); fish oil is mentioned as high in unsaturated fatty acids (animal-derived but unsaturated)

  • Why unsaturated fats stay liquid:

    • Double bonds create kinks that prevent tight packing, reducing van der Waals interactions and melting point

  • Hydrogenation (food industry context):

    • Hydrogenation adds hydrogen across double bonds to convert some unsaturated fats to saturated fats, producing solid fats from liquids

    • This process can create trans fats (trans fatty acids), which have a different spatial arrangement of hydrogens around the double bond

  • Phospholipids and membranes (phospholipid structure):

    • Phospholipids are amphipathic: hydrophilic head (glycerol + phosphate group) and hydrophobic tails (fatty acid chains)

    • In membranes, phospholipids arrange into a bilayer with heads facing the aqueous exterior and interior, and tails tucked inside away from water

  • Steroids and cholesterol:

    • Steroids have four fused carbon rings

    • Cholesterol is given as an example of a steroid and is important in membranes and as a precursor to other steroids

Note on transcript accuracy: Some details in the transcript (e.g., deoxyribose carbon position, specific naming like "transpyratin protein") appear to be misstatements or transcription errors. The notes above reflect the intended biological concepts and commonly accepted details, with clarifications where the transcript itself contained ambiguous or incorrect phrasing.