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Chapter 1. Composition of Living Organisms

Recommended Articles: 【Biology】 Biology Index, 【Organic Chemistry】 Biopolymers: Carbohydrates, Proteins, Lipids, Nucleic Acids

1. Definition of Living Organisms

2. Water and Carbon

3. Biopolymers

4. Carbohydrates

5. Proteins

6. Lipids

7. Nucleic Acids

a. Hydrophobicity Index of Biopolymers

b. Perm hair and Disulfide Bonds

c. Biopolymer Library

1. Definition of Living Organisms

⑴ Definition 1. Organisms grow, move, reproduce, respond to stimuli, and have metabolism.

① Is fire a living organism and a donkey not?

⑵ Definition 2. Defined as an organism if all the following conditions are met:

① Possesses a common set of biomolecules.

② Maintains homeostasis.

③ Capable of evolution.

④ Requires water.

2. Water and Carbon

⑴ H₂O

① Polarity: Oxygen has high electronegativity, attracting electrons from hydrogen, causing a slight negative charge. Conversely, the hydrogen side has a slight positive charge.

② Hydrogen Bonds: Molecular attraction between hydrogen and electronegative atoms (i.e., F, O, N).

○ Water molecules cohere due to hydrogen bonds.

○ A water molecule can form hydrogen bonds at four sites

Figure 1. Hydrogen Bonding in Water

③ High heat capacity due to hydrogen bond: Plays an important role in temperature regulation

④ Excellent solvent (i.e., universal Solvent) due to its polarity

○ Dissolves other polar substances (e.g., salts, alcohols, acids, bases).

○ Facilitates chemical reactions.

○ Hydration Shell: The layer of water molecules surrounding a solute, making ions appear larger in water.

⑤ Expansion upon freezing

○ Reason: Ice forms hexagonal crystals.

○ At atmospheric pressure, water’s density is always greater than ice.

Figure 2. Density of Water and Ice by Temperature

⑵ C (Carbon)

① Carbon can bond with four atoms, used as a backbone for biopolymers.

② Carbon constitutes a significant portion of the biomass.

③ Organic Chemistry: The chemistry of carbon.

○ Molecules based on carbon are called organic compounds.

○ Compounds made of carbon and hydrogen are called hydrocarbons (e.g., CH₄).

④ Meteorites from Mars contain carbonates and hydrocarbon chains.

○ However, there’s no confirmation that these are biopolymers produced by living organisms.

⑶ Functional Groups

Figure 3. Types of Functional Groups

3. Biopolymers (macromolecules)

⑴ Earth’s organisms contain the same set of macromolecules (e.g., carbohydrates, proteins, lipids, nucleic acids).

⑵ Formation of Polymers: All polymers are made through dehydration reactions (water is produced) of monomers.

⑶ Degradation of Polymers: Polymers are broken down into monomers through hydrolysis.

⑷ Benefits of Polymers: Cause less osmotic pressure and maintain a lower concentration of monomers inside cells.

4. Biopolymer 1. Carbohydrates (polysaccharide) = (CH₂O)_n

⑴ Functions: Primary Energy Source, Structural Role

① Energy Source: 4 kcal/g

② Water-soluble molecules

⑵ Glycosidic Bond: Dehydration reaction between sugars.

Figure 4. Glycosidic Bond in Glucose

⑶ Monosaccharides: Glucose(6C), Fructose(6C), Galactose(6C), Others(3C ~ 7C)

Figure 5. Structural Isomers of C₆H₁₂O₆

⑷ Disaccharides

⑸ Oligosaccharides: Referring to C3 ~ C12

⑹ Polysaccharides: Glycogen, Starch, Cellulose, Chitin, Peptidoglycan

① Glycogen

○ A polymer of α-linked glucose with significantly more branches, serving as a relatively short-term energy source in animals.

○ α 1 → 4 linkage, α 1 → 6 linkage

② Starch

○ A polymer of α-linked glucose that serves as a long-term energy source in plants.

③ Cellulose

○ A polymer of β-linked glucose that forms cell walls and is the most abundant carbohydrate on Earth.

○ β 1 → 4 linkage

④ Chitin

○ NAG (N-Acetylglucosamine): The functional group on the second carbon of glucose is substituted with an amine group.

○ Chitin is a polymer of NAG: Forms exoskeletons in insects and crustaceans.

○ β 1 → 4 linkage

Figure 6. Structure of NAG

⑤ Dextrin

○ α 1 → 4 linkage

○ Keep in mind that Dextran is a brand name.

⑺ α Linkage and β Linkage

Figure 7. α Glucose (가) and β Glucose (나)

① α linkage: A type of bond where glucose molecules are connected without flipping upside down, resulting in a slightly twisted three-dimensional structure that forms an α-helix.

② α-linked glucose: The -OH group on the first carbon and the -OH group on the fourth carbon are in the same direction, making the structure unstable → Energy storage.

③ β linkage

○ The glucose molecule on one side is flipped upside down, aligning the first and fourth carbons, forming a straight linear structure in three dimensions.

○ Chains of β-linked glucose are tightly bound through strong hydrogen bonds.

④ β-linked glucose: The -OH group on the first carbon and the -OH group on the fourth carbon are in opposite directions, making the structure stable → Structural formation.

⑻ Starch

① Amylose is an α-linked glucose polymer without branches, formed by the bonding of the first carbon to the fourth carbon.

② Amylopectin is an α-linked glucose polymer with branches, formed by the bonding of the first carbon to the sixth carbon.

③ Starch is insoluble because α-glucose chains form tight crystals through hydrogen bonding.

④ Most digestive enzymes can only break down α linkages because the spatial structure is relatively open, allowing easier access for enzymes.

Figure 8. Amylose and Amylopectin

⑼ Cellulose

① Most abundant carbohydrate on Earth.

② β 1 → 4 linkage

Figure 9. Hydrogen Bonding Between β-Glucose Chains

③ Cellulase

○ Rumen of ruminants: Microbes in the first and second stomachs of ruminants synthesize cellulase.

○ Termites’ intestines: Trichonympha, a symbiotic microbe, synthesizes cellulase.

5. Biopolymers 2. Proteins = Polymers of Amino Acids

⑴ Characteristics

① Constituent elements: C, H, O, N, S

② Functions

○ Enzymes in metabolic activities.

○ Formation of intra- and extracellular structures: Constitutes half of the body’s dry weight.

○ Muscle contraction.

○ Immune function.

○ Hormones or signal proteins.

○ Signal transduction inside cells.

○ Substance transport across membranes.

○ Energy conversion and storage: 4 kcal/g, mainly in fetuses.

○ DNA replication, repair, and recombination.

○ Transcription, translation.

○ Protein transport and secretion.

③ Proteins: Composed of one or more polypeptides.

④ Polypeptides: Made of peptide bonds between amino acids.

⑤ Peptide bond: Dehydration reaction between amino group (-NH₂) and carboxyl group (-COOH).

Figure 10. Dehydration reaction between two amino acids

⑵ Amino Acids

① There are a total of 20 amino acids: 21 including selenocysteine (Sec).

Table 1. Symbols of Amino Acids (ref)

② Structure: Central carbon, amino group, carboxyl group, R group

③ All amino acids have the same backbone, but there are 20 types of side chains (denoted as R).

○ Others do not participate in protein synthesis.

○ Including minor amino acids like selenocysteine, the number can exceed 20.

④ Zwitterion: Acts as an acid or base. Related to isoelectric point.

⑤ Amino acids differ in properties depending on their side chains.

○ Nonpolar amino acids: Ala, Ile, Leu, Met, Phe, Pro, Trp, Val, Gly

○ Polar, uncharged amino acids: Asn, Cys, Gln, Ser, Thr, Tyr

○ Positively charged amino acids: Arg, His, Lys

○ Negatively charged amino acids: Asp, Glu

○ Amino acids containing -OH group: Ser, Thr, Tyr. Phosphate groups can be added to the -OH group, making them useful in signal transduction.

○ Ser, Thr: Involved in phosphorylation cascades in signal transduction.

○ Tyr: Present in tyrosine kinase receptors in signal transduction.

○ Amino acids containing sulfur: Cys, Met. Only Cys forms disulfide bonds.

○ Amino acids containing phenyl group: Phe, Trp, Tyr

○ Phenyl group shows absorbance at 280 nm. Mechanism for quantifying proteins using a UV spectrometer.

○ Amino acids not used in TCA cycle: Leu, Lys

⑥ Titration of Amino Acids

○ Related to each amino acid’s pK_a1, pK_a2, pK_aR, pI, hydrophobicity index, and its proportion in proteins.

⑶ Primary Structure of Proteins

① Amino acid sequence.

② Planar nature of peptide bonds.

○ Amide plane: Forms one peptide bond. Plane formed by two alpha carbons and the C, O, N, H between them.

○ Naming multiple bonds in one plane.

Figure 11. Naming multiple bonds in one plane

○ Φ bond: N - C_α bond

○ ψ bond: C_α - C bond

○ ω bond: C - N bond

○ χ bond: C_α - R (functional group) bond

○ C=O bond resonates with ω bond, making C=O and C-N bonds into 1.5 bonds, thus fixed and non-rotatable.

Figure 12. Planar nature of peptide bonds

⑷ Secondary Structure of Proteins

① A three-dimensional coiling or folding of the amino acid sequence, driven by hydrogen bonding between the backbone atoms (H and O) of amino acids.

② Alpha helix (α-helix)

Figure 13. Alpha helix structure

○ The C=O bond of the N-th amino acid and N-H bond of the (N+4)-th amino acid form hydrogen bonds.

○ On average, 3.6 residues per turn (though there is variation).

○ Elastic, right-handed helix.

○ Hydrophilic amino acids have attractions and repulsions that hinder the formation of alpha helices.

○ Alpha helices are mainly formed by hydrophobic amino acids.

○ Commonly observed in transmembrane proteins.

○ Gly: The functional group R is a hydrogen atom, making it small and unsuitable for forming an alpha-helix structure.

○ Pro: Forms an imino group, which restricts hydrogen bonding → Does not form an alpha-helix structure.

③ Beta pleated sheet (β-pleated sheet): Also known as zigzag conformation.

Figure 14. Beta pleated sheet structure

○ Characteristic: Hydrogen bonds exist not only within amino acids but also between amino acid chains.

○ Common structure in fibrous proteins like silk.

○ Spider webs are a structure with β-pleated sheets and added α-helices.

④ Ramachandran plot

○ A 2D representation of secondary structures, with the Φ bond on the horizontal axis and the ψ bond on the vertical axis.

○ Alpha helix structures are concentrated around (-60°, -60°).

○ Beta pleated sheet structures are concentrated around (-120°, 120°).

○ Purpose: To see if residues are in appropriate positions. Many islands on the plot indicate inappropriate positions.

○ Example

Figure 15. Example of a Ramachandran plot

⑸ Tertiary Structure of Proteins

① Overall three-dimensional structure of a polypeptide.

② Interactions between R groups lead to different three-dimensional structures, which determine different properties.

③ Ionic bond

④ Covalent bond

⑤ Disulfide bridge: Makes the tertiary structure more rigid.

○ Reducing agents: Break disulfide bonds. β-mercaptoethanol, DTT (dithiothreitol), etc.

○ Formation: In eukaryotic cells, disulfide bonds are formed in the rough endoplasmic reticulum; in prokaryotic cells, they are formed in the cytoplasm by PDI (protein disulfide isomerase).

○ Anfinsen’s experiment

○ NEM (N-ethylmaleimide): Covalently binds to the -SH group of cysteine not involved in disulfide bonds.

○ DTT (including β-metcaptoethanol): -S-S- → -SH + HS-. Acts as a reducing agent breaking disulfide bonds. Glutathione (GSH) has a similar function.

○ NEM* → DTT → NEM: Quantifies the amount that originally existed as SH groups. Note that * represents a radioactive isotope.

○ NEM → DTT → NEM*: Quantifies the amount that originally existed as -S-S- (disulfide bonds). Note that * represents a radioactive isotope.

○ Conclusion 1: When denaturing factors are removed, the protein restores its original structure.

○ Conclusion 2: Disulfide bonds contribute irreversibly to the formation of the three-dimensional structure and must be carefully regulated.

⑥ Hydrophobic interactions: Forces arising because the biological environment is water.

⑦ Polar bonds and hydrogen bonds between R groups

⑧ Van der Waals forces

⑨ Other interactions

○ Pseudo hydrogen bond of C=O bond: n → π* interaction, present in more than 45% of protein residues.

○ π-π stacking: Aromatic ring stacking

○ Steric hindrance

○ C5 hydrogen bonds in β-sheet backbone

○ Cation-π interaction

⑩ Specific interactions can be too strong, causing proteins to misfold, necessitating the assistance of protein assembly factors like chaperonins.

○ Example 1. Heat shock protein: Prevents proteins from denaturing due to temperature.

⑹ The quaternary structure of proteins: Interactions between tertiary structure polypeptides.

① Transthyretin (tetramer), hemoglobin (α₂β₂), collagen (3 helix)

⑺ Protein structure determination

① Determining the primary structure

○ Method 1. Edman degradation

○ Degrades amino acids one at a time by binding to the N-terminus of polypeptides in mild alkaline conditions.

○ Only about the first 10 amino acids from the N-terminal can be known.

○ It is a very traditional method that is rarely used nowadays.

○ Method 2. Peptidases

○ Appropriately combining endopeptidases and exopeptidases to appropriately degrade amino acids and determine them one by one.

○ Endopeptidases: Pepsin, trypsin, chymotrypsin, etc.

○ Exopeptidases: Carboxypeptidases, etc.

○ Mechanism of peptidases

○ Method 3. Ab array

○ Method 4. Mass spectrometry

○ 1^st. Electrophoresis & DNA ladder: Can determine whether it’s pure or a mixture.

○ 2^nd. Trypsin treatment

○ 3^rd. First mass spectroscopy: Constructing the MS spectrum.

○ 4^th. Second mass spectroscopy: Constructing the MS/MS spectrum. Also known as tandem MS, MS/MS, fragmentation.

○ 5^th. Reconstruction through the spectrum: Realm of informatics.

○ This method is a first-generation technology and becomes much more complicated when considering post-translational modifications.

② Determining the secondary structure

○ Method 1. Circular dichroism (CD)

○ Method 2. Infrared spectroscopy: Useful for investigating flexible peptide and protein structures.

○ Method 3. Molecular dynamics simulation

③ Determining tertiary and quaternary structures

○ Method 1. X-ray crystallography: About 90% are determined by this method. Allows for inference of 3D coordinates of atoms.

○ Method 2. NMR: About 9% are determined by this method.

○ Method 3. Cryo-EM

○ Resolution is low but is steadily improving and useful for large protein complexes like capsids and amyloids.

○ Protein is immobilized by lowering the temperature to -200 ℃ to observe its 3D structure.

⑻ Protein denaturation

① Denaturation: The three-dimensional structure changes due to factors such as salt concentration, pH, or high temperature, resulting in loss of function.

6. Biomolecules 3. Lipids

⑴ Characteristics

① Mostly composed of carbon and hydrogen, thus high in energy content.

② Hydrophobic: Does not dissolve in water, but dissolves in acetone, alcohol, benzene, etc.

③ Insulating effect (e.g. subcutaneous fat layer), insulation, waterproofing.

⑵ Fat: A triglyceride consisting of glycerol linked to three hydrocarbon-rich fatty acid tails via ester bonds.

① Energy content: 9 kcal/g

② Digestive enzyme, lipase, breaks the ester bonds (ref).

③ Fatty acids: Composed of an even number of carbons because they are biosynthesized from acetyl-CoA.

④ Saturated fatty acid: Fatty acid fully saturated with hydrogen, containing only single bonds. Solid at room temperature, typically of animal origin.

⑤ Unsaturated fatty acid: Contains one or more double bonds (cis configuration). Liquid at room temperature, typically of plant or fish origin.

⑥ Butter and margarine

○ Butter: Saturated fat obtained from milk.

○ Margarine: Made by adding hydrogen to unsaturated fats derived from plants to convert them into saturated fats.

⑦ Trans Fat: Formed during the hydrogenation process when hydrogen is added and then removed, creating trans double bonds.

○ Trans fats have a stacking property, resulting in a higher boiling point.

○ Trans fats have a stacking property, causing them to accumulate in the body, posing health risks.

Figure 16. cis and trans bonds in fatty acid tails

⑶ Steroids: A hydrophobic substance with a planar structure composed of three six-membered rings and one five-membered ring.

① Derived from lipids without monomers (from cholesterol).

② Issues with synthetic steroids

○ Marked mood changes (violent mood swings).

○ Depression, liver damage, high cholesterol, high blood pressure

③ Cholesterol: Found in some animal cell membranes.

○ Refers to steroids with an -OH group.

○ Function 1. Regulating fluidity of animal cell membranes.

○ Function 2. Precursor to various substances: Bile salts, steroid hormones (sex hormones, adrenal cortex hormones, etc.), Vitamin D

○ Function 3. Constituting the protective sheath of nerves

○ Not oxidized in the body to produce energy.

○ 75% of cholesterol is obtained through synthesis.

○ 25% of cholesterol is obtained through diet.

○ Cholesterol is abundant in animal-based foods such as egg yolks, liver, and squid, and it is recommended to consume no more than 300 mg per day.

○ Can cause arteriosclerosis and heart disease.

④ Sterols: Found in some plant cell membranes.

⑤ Sex hormones (estradiol, androgen)

Figure 17. Examples of sex hormones

⑷ Phospholipids = 1 × phosphate head group + 1 × glycerol backbone + 2 × fatty acids + ester bonds. Constituting the phospholipid bilayer. Amphipathic.

① Phospholipid forms in aqueous solutions

○ Micelle: Spherical shape, single layer. Contains a single fatty acid. Used to package and transport hydrophobic substances through blood vessels.

○ Liposome: Ring-shaped structure, bilayer. Contains two fatty acids. Applied in drug delivery.

② Phospholipid Diversity and Membrane Asymmetry: Determined by the types of molecules attached to the phosphate group.

○ Lecithin: The most representative phospholipid. Contains glycerophosphate and adds luster to the skin. Persists in the body for a long time.

Figure 18. Example of phospholipid: Phosphatidylcholine

③ Phospholipid bilayer: Forms hydrophobic boundary of cells. Semi-permeable membrane.

④ Archaea have adapted to extreme environments by utilizing ether (-ROR-) bonds instead of ester (-RCOO-) bonds in the fatty acid linkages of their phospholipids.

Figure 19. Differences Between archaeal phospholipids and those of bacteria and eukaryotes

⑸ Wax

① Ester bond between fatty acids and long-chain alcohols.

② Consists of 40 ~ 60 CH₂ units,

③ Prevents the ingress and egress of water.

④ The Casparian strip, located in the cell walls of the endodermis in plant roots and rich in wax, regulates water transport.

⑹ Fat-soluble vitamins: A, D, E, K

⑺ Carotenoids

① Auxiliary pigments capturing light energy.

② Main reaction: β-Carotene + O₂ → 2 Vitamin A

7. Biomolecules 4. Nucleic Acids: Polymers of nucleotides

⑴ Nucleotide = Phosphate + Nucleoside (e.g., cytidine, uridine, thymidine) = Phosphate + Sugar + Nitrogenous Base

① Sugar: 5-carbon sugar (pentose)

○ Ribose: 2’ carbon has -OH group. Highly reactive.

○ Deoxyribose: 2’ carbon has -H. Less reactive.

② Nitrogenous base

○ Basic ring structure made of carbon-nitrogen covalent bonds.

○ Unshared electron pairs of nitrogen act as H⁺ acceptors.

○ “Base” here refers to the base in acid-base reactions.

○ Aromatic, thus has an absorbance at 260 nm.

○ Note that phenyl groups in proteins have an absorbance at 280 nm.

○ Purity of nucleic acids := Absorbance at 260 nm / Absorbance at 280 nm = Amount of nucleic acids / Total protein

○ N-glycosidic bond: Bond between the nitrogen atom of a base and 5-carbon sugar. The 1st carbon of the sugar participates in bonding.

○ Nitrogenous bases are located inside the double helix to avoid the hydrophilic environment, as they contain hydrophobic aromatic rings.

○ RNA, which cannot form a double helix as DNA does, is less stable.

③ Triphosphate (3 phosphate)

○ A structure containing two high-energy phosphate bonds, providing energy.

○ Triphosphate is located on the outside of the double helix.

○ Reason 1. DNA undergoes polymerization reactions through diphosphate ester bonds, thus DNA polymerase must be accessible.

○ Reason 2. Triphosphate is hydrophilic, thus tends to be on the outside of the double helix.

④ Types ofnucleotides

○ Pyrimidine: Single-ring base. Three types

○ Cytosine (C)

Figure 20. Structure of cytosine

○ Thymine (T)

Figure 21. Structure of thymine

○ Uracil

Figure 22. Structure of uracil

○ Purine: Double-ring base. Three types

○ Guanine (G)

Figure 23. Structure of guanine

○ Adenine (A)

Figure 24. Structure of adenine

○ Inosinic acid (I)

⑵ Polynucleotide

① Phosphodiester bond: Dehydration condensation between the 3’-OH of the first sugar and the 5’-ⓟⓟⓟ of the second sugar in nucleotides.

② Polymerization occurs in the 5’-3’ direction and is an endothermic reaction. Energy is supplied as two molecules of pyrophosphate (PPi) are released from the triphosphate.

③ The 5’ end has a free phosphate group, known as the γ phosphate, exposed.

⑶ DNA (deoxyribonucleic acid)

① Function: Storing genetic information, RNA transcription

② Increase in pH: When the pH exceeds 10, the hydrogen involved in hydrogen bonding dissociates, causing the double strand to separate into single strands.

③ Increase in temperature: Increased kinetic energy of polynucleotides breaks hydrogen bonds between strands, leading to separation into single strands.

④ T_m: Temperature at which 50% of double-stranded DNA becomes single-stranded.

○ Higher G≡C ratio increases bonding strength, thus increasing T_m.

○ Higher amounts of added NaCl counteract repulsion between phosphate groups, thus increasing T_m.

○ Extremely low pH: H⁺ interferes with hydrogen bonds, decreasing T_m. DNA and RNA degrade in strong acids.

○ Extremely high pH: Separates double-stranded DNA into single strands.

⑤ Renaturation kinetics: The study of the extent to which a DNA double helix is restored after denaturation.

○ Regions with high frequency of repetitive sequences denature (ds DNA → ss DNA) first and renature first.

○ High-frequency repetitive sequences: Centromere, etc.

○ Moderate-frequency repetitive sequences: Telomeres, etc.

⑥ DNA Absorbance Experiment

○ At 260 nm, absorbance of 1 corresponds to 50 μg / mL dsDNA concentration.

○ At 260 nm, absorbance of 1 corresponds to 40 μg / mL ssRNA concentration.

⑦ Thermophiles: High G≡C content, increased histones, and supercoiled structures.

⑷ RNA (ribonucleic acid)

① Function: Transmission of genetic information and polypeptide synthesis.

② Increase in pH: The H+ of the 2’-OH group in RNA dissociates → Hydration → Hydrolysis, leading to RNA breaking into fragments.

③ Circular RNA is more stable than linear RNA.

⑸ Comparison of DNA and RNA

Table 2. Comparison of DNA and RNA

① Complementarity: The property that allows restoration of information using the other strand when one strand is damaged.

② Sugar: Deoxyribose has a -H group at the 2nd carbon. Ribose has a -OH (more reactive) group at the 2nd carbon.

③ Instability of RNA

○ Ribose: Increased reactivity due to 2’-OH group.

○ Single-strand: Cannot be corrected or repaired, easily affected by external substances.

○ Deamination process: Amino bases A and C can undergo deamination.

○ Loss of amino group in C base: Becomes U base. A base becomes I.

○ DNA can be corrected, but RNA cannot.

○ RNA undergoes hydrolysis with increased pH.

⑹ Eukaryotic Chromatin

① DNA as genetic material

○ In 1871, Fredrich Miescher first reported DNA in the nucleus.

○ Evidence 1. Chargaff’s rules: [A] = [T], [G] = [C]

○ Evidence 2. X-ray diffraction analysis: Rosalind Elsie Franklin’s diffraction research played a key role in revealing the structure of DNA.

Figure 25. DNA’s 3D diffraction pattern

○ Conclusions by Watson and Crick

Figure 26. DNA structure sketched by Francis Crick

Figure 27. Watson and Crick’s paper

② Structure of DNA

○ Major groove: Phosphate groups are not exposed, making it accessible to transcription factors or enzymes.

○ Minor groove: Phosphate groups are exposed, allowing access to histone proteins.

○ B-form DNA: Watson-Crick model (i.e., DNA in the body). High relative humidity (92 %).

○ A-form DNA: Dehydrated environment (75 %).

○ Example: Double-stranded RNA, DNA-RNA double helix (hairpin, stem loop)

○ Z-form DNA: Zigzag, slender

○ Example: Non-expressed promoters, regions with high G≡C ratio (e.g., centromere)

○ Comparative summary of DNA forms

Table 3. Comparative Summary of DNA Forms

Figure 28. A-form DNA (left), B-form DNA (middle), Z-form DNA (right)

㉠ Minor groove, ㉡ Major groove

③ RNA structure: Most RNA with 3D structure is less than 150 nt in length.

④ Nucleosome (beads-on-a-string, bead-on-string): Also called 10 nm fiber.

○ Structure

○ 146 bp of DNA wraps around a histone octamer (composed of one pair each of H2A, H2B, H3, and H4) with 1.65 turns.

○ Linker DNA: Refers to DNA from H1 to H1. About 200 nucleotides.

○ When treated with endonuclease, H1 to H1 gets cut → visible in electrophoresis.

○ H1: Adjusts nucleosome structure. One per nucleosome. Involved in chromatin condensation.

○ Histone and DNA Binding

○ Over 20% of the amino acids in histones are basic amino acids with a positive charge (e.g., Lys, Arg).

○ Ionic bonds form between the negatively charged phosphate groups of DNA and the positively charged histone proteins.

○ Histone Tail: The N-terminal of the histone molecule within the nucleosome that protrudes outward.

○ Histone Modification: Histone acetylation, histone deacetylation, histone methylation, histone phosphorylation

⑤ 30 nm Fiber: The structure formed when the 10 nm fiber is wound and folded.

Figure 29. 30 nm Fiber

⑥ 300 nm Fiber: A structure in which 30 nm fibers are attached in a looped form around a protein scaffold.

⑦ Chromatin

○ Types of Chromatin

○ Type 1. Euchromatin: Uncondensed chromatin.

○ Type 2. Heterochromatin: Condensed chromatin. Typically centromeres, telomeres exist in heterochromatin form.

○ Structure of Chromatin

○ TAD (topologically associating domain): Chromatin forming loops.

○ The actual shape of TAD is complex and tangled like a ball of yarn.

○ CTCF (11-zinc finger protein, CCCTC-binding factor): A transcription factor encoded by the CTCF gene.

○ CTCF and PDS5A/B determine the boundaries and loop anchors of TAD.

○ WAPL (responsible for releasing cohesin from chromosomes) and PDS5A/B determine the length of the loops.

⑧ Chromosome: The width of a single chromatid is 700 nm.

Figure 30. From nucleosome to chromosome

⑺ Polytene Chromosome (giant chromosome)

① Requirement 1. Related to Mitosis.

② Requirement 2. A giant chromosome formed by repeated DNA replication (only the S phase occurs) without nuclear or cytoplasmic division (no division phase), maintaining a folded state.

③ Endoreduplication

○ Definition: The process of repeatedly synthesizing DNA without the division phase (M phase). Does not form sister chromatids.

○ Location: Ovary nurse cell, follicle cell, abdominal histoblast, fat body cell, gut cell, prepupal salivary gland cell in Drosophila.

○ Result: Formation of polyploidy

④ Composed of more than 1,000 identical DNA molecules.

⑤ Staining reveals alternating dark and light bands.

○ Less condensed light bands are areas of active transcription.

○ Conversely, dark areas are where transcription is suppressed.

⑥ Puff: An area in the polytene chromosome where the light bands locally unravel and expand.

○ Puffs are observed in regions with vigorous gene expression.

○ The location of puffs varies depending on developmental stages and internal or external signals.

⑦ Chromocenter: Not all DNA in chromosomes is polytenic.

○ Exists as highly condensed heterochromatin.

○ Non-polytenic and exhibits minimal transcriptional activity.

○ Salivary gland chromosomes cluster at the chromocenters.

○ DNA in these regions accounts for about 30% of the genome and has very low gene density.

○ Puffs are observed in regions with active gene expression.

⑧ Example: Salivary chromosomes of dipteran insects

Figure 31. Sketch of salivary gland chromosomes by Calvin B. Bridges

○ Facilitates the production of glue needed for pupation.

○ Salivary gland chromosomes have a polyteny level of 1024.

○ Salivary glands degenerate during metamorphosis.

⑻ Lampbrush Chromosome

① Requirement 1. Related to Meiosis.

② Requirement 2. Formed when bivalent chromosomes fail to separate during the first meiotic division.

③ Feature: Lateral Loops

Figure 32. Lateral Loops

⑼ Multinucleate

① Requirement 1. Related to Mitosis.

② Requirement 2. Nuclear division occurs but cytoplasmic division does not.

⑽ Polyploid

① Requirement 1. Related to Meiosis.

② Requirement 2. Treated with colchicine to inhibit separation of homologous chromosomes and then combined with normal gametes.

③ Example: Seedless watermelon (3n)

⑾ Comparison of polytene chromosome, lampbrush chromosome, Multinucleate, and polyploid

Table 4. Comparison of polytene chromosome, lampbrush chromosome, multinucleate, and polyploid

Input: 2015.06.22 22:36

Edit: 2020.03.21 10:16