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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.Biopolymer Library

c.Pharma and Disulfide Bonds

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 (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: Plays an important role in temperature regulation

④ Excellent Solvent (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 Polymer Formation: All polymers are made through dehydration reactions (water is produced) of monomers

⑶ Polymer Degradation: 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

○ α linkage glucose polymer, more branched, short-term energy source in animals

○ α 1 → 4 linkage, α 1 → 6 linkage

② Starch

○ α linkage glucose polymer, long-term energy source in plants

③ Cellulose

○ β linkage glucose polymer, forms cell walls, most abundant carbohydrate on Earth

○ β 1 → 4 linkage

④ Chitin

○ NAG(N-Acetylglucosamin): The 2nd carbon functional group of glucose is replaced with an amino 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

○ Dextran is a trademark name

⑹ α Linkage and β Linkage

Figure. 7. α Glucose (left) and β Glucose (right)

① α Linkage: Glucose units are bonded without flipping upside down, creating an α helix structure

② α Linkage Glucose: The -OH group of the 1st carbon and the -OH group of the 4th carbon are in the same direction, unstable → Energy Storage

③ β Linkage

○ One glucose flips upside down, so the 1st carbon and 4th carbon face each other, forming a straight line

○ β linkage glucose chains cohere tightly due to strong hydrogen bonds

④ β Linkage Glucose: The -OH group of the 1st carbon and the -OH group of the 4th carbon are in opposite directions, stable → Structural Formation

⑺ Starch

① Amylose: α linkage glucose polymer without branches. 1st carbon and 4th carbon are bonded

② Amylopectin: Branched α linkage glucose polymer. 1st carbon and 6th carbon are bonded

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

④ Most digestive enzymes can only break down α linkages due to the spacious arrangement that allows enzyme accessibility

Figure. 8. Amylose and Amylopectin

⑻ 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. 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 - Can add phosphate for signal transduction

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

○ Tyr: Present in tyrosine kinase receptors in signal transduction

○ Sulfur-containing amino acids: Cys, Met. Only Cys forms disulfide bonds

○ Phenyl group containing amino acids: 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

○ Each amino acid’s pKa1, pKa2, pKaR, 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 - Cα bond

○ ψ bond: Cα - C bond

○ ω bond: C - N bond

○ χ bond: Cα - 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 Structure formed by the coiling or folding of the amino acid sequence due to hydrogen bonds between the amino acid backbone (H and O)

② Alpha helix (α-helix)

Figure. 13. Alpha helix structure

○ The C=O bond of the Nth 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: Inappropriate for alpha helix structure due to small size as R group is hydrogen

○ Pro: Forms an imino group, restricting hydrogen bonding → Does not form alpha helix

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

Figure. 14. Beta pleated sheet structure

○ Characteristic: Not only intra-amino acid hydrogen bonds but also inter-amino acid chain hydrogen bonds

○ Common structure in fibrous proteins like silk

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

④ Ramachandran plot

○ Φ bonds on the x-axis and ψ bonds on the y-axis, a two-dimensional representation of tertiary structure

○ 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.

○ In eukaryotic cells, formed in the endoplasmic reticulum. In prokaryotic cells, 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: Initially existing as SH groups quantified, * indicates radioactive isotope

○ NEM → DTT → NEM*: Initially existing as -S-S- quantified, * indicates radioactive isotope

○ Conclusion 1: If denaturing factors of a protein are removed, the protein reverts to its original structure

○ Conclusion 2: Since disulfide bonds contribute irreversibly to the creation of tertiary structure, they must be finely 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

○ Similar hydrogen bonds in C=O bonds: n → π*, 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 Due to certain interactions being strong, proteins can fold incorrectly, necessitating protein assembly proteins like chaperones

○ 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

○ A very traditional method, currently almost unused

○ 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 : Change in tertiary structure due to concentration of salts, pH, high temperatures, 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 : Triglyceride with three hydrocarbon-rich fatty acid tails linked by ester bonds to glycerol

① Energy content : 9 kcal/g

② Digestive enzyme lipase breaks the ester bonds (ref)

③ Fatty acids are synthesized from acetyl coA, so they consist of an even number of carbons

④ Saturated fatty acid : Hydrogen-saturated fatty acids with only single bonds. Solid at room temperature, animal-based

⑤ Unsaturated fatty acid : At least one cis double bond. Liquid at room temperature, plant-based + fish

⑥ Butter and margarine

○ Butter : Saturated fat obtained from milk

○ Margarine : Unsaturated fat obtained from plants, hydrogenated to become saturated fat

⑦ Trans fat : Created during hydrogenation, where hydrogen is added and then removed, creating trans double bonds

○ Trans fats accumulate and have a high boiling point

○ Trans fats accumulate in the body, thus posing a health risk

Figure. 16. cis and trans bonds in fatty acid tails]

⑶ Steroids : Flat structure composed of three hexagonal rings and one pentagonal ring, hydrophobic substance

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 egg yolks, liver, squid, etc., and it’s advisable to consume less 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 solution

○ Micelle : Spherical shape. Single layer. Packs 1 fatty acid, transports hydrophobic substances through blood vessels as micelles

○ Liposome : Ring shape. Double layer. Packs 2 fatty acids, applied in drug delivery

② Diversity and membrane asymmetry of phospholipids : Type of molecule attached to the phosphate group

○ Lecithin : Most representative phospholipid. Contains glycerol phosphate and adds luster to the skin. Remains 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 In extremophiles, the fatty acid bonds in phospholipids are ether (-ROR-) bonds instead of ester (-RCOO-) bonds

Figure. 19. Difference between extremophiles’ phospholipids and those of true bacteria and eukaryotes

⑸ Wax

① Ester bond between fatty acids and long-chain alcohols

② Consists of 40 ~ 60 CH2 units

③ Prevents moisture ingress

④ The Casparian strip, deposited with wax in plant root endodermis cells, 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 (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 contain hydrophobic aromatic rings, thus are located inside the double helix

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

③ Triphosphate (3 phosphate)

○ Contains two high-energy phosphate bonds, provides 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 of Nucleotides

○ Pyrimidine : Single-ring base, three types

○ Cytosine (C, cytosine)

○ Thymine (T, thymine)

○ Uracil (uracil)

○ Purine : Double-ring base, three types

○ Guanine (G, guanine)

○ Adenine (A, adenine)

○ Inosinic acid (I, inosinic acid)

○ Structural variations of nucleotides

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 from 5’ to 3’, an endothermic reaction, energy is supplied by the release of two molecules of pyrophosphate (pi) from triphosphate

③ The 5’ end has a free γ phosphate exposed

⑶ DNA (deoxyribonucleic acid)

① Function : Stores genetic information, RNA transcription

② Increase in pH : At pH above 10, hydrogen bonds forming between bases dissociate, leading to separation of double strands into single strands

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

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

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

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

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

○ Extremely high pH : Separates DNA into single strands

⑤ Renaturation kinetics : Study of the extent of double helix restoration after denaturation

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

○ High frequency repetitive sequences example : Satellites

○ Medium frequency repetitive sequences example : Telomeres

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, high histone content, supercoiled structure

⑷ RNA (ribonucleic acid)

① Function : Transmits genetic information, creates polypeptides

② Increase in pH : RNA 2’-OH group’s H+ dissociates → hydration → hydrolysis, RNA fragments

③ Cyclic RNA is more stable than linear RNA

⑸ Comparison of DNA and RNA

Table. 2. Comparison of DNA and RNA

① Complementarity : If one strand is damaged, the information from the other strand can be restored

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

⑷ Eukaryotic Chromatin

① DNA as genetic material

○ 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. 20. DNA’s 3D diffraction pattern

○ Conclusions by Watson and Crick

Figure. 21. DNA structure sketched by Francis Crick

Figure. 22. Watson and Crick’s paper]

② Structure of DNA

○ Major groove : Phosphate groups not exposed. Accessible to transcription factors and enzymes

○ Minor groove : Phosphate groups exposed. Accessible 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., satellites)

○ Comparative summary of DNA forms

Table. 3. Comparative Summary of DNA Forms

Figure. 23. 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 : Also called 10 nm fiber (bead-on-string)

○ Structure

○ 146 bp DNA wraps 1.65 times around an octamer of histones (i.e., H2A, H2B, H3, H4 pairs)

○ 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 (e.g., Lys, Arg) with a positive charge

○ Ionic bond between the negatively charged DNA with phosphate groups and the positively charged histone proteins

○ Histone Tails : N-terminal ends of histones in the nucleosome protruding outward

○ Histone Modification

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

⑥ 300 nm Fiber : The structure in which the 30 nm fiber is attached in a loop 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 and PDS5A/B determine the length of the loop

⑧ Chromosome : The width of a single chromonema is 700 nm

⑸ Polytene Chromosome (giant chromosome)

① Requirement 1. Related to Mitosis

② Requirement 2. ** Without nuclear division, cytoplasmic division** (No division phase) DNA repeatedly replicates ( only S phase ) and remains in a folded state

③ Endoreduplication

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

○ Location : In Drosophila’s ovary nurse cell, follicle cell, abdominal histoblast, fat body cell, gut cell, prepupal salivary gland cell

○ 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 the developmental stage and external signals

⑦ Chromocenter : Not all DNA in chromosomes is polytene

○ Part exists as strong heterochromatin

○ Do not have polytene nature and almost no transcription occurs

○ Salivary chromosomes are clustered around the chromocenter

○ DNA in these areas makes up about 30% of the total genome and has very low gene density

○ Puffs are observed in regions with vigorous gene expression

⑧ Example : Salivary chromosomes of dipteran insects

Figure. 24. Sketch of Calvin B. Bridge’s Salivary Chromosome]

○ Beneficial for producing glue necessary for becoming a pupa

○ Salivary chromosomes have a polytene degree of 1024

○ Salivary glands degenerate during metamorphosis

⑹ Lampbrush Chromosome

① Requirement 1. Related to Meiosis

② Requirement 2. Created when bivalents do not separate during the first meiotic division

③ Feature : Lateral Loops

Figure. 25. Lateral Loops

⑺ Multinucleate

① Requirement 1. Related to Mitosis

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

⑻ 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)

⑼ Comparison of Polytene Chromosome, Lampbrush Chromosome, Multinucleate, Polyploid

Table. 4. Comparison of Polytene Chromosome, Lampbrush Chromosome, Multinucleate, Polyploid

Input : 2015.06.22 22:36

Edit : 2020.03.21 10:16