Cell Cycle Regulation (General)

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Cell Division (General)

 

Cell Division

Cell division is a fundamental process by which a parent cell divides into two or more daughter cells. This process is essential for growth, repair, tissue regeneration, and reproduction in organisms. Before division, the cell duplicates all its components, including its DNA (genetic material). 

This fundamental biological process ensures genetic continuity across generations.

Types of Cell Division

1. Amitosis (Direct Cell Division)

• A simpler, less precise form of division, typically seen in certain lower organisms or specific cell types.

• The nucleus elongates and divides directly without forming spindle apparatus or chromosome condensation. The cytoplasm divides afterwards.

• Example: bacteria, yeast, and some protozoa

2. Mitosis (Equational Division)

• A process where a single cell divides into two identical daughter cells (daughter cells have the same number of chromosomes as the parent cell, e.g., 2n → 2n).

• It is crucial for growth, repair, and asexual reproduction.

• Example: Division in somatic (vegetative) cells

3. Meiosis (Reductional Division)

• A process where a single cell divides twice to produce four genetically distinct daughter cells, each with half the number of chromosomes as the parent cell e.g., 2n → n.

• It is essential for sexual reproduction and generating genetic variation.

• Example: Division in germ cells (reproductive cells) to form gametes (sperm and egg cells).

Mitosis

Mitosis produces two genetically identical daughter cells, each containing the same number of chromosomes as the parent cell. This process is essential for growth, tissue repair, and asexual reproduction.

Mitosis is preceded by Interphase (G1, S, G2 phases), where the cell grows and the DNA is replicated. The division itself, the M phase, includes Karyokinesis (nuclear division) and Cytokinesis (cytoplasmic division).

Phases of Mitosis

Prophase

This is the first and longest stage of mitosis, where the cell prepares for the separation of chromosomes. The events of this phase are as follows: 

Events of Prophase	Significance
Chromatin Condensation	The loose, thread-like chromatin coils and condenses to form discrete, compact chromosomes. Each chromosome is duplicated, consisting of two identical sister chromatids joined at the centromere.
Nucleolus Disappears	The nucleolus, where ribosomes are synthesized, disintegrates.
Centrosome Migration	In animal cells, the two centrosomes (which were duplicated in Interphase) begin to move away from each other toward opposite poles of the cell.
Mitotic Spindle Formation	Microtubules begin to polymerize from the centrosomes, forming the mitotic spindle, which will later separate the chromosomes.
Nuclear Envelope Breakdown	The nuclear membrane completely fragments towards late prophase. Allows the spindle microtubules to access and interact with the chromosomes.

Metaphase

This phase is defined by the alignment of the chromosomes at the center of the cell. The events of this phase are as follows: 

Events of Metaphase	Significance
Chromosome condensation	Chromosomes attain the maximum condensed stage.
Spindle Attachment	The spindle microtubules attach to the kinetochores (protein structures) located at the centromere of each sister chromatid. The attachment to kinetochores is essential for the precise movement and separation of chromatids.
Chromosome Alignment (Metaphase Plate)	Chromosomes are pulled by the spindle fibers to align along the cell's equatorial plane, forming the Metaphase Plate. This central alignment ensures that sister chromatids will separate correctly and equally into the two daughter cells.

Anaphase

This is the shortest phase, characterized by the separation of sister chromatids. The events of this phase are as follows: 

Events of Anaphase	Significance
Sister Chromatid Separation	The proteins (cohesins) holding the sister chromatids together at the centromere break down, allowing the centromeres to split. This is the crucial step for ensuring that each future daughter nucleus receives a complete and identical set of genetic information.
Movement to Poles	The newly separated sister chromatids (now considered individual daughter chromosomes) are rapidly pulled by the shortening kinetochore microtubules toward opposite poles of the cell. This action separates the two full genomes destined for the daughter cells.
Cell Elongation	Non-kinetochore microtubules lengthen, which pushes the poles apart, causing the entire cell to elongate. Prepares the cell for the physical splitting of the cytoplasm.

Telophase

This is essentially the reversal of prophase, where two new nuclei are formed. The events of this phase are as follows: 

Events of Telophase	Significance
Nuclear Envelope Re-formation	A new nuclear envelope forms around each complete set of chromosomes at the two poles of the cell. This marks the end of karyokinesis (nuclear division) and creates two distinct nuclei.
Chromosomes Decondense	The chromosomes unwind and uncoil, returning to their long, dispersed chromatin form. The DNA returns to its functional state for gene expression in the newly formed daughter cells.
Spindle Disassembly	The mitotic spindle fibers depolymerize and break down. The components are recycled for use in the cytoskeleton of the new cells.
Nucleoli Reappear	The nucleoli re-form within the new nuclei.

Cytokinesis (Not a phase of Mitosis, but part of the M-phase)

Event	Description
Cytoplasm Division	The physical division of the cytoplasm and its contents.
Animal Cells	A cleavage furrow (a groove in the cell surface) forms and deepens, pinching the parent cell into two daughter cells.
Plant Cells	A cell plate (which will become the new cell wall) forms in the middle of the cell, dividing the parent cell into two.

Significance of Mitosis

• Growth: Increases the number of cells in a multicellular organism, leading to growth.

• Repair and Regeneration: Replaces damaged, dead, or worn-out cells (e.g., healing a wound).

• Asexual Reproduction: The basis for reproduction in many unicellular and simple multicellular organisms (e.g., fission in bacteria, vegetative propagation in plants).
• Maintains Chromosome Number: Ensures the two daughter cells receive the exact same number and type of chromosomes as the parent cell (equational division).

Phases of mitosis

Meiosis

Meiosis produces four haploid gametes (sperm or egg cells) with half the chromosome number, ensuring genetic diversity through crossing over and independent assortment. This process is essential for sexual reproduction.

Meiosis involves two sequential cycles of nuclear and cell division: Meiosis I and Meiosis II. It is preceded by a single interphase where DNA is replicated.

Phases of Meiosis

Meiosis I: Reductional Division

Meiosis I is the first division where homologous chromosomes separate, reducing the chromosome number from diploid (2n) to haploid (n).

Phase	Sub-phases	Key Events	Significance
Prophase I		The longest and most complex phase and consists of 5 sub-phases:	Crossing over is crucial for genetic recombination (variation). The paired chromosomes ensure proper separation.
	Leptotene	Chromosome Condensation Begins, Axial Elements Form	The chromatin threads start to coil and condense, making the individual chromosomes (each with two sister chromatids) visible as long, thin strands. Protein scaffolds assemble along the length of each homologous chromosome.
	Zygotene	Synapsis Begins, Synaptonemal Complex Forms, Bivalents/Tetrads Form	Homologous chromosomes begin to align precisely, coming together side-by-side in a process called synapsis. A ladder-like protein structure, the synaptonemal complex, forms between the paired homologous chromosomes, holding them tightly together. The paired structure consisting of two homologous chromosomes (four sister chromatids total) is now fully formed and referred to as a bivalent or tetrad. Precise alignment of homologous chromosomes is established, which is essential for accurate crossing over.
	Pachytene	Synapsis Complete, Crossing Over Occurs	The paired homologous chromosomes are fully synapsed. Genetic exchange (recombination) takes place between the non-sister chromatids of the homologous chromosomes. This happens at specific points called recombination nodules. Genetic Variation is introduced by shuffling alleles between maternal and paternal chromosomes, creating recombinant chromosomes.
	Diplotene	Synaptonemal Complex Dissolves, Homologues Begin to Separate, Chiasmata Become Visible	The protein complex holding the homologues together disintegrates. The homologous chromosomes start to repel and move apart, but they remain attached at the sites where crossing over occurred. The points of attachment where genetic exchange occurred are now physically visible as X-shaped structures called chiasmata (plural; chiasma, singular). In many female mammals, oocytes enter a prolonged resting stage (Dictyotene) during Diplotene, which can last for years or decades.
	Diakinesis	Chromosomes Fully Condensed, Terminalization of Chiasmata, Nuclear Disintegration, Spindle Assembly begins	The chromosomes reach their maximum condensation. The chiasmata move towards the ends (terminalize) of the homologous chromosomes, further separating them while still keeping the pairs linked. The nucleolus disappears, and the nuclear envelope breaks down. The meiotic spindle begins to assemble, marking the end of Prophase I and the transition to Metaphase I.
Metaphase I		Homologous pairs (bivalents) align randomly at the cell's equatorial plate (metaphase plate). Spindle fibers from one pole attach to one full homologous chromosome (both sister chromatids).	Independent Assortment (random orientation) occurs here, which is a second major source of genetic variation.
Anaphase I		Homologous chromosomes separate and are pulled to opposite poles. Sister chromatids remain attached at their centromeres.	This is the point of reduction: each pole receives a haploid set of chromosomes, though each chromosome is still duplicated.
Telophase I & Cytokinesis I		Chromosomes gather at the poles. The nuclear envelope may reform. Cytokinesis divides the cell into two haploid daughter cells (n), each with duplicated chromosomes.	The chromosome number has been reduced by half.22 A brief interphase (Interkinesis) may follow, but no DNA replication occurs.

Sub-phases of Mitotic Prophase I

Phases of Meiosis

Meiosis II: Equational Division

Meiosis II resembles mitosis but begins with a haploid cell (n) and involves the separation of sister chromatids. It is called equational because the chromosome number remains haploid (n).

Phase	Key Events
Prophase II	The nuclear envelope (if reformed) breaks down, and the spindle apparatus re-forms in both haploid daughter cells. Prepares the cell for the second round of division.
Metaphase II	Individual chromosomes (composed of two sister chromatids) align along the equatorial plate of each of the two cells. Kinetochore microtubules attach to the centromere of each sister chromatid. The chromosomes are now set up for the final separation of genetic material.
Anaphase II	The centromeres split, and the sister chromatids separate, moving to opposite poles. Each chromatid is now considered an individual chromosome. Sister chromatid separation is achieved, similar to mitosis.
Telophase II & Cytokinesis II	Chromosomes arrive at the poles and decondense. New nuclear envelopes form around each of the four sets of chromosomes. Cytokinesis fully separates the cells, resulting in four unique haploid (n) daughter cells (gametes). Produces the final, genetically diverse gametes ready for fertilization.

Significance of Meiosis

• Formation of Gametes: Essential for the production of haploid gametes (sex cells) for sexual reproduction.

• Maintenance of Chromosome Number: Ensures that the species-specific diploid chromosome number (2n) is restored after fertilization when two haploid gametes fuse.

• Genetic Variation: Crossing over (Prophase I) and Independent Assortment (Metaphase I) reshuffle genetic material, producing unique combinations and contributing to the diversity necessary for evolution.

Mitosis vs Meiosis

Feature	Mitosis	Meiosis
Type of Cell	Somatic (vegetative) cells	Germ (reproductive) cells
Number of Divisions	One	Two (Meiosis I and Meiosis II)
Daughter Cells	Two	Four
Chromosome Number	Remains the same as parent (Diploid, 2n)	Reduced to half the parent number (Haploid, n)
Genetic Identity	Genetically identical to the parent cell	Genetically different from the parent cell and each other
Purpose	Growth, repair, tissue regeneration, asexual reproduction	Sexual reproduction (gamete formation) and genetic variation
Pairing of Homologous Chromosomes	No	Yes, in Prophase I (synapsis)
Crossing Over	No	Yes, in Prophase I

Proteins

 Proteins are central to nearly all biological processes and possess key properties that enable their wide range of functions.

Crucial Functions of Proteins

Proteins perform diverse, essential roles in living systems:

• Catalysts: Function as enzymes to speed up specific chemical reactions.

• Transport and Storage: Carry and store molecules, such as oxygen.

• Structural Support: Provide mechanical support (e.g., in connective tissue and the cytoskeleton).

• Immunity: Offer immune protection.

• Movement: Generate movement (e.g., in muscle cells).

• Communication: Transmit nerve impulses and signals.

• Regulation: Control growth and differentiation.

Key Properties of Proteins

1. Linear Polymers with Defined Structures

• Building Blocks: Proteins are linear polymers made of monomer units called amino acids, linked end-to-end.

Amino acid structure

• Peptide Bond: Amino acids are linked by a peptide bond (or amide bond), formed by linking the α-carboxyl group of one amino acid to the α-amino group of another, with the loss of a water molecule. This bond is kinetically stable.

Peptide bond formation

• Polypeptide Chain: A series of amino acids joined by peptide bonds forms a polypeptide chain; each amino acid in the chain is called a residue.
• Directionality: A polypeptide chain has directionality:
• N-terminal (α-amino) end: The beginning of the chain.
• C-terminal (α-carboxyl) end: The end of the chain.
• Protein Structure Levels: The amino acid sequence dictates the three-dimensional structure:
• Primary Structure: The specific sequence of linked amino acids
• Secondary Structure: Local three-dimensional structure formed by hydrogen bonds between amino acids near one another (e.g., α-helices, β-sheets).
• Tertiary Structure: Overall long-range three-dimensional structure formed by long-range interactions between amino acids. Protein function depends directly on this structure.
• Quaternary Structure:  Exists in proteins composed of several distinct polypeptide chains (subunits) that assemble into a functional complex.

Protein structure levels

• Cross-links: Polypeptide chains can be cross-linked; the most common are disulfide bonds, formed by the oxidation of a pair of cysteine residues, resulting in a unit called cystine.

2. Wide Range of Functional Groups

• Proteins contain diverse functional groups including alcohols, thiols, carboxylic acids, and basic groups.
• The array and sequence of these chemically reactive groups account for the broad spectrum of protein function, especially the catalytic activity of enzymes.

3. Ability to Form Complex Assemblies

• Proteins can interact with each other and other macromolecules (e.g., DNA, lipids) to form complex, synergistic assemblies or "macromolecular machines."
• Examples include machinery for DNA replication, signal transmission, and muscle contraction.

4. Varying Rigidity and Flexibility

• Some proteins are rigid (e.g., structural elements in the cytoskeleton or connective tissue).
• Others display flexibility and can act as hinges, springs, or levers.
• Conformational changes in flexible proteins enable the transmission of information and the regulated assembly of larger complexes.

Amino Acids: The Building Blocks

• Structure: An α-amino acid consists of a central α-carbon atom linked to:
• An amino group (NH₂)
• A carboxylic acid group (COOH)
• A hydrogen atom (H)
• A distinctive R group (or side chain)

L and D isomers of amino acids

• Chirality: With four different groups attached to the α-carbon, α-amino acids are chiral (except glycine, whose R group is a single H atom, making it achiral).
• Isomers: Chiral amino acids exist as L and D isomers (mirror images). Only L amino acids are constituents of proteins.
• Ionization (Zwitterions): In solution at neutral pH, amino acids exist predominantly as dipolar ions (zwitterions), where the amino group is protonated (-NH₃⁺) and the carboxyl group is deprotonated (-COO^-). The ionization state varies with pH.

The ionization state of amino acids under different pH conditions

• The Set of 20: All proteins are constructed from the same set of 20 common amino acids, with side chains varying in size, shape, charge, hydrogen-bonding capacity, hydrophobic character, and chemical reactivity.

Classification of Amino Acids (Based on R Group)

The 20 common amino acids are categorized into four groups:

1. Hydrophobic Amino Acids (Nonpolar R groups)

• Tend to cluster together in the interior of water-soluble proteins (hydrophobic effect).
• Aliphatic: Glycine (achiral, H side chain), Alanine (CH₃), Valine, Leucine, Isoleucine (includes an additional chiral center), Methionine (includes a thioether -S- group).

 

• Cyclic/Restricted: Proline (side chain bonded to both the N and α-carbon atoms, forming a pyrrolidine ring, which restricts conformation).

• Aromatic: Phenylalanine (purely hydrophobic), Tryptophan (less so due to its NH group in the indole ring).

 

2. Polar Amino Acids (Neutral R groups, Uneven Charge Distribution)

• More hydrophilic (water-loving) than hydrophobic amino acids.
• Hydroxyl Groups (-OH): Serine, Threonine (has an additional asymmetric center), Tyrosine (aromatic ring). The -OH groups make them reactive.

  

• Carboxamide Groups (-CONH₂): Asparagine, Glutamine.

• Sulfhydryl Group (-SH): Cysteine (structurally similar to serine but with a more reactive thiol group; pairs can form disulfide bonds).

3. Positively Charged Amino Acids (Positive Charge at Physiological pH)

• Highly hydrophilic.
• Lysine (primary amino group at terminus).
• Arginine (guanidinium group at terminus).
• Histidine (imidazole group; pK_α near 6, can be uncharged or positively charged near neutral pH, often found in enzyme active sites).

4. Negatively Charged Amino Acids (Negative Charge at Physiological pH)

• Also highly hydrophilic.
• Aspartic acid and Glutamic acid.
• Often called Aspartate and Glutamate to emphasize their negatively charged state (COO^-) at physiological pH.

Significance of Amino Acid Sequence

The amino acid sequence (primary structure) is profoundly important:

• Determines Function: Essential for elucidating a protein's function (e.g., enzyme catalytic mechanism).
• Determines 3D Structure: The sequence is the link between the genetic message (DNA/RNA) and the resulting functional 3D structure.
• Disease: Alterations in a single amino acid can cause severe diseases (e.g., sickle-cell anemia).
• Evolutionary History: Similar sequences indicate a common ancestor, allowing molecular events in evolution to be traced.

Primary Structure: Geometry and Conformation of the Protein Backbone

The specific geometry of the polypeptide backbone is crucial because it limits the number of possible protein folds, allowing proteins to adopt a unique, functional three-dimensional structure.

Key Features of the Peptide Bond

The chemical nature of the peptide bond (linking the carbonyl C and amino N) imposes significant constraints on the backbone:

·     Planar Structure: The peptide bond is essentially planar. Six atoms lie in the same plane: α-carbon and CO (from the first amino acid) and NH, α-carbon (from the second amino acid).

Planar structure of peptide bond

·       Partial Double-Bond Character: The bond resonates between a single bond and a double bond, giving it partial double-bond character.

o    This prevents rotation about the C-N peptide bond, constraining the conformation of the peptide backbone.

Peptide bond resonance

o    The C-N bond length (typically 1.32 Å) is intermediate between a single bond (1.49 Å) and a double bond (1.27 Å).

·   Uncharged: The peptide bond is uncharged, which permits polymers to form tightly packed globular structures.

·      Trans Configuration Preference: Two configurations are possible for the planar peptide bond:

o    Trans: The two α-carbon atoms are on opposite sides of the peptide bond. Almost all peptide bonds in proteins are trans due to fewer steric clashes.

o    Cis: The two α-carbon atoms are on the same side of the peptide bond.

o    Exception: The most common cis peptide bonds are X-Pro linkages, where the cyclic side chain of proline reduces the steric difference between the trans and cis forms.

Configurations of peptide bond

 Freedom of Rotation and Torsion Angles

In contrast to the rigid peptide bond, the adjacent single bonds allow rotation:

·       Single Bonds: The bonds between the N and the C_α atom, and between the C_α and the CO atom, are pure single bonds.

·     Conformational Freedom: The rotation around these two bonds per residue allows proteins to fold in many different ways.

·       Torsion Angles: These rotations are specified by torsion angles:

o    Phi (Φ): Angle of rotation about the bond between the nitrogen (N) and the α-carbon (C_α) atoms.

o    Psi (ψ): Angle of rotation about the bond between the α-carbon (C_α) and the carbonyl carbon (CO) atoms.

o    The Φ and ψ angles determine the path of the polypeptide chain.

Rotation about bonds in a polypeptide chain

Ramachandran Plot and Steric Exclusion

Not all combinations of Φ and ψ angles are possible due to physical limitations:

·      Steric Clashes: Many combinations of Φ and ψ angles are forbidden because of steric collisions (atoms physically occupying the same space).

·    Ramachandran Plot: The allowed combinations of Φ and ψ angles are visualized on a two-dimensional plot called a Ramachandran plot.

·      Limitation: Approximately three-quarters of the possible Φ and ψ combinations are excluded simply by local steric clashes.

·     Thermodynamic Role: The rigidity of the peptide unit and the restricted set of allowed Φ and ψ angles limit the number of possible conformations for the unfolded protein. This reduction in conformational flexibility is essential to overcome the unfavorable entropy of folding, allowing proteins to fold into a unique, defined structure.

Ramachandran plot

Protein Secondary Structure: Helices, Sheets, and Turns

Secondary structure refers to the regular, local folded segments of a polypeptide chain, stabilized by a regular pattern of hydrogen bonds between the peptide N-H and C=O groups of amino acids that are near one another in the linear sequence.

1. The Alpha (α) Helix

The α-helix is a common, rod-like, coiled structure proposed by Linus Pauling and Robert Corey.

·    Structure: A tightly coiled backbone forms the inner part of the rod, with side chains extending outward in a helical array.

·   Stabilization: Stabilized by intrachain hydrogen bonds (within the same polypeptide strand).

·   Hydrogen Bonding Pattern: The C=O group of each amino acid forms a hydrogen bond with the N-H group of the amino acid situated four residues ahead in the sequence (i to i+4). This pattern ensures that almost all main-chain C=O and N-H groups are hydrogen bonded (except near the ends).

H-bonding pattern in a helix

·   Geometry:

o    Residues per turn: 3.6 amino acid residues per complete turn.

o    Rise (Translation) per residue: 1.5 Å along the helix axis.

o    Pitch (Length of one turn): 3.6 residues x 1.5 Å / residue = 5.4 Å.

·   Screw Sense:

o    The α-helices found in proteins are right-handed (clockwise) because this orientation is energetically more favorable due to less steric clash between the side chains and the backbone.

Alpha helix

·   Helix Destabilizers ("Helix Breakers"):

o    Proline: Lacks an N—H group for hydrogen bonding and its rigid ring structure prevents the necessary Φ torsion angle.

o  Amino Acids with β-carbon branching (Valine, Threonine, Isoleucine): Their bulkiness causes steric clashes.

o    Serine, Aspartate, Asparagine: Their side chains can compete for the main-chain N—H and C═O groups, disrupting the regular pattern.

· Occurrence: α-helices are abundant; for example, they make up about 75% of the residues in ferritin. Many proteins that span biological membranes also contain α-helices.

2. The Beta (β) Pleated Sheet

The β-pleated sheet (or β-sheet) is another common periodic structure, markedly different from the rod-like α-helix.

·  Components: Formed by two or more polypeptide chains or segments called β-strands lying next to one another.

·    β-Strand Structure: Each β-strand is almost fully extended (not coiled).

o    Distance between adjacent amino acids: Approximately 3.5 Å (much longer than 1.5 Å in an α-helix).

o    Side chains of adjacent amino acids point in opposite directions (up and down).

· Stabilization: Stabilized by interchain hydrogen bonds (between the N—H and C═O groups of adjacent strands).

·   Arrangements: Adjacent β-strands can run in two ways:

o    Antiparallel β-Sheet: Adjacent strands run in opposite directions. The N—H and C═O of each amino acid are directly hydrogen bonded to the C═O and N—H groups of a partner on the adjacent strand.

o    Parallel β-Sheet: Adjacent strands run in the same direction. The hydrogen bonding is slightly more complex, connecting each residue's N—H to the C═O of one residue on the adjacent strand, and its C═O to the N—H of an amino acid two residues farther along.

·   Shape: β-sheets are structurally diverse; while they can be flat, most adopt a somewhat twisted shape.

·   Occurrence: They are important structural elements, forming the basis of proteins like fatty acid-binding proteins. β-sheets typically contain 4 or 5 strands, but can have 10 or more.

Anti-parallel beta sheet

Parallel beta sheet

3. Turns and Loops

These elements facilitate the compact, globular shape of proteins by reversing the polypeptide chain's direction.

·  Reverse Turn (or β-turn/Hairpin Turn): A common structural element that causes an abrupt reversal in the polypeptide chain's direction.

o    Often stabilized by a hydrogen bond between the C═O groups of residue i and the N—H group of residue i+3.

·   Loops (or Ω-loops): More elaborate structures responsible for chain reversals.

o    Lack regular, periodic structures (unlike α-helices and β-strands).

o    Are often rigid and well defined despite their lack of periodicity.

· Location and Function: Turns and loops invariably lie on the surfaces of proteins and frequently participate in interactions between proteins and other molecules.

Structure of a reverse turn

 

                                             Alpha helix                                                          Beta sheet

Tertiary and Quaternary Protein Structure

1. Tertiary Structure: The Overall Fold

Tertiary structure refers to the overall course of the polypeptide chain; specifically, the spatial arrangement of amino acid residues that are far apart in the linear sequence, and the pattern of any disulfide bonds.

Features of Tertiary Structure

·         It represents the final, stable, three-dimensional shape of a single polypeptide chain.

·         Example (Myoglobin): The oxygen-storage protein in muscle is a single, compact polypeptide chain (153 amino acids) with approximately 70% of the chain folded into eight α-helices connected by turns and loops.

·         Driving Force: The Hydrophobic Effect

o    In an aqueous environment, protein folding is primarily driven by the tendency of hydrophobic residues to be excluded from water (the Hydrophobic Effect).

o    Interior Core: Consists almost entirely of nonpolar residues (e.g., leucine, valine, methionine). Charged residues are excluded from the interior.

o    Exterior Surface: Consists of a mixture of polar and nonpolar residues.

·         Stabilizing Interactions:

o    Hydrogen Bonding: To bury a segment of the main chain in the hydrophobic interior, all peptide N—H and C═O groups must be paired by hydrogen bonding (achieved by forming α-helices or β-sheets).

o    Van der Waals Interactions: These maximize stability when the nonpolar side chains in the core are tightly packed to minimize empty space.

·       Amphipathic Secondary Structures: Many α-helices and β-strands are amphipathic, meaning they have a hydrophobic face (pointing into the protein interior) and a polar face (pointing into the surrounding aqueous solution).

·         Membrane Proteins (The "Exception"): Proteins that span biological membranes, like porins in bacterial outer membranes, are "inside out" because they function in a hydrophobic environment. Their outside surface is covered largely with hydrophobic residues to interact with the membrane's alkane chains, while the interior often contains polar/charged residues surrounding a water-filled channel.

Motifs and Domains

·         Motifs (Super-secondary Structures): Certain combinations of secondary structure that are present in many proteins and often exhibit similar functions.

o    Example: A helix-turn-helix unit, found in many DNA-binding proteins.

·         Domains: Compact globular units into which a polypeptide chain can fold, ranging from 30 to 400 amino acid residues.

o    Domains may be connected by flexible segments and may be shared among proteins with different overall tertiary structures (e.g., the CD4 immune protein has four similar domains).

3-D structure of myoglobin

2. Quaternary Structure: Subunit Arrangement

Quaternary structure refers to the spatial arrangement of multiple polypeptide chains (subunits) and the nature of their interactions. It is the fourth level of protein organization.

·    Subunit: Each individual polypeptide chain in a protein with quaternary structure is called a subunit.

·         Simple Structures:

o    Dimer: Two identical subunits (e.g., the Cro DNA-binding protein).

o    Tetramer: Four subunits.

·     Complex Structures: Proteins can contain more than one type of subunit, often in variable numbers.

·         Example (Hemoglobin): The oxygen-carrying protein in blood is a α₂β₂ tetramer, consisting of two α subunits and two β subunits. Subtle changes in the arrangement of these subunits are critical for its function.

·    Viral Coats: Viruses often utilize quaternary structure to make the most of limited genetic information, forming symmetric capsids using many copies of a few types of subunit (e.g., rhinovirus coat uses 60 copies of each of four subunits).

 

The α2β2 tetramer of human hemoglobin