B - Form and Function

Cell Structure and Function

Ultrastructure of Prokaryotic and Eukaryotic Cells

Prokaryotic and eukaryotic cells represent the two fundamental types of cellular organization in living organisms. While they share some basic features, their structural differences are significant and reflect their evolutionary divergence.

Prokaryotic Cells

Prokaryotic cells, found in bacteria and archaea, are characterized by their simplicity:

• Lack of a membrane-bound nucleus
• No membrane-bound organelles
• Circular DNA located in the nucleoid region
• Ribosomes (70S type)
• Cell wall (usually peptidoglycan in bacteria)
• Flagella for motility in some species

Example

A typical bacterial cell, like Escherichia coli, measures about 1-2 μm in length and has a simple internal structure with a nucleoid region containing its genetic material.

Eukaryotic Cells

Eukaryotic cells, found in protists, fungi, plants, and animals, have a more complex structure:

• Membrane-bound nucleus containing linear DNA organized into chromosomes
• Numerous membrane-bound organelles (e.g., mitochondria, endoplasmic reticulum, Golgi apparatus)
• Larger ribosomes (80S type)
• Cytoskeleton (microfilaments, intermediate filaments, and microtubules)
• In plants: cell wall (made of cellulose) and chloroplasts

Note

The presence of a nucleus and membrane-bound organelles in eukaryotic cells allows for compartmentalization of cellular functions, enabling more complex metabolic processes.

Functions of Organelles

Eukaryotic cells contain various organelles, each with specific functions:

1. Nucleus: Houses genetic material and controls cellular activities
2. Mitochondria: Site of cellular respiration and ATP production
3. Endoplasmic Reticulum (ER):
   • Rough ER: Protein synthesis and modification
   • Smooth ER: Lipid synthesis and detoxification
4. Golgi Apparatus: Modification, packaging, and distribution of proteins
5. Lysosomes: Breakdown of cellular waste and foreign materials
6. Chloroplasts (in plants): Site of photosynthesis
7. Vacuoles: Storage of water, nutrients, and waste products
8. Peroxisomes: Breakdown of fatty acids and detoxification of hydrogen peroxide

Example

In a pancreatic cell, which produces digestive enzymes, the rough ER and Golgi apparatus are particularly well-developed to support the high rate of protein synthesis and secretion.

Cell Specialization and Differentiation

Cell specialization refers to the process by which cells develop specific structures and functions to perform particular roles within an organism. This process is crucial for the development of complex multicellular organisms.

Mechanisms of Cell Differentiation

1. Gene Expression: Different genes are activated or repressed in different cell types
2. Epigenetic Modifications: Chemical modifications to DNA or histones that affect gene expression without changing the DNA sequence
3. Cell Signaling: External signals can trigger specific developmental pathways

Common Mistake

Students often confuse cell specialization with adaptation. While adaptation occurs over generations in response to environmental pressures, cell specialization happens during the development of an individual organism.

Examples of Specialized Cells

1. Neurons: Elongated cells specialized for transmitting electrical signals
2. Red Blood Cells: Biconcave disc-shaped cells optimized for oxygen transport
3. Muscle Cells: Elongated cells containing contractile proteins for movement
4. Plant Root Hair Cells: Thin extensions that increase surface area for water and nutrient absorption

Tip

When studying cell specialization, focus on how the structure of each specialized cell type relates to its function. This structure-function relationship is a key concept in biology.

Membrane Structure and Transport

Fluid Mosaic Model of Membranes

The fluid mosaic model, proposed by Singer and Nicolson in 1972, describes the structure of biological membranes. Key features include:

1. Phospholipid Bilayer: Forms the basic structure of the membrane
2. Membrane Proteins: Embedded in or associated with the lipid bilayer
3. Cholesterol: Provides stability and fluidity to the membrane
4. Glycolipids and Glycoproteins: Present on the outer surface, involved in cell recognition

The model is described as "fluid" because the lipids and proteins can move laterally within the membrane plane, and "mosaic" due to the varied distribution of proteins within the lipid bilayer.

Note

The fluidity of the membrane is crucial for many cellular processes, including cell signaling and membrane fusion events like endocytosis and exocytosis.

Passive and Active Transport Across Membranes

Cells require mechanisms to move substances across their membranes. These mechanisms can be broadly categorized into passive and active transport.

Passive Transport

Passive transport does not require energy input and moves substances down their concentration gradient.

1. Simple Diffusion: Direct movement of small, nonpolar molecules through the lipid bilayer

Example

Oxygen diffuses from areas of high concentration in the lungs to areas of lower concentration in the blood and tissues.

1. Facilitated Diffusion: Movement of polar molecules or ions through protein channels or carriers

Example

Glucose enters cells via GLUT proteins, which act as facilitated diffusion channels.

1. Osmosis: Diffusion of water across a selectively permeable membrane

Example

In plant cells, water moves into the cell by osmosis when the cell is placed in a hypotonic solution, causing the cell to become turgid.

Active Transport

Active transport requires energy (usually in the form of ATP) to move substances against their concentration gradient.

1. Primary Active Transport: Directly uses ATP to move substances

Example

The sodium-potassium pump uses ATP to maintain the concentration gradients of sodium and potassium ions across cell membranes.

1. Secondary Active Transport: Uses the energy stored in electrochemical gradients established by primary active transport

Example

The sodium-glucose cotransporter in intestinal cells uses the sodium gradient to drive glucose uptake against its concentration gradient.

Common Mistake

Students often confuse facilitated diffusion with active transport. Remember, facilitated diffusion does not require energy input and only moves substances down their concentration gradient, while active transport requires energy and can move substances against their concentration gradient.

Cell Division

Mitosis and the Cell Cycle

The cell cycle is a series of events that lead to cell division and the production of two daughter cells. It consists of interphase (G1, S, and G2 phases) and the mitotic phase (mitosis and cytokinesis).

Interphase

1. G1 Phase: Cell growth and preparation for DNA synthesis
2. S Phase: DNA replication
3. G2 Phase: Further growth and preparation for mitosis

Mitotic Phase

Mitosis is the process of nuclear division, followed by cytokinesis (division of the cytoplasm). The stages of mitosis are:

1. Prophase: Chromatin condenses into chromosomes, nuclear envelope breaks down
2. Metaphase: Chromosomes align at the metaphase plate
3. Anaphase: Sister chromatids separate and move to opposite poles
4. Telophase: Nuclear envelopes reform, chromosomes decondense

Example

In the root tip of an onion, cells undergo rapid mitosis to promote growth. Observing these cells under a microscope allows students to identify the different stages of mitosis.

Control of the Cell Cycle

The cell cycle is tightly regulated to ensure proper cell division and prevent uncontrolled growth. Key regulatory mechanisms include:

1. Cyclins and Cyclin-Dependent Kinases (CDKs): Protein complexes that drive the cell cycle forward
2. Checkpoints: Points in the cell cycle where progress is halted if certain conditions are not met
   • G1 checkpoint: Ensures the cell is ready for DNA synthesis
   • G2 checkpoint: Ensures DNA is properly replicated and the cell is ready for mitosis
   • Metaphase checkpoint: Ensures all chromosomes are properly attached to the spindle
3. p53 Protein: A tumor suppressor that can halt the cell cycle or trigger apoptosis in response to DNA damage

Note

Dysregulation of the cell cycle control mechanisms can lead to cancer, characterized by uncontrolled cell division.

Tip

When studying the cell cycle, create a timeline or circular diagram to visualize the sequence of events and the points at which different regulatory mechanisms act.

DNA Structure and Replication

Structure of DNA and RNA

DNA (Deoxyribonucleic Acid) and RNA (Ribonucleic Acid) are nucleic acids that play crucial roles in storing and transmitting genetic information.

DNA Structure

• Double-stranded helix
• Composed of nucleotides: deoxyribose sugar, phosphate group, and nitrogenous base (A, T, C, G)
• Complementary base pairing: A with T, C with G
• Antiparallel strands (5' to 3' in opposite directions)

The structure of DNA can be represented by the following equation:

$$ \text{DNA} = \text{deoxyribose} + \text{phosphate} + \text{nitrogenous base (A, T, C, G)} $$

RNA Structure

• Usually single-stranded (some exceptions exist)
• Composed of nucleotides: ribose sugar, phosphate group, and nitrogenous base (A, U, C, G)
• U (uracil) replaces T (thymine) found in DNA

Example

The structure of DNA allows for its function in genetic storage and replication. For instance, the complementary base pairing enables accurate copying of genetic information during DNA replication.

DNA Replication Process

DNA replication is the process by which a cell creates an exact copy of its DNA before cell division. It is semi-conservative, meaning each new double helix contains one original strand and one newly synthesized strand.

Key steps in DNA replication:

1. Initiation:
   • Helicase unwinds the DNA double helix at specific sites called origins of replication
   • Single-strand binding proteins stabilize the separated strands
2. Elongation:
   • Primase synthesizes short RNA primers
   • DNA polymerase III extends the primers, adding nucleotides in the 5' to 3' direction
   • Leading strand: Continuous synthesis
   • Lagging strand: Discontinuous synthesis (Okazaki fragments)
   • DNA polymerase I removes RNA primers and fills gaps
   • DNA ligase joins Okazaki fragments
3. Termination:
   • Replication forks meet and fusion occurs
   • Topoisomerases resolve any remaining tangles

Note

The enzymes involved in DNA replication work together in a large complex called the replisome.

Common Mistake

Students often forget that DNA replication is bidirectional, occurring simultaneously in both directions from the origin of replication.

Tip

When studying DNA replication, focus on understanding the roles of each enzyme and how they work together to ensure accurate and efficient copying of the genetic material.

Protein Synthesis

Transcription and Translation

Protein synthesis is the process by which cells create proteins based on the information encoded in DNA. It occurs in two main stages: transcription and translation.

Transcription

Transcription is the process of creating an RNA copy of a gene sequence. It occurs in the nucleus of eukaryotic cells.

Key steps in transcription:

1. Initiation:
   • RNA polymerase binds to the promoter region of the gene
   • Transcription factors assist in positioning the RNA polymerase
2. Elongation:
   • RNA polymerase moves along the template DNA strand in the 3' to 5' direction
   • Complementary RNA nucleotides are added to the growing RNA strand in the 5' to 3' direction
   • Base pairing rules: A-U, C-G (U in RNA pairs with A in DNA)
3. Termination:
   • In prokaryotes: Termination occurs at specific sequences
   • In eukaryotes: Poly-A tail is added, and the transcript is cleaved

Example

During transcription of the insulin gene, RNA polymerase creates an mRNA copy of the gene sequence, which will later be translated into the insulin protein.

Translation

Translation is the process of creating a protein based on the sequence of an mRNA molecule. It occurs on ribosomes in the cytoplasm.

Key steps in translation:

1. Initiation:
   • Small ribosomal subunit binds to the 5' end of mRNA
   • Initiator tRNA carrying methionine binds to the start codon (AUG)
   • Large ribosomal subunit joins to form the complete ribosome
2. Elongation:
   • tRNAs bring amino acids to the ribosome based on codon-anticodon matching
   • Peptide bonds form between amino acids
   • Ribosome moves along the mRNA, reading one codon at a time
3. Termination:
   • Stop codon (UAA, UAG, or UGA) is reached
   • Release factors cause the release of the completed polypeptide chain

Note

The genetic code is degenerate, meaning that multiple codons can code for the same amino acid. This redundancy helps to minimize the impact of some mutations.

Gene Expression and Regulation

Gene expression refers to the process by which the information encoded in a gene is used to synthesize a functional gene product, typically a protein. Regulation of gene expression is crucial for cellular function and development.

Levels of Gene Regulation

1. Transcriptional Regulation:
   • Promoter and enhancer sequences
   • Transcription factors (activators and repressors)
   • Chromatin remodeling and epigenetic modifications
2. Post-transcriptional Regulation:
   • mRNA processing (splicing, capping, polyadenylation)
   • mRNA stability and degradation
   • RNA interference (RNAi)
3. Translational Regulation:
   • Regulation of initiation factors
   • mRNA sequestration
4. Post-translational Regulation:
   • Protein modification (e.g., phosphorylation, glycosylation)
   • Protein degradation

Example

The lac operon in E. coli is a classic example of gene regulation. In the absence of lactose, the lac repressor protein binds to the operator region, preventing transcription of the lac genes. When lactose is present, it binds to the repressor, causing it to release from the DNA and allowing transcription to occur.

Common Mistake

Students often think that all genes are constantly being expressed. In reality, most genes are regulated and only expressed when needed, saving energy and resources for the cell.

Tip

When studying gene regulation, consider how different regulatory mechanisms allow cells to respond quickly to environmental changes or developmental signals.

Enzymes

Enzyme Structure and Function

Enzymes are biological catalysts that speed up chemical reactions in living organisms without being consumed in the process. They are typically proteins, although some RNA molecules (ribozymes) can also act as enzymes.

Structure of Enzymes

Enzymes have a specific three-dimensional structure that is crucial to their function:

1. Primary Structure: The sequence of amino acids
2. Secondary Structure: Local folding patterns (α-helices and β-sheets)
3. Tertiary Structure: Overall 3D shape of the protein
4. Quaternary Structure: Arrangement of multiple polypeptide chains (if applicable)

The active site is a region within the enzyme where the substrate binds and the reaction occurs. It is often a pocket or cleft in the enzyme's structure.

Note

The specificity of enzymes is due to the precise shape and chemical properties of their active sites, which complement the shape and properties of their specific substrates.

Function of Enzymes

Enzymes lower the activation energy of reactions, allowing them to proceed much faster than they would without a catalyst. They do this by:

1. Bringing substrates together in the correct orientation
2. Straining bonds to make them easier to break
3. Providing an alternative reaction pathway with lower activation energy

The function of an enzyme can be represented by the following equation:

$$ \text{Enzyme} + \text{Substrate} \rightleftharpoons \text{Enzyme-Substrate Complex} \rightarrow \text{Enzyme} + \text{Product} $$

Example

The enzyme catalase, found in many organisms, catalyzes the decomposition of hydrogen peroxide into water and oxygen. This reaction is crucial for protecting cells from oxidative damage.

$$ 2H_2O_2 \xrightarrow{\text{catalase}} 2H_2O +