Chapter 3: Cellular Level

• Cell Membrane Overview:

  • The cell membrane separates the internal environment of the cell from the external environment.

  • It acts as a protective barrier and regulates the exchange of materials.

• Structure of the Cell Membrane:

  • Composed of a phospholipid bilayer.

  • Hydrophilic (water-attracting) heads face the inner and outer environments while hydrophobic (water-repelling) tails face inward.

  • Contains embedded proteins for various functions, including cell recognition, transport, and communication.

• Transport Mechanisms:

  • Passive Transport: Requires no energy for movement.

    • Simple diffusion: Movement of small, nonpolar molecules across the membrane.

    • Facilitated diffusion: Involves membrane proteins to assist the movement of larger or polar molecules.

    • Osmosis: Diffusion of water through the membrane.

  • Active Transport: Requires energy (ATP) to move substances against their concentration gradients.

    • Examples include sodium-potassium pumps and endocytosis mechanisms.

• Cystic Fibrosis:

  • A genetic disorder caused by a defective ion channel, impacting chloride ion transport.

  • Results in thick mucus in the lungs, impairing respiratory function due to disrupted osmotic processes related to ion transport.

Overview of a Prototypical Human Cell

All living cells, particularly those in multicellular organisms, have a cell membrane that encases an internal compartment known as the cytoplasm, which contains the nucleus and cytosol (a gel-like substance crucial for biochemical reactions). Eukaryotic cells, which include animal cells, contain numerous organelles that work together to maintain cell health, functioning similarly to bodily organs. The nucleus is notably the central organelle housing DNA.

Organelles of the Endomembrane System

The endomembrane system is comprised of three key organelles: the endoplasmic reticulum (ER), Golgi apparatus, and vesicles. These organelles collaborate in various cellular processes, particularly in production, packaging, and export of molecules.

Endoplasmic Reticulum (ER)

The ER is a continuous network of channels connected to the nuclear membrane, functioning like a transportation system within the cell. It exists in two forms:

• Rough ER (RER): Studded with ribosomes that synthesize proteins.

• Smooth ER (SER): Lacks ribosomes, involved in lipid synthesis and detoxification.

Golgi Apparatus

The Golgi apparatus sorts, modifies, and dispatches products from the rough ER. It consists of stacked, membranous discs that receive vesicles containing materials, sorting them for further processing and preparing them for secretion or transport.

Lysosomes

These organelles contain digestive enzymes that break down waste and unwanted cellular components. They play a critical role in autophagy (self-digestion of cell components) and can trigger controlled cell death through a process called autolysis.

Energy Production and Detoxification

Cells also need to produce energy and detoxify harmful substances.

Mitochondria

Mitochondria are known as the "energy transformers" of the cell, converting nutrients like glucose into ATP (adenosine triphosphate), the energy currency of the cell. They are crucial for energy-consuming processes like muscle contractions.

Peroxisomes

These are membrane-bound organelles containing enzymes for lipid metabolism and detoxification, converting harmful byproducts like hydrogen peroxide (H2O2) into safe byproducts.

Overview of the Nucleus

• Largest organelle; control center of the cell.

• Stores genetic instructions for protein manufacturing.

• Some cells have multiple nuclei (e.g., skeletal muscle cells: multinucleated).

• Red blood cells (RBCs) lack a nucleus; eject during maturing to accommodate hemoglobin.

Structure of the Nucleus

• Surrounded by a nuclear envelope: two lipid bilayers with nuclear pores.

• Contains nucleoplasm and nucleolus (responsible for RNA manufacturing).

• Chromatin: DNA wrapped around histone proteins.

• Chromatin condenses into chromosomes during cell division; humans have ~22,000 genes across 46 chromosomes.

DNA Replication

• Cells reproduce by cell division, ensuring two daughter cells have full DNA complement.

• DNA made of two antiparallel strands (double helix) with complementary bases:

  • Adenine (A) pairs with Thymine (T)

  • Cytosine (C) pairs with Guanine (G)

Stages of DNA Replication:

1. Initiation: Strands are separated by helicase enzymes.

2. Elongation: DNA polymerase synthesizes new strands complementary to templates.

3. Termination: Completed strands formed; each new DNA molecule is semiconservative (one old strand, one new).

• Importance of precise replication due to potential for errors in DNA sequence, which can cause dysfunctions.

• DNA as Blueprint for Proteins

  • DNA holds information necessary for building proteins, crucial for cellular structure and functions.

  • Proteins include enzymes that facilitate biochemical reactions (e.g., DNA replication, energy harvesting).

  • A cell's genome is its DNA, while its proteome is its complete set of proteins.

• Gene Functionality

  • A gene is a DNA segment coding for a specific protein.

  • Proteins are formed from amino acids, determined by the sequence of nucleotides in DNA.

  • Codons (three-base sequences in mRNA) define specific amino acids.

Transcription: From DNA to RNA

• Overview

  • Involves synthesizing mRNA from a DNA template.

  • mRNA is single-stranded and uses uracil instead of thymine.

  • takes place in the nucleus

• Stages of Transcription

  1. Initiation: Promoter region initiates transcription.

  2. Elongation: RNA polymerase unwinds DNA, synthesizes mRNA.

  3. Termination: Sequence at end of gene signals RNA separation.

• mRNA Modification: Includes splicing to remove non-coding regions (introns), connecting coding segments (exons).

Translation: From RNA to Protein

• Overview

  • mRNA is translated into a polypeptide (chain of amino acids).

  • Ribosomes serve as the site of translation.

  • takes place in the cytoplasm

• Components of Translation

  • Ribosomal RNA (rRNA) makes up ribosome structure.

  • Transfer RNA (tRNA) brings amino acids to ribosome, ensures correct sequence through anticodon-codon pairing.

• Stages of Translation

  1. Initiation: Ribosome binds to mRNA.

  2. Elongation: tRNA brings appropriate amino acids, forming polypeptide chain.

  3. Termination: Stop codon signals completion and release of the new protein.

• Efficiency of Translation: Multiple ribosomes can translate a single mRNA simultaneously, enhancing protein production.

Cell Growth and Division

Overview of Cell Division

• Significance of Cell Division

  • Vital for growth and maintenance.

  • Most somatic cells divide; exceptions include gametes, red blood cells, and some neurons.

  • Somatic cells (body cells) vs. germ cells (eggs and sperm).

• Chromosome Composition

  • Somatic cells have 2 copies of chromosomes (diploid).

  • Each has 23 homologous pairs from both parents.

• Cell Renewal

  • Cells undergo self-repair and regeneration over a lifespan.

  • Example: Gastrointestinal tract lining cells are renewed frequently due to wear.

• Cell Cycle

  • Describes the process from cell creation to division into two new cells.

Phases of the Cell Cycle

• Two Primary Phases

  • Interphase:

    • Period of cell growth and preparation; no division occurs.

    • Majority of cell lifecycle is spent here.

  • Mitosis and Cytokinesis:

    • Mitosis: Division of genetic material, forms two nuclei.

    • Cytokinesis: Division of cytoplasm, resulting in two distinct cells.

Interphase Breakdown

• G1 Phase: The cell grows and performs metabolic functions.

• S Phase: DNA replication occurs, doubling the DNA content.

• G2 Phase: The cell continues to grow and prepares for mitosis.

• G0 Phase: A resting phase where cells temporarily or permanently cease dividing.

DNA Synthesis and Mitosis

• DNA Synthesis

  • Each chromosome has a sister chromatid connected by a centromere.

  • Human cells have 92 chromatids post-synthesis (46 duplicated chromosomes).

• Mitosis (1 to 2 hours)

  • Processes:

    1. Separation of genetic material.

    2. Cytokinesis (divides cytoplasm).

  • Stages of Mitosis:

    • Prophase: Chromosomes condense; nuclear envelope breaks down.

    • Metaphase: Chromatids align at the metaphase plate.

    • Anaphase: Sister chromatids separate to opposite poles.

    • Telophase: Two nuclei form, nearing end of division.

• Cytokinesis: Formation of cleavage furrow leading to two cells.

  • Abnormalities may result in multiple nuclei, indicating cancer.

Cell Cycle Regulation

• Regulatory System:

  • Manages transitions between cell cycle phases using internal and external signals.

  • Key Components:

    • Cyclins and cyclin-dependent kinases (CDK).

  • Ensures cell readiness for phase transitions.

• Consequences of Failures:

  • Uncontrolled cell division and cancer due to genetic mutations or environmental factors.

  • Classifies uncontrolled cells as benign or malignant based on harm potential.

Homeostatic Imbalances Causing Cancer

• Cancer arises from genetic and environmental causes linked to failed cell cycle control.

  • Disruptions:

    • Imbalance between proto-oncogenes (stimulate division) and tumor suppressor genes (prevent division).

    • Can lead to overactive cell proliferation or inhibited growth regulation

Cell Differentiation

Introduction to Differentiation

Humans develop from a single fertilized egg into specialized cell types (nerve, muscle, epithelial) through cellular differentiation, where unspecialized cells gain distinct shapes and functions.

Stem Cells

• Definition: Stem cells are unspecialized cells capable of infinite division and differentiation under specific conditions.

• Categories of Stem Cells:

  • Totipotent: Found in initial zygote divisions, these cells can become any cell type necessary for organism development.

  • Pluripotent: Derived from totipotent cells, capable of becoming any human tissue but not able to develop into a whole organism.

  • Multipotent: Can differentiate into several specific cell types within a limited lineage (e.g., red and white blood cells).

  • Oligopotent: Limited to differentiating into a small range of cell types.

  • Unipotent: Fully specialized and can only produce more of its kind.

Stem cells play a role throughout life stages: embryonic, fetal, and adult. For example, epithelial stem cells in the skin become keratinocytes. Adult bone marrow contains various stem cells, including:

• Hematopoietic stem cells: Produce blood and immune cells.

• Endothelial stem cells: Form the lining of blood vessels.

• Mesenchymal stem cells: Give rise to muscle cells.

Differentiation Process

As cells differentiate, they undergo changes in size, shape, metabolic activity, and function, despite all cells having the same DNA. This process is like actors in a movie script—while they share the script, they perform different roles based on their lines. Similarly, cells express only the genes crucial to their function, known as unique genetic expression

Regulation of Gene Expression

Differentiation relies on transcription factors that regulate gene expression, determining which genes are activated or suppressed as cells specialize.

Everyday Connection: Stem Cell Research

Stem cell research aims to create methods for regeneration and repair cell damage related to aging and dysfunction. Stem cells are classified by origin and differentiation capability:

• hESCs: Pluripotent cells from embryos.

• Adult stem cells: Multipotent cells in tissues like skin and bone marrow.

• iPSCs: Reprogrammed adult cells mimicking embryonic stem cells for potential disease therapies (e.g., diabetes, heart disease).Challenges persist due to ethical, legal, and immunological issues, especially with embryonic stem cells causing immune responses. Adult stem cells pose less rejection risk as they are accepted by the body. The regenerative medicine field is growing through exploring stem cell potential and therapies.

Review Questions:

Here are the correct answers along with explanations for each question:

1. Ion channels are examples of: integral proteins.*Explanation: Ion channels are embedded within the cell membrane, allowing the facilitated transport of ions across the membrane, classifying them as integral proteins.

2. The diffusion of substances within a solution tends to move those substances down; concentration.*Explanation: Substances move from an area of higher concentration to an area of lower concentration, which is known as moving down their concentration gradient.

3. Ion pumps and phagocytosis are both examples of: active transport.*Explanation: Both processes require energy (ATP) to move substances across the membrane, either against their concentration gradient (in the case of ion pumps) or through engulfing particles (phagocytosis).

4. Choose the answer that best completes the following analogy: Diffusion is to solutes as endocytosis is to fluid.*Explanation: Diffusion primarily involves the movement of solutes, whereas endocytosis can involve the uptake of fluids (pinocytosis).

   Correct answer: diffusion is to osmosis as endocytosis is to pinocytosis

5. Cytoplasm is to cytosol as a swimming pool containing chlorine and flotation toys is to: the pool water containing chlorine.*Explanation: Cytoplasm consists of the cytosol (the liquid portion) and organelles; thus, the analogy parallels with the swimming pool's water as the solvent carrying the substances.

6. The rough ER has its name due to what associated structures? ribosomes.*Explanation: The rough endoplasmic reticulum (RER) is studded with ribosomes, which give it a rough appearance under a microscope.

7. Which of the following is a function of the rough ER? production of proteins.*Explanation: The rough ER is primarily involved in synthesizing proteins due to the presence of ribosomes.

8. A feature common to all three components of the cytoskeleton is: They are all polymers of protein subunits.*Explanation: Microfilaments (actin), intermediate filaments, and microtubules (tubulin) are all made of protein subunits.

9. Which of the following organelles produces large quantities of ATP when both glucose and oxygen are available to the cell? mitochondria.*Explanation: Mitochondria convert glucose and oxygen into ATP through cellular respiration, making them central to energy production in cells.

10. The nucleus and mitochondria share which of the following features? a double cell membrane.*Explanation: Both the nucleus and mitochondria are surrounded by a double membrane that separates their internal contents from the cytoplasm.

11. Which of the following structures could be found within the nucleolus? ribosomes.*Explanation: The nucleolus is where ribosomal RNA (rRNA) is synthesized and combined with proteins to form ribosome subunits.

12. Which of the following sequences on a DNA molecule would be complementary to GCTTATAT? CGAATATA.*Explanation: Complementary base pairing means that G pairs with C and A pairs with T.

13. Place the following structures in order from least to most complex organization: DNA, nucleosome, chromatin, chromosome. Correct Order: DNA, nucleosome, chromatin, chromosome.*Explanation: DNA wraps around histones to form nucleosomes, which coil into chromatin, which then condenses into chromosomes during cell division.

14. Which of the following is part of the elongation step of DNA synthesis? attaching complementary nucleotides to the template strand.*Explanation: During elongation, DNA polymerase attaches complementary nucleotides to the growing daughter strand.

15. Which of the following is not a difference between DNA and RNA? DNA contains alternating sugar-phosphate molecules whereas RNA does not contain sugars.*Explanation: This statement is inaccurate because both DNA and RNA do contain sugars; DNA contains deoxyribose while RNA contains ribose, implying this is not true.

16. Transcription and translation take place in the nucleus; cytoplasm.*Explanation: Transcription occurs in the nucleus where DNA is converted to mRNA, while translation takes place in the cytoplasm where mRNA is used to synthesize proteins.

17. How many “letters” of an RNA molecule, in sequence, does it take to provide the code for a single amino acid? 3.*Explanation: Each amino acid is specified by a sequence of three nucleotides called a codon in mRNA.

18. Which of the following is not entirely or mostly made out of RNA? the intron.*Explanation: Introns are non-coding sections of a gene found in DNA; they are not ribonucleic in nature.

19. Which of the following phases is characterized by preparation for DNA synthesis? G1.*Explanation: The G1 phase is when the cell grows and prepares to duplicate its DNA, occurring prior to S phase.

20. A mutation in the gene for a cyclin protein might result in: cancer.*Explanation: Mutations in cyclin genes can disrupt cell cycle regulation, leading to uncontrolled cell division, commonly associated with cancer. This is the incorrect answer. I think it’s all of the above

21. What is a primary function of tumor suppressor genes? stop certain cells from dividing.*Explanation: Tumor suppressor genes inhibit cell division, preventing uncontrolled proliferation that can lead to cancer.

22. Arrange the following terms in order of increasing specialization: multipotency, pleuripotency, oligopotency, unipotency.*Explanation: Unipotent cells can produce one cell type, while multipotent can develop into multiple cell types, hence the arrangement reflects increasing specialization. WRONG

    Correct answer: Pluri, multi, oligo, uni

23. Which type of stem cell gives rise to red and white blood cells? hematopoietic.*Explanation: Hematopoietic stem cells are responsible for generating all blood cell types, including red and white blood cells.

24. What multipotent stem cells from children sometimes banked by parents? cells from the umbilical cord and from baby teeth.*Explanation: These stem cells (from umbilical cord blood and teeth) are often banked due to their potential regenerative properties.