Cell Biology 1 dont need meh

Cell Biology BISC-3754 Notes

Introduction to Cell Biology

• Welcome to Cell Biology!

Course Textbook and Digital Platform

• Required Textbook (Ebook) and Digital Platform:

  • Essential Cell Biology, 6th edition, 2023.

  • Authors: Bruce Alberts, Karen Hopkin, Alexander Johnson, David Morgan, Keith Roberts, Peter Walter, Rebecca Heald.

  • Publisher: W. W. Norton and Company, New York, NY.

  • Includes Ebook and Smartwork.

  • Alternative: Print textbook and Smartwork.

• Cell Biology Spring 2025

Recommended Textbook

• Recommended (not required) Textbook:

  • Molecular Biology of the Cell, 6th edition, 2015.

  • Authors: Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, and Peter Walter.

  • Publisher: Garland Science, New York, NY.

  • Cell Biology Spring 2025

Course Requirements and Grading

• Textbook (Ebook): Read and take notes.

• Classes: Take notes and review.

• Midterm Exams:

  • 3 midterm exams.

  • The midterm exam with the lowest score is worth 16% of the final grade.

  • Each of the other two midterm exams is worth 22% of the final grade.

• Cumulative Final Exam: 25%

• Participation, Attendance, In and Out of Class Assignments (including Smartwork): 15%

Introduction to Cells and Their Components

• Discovery of cells

• Prokaryotic cells

• Eukaryotic cells

• Cell constituents

Discovery of Cells

• Advances in lens grinding led to being able to observe cells.

• Key figures:

  • Robert Hooke (1635-1703)

  • Van Leeuwenhoek

Observations by van Leeuwenhoek

• Drawings by van Leeuwenhoek:

  • Bacteria from between his teeth.

  • Drawing of eukaryotic green alga Volvox.

• Contemporary photomicrograph of Volvox, similar to what was seen in the lab.

Hooke's Observations

• Hooke observed thick cell walls in cork plant cells using a primitive light microscope in 1663 and published his findings in 1665.

• Photo of cork tree with pliable bark exposed.

Hooke's Terminology

• Hooke reported that cork was composed of a mass of chambers, which he called “cells” based on their resemblance to cells occupied by monks in a monastery.

Cell Walls and Plasma Membranes

• Image of electron micrograph of plant cell walls.

• Question: Where are the cell walls? Where are the plasma membranes?

Development of Cell Theory

• Schwann (zoologist) and Schleiden (botanist) systematically investigated and documented animal and plant tissues with a light microscope in the 1830s.

• They showed that cells are the universal building blocks of all living tissues.

• Cell theory, as fundamental as atomic theory (all matter is made up of atoms), was created.

Schwann Cell and Myelin Sheath

• Schwann cells wrap their plasma membrane concentrically around the axon to form a segment of myelin sheath (approximately 1mm long).

• Membrane layers in the schematic are shown less compacted than they are in reality.

Cell Theory - Formation of New Cells

• All living cells are formed by growth and division of existing cells.

• This was confirmed in Louis Pasteur’s famous experiments.

• What were the experiments?

Cell Division

• Figure 1–5: New cells form by growth and division of existing cells.

• (A) Drawing of living hair cell from a Tradescantia spiderwort flower, dividing in two over 2.5 hours.

• Inside the cell, DNA can be seen condensing into chromosomes, which are then separated into two daughter cells.

• Figure 1–5 New cells form by growth and division of existing cells.

• (B) A comparable living plant cell photographed through a modern light microscope.

Basic Characteristics of Cells

• Small

• Membrane-enclosed units

• Filled with concentrated aqueous solution of chemicals

• Endowed with extraordinary ability to create copies of themselves by growing and then dividing in two

• All living things are built from Cells, which are:

Key Aspects of Cells

• Great variety of forms that cells can adopt

• Chemical machinery all cells have in common

• How cells are made visible under the microscope (next class)

• Similarities of living things (model organisms)

Unity and Diversity of Cells

• Cells Vary Enormously in Appearance and Function

• Living Cells All Have a Similar Basic Chemistry

• Living Cells Are Self-Replicating Collections of Catalysts

• All Living Cells Have Apparently Evolved from the Same Ancestral Cell

Cell Diversity in Appearance

• Cells vary in:

  • Size (e.g., bacterial cell is a few microns, whereas a frog egg cell is ~1 mm in diameter)

  • Shape (e.g., typical nerve cell in the brain is enormously extended, whereas Paramecium is relatively compact and submarine-shaped)

  • Chemical requirements (e.g., some require oxygen, but oxygen is deadly for others; autotrophs, heterotrophs, chemolithoautotrophs)

• Frog egg cells are an example.

Cell Diversity in Function

• Some Examples of Cells’ Functions:

  • Specialized factories for production of particular substances, e.g., hormones, starch, fat, latex, or pigments.

  • Muscle cells - engines that burn fuel to do mechanical work.

  • Modified muscle cells in electric eel - electricity generators that generate high-voltage pulses.

Variety of Cell Shapes and Sizes

• Figure 1–1: Cells come in a variety of shapes and sizes

• Examples:

  • (A) Nerve cell

  • (B) Paramecium

  • (C) Snapdragon flower petal cells

  • (D) Macrophage

  • (E) Fission yeast

• Note the very different scales of these micrographs

Nerve Cell Structure

• Drawing of a single nerve cell from a mammalian brain.

  • Single, unbranched extension (axon) projects toward the top of the image, through which it sends electrical signals to other nerve cells.

  • Huge branching tree of projections (dendrites) through which it receives signals from as many as 100,000 other nerve cells.

Paramecium

• (B) Paramecium

• This protozoan—a single giant cell—swims by means of beating cilia covering its surface.

Snapdragon Flower Petal Cells

• (C) Surface of a snapdragon flower petal displays an orderly array of tightly packed cells.

• Each cell is squat, immobile, and surrounded by a rigid box of cellulose with an outer waterproof covering of wax.

Macrophage

• (D) A macrophage spreads itself out as it patrols animal tissues.

• It crawls through tissues, constantly pouring itself into new shapes as it searches for and engulfs debris, foreign microorganisms, and dead or dying cells.

• What kind of cell is a macrophage?

Fission Yeast

• (E) A fission yeast caught in the act of dividing in two.

• The medial septum (stained red with a fluorescent dye) is forming a wall between two nuclei (also stained red) that have been separated into two daughter cells; in this image, the cells’ membranes are stained with a green fluorescent dye.

• Can be shaped as rod or spherical as in budding yeast.

Similar Basic Chemistry of Living Cells

• Living Cells - All Have a Similar Basic Chemistry.

• Although cells of all living things are enormously varied when viewed from the outside, they are fundamentally similar inside.

• Cells resemble each other to an astonishing degree in their chemical details:

  • In all organisms, genetic information is carried in DNA molecules, written in the same chemical code, constructed out of the same chemical building blocks, and interpreted by essentially the same chemical machinery.

  • Composed of the same sorts of molecules which participate in the same types of chemical reactions.

The Central Dogma

• The Central Dogma

  • ${DNA} <br>Arr^{REPLICATION} {DNA}$

  • ${DNA} <br>Arr^{TRANSCRIPTION} {RNA}$

  • ${RNA} <br>Arr^{TRANSLATION} {PROTEIN}$

  • Replication: DNA synthesis using nucleotides.

  • Transcription: RNA synthesis.

  • Translation: Protein synthesis using amino acids.

Biochemical Factories and Plasma Membranes

• All Cells Function as Biochemical Factories Dealing with the Same Basic Molecular Building Blocks.

• All Cells Are Enclosed in a Plasma Membrane Across Which Nutrients and Waste Materials Must Pass.

Role of Amino Acids and Proteins

• All organisms use the same set of 20 amino acids to make their proteins.

• The appearance and behavior of a cell are largely dictated by its protein molecules, which serve many functions, including:

  • Structural supports

  • Chemical catalysts

  • Molecular motors

Common Chemistry in Living Organisms

• All living organisms are constructed from cells that have a fundamentally similar chemistry and operate according to the same basic principles

• Examples:

  • (A) A colony of bacteria

  • (B) A butterfly

  • (C) A rose

  • (D) A dolphin

Heterotrophic Energy Source

• One protozoan eats another (heterotrophic) for energy.

• Images provided.

Free-Energy Sources for Cells

• Cells Can Be Powered by a Variety of Free-Energy Sources.

• Example: Hydrothermal vents in the sea.

Nitrogen and Carbon Dioxide Fixation

• Some Cells Fix Atmospheric Nitrogen and Carbon Dioxide.

Cellular Dimensions

• Units used to measure cells and organelles:

  • Micrometer ($\"\mu m$) - also called micron - one millionth of a meter ($10^{-6} m$)

  • Bacterial cells - one to a few $\mu m$ in diameter.

  • Cells of plants and animals - 10–20 times larger.

Cells Forming Tissues in Plants

• Cells form tissues in plants.

• (A) Cells in the root tip of a fern:

  • DNA-containing nuclei stained red

  • Each cell is surrounded by a thin cell wall (light blue)

  • Red nuclei of densely packed cells are seen at the bottom corners of the prep.

Cells Forming Tissues in Animals

• Cells form tissues in animals.

• (B) Cells in crypts of the small intestine:

  • Each crypt appears in this cross-section as a ring of closely packed cells (nuclei stained blue)

  • Rings are surrounded by the extracellular matrix, which contains scattered cells that produced most of the matrix components.

Tree of Life

• Tree of Life Has Three Primary Branches: Bacteria, Archaea, and Eukaryotes.

• Examples provided for each branch.

Prokaryotic Cells

• Most diverse and numerous cells on Earth.

• Pro means “before,” and karyon means “kernel” or “nucleus.”

• No organelles; they do have ribosomes.

• Divided into two domains: Bacteria and Archaea.

Biochemical Diversity Among Prokaryotic Cells

• Greatest Biochemical Diversity Exists Among Prokaryotic Cells.

• Bacteria come in different shapes and sizes:

  • Typical spherical, rodlike, and spiral-shaped bacteria, drawn to scale.

  • Spiral cells shown are the organisms that cause syphilis.

Prokaryotic Cell Structure

• Diagram of a prokaryotic cell showing:

  • Plasma membrane

  • DNA

  • Cell wall

  • Flagellum

  • Ribosomes

Bacterium Escherichia coli (E. coli) as a Model Organism

• Electron micrograph of a longitudinal section:

  • The cell’s DNA is concentrated in a lightly stained region.

  • E. coli has an outer membrane and an inner (plasma) membrane, with a thin cell wall in between.

  • Many flagella are distributed over its surface (not visible in this micrograph).

Photosynthetic and Nitrogen-Fixing Bacteria

• Some bacteria are photosynthetic and fix nitrogen.

• Anabaena cylindrica - a cyanobacterium that forms long, multicellular chains, has specialized cells that:

  • Fix nitrogen (labeled H, abbreviation for heterocyst) that captures $N_2$ from the atmosphere and incorporates it into organic compounds.

  • Fix $CO_2$ through photosynthesis (labeled V, for vegetative).

  • Become resistant spores (labeled S) that can survive under unfavorable conditions.

  • Light micrograph from a light microscope.

Photosynthetic Prokaryotes

• Some bacteria are photosynthetic.

• An electron micrograph of a related species, Phormidium laminosum, shows intracellular membranes where photosynthesis occurs.

  • Some prokaryotes can have intracellular membranes and form simple multicellular organisms.

Cell Architecture Comparison

• Cell architecture of bacterial, plant, and animal cells.

• Note different scales.

• Diagrams highlighting the key components of each cell type.

Animal Cell Structure

• Animal cell drawing based on a fibroblast, a cell that inhabits connective tissue and deposits extracellular matrix.

• Note the scale.

Eukaryotic Cell - Cytoplasm, Plasma Membrane, and Nucleus

• Image of a eukaryotic cell showing cytoplasm, plasma membrane, and nucleus.

Plant Cell Structure

• Plant cell drawing typical of a young leaf cell.

• Note the scale.

Bacterial Cell Structure

• Rod-shaped bacterial cell with a single flagellum for motility.

• Note the scale.

Origin of Eukaryotic Cells

• Eukaryotic Cells May Have Originated as Predators.

• One protozoan eats another: SEM shows Didinium ingesting a Paramecium (artificial color).

Evolution of Eukaryotic Cells

• Where did eukaryotic cells come from?

• Eukaryotic, bacterial, and archaean lineages diverged from one another >3 billion years ago—very early in the evolution of life on Earth.

• Mitochondria are essentially the same in plants, animals, and fungi and, therefore, were presumably acquired before these lines diverged ~1.5 billion years ago.

• Some time later, eukaryotes are thought to have acquired mitochondria.

• Later still, a subset of eukaryotes acquired chloroplasts.

Modern Eukaryotic Cells Evolved from Symbiosis

• Endosymbiotic theory diagrams.

Evolution of Mitochondria

• Virtually certain that mitochondria evolved from aerobic bacteria that were engulfed by an archaea-derived, early anaerobic eukaryotic cell and survived inside it, living in symbiosis with their host.

• The model shows the double membrane of present-day mitochondria, which is thought to have been derived from the plasma membrane and outer membrane of the engulfed bacterium.

  • The membrane derived from the plasma membrane of the engulfing ancestral cell was ultimately lost.

Symbiotic Evolution of Chloroplasts

• Photosynthetic bacteria are thought to have been taken up by early eukaryotic cells that already contained mitochondria.

Complexity in Protozoan Anatomy

• Although they are single-celled, protozoan anatomy is often elaborate and includes such structures as:

  • Mouthparts

  • Photoreceptors

  • Flagella

  • Beating cilia

  • Sensory bristles

  • Stinging darts

  • Stalklike appendages

  • Musclelike contractile bundles

Model Organisms

• Small

• Easy and inexpensive to breed and maintain

• Short generation time

• Genome well-studied

• May be transparent

Saccharomyces cerevisiae as a Model Organism

• Saccharomyces cerevisiae is a Simple Eukaryote and Model Organism.

• Budding yeast.

Arabidopsis as a Model Plant

• Arabidopsis Has Been Chosen as a Model Plant.

• Can be grown indoors in large numbers.

• Genes have counterparts in agricultural species.

Model Animals

• Model Animals Include Flies, Worms, Fish, and Mice.

Studying Human Cells Directly

• In addition to model organisms, biologists also directly study humans and their cells.

• Given appropriate conditions, many human cell types–and many cell types of animals or plants–will survive, grow, and express specialized properties in a culture dish.

• Experiments using cultured cells are carried out in vitro (“in glass”) vs. experiments carried out on intact organisms, i.e., in vivo.

Fibroblasts from Human Skin

• A Fibroblasts from human skin.

  • Major cell type in connective tissue

  • Even in cell culture, continue to secrete proteins that form ECM

• Cells in culture often display properties that reflect their origin

• These (A, B, C) phase-contrast micrographs show a variety of cell types that can grow in culture.

Human Nerve Cells in Culture

• (B) Human nerve cells make connections with other nerve cells, even in culture.

Epithelial Cells from Human Cervix

• (C) Epithelial cells from the human cervix join together to form a cell sheet in culture, just as they do in the body.

Embryonic Heart Muscle Cells

• Embryonic heart muscle cells contract spontaneously even though they are grown in a culture dish.

Euglena - Eukaryotic Cell

• Euglena.

• Is this a multicellular organism?

• Is it a eukaryote?

• Key components listed.

Review: Eukaryotic Cells - Organelles

The Eukaryotic Cell

• Nucleus – information store of cell

• Mitochondria - generate usable energy from food molecules

• Chloroplasts - capture energy from sunlight

• Internal Membranes – create intracellular compartments with different functions

• Cytosol – concentrated aqueous gel of large and small molecules

• Cytoskeleton - responsible for directed cell movements

• Cytosol - far from static

Nucleus - Information Store

• Usually most prominent organelle

• Enclosed in two concentric membranes that make the nuclear envelope

• Contains molecules of DNA, visible as chromosomes when the DNA condenses before a cell divides

Microscopic View of Nucleus

• Images showing the cytoplasm, mitochondrion, nuclear envelope, and nucleus.

Condensed Chromosomes

• Image of nucleus with condensed chromosomes.

Mitochondria - Energy Generation

• Generate Usable Energy, ATP, from Food Molecules

• Consume $O<em>2$ and release $CO</em>2$ (respiration, chapter 14)

• Present in essentially all eukaryotic cells (notable exception is red blood cells)

• Two separate membranes, with the inner membrane formed into folds that project into the mitochondrial matrix

• Contain their own DNA

• Reproduce by dividing

• Acquired by endosymbiotic event

Mitochondrial Networks

• This budding yeast cell, which contains a green fluorescent protein in its mitochondria, was viewed in a super-resolution confocal fluorescence microscope.

• In this three-dimensional image, mitochondria are seen to form complex branched networks.

• Mitochondria can vary in shape and size.

Mitochondrial Structure

• (A) An electron micrograph of a cross-section of a mitochondrion reveals extensive infolding of the inner membrane.

• Mitochondria have a distinctive internal structure.

Mitochondrial Membranes

• (B) Mitochondrial membranes:

  • Smooth outer membrane (gray)

  • Highly convoluted inner membrane (red)

• Inner membrane:

  • Contains most of the proteins responsible for energy production in eukaryotic cells

  • Is highly folded to provide a large surface area for this activity

Mitochondrial Compartments

• (C) Innermost compartment of the mitochondrion shown in orange.

Chloroplasts - Photosynthesis

• Capture energy from sunlight in photosynthesis

• Make sugar molecules, fix $CO<em>2$, release $O</em>2$

• In plants and algae

• Even more complex structure than mitochondria

• Two surrounding membranes

• Internal stacks of membranes containing chlorophyll

• Contain own DNA

• Reproduce by dividing in two

• Likely engulfed by early aerobic eukaryotic cell by endosymbiosis

Chloroplasts in Plant Cells

• Chloroplasts in plant cells capture the energy of sunlight.

• Images showing chloroplasts and their components.

Intracellular Compartments

• Internal Membranes Create Intracellular Compartments with Different Functions

• Many organelles are surrounded by single membranes

• Most of these structures are involved with importing raw materials and exporting useful materials and waste products

Endoplasmic Reticulum (ER)

• Irregular maze of interconnected spaces enclosed by a membrane

• Most cell membrane components are made here

• Most materials destined for export are made here

• Enormously enlarged in cells specialized for secretion of proteins (e.g., goblet cells in intestinal epithelial cells)

ER Structure

• Images showing the nucleus, nuclear envelope, endoplasmic reticulum, and ribosomes.

Golgi Apparatus

• Stacks of flattened, membrane-enclosed sacs

• Modifies and packages molecules made in the ER, destined to be secreted from the cell or transported to another cell compartment

Golgi Apparatus Structure

• Images showing the nuclear envelope, membrane-enclosed vesicles, Golgi apparatus, and endoplasmic reticulum.

Lysosomes - Intracellular Digestion

• Small, irregularly shaped organelles

• Intracellular digestion occurs in lysosomes

• Release nutrients from ingested food particles in the cytosol

• Break down unwanted molecules for recycling or excretion

Peroxisomes and Transport Vesicles

• Peroxisomes:

  • Small, membrane-enclosed vesicles

  • Provide a sequestered environment for a variety of reactions in which $H<em>2O</em>2$ is used to inactivate toxic molecules

• Transport Vesicles:

  • Membranes form many types of small transport vesicles

  • Ferry materials between one membrane-enclosed organelle and another

Organelle Overview

• Diagram showing the relationships between lysosomes, mitochondria, peroxisomes, cytosol, nuclear envelope, Golgi apparatus, transport vesicles, endoplasmic reticulum, and plasma membrane.

• Cytosol (blue) - Cytoplasm that fills the space outside of organelles

Cytosol - Aqueous Gel

• Part of cytoplasm that is not contained within intracellular membranes

• The largest compartment in most cells

• Packed with large and small molecules so that it behaves more like a water-based gel than liquid

• Site of many chemical reactions in the cell

• Most proteins made here on ribosomes

• Cytosol Is a Concentrated Aqueous Gel of Large and Small Molecules

Cytoskeleton

• Cytoskeleton Is Responsible for Directed Cell Movements

• The cytosol is not just a structureless soup of chemicals and organelles

• With an electron microscope, one can see that in eukaryotes, the cytosol is criss-crossed by long, fine filaments

Functions of the Cytoskeleton

• Protein filaments and proteins that attach to them form a system of girders, ropes, and motors that gives the cell its:

  • Mechanical strength

  • Controls its shape

  • Drives and guides its movements

• Cytoskeleton

Crawling Locomotion

• Crawling Amoeba

• With the notable exception of swimming sperm, in animals, almost all locomotion occurs by crawling, long-distance crawling in the construction of the nervous system

Cytoplasmic Streaming video clip

• See cytoplasmic streaming video clip next slide

• In plant cells, although the cell itself is not moving the way animal cells can, within plant cells, cytoskeletal tracks provide a way for chloroplasts, for example, to move in a constant stream around the cell interior

Microtubules and Chromosomes

• Microtubules and chromosomes are seen during cell division.

Dynamic Nature of Cytosol

• Cell interior is in constant motion

• The cytoskeleton is a dynamic tangle of protein ropes constantly being strung together and taken apart

• Cytoskeletal filaments can assemble and then disappear in minutes

Motor Proteins

• Motor proteins use energy stored in ATP to move along tracks and cables

• Carry organelles and proteins throughout the cytoplasm

• Race across the width of the cell in seconds

Molecular Motion in Cytosol

• Large and small molecules fill every free space in the cell

• Are knocked to and fro by random thermal motion

• Constantly colliding with each other and other cell structures

Cytosol Crowded and Fast Molecular Movement

Cytosol Crowded and Movement of Molecules is Rapid (slowed down at end of video clip)