Chapter 1: Cells: The Fundamental Units of Life

Even bacteria contains proteins that are distantly related to those that form the cytoskeletal elements involved in eukaryotic cell division.

How do we know that the cytoskeleton's role in cell division may be its most ancient function?

The exchange is mediated by transport vesicles that pinch off from the membrane of one organelle and fuse with another

How does a continual exchange of materials take place between the ER, Golgi, lysosomes and plasma membrane?

model organisms

organisms that are easier to study in the laboratory so they are used more commonly

eukaryotes

organisms whose cells contain a nucleus

prokaryotes

organisms whose cells do not contain a nucleus

scanning electron microscope

electron microscope used to look at the surface detail of cells and other structures; works by scattering electrons off the surface of the sample

transmission electron microscope

electron microscope used to look at thin sections of tissue; similar to a light microscope except that it transmits a beam of electrons rather than a beam of light through the sample

plasma membrane

enclosing membrane of the cell that separates the interior of the cell from its external environment

mitochondria

One of the most visible organelle's in the cell; enclosed in two separate membranes, with the inner membrane formed into folds that project into the interior of the organelle Generators of chemical energy for the cell. They harness the energy from the oxidation of food molecules, such as sugars to produce adenosine triphosphate (ATP), the basic chemical fuel that powers most of the cell's activities. Because it consumes oxygen and releases carbon dioxide in the course of this activity, the entire process is called cell respiration. These organelles contain their own DNA and reproduce by dividing.

bacteria

cells that have the simplest structure and come closest to showing life stripped down to its essentials; contains no organelles other than ribosomes

microtubules

Thickest filaments of the cytoskeleton. They have the form of minute hollow tubes. In dividing cells, they become reorganized into a spectacular array that helps pull the duplicated chromosomes apart and distribute them equally to the two daughter cells.

actin filaments

Thinnest filaments of the cytoskeleton which are abundant in all eukaryotic cells but occur in especially large numbers inside muscle cells, where they serve as a central part of the machinery responsible for muscle contraction.

motor proteins

Use the energy stored in molecules of ATP to trundle along the cytoskeleton, carrying organelles and proteins throughout the cytoplasm, and racing across the width of the cell in seconds

When a cell replicates its DNA in preparation for cell division, the copying is not always perfect. On occasion, the instructions are corrupted by mutations that change the sequence of nucleotides in the DNA. For this reason, daughter cells are not necessarily exact replicas of their parent. Mutations can create offspring that are changed for the worse (less able to survive and reproduce), changed for the better (better able to survive and reproduce) or changed in a neutral way (genetically different but equally viable).

What are mutations in DNA?

carbohydrates, lipids, proteins, nucleic acids

What are the four groups of biomolecules?

eukaryotes, bacteria, archaea

What are the three domains of life?

Bacteria and Archaea (which are thought to have diverged from a common prokaryotic ancestor 3.5 billion years ago). At a molecular level, these two are as different from each other as each are from eukaryotes

What are the two domains of prokaryotes?

All living things are built from cells

What distinguishes something living from something nonliving?

DNA is composed of long polymer chains that are made from the same set of four monomers, called nucleotides strung together in different sequences.

What is DNA?

When the information encoded in DNA molecules is transcribed, it is transcribed into a related set of polynucleotides called RNA. Some RNA molecules have their own regulatory, structural, or chemical activities, but most are translated into a different polymer called a protein.

What is RNA?

In broad terms, life is related to growth, reproduction, and an ability to actively alter their behavior in response to the environment

What is the basic definition of life?

The flow of information from DNA to RNA to protein that makes reproduction of cells possible

What is the central dogma?

Bacteria are more familiar with our everyday life-the species that live in the soil or make us ill. Archaea are found not only in these habitats but also in environments that are too hostile for most other cells: the concentrated brine, the hot acid of volcanic springs, the airless depths of marine sediments etc. (many of these extreme environments resemble the harsh conditions that must have existed on primitive earth, where living things first evolved before the atmosphere became rich in oxygen.)

Where are bacteria and archaea found?

Viruses contain information in the form of DNA or RNA but they do not have the ability to reproduce by their own efforts. Instead, they parasitize the reproductive machinery of the cells that they invade to make copies of themselves.

Why aren't viruses considered living?

The parts are small, transparent, and mostly colorless.

Why is distinguishing the internal structure of a cell so difficult?

extracellular matrix

a dense material often made of protein fibers embedded in a gel of long sugar chains that lies between cells

ribosome

a large macromolecular complex in which RNAs are translated into proteins

florescence microscope

a new type of light microscope that uses sophisticated methods of illumination and electronic image processing to see fluorescently labeled cell components in much finer detail. The newest kinds can see down to 20 nanometers, the size of a single ribosome

cytoplasm

a transparent substance around the nucleus and filling the cell's interior

chromosomes

long polymers of DNA that become more visible when they become more compact before a cell divides into two daughter cells

transport vesicles

membrane enclosed vesicles that ferry materials between one membrane enclosed organelle and another

light microscope

microscope that uses visible light to illuminate specimens; first microscopes created

electron microscope

microscopes that use beams of electrons instead of beams of light to illuminate objects. Because electrons have a much shorter wavelength, these instruments greatly extend our ability to see the fine details of cells. Cannot be used to view living cells.

protozoans

A class of free-living, motile, unicellular organisms. Can be predators (such as Didinium), photosynthetic, carnivorous, motile, or sedentary. Their anatomy is often elaborate and includes such structures as sensory bristles, photoreceptors, beating cilia, stalklike appendages, mouthparts, stinging darts, and muscle like contractile bundles. Although they are single-cells, they can be as intricate and versatile as many multi-cellular organisms.

.2 micrometers

A conventional light microscope has a resolution of about

endocytosis

A process in which portions of the plasma membrane tuck inward and pinch off to form vesicles that carry materials captured from the external medium into the cell. Animal cells can engulf very large particles or even entire foreign cells through this.

exocytosis

A process in which vesicles from inside the cell fuse with the plasma membrane and release their contents into the external medium. Most of the hormones and signal molecules that allow cells to communicate with one another are secreted from cells by this process.

endoplasmic reticulum

An irregular maze of interconnected spaces enclosed by a membrane. It is the site where most cell-membrane components as well as materials destined for export from the cell, are made. This organelle is enormously enlarged in cells that are specialized for the secretion of proteins.

The cytoskeleton is a dynamic jungle of protein ropes that are continually being string together and taken apart. Motor proteins move across these tracks. In addition, the large and small molecules that fill every free space in the cell are knocked to and fro by thermal motion, constantly colliding with one another and with other structures in the cell's crowded cytosol.

Describe how the cytosol is dynamic, not static.

The ancestral eukaryotic cell was a predator that fed by capturing other cells. Such a way of life requires a large size, a flexible membrane, and a cytoskeleton to help the cell move and eat. The nuclear compartment may have evolved to keep the DNA segregated from this physical and chemical hurly-burly, so as to allow more delicate and complex control of the way the cell reads out its genetic information. Such a primitive eukaryotic cell with a nucleus and cytoskeleton was most likely the sort of cell that engulfed free-living, oxygen-consuming bacteria that were the likely ancestors of mitochondria. This partnership is thought to have been established 1.5 billion years ago, when the earth's atmosphere first became rich in oxygen

Describe the theory that eukaryotic cells may have originated as predators

Eukaryotic cells in general are bigger and more elaborate than prokaryotes. Some live as single-celled organisms such as amoebae and yeasts and others live in multicellular assemblies. ALL complex multicellular organisms are formed from eukaryotic cells. By definition, these cells have a nucleus which go hand in hand with possession of a variety of other organelles common to all eukaryotic organisms. Reproduce sexually or asexually. Some have cell walls.

Describe typical eukaryotes.

1. Prokaryotes are typically spherical, rodlike, or corkscrew shaped. 2. They are small (.2-10 micrometers long), although some giant species are much longer. 3. They often have a tough protective coat or cell wall surrounding the cytoplasm and the DNA. 4. In the electron microscope, the cell interior appears as a matrix of varying texture without any obvious internal structure. 5. The cells divide quickly by dividing in two (asexually/binary fission). Thanks to their large numbers, rapid proliferation, and ability to exchange bits of genetic material by a process akin to sex, populations of prokaryotic cells can evolve fast, rapidly acquiring the ability to use a new food source or to resist being killed by a new antibiotic. Circular chromosomes. 6. Most live as single-celled organisms, although some join together to form chains, clusters, or other organized multicellular structures. 7. They are the most diverse class of cells on the planet. Members of this class exploit an enormous range of habitats and they vastly outnumber all eukaryotic organisms on earth.

Describe typical prokaryotes

Cells use their genes to produce some RNAs and proteins and others do not, depending on their internal state and on cues that they and their ancestor cells have received from their surroundings- mainly signals from other cells in the organism. Therefore, each cell is capable of carrying out a variety of biological tasks, depending on its environment and its history, and it selectively uses the information encoded in its DNA to guide its activities. For example, every cell in the human body generated from a single fertilized egg. Yet, every cell is not the same; they have many different functions.

Different cells express different genes. Explain.

photosynthesis

Function of the chloroplasts in which energy from sunlight is trapped in chlorophyll molecules and used to drive the manufacture of energy rich sugar molecules. In the process, they release oxygen as a molecular by-product.

homologous

Genes (and their protein products) from different organisms that have very similar nucleotide sequences. These are very likely to have descended from a common ancestral gene.

The vast bulk of our DNA does not code for proteins or for functional RNA molecules. Instead, it includes a mixture of sequences that help regulate gene activity, plus sequences that seem to be dispensable. The large quantity of regulatory DNA contained in the genomes of eukaryotic multicellular organisms allows for enormous complexity and sophistication in the way different genes are brought into action at different times and places. In the end, the basic list of proteins that the cells can make, as specified by the DNA, is not much longer than the parts list of an automobile.

Genomes contain more than just genes. Explain.

Mitochondria are thought to have evolved from aerobic bacteria that took to living inside the anaerobic ancestors of today's eukaryotic cells. This created a symbiotic relationship in which the host eukaryote and the engulfed bacterium helped each other survive and reproduce. Thus, our own oxygen-based metabolism can be regarded as a product of the activities of bacterial cells.

How are mitochondria related to prokaryotes?

1. All cells are composed of the same sorts of molecules which participate in the same types of chemical reactions. 2. In all organisms, genetic information in the form of genes is carried in DNA molecules. This information is written in the same genetic code, constructed out of the same chemical building blocks, interpreted by essentially the same chemical machinery, and replicated in the same way when a cell or organism reproduces.

How do all cells have a similar basic chemistry?

1. size 2. shape 3. chemical requirements- for example some require oxygen to live, and for others the gas is deadly 4. function

How do cells vary?

They have all inherited their genetic information from the same common ancestral cell. Through a long process of mutation and natural selection, the descendants of this ancestral cell have gradually diverged to fill every habitat on earth with different organisms.

How does evolution offer an explanation of why present-day cells are so similar in their fundamentals?

DNA encodes the information that ultimately directs the assembly of proteins. Proteins, in turn, catalyze the replication of DNA and the transcription of RNA into proteins. This feedback loop between proteins and polynucleotides underlies the self-reproducing behavior of living things.

How does the central dogma make reproduction possible?

1. Stain the cells with dyes that color particular components differently. 2. One can exploit the fact that cell components differ slightly from one another in refractive index, just as glass differs in refractive index from water, causing light rays to be deflected as they pass from one medium into the other.

How is it possible to study the internal structure of a cell through a microscope?

Proteins also catalyze the many other chemical reactions.

In addition to their roles in polynucleotide and protein synthesis, what else do proteins do?

chloroplasts

Large green organelles that are found in the cells of plants and algae, but not in the cells of animals or fungi. These organelles have an even more complex structure than mitochondria: in addition to their two surrounding membranes, they possess internal stacks of membranes containing the pigment chlorophyll. They carry out photosynthesis, thus enabling plants to get energy directly from sunlight and to produce the food molecules and oxygen that mitochondria use to generate chemical energy. Like mitochondria, chloroplasts contain their own DNA, reproduce by dividing in two, and are thought to have evolved from bacteria.

E. Coli

Model organism that is a small rod shaped cell that normally live in the guts of humans or other vertebrates, but also grows and reproduces rapidly in a simple nutrient broth in a culture bottle. Most of our knowledge of the fundamental mechanisms of life, including how cells replicate their DNA and how they decode these genetic instructions to make proteins, have come from this organism.

s. cerevisiae

Model organism that is a small, single celled fungus that is at least as closely related to animals as it is to plants. Like other fungi, it has a rigid cell wall, is relatively immobile, and possesses mitochondria but not chloroplasts. Genetic and biochemical studies in yeast have been crucial to understanding many basic mechanisms in eukaryotic cells, including the cell division cycle.

Golgi apparatus

Sacks of flattened, membrane-enclosed sacs which modify and package molecules made in the ER that are destined to be either secreted from the cell or transported to another cell compartment

cytoskeleton

System of protein filaments criss-crossed through the cytosol, anchored at one end of the plasma membrane or radiating out from a central site adjacent from the nucleus. Composed of three major filament types. These three types of filaments, together with other proteins that attach to them, form a system of girders, ropes and motors that gives the cell its mechanical strength, controls its shape, and drives and guides its movements. Governs the internal organization of the cell as well as its internal features. So it is as necessary to a stationary plant cell boxed in by a cell wall, as it is to an animal cell, which freely bends, stretches, swims, etc.

intermediate filaments

The filaments of intermediate thickness of the cytoskeleton. They serve to strengthen most animal cells.

electron microscope

The highest magnification and best resolution microscope, which can reveal details down to a few nanometers. Cannot be used to look at living cells because the cells must be fixed (preserved by pickling in a reactive chemical solution), supported by embedding in a solid wax or resin, cut or sectioned into thin slices, and stained before it is viewed

cytosol

The part of the cytoplasm that is not contained within intracellular membranes. The largest single compartment, which contains a host of large and small molecules, crowded together so closely it behaves more like a water-based gel than a liquid solution. The site of many chemical reactions that are fundamental to the cell's existence. ex) breakdown of nutrient molecules

cells

The simplest form of life. Small, membrane enclosed units filled with a concentrated aqueous solution of chemicals and endowed with the ability to create copies of themselves by growing and then dividing in two.

lysosomes

small, irregularly shaped organelles in which intracellular digestion occurs, releasing nutrients from ingested food particles into the cytosol and breaking down unwanted molecules for either recycling within the cell or excretion from the cell.

peroxisomes

small, membrane enclosed vesicles that provide a sequestered environment for a variety of reactions in which hydrogen peroxide is used to inactivate toxic molecules

organelles

substructures within the cell surrounded by internal membranes that have specialized functions; often only hazily defined using a light microscope

genome

the entire sequence of nucleotides in an organism's DNA that provides a genetic program that instructs a cell how to behave

nucleus

the most prominent organelle in a eukaryotic cell. It is enclosed within two concentric membranes that form the nuclear envelope, and it contains molecules of DNA- extremely long polymers that encode the genetic info of the organism.

cell theory

the principle that all living cells are formed by the growth and division of existing cells

evolution

the process by which living species become gradually modified and adapted to their environment in more and more sophisticated ways