A Preview of Cell Biology

A Preview of Cell Biology

• The cell is the basic unit of biology.

• Cells are constantly changing.

• The convergence of cytology, genetics, and biochemistry

has made modern cell biology one of the most exciting

and dynamic disciplines in biology.

1.1 The Cell Theory: A Brief History

• Robert Hooke (1665) observed compartments in cork,

under a microscope, and first named them cells.

• He had observed the compartments formed by cell walls

of dead plant tissue.

Advances in Microscopy Allowed Detailed Studies of Cells

• Two factors restricted progress in early cell biology

– Microscopes had limited resolution, or resolving power

(ability to see fine detail)

– The descriptive nature of cell biology: the focus was on

observation, with little emphasis on explanation

Compound Microscopes

• By the 1830s, compound microscopes were used

– These had two lenses

– Both magnification and resolution were improved

– Structures only 1 μm in size could be seen clearly

The Cell Theory Applies to All Organisms

• Using a compound microscope, Robert Brown identified

the nucleus, a structure inside plant cells.

• Matthias Schleiden concluded that all plant tissues are

composed of cells.

• Thomas Schwann made the same conclusion for animals.

The Cell Theory

• In 1839, Schwann postulated the cell theory:

1. All organisms consist of one or more cells.

2. The cell is the basic unit of structure for all organisms.

• Later, Virchow (1855) added:

3. All cells arise only from preexisting cells.

1.2 The Emergence of Modern Cell Biology

• Three strands of biological inquiry weave into modern cell biology:

– Cytology focuses mainly on cellular structure and

emphasizes optical techniques.

– Biochemistry focuses on cellular structure and function.

– Genetics focuses on information flow and heredity and

includes sequencing of the entire genome (all of the DNA)

in numerous organisms.

The Cytological Strand Deals with Cellular Structure

• Historically, cytology deals primarily with cell structure and observation using optical techniques.

• Microscopy has been invaluable in helping cell biologists deal with the problem of small size of cells and their components.

Cellular Dimensions

• The units used to measure cells and organelles may not

be familiar.

• The micrometer (μm), also called the micron, is one

millionth of a meter (10−6 m).

• Bacterial cells are a few micrometers in diameter, whereas the cells of plants and animals are 10–20 times larger.

• Organelles are comparable to bacterial cells in size

Measurements in Cell Biology

• The nanometer (nm) is used for molecules and

subcellular structures that are too small to be seen using

the light microscope.

– The nanometer is one-billionth of a meter (10−9 m).

• The angstrom (Å), which is 0.1 nm, equals about the size

of a hydrogen atom.

– It is used in cell biology to measure dimensions within

proteins and DN A molecules.

The Light Microscope

• The light microscope was the earliest tool of cytologists.

• It allowed identification of nuclei, mitochondria, and

chloroplasts within cells.

• Light microscopy is also called brightfield microscopy

because white light is passed directly through a specimen.

• Brightfield microscopy samples are dead, fixed, and stained. The preparation process can introduce distortions not typical to living cells.

Specialized Light Microscopes

• A variety of special optical techniques have been developed for observing living cells directly. These include:

– Phase-contrast microscopy

– Differential interference contrast microscopy

– Fluorescence microscopy

– Confocal microscopy

Enhancements to Microscopy

• Phase contrast and differential interference contrast microscopy make it possible to see living cells clearly.

• The phase of transmitted light changes as it passes through a structure with a different density from the

surrounding medium.

• These types of microscopy enhance and amplify these slight changes.

Fluorescence Microscopy

• Fluorescence microscopy allows detection of proteins, DNA sequences, or molecules that have been made fluorescent by binding to antibodies.

• An antibody is a protein that binds a particular target molecule, called an antigen.

• The antibody can be coupled to a fluorescent molecule, which emits fluorescence wherever the target molecule is bound by the antibody.

• Green fluorescent protein (G F P) can also be used to study the temporal and spatial distribution of proteins in a

living cell.

• Confocal microscopy uses a laser beam to illuminate a single plane of a fluorescently labeled specimen.

• Digital video microscopy uses video cameras to collect digital images.

Limits of Resolution

• The limit of resolution refers to how far apart objects must be to appear as distinct.

• The smaller the microscope’s limit of resolution, the greater is its resolving power (ability to see fine details).

• The resolution for a light microscope is related to the physical nature of light.

• For visible light, the limit of resolution is about 200–350

nm.

Electron Microscopy

• The electron microscope, which uses a beam of

electrons rather than light, was a major breakthrough for

cell biology.

• The limit of resolution of electron microscopes is about

100 times better than light microscopes.

• The magnification is much higher than light microscopes—up to 100,000×.

• In transmission electron microscopy (T E M), electrons

are transmitted through the specimen.

• In scanning electron microscopy (SE M), the surface of

a specimen is scanned by detecting electrons deflected

from the outer surface.

• Specialized approaches in electron microscopy allow for

visualization of specimens in three dimensions, and allow

for the determination of protein macromolecular structures.

The Biochemical Strand Studies the Chemistry of Biological Structure and Function

• Around the same time cytologists were studying cells

microscopically, others began to explore cellular function.

• These scientists began to try to understand the structure and function of biological molecules.

Biological Reactions and Pathways

• In 1828, Fredrich Wöhler showed that a compound made

in a living organism could be synthesized in the lab.

• Prior to this work, it was thought that living organisms

were unique and not governed by the laws of physics and

chemistry.

Key Observations in Early Biochemistry

• Louis Pasteur (1860s) showed that yeasts could ferment

sugar into alcohol.

• The Buchners (1897) showed that yeast extracts could do

the same.

• This led to the discovery of enzymes, biological catalysts.

Early Biochemistry

• Steps of the pathways of fermentation and other cellular

processes were elucidated in the 1920s,1930s, and

1940s.

• Gustav Embden, Otto Meyerhof, Otto Warburg, and Hans

Krebs described the steps of glycolysis (the Embden–

Meyerhof pathway) and the Krebs cycle.

• Fritz Lipmann showed that adenosine triphosphate (ATP)

is the principal energy storage compound in most cells.

• Melvin Calvin and colleagues elucidated the Calvin cycle.

Biochemistry Methods

• Subcellular fractionation—uses centrifugation to

separate/isolate different structures and macromolecules

• Ultracentrifuges—are capable of very high speeds (over

100,000 revolutions per minute)

• Chromatography—techniques to separate molecules

from a solution based on size, charge, or chemical affinity

• Electrophoresis—uses an electrical field to move

proteins, DNA, or RNA molecules through a medium

based on size/charge

• Mass spectrometry—is used to determine the size and

composition of individual proteins

The Genetic Strand Focuses on Information Flow

• The genetic strand is the study of the inheritance of

characteristics from generation to generation.

• It was not until the nineteenth century that scientists

discovered the nature of inherited physical entities, now

called genes.

Classical Genetics

• Gregor Mendel’s experiments with peas (1866) laid the

foundation for understanding the passage of “hereditary

factors” from parents to offspring.

• The hereditary factors are now known to be genes.

Chromosomes

• Walther Flemming (1880) saw threadlike bodies in the

nucleus called chromosomes.

• He called the process of cell division mitosis.

• Wilhelm Roux (1883) and August Weisman (shortly after)

suggested that chromosomes carried the genetic material.

Chromosome Theory

• Three geneticists formulated the chromosome theory of

heredity, proposing that Mendel’s hereditary factors are

located on chromosomes.

• Morgan, Bridges, and Sturtevant (1920s) were able to

connect specific traits to specific chromosomes in the

model organism, Drosophila melanogaster (the common

fruit fly).

DNA

• Friedrich Miescher (1869) first isolated DN A, which he

called “nuclein.”

• Known to be a component of chromosomes by 1914

• Known to be composed of only four different nucleotides

by the 1930s

• Proteins, composed of 20 different amino acids, were

thought more likely to be a genetic material.

DNA is the Genetic Material

• Experiments with bacteria and viruses in the 1940s began

to implicate DNA as the genetic material.

• Beadle and Tatum formulated the one gene–one enzyme

concept (each gene is responsible for the production of a

single protein).

Molecular Genetics

• In 1953, Watson and Crick, with assistance from Rosalind

Franklin, proposed the double helix model for DN A

structure.

• In the 1960s, there were many advances toward

understanding DN A replication, RN A production, and the

genetic code

• Crick coined the central dogma of molecular biology,

which can be summarized as:

RNA

• Three important kinds of RNA molecules:

– mRNAs (messenger RNA s)—translated to produce

protein

– rRNAs (ribosomal RNA s)—components of ribosomes

– tRNAs (transfer RNA s)—bring the appropriate amino

acid for protein synthesis

• Exceptions to the central dogma include viruses with RN A

genomes

• Reverse transcriptase is an enzyme that uses viral RN A to

synthesize complementary DN A.

Working with DNA

• Recombinant DN A technology uses restriction enzymes

to cut DNA at specific places, allowing scientists to create

recombinant DN A molecules with DN A from different

sources.

• DNA cloning is the generation of many copies of a specific

DNA sequence.

• DNA transformation is the process of introducing DN A

into cells

Sequencing DNA

• DNA sequencing methods are used routinely for rapidly

determining the base sequences of DN A molecules.

• It is now possible to sequence entire genomes (entire DN A

content of a cell).

Bioinformatics and “-Omics”

• Bioinformatics merges computer science with biology to

organize and interpret enormous amounts of sequencing

and other data.

• Genomics is the study of all the genes of an organism.

• Proteomics is the study of the functions and interactions of

all the proteins present (or proteome) in a particular cell.

Bioinformatic Tools

• Numerous bioinformatic tools are publicly available

through NCB I (National Center for Biotechnology

Information).

• High-throughput methods allow for dramatic increases in

the speed of molecular analysis.

• Expression levels of hundreds or thousands of genes can

be monitored simultaneously.

-Omics

• Transcriptomics—the study of all the genes transcribed in a cell

• Metabolomics—the analysis of all metabolic reactions

happening at a given time in a cell

• Lipidomics—study of all the lipids in a cell

• Ionomics—study of all the ions in a cell

• There are likely more “-omics” to come.

CRISP R Genome Editing

• Clustered regularly interspaced short palindromic repeats

(CRI SP R; pronounced “crisper”)

• Discovered as a prokaryotic defense against viral infection

• Used as a tool to for genome editing

• A double stranded break is introduced in the genome at a

precise location.

• This location is targeted by a short nucleotide called a

guide RNA (gRNA).

• When double stranded breaks are repaired, the cell often

introduces errors.

• If a piece of DNA called a repair template is included, the

cell can repair the break using a process called homology-

directed repair.

1.3 How Do We Know What We Know?

• What we think of as “facts” today, things known to be true,

are ideas that replaced earlier “facts,” now know to be

misconceptions.

Biological “Facts” May Turn Out to Be Incorrect

• In science, “facts” are provisional pieces of information.

• These are dynamic and subject to change.

• To a scientist, a “fact” is an attempt to state our best

current understanding of the world, based on observations

and experiments.

Experiments Test Specific Scientific Hypotheses

• Researchers first search the scientific literature, using

peer-reviewed sources in scientific or medical journals.

• They formulate a hypothesis, a tentative explanation that

can be tested experimentally.

• This may take the form of a model, which appears to be a

reasonable explanation for the phenomenon.

Testing Hypotheses

• Experimenters then design a controlled experiment,

collecting the data and interpreting the results.

• Scientists seek to prove the null hypothesis, which is

opposite to their hypothesis.

• The certainty of a particular hypothesis is strengthened

when multiple attempts fail to confirm the null hypothesis.

Model Organisms Play a Key Role in Modern Cell Biology Research

• Scientists have developed a number of model systems to

study cellular processes directly in living cells and

organisms.

Cell and Tissue Cultures

• Cell cultures are commonly used as model systems.

• Cell cultures are used to study cancer, viruses, proteins,

and cellular differentiation.

• Some of what is learned from cultured cells may not reflect

what happens within an intact organism.

Model Organisms

• A model organism is a species widely studied, well characterized, and easy to manipulate.

• Each has particular advantages, useful for experimental

studies.

• Much of our knowledge is based on research using

relatively few organisms.

Well-Designed Experiments Alter Only One Variable at a Time

• In a typical experiment, one condition is varied, called the

independent variable.

• All other variables are kept constant.

• The outcome is called the dependent variable.

• In vivo experiments involve living organisms.

• In vitro experiments are done outside the living organisms,

for example, in a test tube.