BIO 415 Chapter 1

Two types of cells:

Prokaryotic (bacteria)—lack a nuclear envelope.Eukaryotic—have a nucleus that separates genetic material from cytoplasm.

RNA is able to both serve as a _______________ for, and to ______________ its own _____________.

Template, catalyze, replication

Who discovered that RNA is capable of acting as a template and catalyst of its own replication?

Altman and Cech

_________ is generally believed to have been the initial genetic system in evolution.

RNA RNA world


nucleotide gene sequence is copied into RNA.


nucleotide sequence of RNA is used to specify the order of amino acids in a protein

Define Amphipathic

one end of the molecule is soluble in water and the other is not- Water soluble - hydrophilic- Water insoluble - hydrophobic

_________________ are the basic components of all present-day biological membranes


When placed in water, phospholipids....

spontaneously aggregate into a bilayer

What do cells use for source of metabolic energy?

ATP (Adenine 5' Triphosphate)

What are the three developmental "Stages" of metabolism according to evolution

1. Glycolysis - because it is anaerobic (2 ATP)- All-present day cells do this- Glucose is broken down to lactic acid2. Photosynthesis - first photosynthetic bacteria probably used H2S to convert CO2 to organic molecules- Use of H2O in photosynthesis evolved later- Changed the Earth's atmosphere to Oxygen rich environment3. Oxidative Metabolism - most efficient (36-38 ATP)

Two types of prokaryotes

Archaebacteria—many live in extreme environments.Eubacteria—a large group that live in a wide range of environments.

What are some general characteristics of prokaryotes?

1. Absent nucleus2. Cytoplasmic organelles absent3. Smaller than Eukaryotes (generally)

What are important characteristics of Cyanobacteria

1. The group in which photosynthesis evolved (according to evolution)2. Are the largest and most complex prokaryotes.

Escherichia coli (E. coli)

1. Is a typical prokaryotic cell.2. Has a rigid cell wall of polysaccharides and peptides3. Beneath the cell wall is the plasma membrane, a phospholipid bilayer with associated proteins4. DNA is a single circular molecule in the nucleoid 5. cytoplasm contains approximately 30,000 ribosomes

What are the general characteristics of eukaryotic cells?

1. Much larger and more complex2. Have a nucleus3. Have cytoplasmic organelles


1. The largest organelle2. The site of DNA replication3. The site of RNA synthesis


The side of oxidative metabolism (in animal cells)


Site of photosynthesis

Lysosomes and Peroxisomes

specialized metabolic compartments for the digestion of macromolecules and for various oxidative reactions


1. Digestion of macromolecules2. Storage of waste products and nutrients

Endoplasmic reticulum

Network of intracellular membranes, extending from the nuclear membrane throughout the cytoplasm.Function: processing and transport of proteins and lipid synthesis

Golgi apparatus

Compartment for further protein modification, packaging, and transport to final destination either in the cell or out of the cellAlso serves as a site of lipid synthesis In some plant cells, site of synthesis of some polysaccharides that compose the cell wall.


Network of protein filaments extending throughout the cytoplasm. Function:1. Provides structural framework2. Determines cell shape and organization3. Involved in movement of whole cells, organelles, and chromosomes during cell division.

Eukaryote organelles are thought to have arisen by...

Endosymbiosis (prokaryotic cells living inside the ancestors of eukaryotes)

Possible evidence for endosymbiotic theory:

1. Mitochondria and chloroplasts are similar to bacteria in size.2. Like bacteria, they reproduce by dividing in two. 3. Both contain their own DNA, which encodes some of their components.

What is the evolutionary explanation of the differences between archaebacteria and bacteria, as well as the formation of the eukaryotic genome?

Archaebacteria and eubacteria probably diverged very early in their evolutionary historyOne hypothesis is that the eukaryotic genome arose from the fusion of archaebacterial and eubacterial genomes.


1. It is the most simple eukaryote2. It is a single-celled organism

What are the 3 main plant tissue systems?

1. Ground tissue- Parenchyma cells: site of metabolic reactions, including photosynthesis- Collenchyma and sclerenchyma: have thick cell walls and provide structural support.2. Dermal tissue—covers the surface of the plant; forms a protective coat and allows absorption of nutrients.3. Vascular tissue (xylem and phloem)—elongated cells which transport water and nutrients throughout the plant.

What are the major tissue types for animals?

1. Epithelial cells form sheets that cover the surface of the body and line internal organs.2. Connective tissues include bone, cartilage, and adipose tissue. Loose connective tissue is formed by fibroblasts.3. Blood contains several different types of cells: (Has this changed?)- RBC- WBC4. Nervous tissue is composed of supporting cells and nerve cells, or neurons, and various types of sensory cells.5. Muscle cells are responsible for the production of force and movement.

What is the most thoroughly studied species of bacteria? In what ways has it advanced the understanding of cell biology?

E. coliOur understanding of DNA replication, the genetic code, gene expression, and protein synthesis derive from studies of this bacterium.It has especially helped with our study of genetics due to it's small genome and rapid growth rate (every 20 minutes)

What organism is a model for fundamental studies of eukaryote biology? Why?

YeastColonies from a single cell and can be used for genetic manipulations on eukaryotic cells

The unity of molecular cell biology

General principles of cell structure and function revealed by studies of yeasts apply to all eukaryotic cells.

What species of organism have helped grow our understanding of early development of multicellular organisms? Why?

Caenorhabditis elegans (type of nematode)1. Adult worms consist of only 959 somatic cells. 2. The embryonic origin and lineage of all the cells has been traced.3. Genetic studies of C. elegans have identified many mutations responsible for developmental abnormalities.

In what ways is the fruit fly Drosophila melanogaster a model organism for understanding developmental biology?

1. Short reproductive cycle (2 weeks) make it useful for genetic studies2. Has advanced the understanding of molecular mechanisms that govern animal development, particularly with respect to formation of the body plan of complex multicellular organisms.

What organism is a model for plant molecular biology?Why?

Arabidopsis thalianaIt has a small genome and is easy to grow in the lab

___________ ______________ cells are important models for studying particular aspects of cell biology:Provide examples:

Highly differentiatedMuscle cells are a model for studying cell movement at the molecular levelGiant neurons are used to study ion transport and cytoskeleton function

What two organisms are important for studying vertebrate cell development? Why?

1. The frog Xenopus laevis - produces large eggs in large numbers, facilitating laboratory study and biochemical analysis2. Zebrafish - embryos develop outside of the mother and are transparent, so early stages of development can be easily observed.

What is the most common mammal model?Why?

The mouse1. The human and mouse genomes are similar2. mutations in homologous genes result in similar developmental defects in both species. 3. Genetically engineered mice with specific mutant genes are now used to study the functions of these genes in the context of the whole animal.

What are some major history points of light microscopy?

1. Robert Hooke coined the term "cell" from observations of a piece of cork in 1665.2. In the 1670s Antony van Leeuwenhoek was able to observe a variety of cells, including sperm, red blood cells, and bacteria.3. Schleiden and Schwann in 1838 proposed the cell theory after studying plant and animal cells with a microscope

Resolution of contemporary light microscopes:

about 1000X

Define resoltuion

The ability to distinguish objects separated by small distancesMORE IMPORTANT THAN MAGNIFICATION

What are the different types of microscopy?

1. Bright-field microscopy2. Phase-contrast microscopy + Differential Interference-Contrast3. Video-enhanced DIC microscopy 4. Fluorescence microscopy 5. Confocal microscopy 6. Multi-photon excitation microscopy7. TEM8. SEM

Bright-field microscopy

1. Light passes through the sample2. Cells are often preserved with fixatives since the dye usually kill the cells

Phase-contrast microscopy + Differential Interference-Contrast

1. Convert variations in density or thickness to differences in contrast2. Will get a 3-D image

Video-enhanced DIC microscopy

1. Allows visualization of the movement of organelles along microtubules. Can calculate the rate of motion by knowing the flicker rate (frames / second) and the distance. - Kinesin move vesicles along microtubules are quantized (we know the rate at which kinesin move vesicles)- Vesicles that move at different rates - we can determine how many kinesin are pulling the vesicles 2. Resolution is as much as .025 micrometers

Fluorescence microscopy

1. fluorescent dye is attached to a molecule of interest in fixed or living cells.2. Dye absorbs light at one wavelength and emits light at another wavelength (The emitted light is a lesser energy than absorbed)3. Illuminate the specimen with a wavelength of light that excites the fluorescent dye.4. Filters are used to detect the specific wavelength of light that the dye emits.Some parts of the image blurry from image that is not in focus

Examples of Fluorescence microscopy

1. Green Fluorescent Protein (GFP)- Jellyfish protein that can be fused to any protein of interest - Tagged protein is expressed in cells and detected by fluorescence microscopy2. Fluorescence Recovery After Photobleaching (FRAP): - Region of GFP-protein is bleached with light (over excitement)- The region is burned out-Observe the recovery time as GFP-labeled molecules move into the bleached region- Study rate of protein movement in living cells3. Fluorescence resonance energy transfer (FRET): - two proteins are coupled to different fluorescent dyes- light emitted by one GFP variant excites the second- Used to study interactions between proteins in a cell

Image Deconvolution.

The images of fluorescence microscopy can sometime be out of focusThe computer analyzes different depths of focus and generates an image that is deconvoluted

Confocal microscopy

1. Increased the contrast and detail by analyzing the fluorescence from a single point.2. Gets rid of all of the unfocused light3. Allows for the z-plane (this allows better understanding on getting a better 3-D perspective of images)

Electron Microscopy

1. Much better resolution - down to .2 nm2. This is because of the short wavelength of electron beam3. resolution for biological sample is 1-2 nm because of the inherent lack of contrast

Types of Electron Microscopy

1. Transmission (more common)- Fixed, heavy metal, and electron beam reflects off the metal- darker images are more electron-dense - Can determine parts of the membrane - hydrophilic head - more electron dense (darker) - hydrophobic tail - less electron dense (lighter)2. Electron Tomography (scanning)- 3-D image- A computer analyzes multiple 2-D dimensional images over a range of viewing directions

Metal Shadowing

1. Used to visualize the surface of subcellular structures or macromolecules.2. Specimen is sprayed with a thin layer of metal such as platinum, from an angle, which results in a shadowing effect.

Freeze fracturing

1. Specimens are frozen in liquid nitrogen and then fractured with a knife blade. 2. The specimen is then shadowed with platinum.3. Often splits the lipid bilayer

Differential centrifugation

1. Developed in the 1940s and 1950s 2. Uses ultracentrifuge3. Separate cell components on the basis of size and density - nuclei are large and dense and will pellet at relatively low speed 800xg- mitochondria are smaller and less dense and require about 8,000xg- ER vesicle need about 60,000 - 100,00xg

Density-gradient centrifugation

1. Organelles are separated by sedimentation through a gradient of a dense substance, such as sucrose2. Two Types:- Continuous gradient- Discontinuous gradient-- Different densities with different refraction indexes-- A sample of 1.4 M will not move further than the 1.4 M solution because higher Molar solution are too dense

Velocity centrifugation

Starting material is layered on top of the sucrose gradient. Particles of different sizes sediment through the gradient at different rates.

Equilibrium centrifugation

Used to separate subcellular components on the basis of their buoyant densityThe sample particles are centrifuged until they reach an equilibrium position at which their buoyant density is equal to that of the surrounding sucrose or cesium chloride solution

Cell Culture:

1. In vitro - enables scientists to study cell growth, differentiation, and perform genetic manipulation.2. Most animal cells will grow on the plastic surface of the Petri dish.3. Embryos and tumors are typically used as the starting material because still contain rapid growing cells4. Embryonic fibroblasts grow particularly well in culture and are one of the most widely studies types of animal cells

What are the two common starting materials for cell cultures? Why?

Embryos and tumorsBecause still contain many rapid growing cellsEmbryonic Fibroblasts grow particularly well in culture and are one of the most widely studied types of animal cells (easy to grow and grow fast)

What is one of the most widely studied cell types of animal cells? Why?

Embryonic Fibroblasts Grow particularly well in culture and are one of the most widely studied types of animal cells (easy to grow and grow fast)

What are the advantages and disadvantages of using embryonic stem cells research?

Advantages:1. Maintain ability to differentiate into all cell types2. Played important role in studying gene functions and offer possibility of treating human diseases.Disadvantages:1. Major moral problem - must kill the embryo2. There is more plasticity leading to less control of what is grown - this is where adult stem cells show more promise!

Culture media for animal cells:

1. Complex and must include:- Salts - Glucose - Various essential amino acids and vitamins2. Serum provides polypeptide growth factors. 3. The identification of individual growth factors makes it possible to culture cells in serum-free media.

What is Harry Eagle known for? Why is it important?

1. The first researcher to describe a defined medium for animal cells in 19552. Enabled scientists to grow a wide variety of cells under defined experimental conditions

Primary Culture

1. An initial cell culture from tissue2. Can be replated at a lower density to form secondary cultures many times 3. Most normal cells such as fibroblasts CANNOT be grown in culture indefinitely

Cell Lines

1. Embryonic stem cells and tumor cells can proliferate indefinitely 2. Provide a continuous and uniform source of cells for many types of experiments


Mass of undifferentiated cells that is produced as a cell culture

What is the purpose of using Phenyl Red in a media?

It acts as a pH indicator to help keep experiment at the right pH. Initially it is a orangish pink. When yellow, it is time to change.

What are the advantages and disadvantages of cell line and primary cultures?

Cell Line:Advantages1. Infinite supply2. Conservation of uniformityDisadvantages:1. It's a tumor and it's genetics are messed upPrimary Culture:Advantages:1. Cell are not messed up geneticallyDisadvantages:1. Limited time and cell replications2. Lack of uniformity3. Limitations because out of original context of the body and now are in 2-D plane rather than 3-D plane.

What is one of the most widely studied cell types of animal cells? Why?