Cell Biology Quest 1

Robert Hooke

He coined the word cell; they reminded him of the cells inhabited by monks living in a monastery. He looked at thin layers of cork through a double-lens microscope.

Antonie Van Leeuwenhoek

Dutchman who sold cloths and buttons but in his spare time ground lenses and constructed simple microscopes with good quality (single lens microscope). He was first to examine a drop of pond water under the microscope and saw “animalcules” that moved.

Matthias Schleiden and Theodor Schwann

Created the first two ideas of cell theory: All organisms are composed of one or more cells. The cell is the structural unit of life. (1838-1839)

Rudolf Virchow

A German pathologist who proposed the third tenet of cell theory: Cells can arise only by division from a preexisting cell (1855)

Shinya Yamanaka

won the 2012 Nobel Prize in Physiology and Medicine for cell reprogramming (iPS Stem Cells). The experiment where they gave mice sicke cell, collected their skin cells, reprogrammed them into embryonic stem cell-like iPS cells which gave them genetically identical mutant iPS cells, then corrected sickle cell mutation, then differentiated them into blood stem cells, transplanted them and cured the mice.

Lynn Margulis

She resurrected the idea that organelles from a eukaryotic cell (mitochondria and chloroplasts) had evolved from smaller prokaryotic cells that had taken up residence in the cytoplasm of a larger host cell. This hypothesis is referred to as the endosymbiont theory.

What are some properties of cells?

Cells acquire and utilize energy, carry out a variety of chemical reactions, engage in mechanical activities, can respond to stimuli, are capable of self-regulation, are highly complex and organized, and evolve

What is the difference between light microscopy and electron microscopy?

Light microscopy has a lower-level quality and is less detailed when compared to electron microscopy. Light has color and electron is in black and white

What are some similarities and differences between prokaryotic and eukaryotic cells?

Eukaryotes are more complex, include animals/plants/fungi, have a nucleus and membrane-bound organelles, are large, reproduce through miosis and fertilization, and are usually multicellular. Prokaryotes are simpler, include bacteria/archaea, have no nucleus and membrane-bound organelles, are small, often have circular DNA, and are usually unicellular.

What are the three domains of life?

Archaea, Bacteria, and Eukarya

How can we classify organisms using molecular biology into the various taxa? For example, how can we use metagenomics to identify microbiome composition?

You can use 16S Ribosomal RNA or 18S Ribosomal RNA to identify what domain/species an organism is in. They are in a universally conserved region which makes it easier to amplify a gene using primers based on sequences. They have varied regions and can sometimes get to species level.

What is a microbiome and how do we identify the microbiomes that make up a particular sample?

A microbiome is the collection of microbes and is the subject of several international research efforts aimed at identifying and characterizing these organisms. Sequencing techniques can help identify the microbiomes.

What is differentiation?

A process in which specialized cells are formed.

Stem Cells

Undifferentiated cells that can turn into multiple cell types. They serve as a repair system for the body

Multipotent

Capable of differentiating into a limited range of cell types related to a specific tissue or organ. Lowest potency

Pluripotent

Can give rise to almost all cell types in the body but cannot develop into an entire organism on their own. They can form any cell type except for extra-embryonic tissues

Totipotent

can differentiate into any cell type in the organism, including extra-embryonic tissues like the placenta. They have the highest potency

Adult Stem Cells

Undifferentiated cells found throughout the body after development. Found in mature tissues. restricted to forming types of cells found in the tissues where they reside

Hematopoietic Stem Cells

Multipotent primitive cells that can develop into all types of blood cells. Can produce blood cells in bone marrow.

Mesenchymal Stem Cells

multipotent. Produce a variety of other cell types found in various tissues and organs

Embryonic stem cells

Have greater potential for differentiation (pluripotent) than adult stem cells. They must be differentiated in vitro. Involves ethical considerations

Somatic Cell Nuclear Transfer

When the nucleus of the unfertilized egg is replaced by the nucleus of a cell from the patient to be treated, to give the egg the same chromosome composition as that of the patient. It then is developed to an early embryonic stage and the ES cells would be removed, cultured, and induced to differentiate the cell type needed by the patient

Induced Pluripotent Stem Cells

reprogramming another cell in the body and revert to stem cell, then differentiate into a different cell type. They are made by reprogramming somatic cells to a pluripotent state, meaning they can differentiate into almost any cell type.

Protein induced Pluripotent stem cells

type of pluripotent stem cell generated by introducing specific proteins into somatic cells. These proteins reprogram the somatic cells to revert to a pluripotent state, meaning they can differentiate into almost any cell type in the body

direct cell reprogramming

also known as transdifferentiation. where one type of somatic cell is converted directly into another type of somatic cell without passing through an intermediate pluripotent state.

What are the 6 model organisms for cell biology?

E. coli Bacteria, Brewers and bakers yeast, mustard plant, nematode, fruit fly, and mouse.

advantages of using E. coli

rapid growth and simple genetics

advantages for using yeast

eukaryotic organism with simple genetics and easily manipulated

Advantages for using nematodes

transparent body, well-characterized development, and simple nervous system

advantages for using fruit flies

short life cycle, large number of offspring, and well understood genetics

advantages for using mice

genetic and physiological similarities to humans, well-developed genetic tools, and the ability to create transgenic and knockout models

Advantages for using mustard plants

genetic simplicity, short life cycle, ease of cultivation, extensive genetic tools, relevance to other plants

What is the size range for many eukaryotic cells?

10 to 30 micrometers

What is the size range for prokaryotes?

1 to 5 micrometers

How big are nuclei?

5 to 10 mincrometers

How big are mitochondria?

about 2 micrometers

How big are Bacterium?

about 1 micrometer

How big are viruses

about 20 to 300 nanometers

How big is a hydrogen atom?

1 A

How big is a paramecium?

1.5 mm

How big is a DNA molecule?

2 nm

Convert one centimeter into meters

0.01 m

Convert one Millimeter into meters

0.001 m

Convert one micrometer or micron into meters

0.000001 or 1×10^-6 m

Convert one nanometer into meters

0.000000001 or 1×10^-9 m

convert one angstrom into meters

0.0000000001 or 1×10^-10 m

convert one picometer into meters

0.000000000001 or 1×10^-12 m

synthetic biology

a field oriented to create a living cell in the laboratory. ex. Jurassic Park

mirror life

hypothetical form of life with molecular building blocks that are mirror images of those found in natural life.

What is the synthetic biology toolbox?

Nucleic acids, proteins, and lipids

viruses

obligate intracellular parasites. some need hosts to reproduce which blur lines

virion

a virus particle outside of the host cell. can’t replicate but found that some viruses can self assemble

Viral genetic material

can be single strand or double strand or DNA or RNA

What does the protein capsid do in viruses?

surrounds the genetic material. protein coat. can be different shapes

every virus is made from…

nucleic acid, protein coat, maybe envelope which is derived from host cell membrane

identavirus

delivery for gene therapy

Adenovirus

common. icosahedral shape (20 sides). each triangle is a capsomere which makes up a capsid

Human immunodeficiency Virus (HIV)

envelope derived from human cytoplasmic membrane. glycoprotein has sugar group. spherical

T-even bacteriophage

icosahedral head and a long contractile tail. head contains the viral DNA while the tail is used to inject the DNA into host cell

What is viral specificity for a certain host determined by?

the virus’ surface proteins

Lytic infection

the virus redirects the host into making more virus particles, the host cell bursts and releases the virus

Integration infection

the virus puts its DNA into the host cell’s chromosomes

provirus

virus that integrates its DNA into host cell

Viroids

pathigens, each consisting of a small, naked RNA molecule. Not a virus. can cause disease by interfering with gene expression in host cells. infect plants

Endosymbiont theory

organelles in eukaryotic cells (mitochondria and chloroplasts) evolved from smaller prokaryotic cells.

evidence for endosymbiont theory

have their own DNA, about the right size (bacteria size), double membrane, lineage, binary fission, can divide on own, chloroplasts use FTSZ like bacteria

How might early life have arisen on earth?

Ancient microbes are thought to have formed stratified rock formations, called stromatolites, suggesting that life may have proliferated as early as 3.5 billion years ago

What are the most common elements in living organisms?

CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur)

covalent bonds

pairs of electrons are shared between pairs of atoms

If two electron pairs are shared the covalent bond is a…

double bond

If three pairs of electrons are shared it is a…

triple bond

what is an important consequence in determining the shapes of molecules?

the type of bond between atoms

polar molecules

have an asymmetrical distribution of charge (dipole) ex. oxygen

nonpolar molecules

molecules that lack electronegative atoms and strongly polarized bonds. ex. carbon

dipole

pair of equal and oppositely charged or magnetized poles separated by a distance

important properties of carbon

carbon has 4 valence electrons allowing it to form 4 covalent bonds with other atoms, carbon atoms can bond with each other to form long chains and complex structures, carbon can form single, double, and triple bonds with other atoms, generally stable

electronegative

the shared electrons tend to be located more closely to the atom with the greater attractive force

What are some highly electronegative elements?

Fluorine, oxygen, chlorine, nitrogen, bromine

anion

extra negative charged ion. extra electrons

cation

extra positive ion. lost electron

ion

result when strongly electronegative nuclei capture electrons

free radicals

unstable atoms or molecules with unpaired electrons. formed during normal metabolism. highly reactive and damage macromolecules such as DNA. May play a role in aging

SOD (superoxide dismutase)

an enzyme that destroys the superoxide radical (o2-). protects cells from damage due to the superoxide radical. extends the lifespan of lab animals that overproduce it

calorie restriction can…

extend lifespan of experimental animals, result in decreased production of free radicals, diet containing 25% fewer calories show reduced levels of DNA damage

types of non-covalent bonds

ionic bonds, hydrogen bonds, hydrophobic interactions, van der waals forces

noncovalent bonds

interactions that do not involve the sharing of pairs of electrons

ionic bonds

attractions between charged atoms. Are weakened in the presence of water. May be significant within large biological molecules

hydrogen bonds

when covalently bound hydrogen has a partial positive charge and attracts electrons of a second atom. They determine the structure and properties of water. They occur in biological molecules, such as between DNA strands

hydrophobic interactions

occur when nonpolar molecules associate and minimize their exposure to polar molecules

van der waals forces

attractions between nonpolar molecules. due to transient dipole formation. operate at optimum distances and are maximized by complementary surfaces

why is water so conductive to supporting life?

it is asymmetric (both h atoms are on one side), both covalent O-H bonds are highly polarized, and all three atoms readily form H bonds

acids

release protons

bases

accept protons

amphoteric molecules

act as either acids or bases. ex, water

How do you measure acidity?

use a pH scale to measure

Changes in pH can affect …

ion state and function of proteins

buffers

resist changes in pH

biochemicals

carbon-containing molecules produced by living organisms

hydrocarbons

contain only carbon and hydrogen. vary in number of carbons and the double and triple bonds between carbons

functional groups

groups of atoms giving organic molecules different characteristics and properties