cell structure and function exam 1

robert hooke

• observed compartments in cork under a microscope

• first named them “cell”

• 1665

anton von leeuwenhoek

• improved microscope

• observed single-cell microorganisms

• late 17th century

the cell theory matthias schleiden and thomas schwann

matthias schleiden: concluded that all plant tissues are composed of cells

thomas schwann: made the same conclusion for animals (concluded that all animal tissues are composed of cells)

the cell theory

1. all organisms consist of one or more cells

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

3. all cells arise only from preexisting cells “omnis cellula e cellula”

schwann (1839) 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 ____ to the cell theory

3. all cells arise only from preexisting cells “omnis cellula e cellula”

three strands of biological inquiry that weave into modern cell biology

• cytology

• biochemistry

• genetics

strand of biological inquiry: cytology

focuses mainly on cellular structure and emphasizes optical techniques

strand of biological inquiry: biochemistry

focuses on cellular structure and function

strand of biological inquiry: genetics

focuses on information flow and heredity and includes sequencing of the entire genome (all of the DNA) in numerous organisms

the micrometer (µm)

• also called the micron

• 10^-6 m

the nanometer (nm)

10^-9

the angstrom (Å)

• 0.1 nm

• equals about the size of a hydrogen atom

types of light microscopy

• brightfield

  • unstained specimen

  • stained specimen

• phase contrast

• differential interference contrast

• fluorescence

• confocal

type of light microscopy: brightfield (unstained specimen)

• passes light directly through specimen

• unless cell is naturally pigmented or artificially stained, the image has little contrast

type of light microscopy: brightfield (stained specimen)

• staining with various dyes enhances contrast

• most staining procedures require that cells be fixed (preserved)

type of light microscopy: phase contrast

• enhances contrast in unstained cells by amplifying variations in refractive index - within specimen

• especially useful for examining living, unpigmented cells

type of light microscopy: differential interference contrast

also uses optical modifications to exaggerate differences in refractive index

type of light microscopy: fluroescence

• shows the locations of specific molecules in the cell

• fluorescent substances absorb ultraviolet radiation and emit visible light

• the fluorescing molecules may occur naturally in the specimen but more often are made by tagging the molecules of interest with fluorescent dyes or antibodies

type of light microscopy: confocal

• uses lasers and special optics to focus illuminating beam on a single plane within the specimen

• only those regions within a narrow depth of focus are imaged

• regions above and below the selected plane of view appear black rather than blurry

electron microscopy

• transmission EM

• scanning EM

electron microscopy: transmission EM

you can see the organelles in a cell

electron microscopy: scanning EM

you only see the surface of the cell

individuals who formed key observations in early biochemistry

• fredrich wohler

• louis pasteur

• the buchners

key observations in early biochemistry: fredrich wohler (1828)

showed that a compound made in a living organism could be synthesized in the lab

key observations in early biochemistry: louis pasteur (1860s)

showed that yeasts could ferment sugar into alcohol

key observations in early biochemistry: the buchners (1897)

showed that yeast extracts could do the same

what the key observations in early biochemistry led to

this all led to the discovery of enzymes - biological catalysts

biochemistry methods - separation techniques

• subcellular fractionation

• ultracentrifugation

• chromatography

• electrophoresis

separation technique: subcellular fractionation

uses centrifugation to separate/isolate different structures and molecules

separation techniques: ultracentrifugation

capable of very high speeds (over 100,000 revolutions per minute) to separate tiny particles based on shape, size, and density

separation techniques: chromatography

techniques to separate molecules from a solution based on size, charge, or chemical affinity

• gel filtration chromatography: size exclusion; molecules separated based on size; largest proteins first and smallest last

• ion exchange chromatography: molecules separated based on charge; bound proteins are eluted by raising salt concentration (competing ions)

  • cation exchange - cationic proteins bind to negatively charged beads

  • anion exchange: anionic proteins bind to positively charged beads

separation techniques: electrophoresis

uses an electrical field to move proteins, DNA, or RNA molecules through a medium based on size/charge

• separates biomolecules like proteins or nucleic acids based on their size (molecular weight) and charge using an electric field

• molecules are loaded into a porous gel matrix, an electric current is applied, negatively charged molecules move toward the positive electrode (anode)

• rRNAs can be separated by electrophoresis

more on electrophoresis

• SDS page: most common for proteins; proteins are denatured and coated with a detergent called SDS

• 2D gel electrophoresis: combines isoelectric focusing (IEF) and SDS-PAGE to separate complex mixtures of hundreds or thousands of proteins with extremely high resolution

biochemistry methods - identification techniques

• mass spectrometry

• x-ray crystallography

identification techniques: mass spectrometry

used to determine the size and composition of individual proteins

identification techniques: x-ray crystallography

used to determine 3-D structure of individual molecules and complexes

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

genetic strand timeline

• 1953: watson and crick, with assistance from rosalind franklin, proposed the double helix model for DNA structure

• 1960s: many advances toward understanding DNA replication, RNA production, and the genetic code

crick coined the central dogma of molecular biology, which can be summarized as…

1. DNA replication

2. transcription

3. translation

central dogma: DNA replication

nuclear DNA is fully copied one time each cell division

central dogma: transcription

nuclear DNA directs the synthesis of specific mRNA molecules

central dogma: translation

a ribosome synthesizes the specific protein encoded by the mRNA

working with DNA: recombinant DNA technology

uses restriction enzymes to cut DNA at specific places, allowing scientists to create recombinant DNA molecules with DNA from different sources

working with DNA: DNA cloning

the generation of many copies of a specific DNA sequence

working with DNA: DNA transformation

the process of introducing DNA into cells

sequencing DNA

• DNA sequencing methods for rapidly determining the base sequences of DNA molecules are used routinely

• it is now possible to sequence entire genomes (entire DNA content of a cell)

CRISPR genome editing

a biotechnology tool that allows scientists to precisely alter DNA sequences and modify gene function in living organisms

bioinformatics

merges computer science with biology to organize and interpret enormous amounts of sequencing and other data

bioinformatis’ “-omics”

• genomics

• proteomics

• transcriptomics

• metabolomics

• lipidomics

• ionomics

bioinformatics: genomics

the study of all the genes of an organism

bioinformatics: proteomics

the study of the functions and interactions of all the proteins present (or proteome) in a particular cell

bioinformatics: transcriptomics

the study of all the genes transcribed in a cell

bioinformatics: metabolomics

the analysis of all metabolic reactions happening at a given time in a cell

bioinformatics: lipidomics

the study of all the lipids in a cell

bioinformatics: ionomics

the study of all the ions in a cell

cell biology experiments often involve

combining all three threads: cytology, biochemistry, genetics

the 4 types of macromolecules

• proteins

• polysaccharides (carbohydrates)

• lipids (fats)

• nucleic acid

macromolecules are built up of…

simple units called monomers; they are called polymers

basic information regarding atomic structure

• subatomic particles and atomic numbers

• valence shells and the octet rule

• chemical bonds in cell biology

info. regarding atomic structure: subatomic particles and atomic numbers

• protons: +1 charge; 1 amu

• neutrons: 0 charge; 1 amu

• electrons: -1 charge; 0 amu

info. regarding atomic structure: valence shells and the octet rule

• valence electrons: electrons in the outermost shell

• octet rule: atoms are most stable when their outer shell contains 8 electrons

• electronegativity: an atom’s affinity or “pull” for shared electrons

info. regarding atomic structure: chemical bonds in cell biology

• covalent bonds (polar and non-polar)

• ionic bonds

• hydrogen bonds

• van der waals

non-polar covalent bonds

equal sharing of electrons with similar electronegativities; strong in water

polar covalent bonds

unequal sharing of electrons where one atom is more electronegative; strong in water

ionic bond

full transfer of electrons creating charged ions (Na+, Cl-); weakened by water