Cell Biology Ch. 1

basic unit of life and biology? what does this mean?

cell / smallest thing to exhibit all the characteristics of life

basic characteristics of cells

every organism consists of them, carry out necessary functions for life, are constantly changing and have capacity to grow, reproduce, and become specialized

3 parts of cell theory

all cells come from preexisting cells, all living things are made of cells, cell is basic unit of life

what is cell biology and what are the 3 areas of study that contribute to the overall field of cell bio

study of cell structure and function / cytology, biochemistry, and genetics

describe cytology

studies cellular structure, uses microscope, based on direct observations, easier

first to view and name cells? what type of cells?

Robert Hooke / dead cork

first to see living cells

antonie van leeuwenhoek

discovered and name nucleus

Robert Brown

said cells come from preexisting cells

Virchow

said all plants and animals are made of cells

Schleiden and Scwann

describe biochemistry

studies chemistry of living systems, function, isolating/separating (molecular level), and how the things we see work

describe genetics

study of behavior of genes and storage of hereditary information, PCR

define micro unit, value, and symbol

10^-6 m (um) / 1 millionth of a meter

define nano unit, value, and symbol

10^-9 m (nm) / 1 billionth of a meter

3 necessary parts of microscopy

illumination source, specimen, and lenses

light microscopy:

illumination source, lenses, mag limit, typically?

light or photons / glass / 1000X / compound

electron microscopy:

illumination source, lenses, mag limit

electrons / magnets / 10^6X

simple vs. compound microscope

simple using single convex lense to focus light while compound uses many lenses

identify 2 types of microscopy and the different types within those

light microscopy (brightfield, phase-contrast/differential interference contrast, fluorescence/confocal) and electron miscroscopy (transmission electron miscroscope TEM and scanning electron microscope SEM)

define magnification

increasing virtual size of sample (how large it looks)

define resolution

distinguishing between two points as separate

higher mag = (__) res

increased (but not always better); think beach ball and softball example with rope

t or f: monocular microscopes can be compound

t

how does a brightfield microscope work

light passes through specimen and glass lenses focus image onto eye

brightfield microscopes are usually (__) and can utilize chemical (__). background is (__) and has (__) look what can be seen without stains/dyes?

compound / dyes or stains / white / watercolor / nucleus, cell membrane, cytoplasm

phase contrast/differential interference contrast microscope has (__) background and (__) are visible. (__) appearance

white/gray / shadows and highlights / 3D

how does phase contrast/differential interference contrast microscope work?

converting small phase shifts in transmitted light into visible differences in image brightness and contrast.

identify microscope used

brightfield

identify microscope used

phase contrast/ differential interference contrast

identify two types of immunofluorescence

primary (direct) and secondary (indirect)

describe basic antibody structure

protein made by B lymphocytes in immune system that binds a target antigen. it has a constant region (C) that is the same for all antibodies and variable (V) that are identical to each other but unique for each antibody and antigen-binding site.

explain how cytology is different from biochem in discipline of cell bio

cytology explores the structures while biochem exlains and clarifies the structures

list diff biochemical techniques used by cell biologists

centrifugation (subcellular fractionation), ultracentrigue, chromatograophy, electrophoresis, mass sepctrometry

differentiate between classical genetics and molecular genetics

classical genetics studied chromosomes, DNA, and how genetic information is passed. molecular genetics studies the chemical structure and function of genes

identify 3 parts of central dogma of molecular biology

DNA replication, transcription, and translation

differentiate between a hypothesis and null hypothesis

a hypothesis is a tentative explanation that can be tested experimentally or by observation; a null hypothesis is the opposite of the original hypothesis. failure to confirm null hypothesis verifies the hypothesis

what is bioinformatics

allows us to compare and analyze many genes or other molecules at the same time

what is chromatography

separates mixture into parts based on charge or affinity or size

chromosome theory of heredity

characteristics of organisms passed down generations results from inheritance of chromosomes carrying genes

CRISPR

genome editing

DNA sequencing

rapidly determines base sequences of DNA molecules

electrophoresis

electricity separates proteins, DNA, or RNA by size and electric charge

antibodies can be linked to an (___) to perform a chemical reaction resulting in a colored precipitation product that can be seen with standard microscope

enzyme

guide RNA

helps Cas9 target a specific place within the genome wehre Cas9 causes a double-stranded break in DNA

mass spectrometry

determines size and composition of individual proteins

recombinant DNA

contain DNA sequences from 2 different sources

subcellular fractionation

isolating structures based on size, shape, or density by ultracentrifugation. used to isolate organelles and speeding up pulls out smaller things

hypothesis

proposed explanation for a specific phenomenon that is testable

theory

predictive, repeatable, tested abundantly, not proven

explain how fluorescence/confocal microscopy works

light is projected onto the sample and emitted back to the detector

fluoresence/confocal microscopy is also called (__) microscopy and requires the use of (__). what do the images look like? what can it detect?

darkfield / fluorophores / dark background with very clear not blurry colorful images / specific molecules and ions

fluorophores (__) energy at shorter or (__) energy wavelengths. they (__) energy at longer or (__) energy wavelengths

absorb / high / release / low

fluorophores can be in stand-alone (__) and (__) and used to?

dyes / stains / tag antibodies for immunofluorescence microscopy

immnunofluorescence microscopy specifically identifies the location of (___) and uses (__). what are the two types

various molecules / fluorescently tagged antibodies / primary and secondary immunofluorescence

what is the epitope

specific part of foreign particle or antigen that the antibody binds to

how does primary/direct immunofluorescence work

antibodies are labeled with a fluorescent dye and then they bind directly to target antigen

specificity, background, and signal or primary/direct immunofluorescence

high specificity / low background / low signal

how does secondary/indirect immunoflourescence work

unlabeled primary antibody binds to the target antigen (it will not light up). then a secondary fluoro-tagged antibody binds to the primary antibodies

specificity, background, and signal of secondary/indirect immunoflourescence

lower specificity / higher background / high signal (greater ratio of binding)

fluorescent staining dye that binds to AT-rich regions of fixed cells in DNA

DAPI

fluorescent staining dye that binds to AT-rich regions of live cells in DNA

hoechst

fluorescent staining dye that intercalates with DNA

propidium iodide

fluorescent staining method for protein is (__). how does it work?

green fluorescent protein (GFP) / GFP amino sequence added to protein gene and then expresses green to show where protein is but may change how protein behaves

what type of microscope used

fluorescence/confocal microscopy

how does transmission electron microscope work

electron passed through specimen

how does scanning electron microscope work?

electrons projected onto specimen coated in gold and then bounce off

how to distinguish transmission vs. scanning EM and what can you see

transmission look like a more detailed brightfield image and you can see individual ribosomes and scanning are 3-D

for transmission EM, darker parts mean more

solid because electrons not passing through but bouncing back

what microscope used

transmission electron microscope

what type of microscope used

scanning electron microscope

how are antibodies used in EM

antibodies labeled with gold particles which show up as darker spots

how does centrifugation separate things

using centrifugal force to separate heavier things to bottom

how does immunoaffinity column chromatography work

beads coated with anti-specific antibodies and packed into a column. cell membranes are destroyed and mixture of molecules allowed to separate by gravity and antibodies bind to target protein but you also get non specific binding. Then washed to get rid of non specific binding proteins and then a final step to break off protein of interest from antibody

what type of gel is used in DNA electrophoresis

porous agarose

how does DNA electrophoresis work

smaller pieces go through gel more quickly and end up farther away from negative end (more towards positive end). thicker bands show that there is more DNA of that size there