Cell Bio Ch. 1

Parts of cell theory

all living things are made of cells, the cell is the fundamental unit of life, cells arise from pre-existing cells

cells

membrane-enclosed units filled with a concentrated aqueous solution of chemicals that can grow and divide; form dictates function, function dictates form.

What does the solution of chemicals that can grow and divide do?

gives cells their properties

How big are most cells

0.5-few hundred micrometers

How many cell types do humans have?

around 200 different types organized into tissues

Different sizes in the body (cell-organism)

cell, tissues, organs, organ systems, organism

What drives cell differentiation?

proteins

Epithelial cells

forms the outer surface of tissue layers, such as the intestine, kidneys, and skin; acts as a barrier between its tissue and the rest of the body; structure: tightly compact into a barrier

Myocytes

long, tubular cells that develop from myoblasts to form muscles. Specialized for contraction.

Why are myocytes multinucleated?

myoblasts fuse to make myocytes → multinucleated; also called striated tissue that allows for contraction

Neutrophils

leukocytes (WBCs) that can crawl out of the blood vessels and migrate towards site of inflammation; phagocytic cells.

Central dogma

living cells all replicate, do transcription, and translation

Replication

DNA synthesis

Transcription

RNA synthesis; where gene expression occurs

Translation

protein synthesis; takes RNA and decodes it to make proteins

Genomes

all DNA inside of an organism; makes organisms different

Transcriptome

All RNA in an organism; cells from the same organism differ by transcriptome → gene expression drives differentiation

Proteome

all proteins in an organism; cell’s proteome dictates its physical/chemical properties

3 domains

Bacteria, archaea, and eukaryotes

Eukaryotes contain a combination of genomes that originally derived from ______

prokaryotes (archaea and bacteria)

Cell membrane

made up of phospholipids and proteins

Cytosol

gelatinous aqueous interior

Ribosomes

a complex of RNA and protein that carry out protein synthesis

Nucleus

• Site for DNA replication and transcription

• enclosed by 2 membranes → nuclear envelope

• encloses the cell’s chromosomes

• reactions for interpreting the genetic instructions take place here

• surrounded by nuclear envelope

• Nucleolus - site of ribosome assembly

Nuclear pore complex

made of proteins to allow things in and out of the nucleus

Endoplasmic reticulum

• site of protein and lipid synthesis

• extensive membranous network

• Rough ER - have ribosomes that make proteins

• Smooth ER - makes lipids

• both lipids and proteins destined for secretion when made in ER

• proteins made in cytosol are not secreted

• ER = cell’s factory; stuff gets made and sent away

Golgi Apparatus

• distribution center

• stacked membranous discs

• processes, packages, and transports proteins

• Materials made in ER get sent here

• vesicles deliver from ER → Golgi → final destination

Mitochondria

• Responsible for aerobic respiration and making ATP

• extract energy from food and convert it to a useful form

• have 2 membranes → outer membrane and highly folded inner membrane (more folds = more ATP)

• have their own circular chromosome and ribosomes

• similar to modern day bacteria

• has ability to follow central dogma on its own

Lysosome

• site of digestion for macromolecules

• full of digestive enzymes; highly acidic for enzymes to work

• break down worn-out cell parts or molecules taken in by the cell

• materials are also brought in from outside via endocytosis, and sent to lysosome for digestion

• food and other particles are taken into vesicles that fuse with a lysosome for digestion, digestive enzymes are processed in the golgi and enclosed in lysosome compartments, damaged or worn-out cell components can be directed to lysosomes for digestion

Peroxisomes

• small membrane-enclosed compartments

• Makes CO2 as a byproduct

• liver contains lots of peroxisomes for detoxing

• break down toxins, fatty acids, and alcohol by H2O2 producing oxidative reactions

• differs from lysosome because of materials digested

Cytoskeleton

• network of protein fibers

• functions include cell support, cell movement, cell shape, and movement of structures within cells.

3 types of filaments that make up cytoskeleton

actin filaments, microtubules, and intermediate filaments

How to tell if a cell is undergoing mitosis

chromatin and no mitotic spindle indicates cell is not undergoing mitosis; condensed chromatin = mitosis

Chloroplasts

• only found in photosynthetic organisms

• plant and algae have them

• sites of photosynthesis

• have their own chromosome and ribosomes to perform central dogma

• have outer membrane and stacked discs (photosynthesis site)

What is cell wall made of?

cellulose

Vacuole

water filled; adds or removes water from cell

3 types of microscopy

compound light microscope, electron microscope, fluorescence microscopy

Magnification

makes image bigger → larger number = better

Resolution

distance between 2 points that can still be distinguished (makes image less blurry) → smaller number = better

What is the smallest the eye can see

20 mm

Light microscope

• uses 2 glass lenses

• specimen must be thin enough for light to pass through

• as light passes, see shadow of specimen except magnified

• light is focused on specimen by lenses in the condenser

• objective and eyepiece lenses focus image in eye

Limits of magnification and resolution for light microscope

1000x magnification and 0.2 micrometer resolution

3 types of light microscopes

• brightfield: not much contrasts, specimen isn’t dense

• phase-contrast (nomarksi): add more contrast to specimen (halo around specimen)

• interference-contrast: increases contrast on edges of thicker areas (shows edges more)

• magnification and resolution are the same for all 3 types, only contrast is changed

What does staining with dyes do?

• creates contrast

• typically used on dead cells because dyes are toxic

• dyes stick to different molecules (ex: lipid stains, DNA stains, protein stains, etc.)

TEM

• flat view

• viewing shadow of specimen

• electrons provide image instead of glass

• pass electrons through specimen

• specimen is sliced thinly and coated in heavy metals → specimen is dead

• heavy metals on denser parts blocks electrons

• uses beams of electrons instead of light

• magnetic coils focus the beam instead of glass lenses

• contrast introduced by staining specimen or background with heavy metals that absorb or scatter electrons

What makes up mitotic spindle?

microtubules

SEM

• 3D images

• produces an image of the surface of a specimen

• SEM is usually smaller, simpler, and cheaper than TEM

• specimen coated with heavy metal, scanned by beam of electrons, detector measures the electrons scattered from specimen’s surface

Limits for TEM

10^6 magnification and 1nm resolution

Limits for SEM

• 3-20 nm resolution

• 20,000 x magnification

Fluorescent molecules

• absorb and emit light

• has special property with light and electrons absorb light and get excited before going back to ground state

• energy from excitement is given off as light; lose some energy in the form of heat

fluorescent probes

• can reveal the location of particular molecules in a cell

• used to locate a particular structure or molecule within the cell

• some fluorescent dyes bind to certain molecules in a cell

• some can be coupled to highly specific antibodies

• some proteins are fluorescent

• have to take 2 different pictures for 2 different colors

Fluorescence microscopy

• type of light microscope

• shine light at specimen, fluorophors get excited, and shine light back

• 1st barrier filters: passes only wavelengths that excite the particular dye

• 2nd barrier filter: passes only wavelengths emitted when the dye fluoresces

• beam-splitting mirror: redirects light onto specimen

• objective lens: magnifies

Immunofluorescence microscopy

to localize (probe) a specific protein:

• cells are incubated with primary antibody (binds to thing you want to localize) → this doesn’t glow; add detergent to cell to poke holes in membrane and allow primary antibody through (specimen is dead)

• incubate with a secondary antibody that’s coupled to a fluorescent molecule (designed to recognize primary; also has a fluorophor attached to it

• thing you probe for = antigen

• ex: anti-tubulin antibody binds to tubulin

• epitope = part of antigen being recognized

Fluorescent proteins

• can be used as a probe in living cells

• GFP was the first of these to be used

• can be used on living cells because it comes from living organisms

Probing for tubulin using GFP

• take gene, cut gene, paste it with another gene that codes for what you probe for

• cell undergoes transcription and translation → fusion gene fluoresces

• if done a certain way - fusion gene can be passed down to progeny

Super-resolution light microscopy

• several techniques

• allows images with a high resolution than the one imposed by a diffraction limit

• have lasers and fluorophors to make it more focused

• light scatters, so they use lasers to bleach surrounding area for a sharper image

Why do we study model organisms?

• rapid reproduction

• easy to manipulate genetically

• easily identifiable phenotypes

• pool of information

• biologists tend to study different aspects of same model organism

Why have scientists focused on E. coli?

• most knowledge of fundamental mechanisms of life has come from studies of prokaryote E. coli

• easily grown

• adapts to variable chemical conditions

• rapid reproduction

• small genome

organisms vary enormously in the side of their genomes

simpler life form = smaller genome

Saccharomyces cerevisiae

• simple eukaryote

• brewer’s yeast

• have asexual and sexual life cycles (can undergo mitosis and meiosis)

• easy to culture

• rapid reproduction

• small genome

• studies on yeast help scientists with the steps of the cell division cycle

Cell division machinery between yeast and humans

very well conserved; such genes and their protein products are homologous

Drosophila melanogaster

• foundations of classical genetics were built on studying fruit flies

• 9 day life cycle

• small genome

Caenorhabditis elegans

• nematode

• used to study development and apoptosis

• apoptosis = programmed cell death

• develops like clockwork precision from a fertilized egg into an adult with 959 body cells

• survive freezing

• first multicellular organism to have its complete genome sequenced

Danio rerior

• zebrafish

• used to study vertebrate development

• transparent for first 2 weeks

• embryos develop outside the mother

Mus musculus

• mouse

• serves as a model for mammals

• small, hardy, rapid breeders

• study immunology, cancer development, obesity, behavior

• tumor growth can be followed directly by attaching a fluorescent protein to a tumor and injecting it into mouse