AP Bio ~ chap 6-7

microscopy

use of microscope (3 important parameter = magnification, resolution, contrast)

• LM

• EM

magnification

ration of an object’s image size to real size

resolution

measure of the clarity of the image; minimum distance 2 points can be separated and still be distinguished as different

contrast

difference in brightness between the ligfht and dark areas of an image (stain/label)

light microscope (LM)

visible light passed through the slide and lenses bend light so the image is magnified

Brigthfield (staided/unstained)

light passes directly through and without stain there is little contrast

Phase-contrast

variations in density is amplified to enhance contasted in unstained cells (helpful for living/unpigmented cells)

Differential-interference-contrast (Nomarski)

optical modifications to exaggerate differences in density (almost #D looking image)

Fluorenscence

some specific molecules can be revealed with fluorescent dyes/antibodies (some have their own). It absorbs ultraviolet radiation and emits visible light

Confocal

laser eliminates out-of-focus light from a thick sample

Deconvolution

process of digitally removing out-of-focus light and reassigns it to its source (much shaper 3D image)

Super-resolution

light up individual fluorescent molecules and record position. Sharp greenish dots from combining info from a bunch of molecules

electron microscopy (EM)

focuses a beam of electrons through a specimen or onto its surface. The wave-like characteristics allows for magnification and resolution

Scanning electron microscopy (SEM)

specially useful for detailed study of topography (natural arrangement) of a specimen. An electron beam scans and excites the electrons on the surface. Results are 3D (electromagnets as lenses-image on monitor)

Transmission electron microscopy (TEM)

used for study of the internal strx of cells. Electron beam that provides a thin section of specimen. Specimens stained with atoms of heavy metals to enhance electron density in parts (electromagnets as lenses-image on monitor)

organelles

organized membrane-enclosed structures within cell

cytology

study of cell strx

biochemistry

study of chemical processes

Cell fractionation

useful technique for study cell strx and fxn. takes apart/separates major organelles and other subcellular strx from each other. Equipment = centrifuge (fast spins force appart; slower = lger components)

cytosol

jelly-like substance that suspends subcellular components

eukaryotic/prokaryotic cell

major diff = DNA location

e(true) = nucleus (mem enclosed) - bigger (better for fxn of metabolism)

p(before) = nucleoid (not mem enclosed)

nucleoid

irregularly shaped area containing the genetic material (DNA) of the prokaryotic cell

cytoplasm

gelatinous liquid that fills the inside of a cell (composed of water, salts, and various organic molecules)

plasma membrane strx

• double layer (bilayer) of phospholipids

• proteins embedded or attached (specific to cell for fxn)

• hydrophobic parts of pl are inside while outside is hydrophilic

• carb side chains might be attached to proteins or outer layer of mem

• fxn = passage

nucleus strx

• Nuclear envelope

• Nucleolus

• Chromatin (DNA)

nuclear envelope

• encloses nucleus

• 2/double nuclear membrane (each lipid bilayer with associated proteins)

• underlying lamina (netlike array of protein filaments)

• nuclear pore complexes (regulate passage)

nuclear latima

netlike array of protein filaments that maintain shape through mechanical support

chromosomes

strx that carry out genetic info - one strand of long DNA with proteins to coil/reduce length

chromatin

complex of coiled DNA and proteins that make up chromosomes

nucleolus (nucleoli)

• prominent strx within nucleus

• creation of rRNA

• creation of ribosomes (later exit through pores)

Ribosome

• complexes of rRNA and protein

• not organelles - not mem bound

• free and docked/bound

endomembrane system

Carry out variety tasks (creation and transport of proteins, metabolism and movement of lipids, detoxification of poisons)

• nuclear envelope

• ER

• golgi apparatus

• lysosomes

• vesicles

• vacuoles

• plasma mem

vesicles

sacs made of membranes that stores and transports products and wastes

glycoproteins

proteins w carbohydrates covalently bonded to them

transport vesicles

in transit from one part to another part within cell

golgi apparatus

• series of flattened stacked pouches (cisternae)

• cis face (close to ER)

• trans face (away from ER)

• membrane bound organelles

• polar in both strx and fxn

• fxn = modify and store ER products and manufacturer macromolecules

endoplasmic reticulum (ER)

extensive network of membranes that accounts for more than ½ total mem in eukaryotic cells. COnsists of cisternae

Smooth ER

w/o ribosomes

• fxn = creation of lipids, metabolism of carbs, detoxification, storage of calcium ions

rough (ER)

w/ ribosomes

• fxn = secrete proteins produced by ribosomes and add proteins to own membrane

lysosome

membranous sac of hydrolytic enzymes used to digest macromolecules (if breaks acidic can lead to cell death)

• fxn = breakdown harmful and big units

phagocytosis

a process of eating by engulfing smaller organisms or food particles

vacuoles

lg vesicles derived from ER and Golgi

• fxn = transport (selective) solutes and isolate waste products

food vacuoles

digestive fxn

contractile vacuoles

pump excess water out of cell (maintain suitable concentration of ions and molecules inside cell)

central vacuole

in mature plant cells

• major role = growth bc fill w water

mitochondria

convert energy to forms for cell to work

• sites of cellular respiration (process use oxygen to drive generation of ATP by extracting energy from sugars, fats, and other fuels)

chloroplasts

convert energy to forms for cell to work

• sites of photosynthesis (convert solar energy to chemical energy by absorbing sunlight and use it to drive creation of organic compounds)

endosymbiont theory

states that an early ancestor of eukaryotic cells engulfed an oxygen-using non-photosynthetic prokaryotic cell. eventually the engulfed cell form relationship w host becoming an endosymbiont (a living cell within another cell) they later merge and determine if mitochondria or chloroplast

criste

infoldings on inner membrane that divides into 2 internal compartments

• strx = frx : criste is more sa meaning more area for productivity of cr

mitochondrial matrix

• enclosed by inner membrane

• contains diff enzymes as well as mito. DNA and ribosomes

thylakoids

interconnected sacs

granum (grana)

stack of thylakoids

stroma

liquid outside thylakoids (contains chlor. DNA, ribosomes, and diff enzymes)

plastids

any class of small organelles in cytoplasm of plant cells that contain pigment or food

peroxisome

• specialized metabolic compartment bound by single mem

• contain enzymes that remove hydrogen atoms and transfer them to oxygen atoms from various substrates

• strx = fxn : enzymes that produce hydrogen peroxide and those that dispose are isolated from components that could be damaged

cytoskeleton

network of fibers extending throughout cytoplasm (microtubules, microfilaments, intermediate filaments)

• fxn = mechanical support

cell motility

changes in cell location and movements of cell parts

motor proteins

move along cytoplasm

microtubules

thickest fiber that makes up cytoskeleton

• hollow rod

• sape/support cell

• guides vesicles from Er to golgi to plasma mem

• involved in speration of chromosomes during cell division

centrosome

• region often near nucleus

• microtubules grow out of these

centrioles

• pair within centrosome

cilia (cilium)

microtubule-containing extensions that project from some cells - work like oars as it alternates power and recovery strokes

flagella (flagellum)

microtubule-containing extensions that project from some cells - undulating motion like tail of fish

basal body

an organelle that forms the base of a flagellum or cilium

dyneins

lg motor protein that is attached along each outer microtubule doublet (typically has 2 feet)

microfilaments/actin filaments

thin solid rods that make up cytoskeleton

• built from molecules of actin

• twisted double chain of actin subunits

• form structural networks

• bear tension/pull force

actin

globular protein

cortex

outer cytoplasmic layer of cell

myosin

protein that causes contraction of muscle cells

pseudopodia

surface by extending extensions

cytoplasmic streaming

circular flow of cytoplasm within cells (common in lg plant cells)

intermediate filaments

mid thickness of fiber in cytoskeleton

• only in some animals

• specialized for bearing tension

• constructed from particular molecular subunit from protein family

• specially sturdy and play important role in reinforce shape

cell wall

• extracellular strx of plant cells (distinguish from animal)

• maintain shape

• prevent excessive water intake

• strong to hold against force of gravity

primary cell wall

relitively thin and flexible wall on young plant cells

middle lamella

thin layer of sticky polysaccharides called pectins (between primary walls of adjacent cells)

secondary cell wall

some add this to strengthen the wall as it stops growing

extracellular matrix (ECM)

• main ingredients - glycoproteins and other carb-containing molecules

• most abundant = collagen

collagen

forms strong fibers outside cells embedded in network woven out of proteoglycans (40% total protein in human body)

proteoglycans

consists of small core protein with many carb chains covalently bonded

fibronectin

type of glycoprotein that binds to integrins

integrins

cell-surface receptor proteins that are built into plasma mem (in position to transmit signals between ECM and cytoskeleton)

plasmodesmata

a narrow thread of cytoplasm that passes through the cell walls of adjacent plant cells and allows communication between them (jxn in plant cells - similar to gap but only works in corresponding hole on other plant cell)

cell junctions

connection between cells

tight junctions

• mem pressed tightly together

• extreme version of desmosome

• doesn’t allow for movement since there is no room for passage

desmosomes

• proteins stick together and form channel

• allows passage between cells

gap junctions

• direct connection between cells

• inside cells and in mem

selective permability

allows some substances to cross it more easily than others (ex=plasma mam)

amphipathic

has both hydrophilic and hydrophobic regions

fluid mosaic model

• how scientists show/picture what the cell looks and functions like

• helps explain how mem regulate the cell’s molecular traffic

integral proteins

protein that penetrates the hydrophobic interior of the lipid bilayer (majority = transmembrane/span mem)

peripheral proteins

proteins that aren’t embedded in lipid bilayer at all but rather appendages loosely bound to mem surface

Functions of membrane proteins

• transport

• enzymatic activity

• signal transduction

• cell-cell recognition

• intercellular joining

• attachment to cytoskeleton and ECM

transport (protein fxn)

• protein spans mem

• hydrophilic channel across mem

• selective for particular solute

enzymatic activity (protein fxn)

• protein built into mem may be an enzyme w it's active site exposed to substance in adjacent solution

signal transduction (protein fxn)

• mem protein w binding site

• specific shape that fits ahpe of chemical messenger

• external messenger = may cause shape change (allow message inside)

cell-cell regognition (protein fxn)

• identification tag

• specifically recognized by mem of other cells

• shorter lasting than intercell.

intercellular joining (protein fxn)

• protein of adjacent cells hook together in various kinds of junctions

• longer lasting than cell-cell

attachment to cytoskeleton and extracellular matrix (protein fxn)

microfilaments/other elements of cytoskeleton noncovalently bound to mem proteins

help maintain shape and stabilize location of certain mem proteins

glycolipids

carbohydrate-attached lipids, which are associated with cell membranes

transport proteins

• channel proteins = fxn by having hydrophilic channel so certain pass

• carrier proteins = fxn by holding onto passengers and change shape to allow passage