IB HL BIO YR 1 UNIT FOUR

cell wall

structure: external outer covering made of cellulose

function: provides support and mechanical strength, prevents excess water uptake

types of cells: bacterium and plant

not considered organelle

centrosome

structure: microtube organizing center

function: microtubes form spindle fibers and contribute to cell division (mitosis/meiosis)

types of cells: animals

chloroplast

structure: double membrane structure with internal stacks of membranous discs

function: site of photosynthesis, manufactured organic molecules are stored in various plastids

types of cells: plants

contains three membranes (outer, inner and thylakoid) that creates three distinct compartmentalized areas (intermembrane space, stroma and thylakoid space)

cytoskeleton

structure: filamentous scaffolding within the cytoplasm

function: provides internal structure and mediates intracellular transport

types of cells: bacterium, plants, animals

not considered organelle

cytosol

structure: mostly water, but full of enzymes and other molecules

function: hold organelles in place and catalyses reactions (like glycosis)

types of cells: bacterium, plants, animals

endoplasmic reticulum (rough), aka RER

structure: folded membrane studded with bound ribosomes, forms series of flattened sacs and tubes

function: protein synthesis and modification for export

types of cells: plants and animals

endoplasmic reticulum (smooth)

structure: folded membrane continuous with the nuclear envelope

function: production of lipids and metabolism of toxins

types of cells: plants and animals

golgi apparatus

structure: an assembly of vesicles and folded membranes located near the cell membrane

function: involved in the sorting, storing, modification, and export of secretory products, exocytosis

types of cells: plants and animals

organized into cis, medial and trans compartments

lysosome

structure: membranous sacs filled with hydrolytic enzymes

function: breakdown / hydrolysis of macromolecules and waste

types of cells: animals

requires enzymes

mitochondrion

structure: double membrane structure, inner membrane highly folded into internal cristae, outer membrane is permeable to many small molecules and ions

function: site of aerobic respiration, produce ATP through the breakdown of molecules (glucose)

types of cells: plants and animals

contains transport proteins that assist in moving larger molecules to mitochondria

nuclear envelope

structure: double membrane that surrounds nucleus

function: control movement in and out of nucleus

types of cells: plants and animals

nucleoid region

structure: area in prokaryotes where the bacterial DNA is concentrated

function: holding place for DNA

types of cells: bacterium

nucleolus

structure: dense, darker region in the nucleus

function: site of ribosome synthesis

types of cells: plants and animals

nucleus

structure: double membrane structure with pores (outer membrane is part of RER)

function: stores genetic material (DNA) and chromatin, protects DNA from damage, double membrane regulates gene expression

types of cells: plants and animals

peroxisome

structure: membranous sac containing a variety of catabolic enzymes

function: catalyzes breakdown of toxic substances (eg H2O2) and other metabolites

types of cells: plants and animals

similar to lysosomes but have a different set of enzymes that are involved in detoxification of harmful compounds and lipid metabolism

plasma membrane

structure: phospholipid bilayer embedded with proteins

function: semi-permeable and selective barrier surrounding the cell

types of cells: bacterium, plants, and animals

ribosome

structure: two subunits made of RNA and protein, larger in eukaryotes (80S) than prokaryotes (70S)

function: site of polypeptide synthesis (called translation)

types of cells: bacterium, plants, and animals

vacuole

structure: fluid-filled internal cavity surrounded by a membrane (tonoplast)

function: maintains hydrostatic pressure (animal cells may have small, temporary vacuoles)

types of cells: plants and sometimes animals

organelle

subunits of cells that perform specific functions

both prokaryotic and eukaryotic cells, but membrane-bound organelles only found in eukaryotic

compartmentalization

organization or different functions and processes within specific areas or structures within the cell that are separated by plasma membranes

allows for the development of specialized cell structures (chloroplasts and mitochondria)

allows specific reactions to occur in specific places

can delay a cell’s ability to respond to the environment

cytoplasm

matrix that surrounds organelles and other structures in the cell

not a discrete structure with specific function, so not an organelle

responsible for metabolic processes (including translation of mRNA to protein on the ribosomes)

ribosomes

structures that make proteins out of mRNA from nucleus

not membrane-bound but are considered organelles because they have a specific function

can be bound or free (have same structure and function either way)

post-transcriptional modification

eukaryotic cells

mRNA produced in the nucleus needs to be changed by removing pieces of it, which makes a working protein

cristae (mitochondria)

allow more of the enzymes needed for ATP production to be present on membranes in mitochondria by increasing surface area

increases efficiency and speed of cell respiration by increasing number of enzymes available for various reactions

matrix (mitochondria)

space between inner membranes in mitochondria

contains a lot of enzymes and other molecules in high concentration needed for the Krebs cycle

a key pathway in cell respiration

intermembrane space (mitochondria)

small space between outer and inner membranes of mitochondria

allows high concentrations of molecules to accumulate

creates concentration gradient across inner membrane that is used to generate ATP

thylakoid membrane (chloroplast)

form thylakoids (look like stacked pancakes), where the light dependent reactions of photosynthesis take place

absorbs light energy and uses it to generate ATP to power photosynthesis

separate the stroma from the thylakoid space (small space, allows chloroplast to quickly generate a high concentration gradient)

granum (chloroplast)

many thylakoids together in a stack

maximize the amount of sunlight absorbed by chloroplast

connected to thylakoid membranes called lamellae

stroma (chloroplast)

space between inner and thylakoid membranes

contains all enzymes/substrates required for remaining steps of photosynthesis (Calvin cycle) that will make glucose molecules

gene expression

process by which the information in DNA is translated into proteins

entry and exit of signaling molecules and transcription factors are critical components in regulation of it

nuclear pores

allow entry and exit of molecules into nucleus

integral proteins

serve as channel proteins that also regulate mRNA leaving nucleus for RER or free ribosomes

bound ribosomes

ribosome bound to cytosolic side of RER

proteins it produces ends up inside RER and will be exported outside of cell

tend to be more numerous

free ribosomes

located in cytoplasm

tend to be less numerous

endoplasmic reticulum lumen

inside of flattened sacs in the RER system

cis compartment (golgi)

receives newly modified proteins from RER

vesicle fuses with it and releases protein inside golgi

medial compartment (golgi)

contains proteins destined for use within the cell (lysosomes)

proteins undergo further modifications before final destination

trans compartment (golgi)

contains proteins destined for export outside of cell

packages proteins into vesicles for secretion

vesicles

small membrane-bound cell structures

play a key role in transport and storage of protein and other products , act as delivery trucks

transport and release proteins, lipids, and RNA from one part of cell to another

types of cells: plants and animals

transport vesicles

transport materials from one part of a cell to another

intracellular

secretory vesicles

store and transport molecules (hormones, neurotransmitters, digestive enzymes) to be secreted outside the cell

clathrin

protein that plays important role in formation of vesicles

brings together the cytoskeleton and other proteins necessary for budding/scission of vesicles from membranes

involved in endocytosis, phagocytosis, transport of cargo from golgi to plasma membrane, and formation of lysosomes

forms cage-like structure, protects vesicle

phospholipid

amphipathic (both hydrophilic and hydrophobic)

form bilayer (heads on outside, tails on inside)

major structural component of almost all membranes

hydrophobic tails make bilayer selectively permeable

protein

amino acid side chains determine properties

3D structure determines function

conjugated proteins (glycoproteins) contain non-protein parts

selective permeability

only certain substances can cross bilayer without assistance

polarity/size/charge of substance determines permeability

permeable molecules

small non-polar molecules

“lipid soluble” molecules

ex: O2, CO2, N2, steriods

mostly permeable molecules

small uncharged polar molecules

ex: H2O and glycerol

mostly impermeable molecules

large uncharged polar molecules

ex: glucose, sucrose, other mono/disaccharides

impermeable molecules

ions and anything with a charge

ex: Na+, K+, Cl-, H+, Ca2+

integral proteins

membrane protein

embedded in bilayer

amphipathic (part inside bilayer = hydrophobic, part outside bilayer = hydrophilic)

mostly transmembrane

difficult to isolate

transmembrane

spans across entire membrane

parts outside cell, inside bilayer, and inside cell

peripheral proteins

membrane protein

located on surface of bilayer (either side)

hydrophilic

easier to isolate

functions of membrane proteins

transport

ID tags, cell-cell recognition

receive chemical signals (when bonded to receptor proteins)

enzymes (can be embedded in/associated with bilayer)

adhesion (cells with same tissue are joined by membrane proteins)

transport proteins

membrane protein

transmembrane

transport materials across bilayer

ex: channels, carriers, pumps

glycoproteins

conjugated proteins

carb chain (oligosaccharide) covalently bonded to protein

on extracellular side of bilayer

glycolipids

carb chain (oligosaccharide) covalently bonded to lipid

on extracellular side of bilayer

amphipathic

carb groups are polar and extend into extracellular environment

lipid groups are nonpolar and embedded in bilayer

contribute to membrane stability and form hydrogen bonds to water molecules surrounding cell

functions of glycoproteins and glycolipids

cell recognition (carb chains = ID tags)

cell adhesion (carb chains bind to chains on other cells)

cell signaling (receptor for chemical messengers)

cell protection (carb creates glycocalyx)

glycocalyx

carb groups create sticky layer on extracellular surface of cell

forms protective layer

glycoproteins and glycolipids

cholesterol

steriod

found in animal cell membranes

amphipathic

prevents fatty acid chains from sticking together and freezing at low temperatures, increases fluidity

stabilizes membrane and decreases fluidity at high temperatures

fluid mosaic model

proposed by singer and nicolson (1972)

“fluid” - bilayer = viscous, move around and flow past each other

“mosaic” - embedded with proteins, mosaic of components

membrane fluidity trends

temperature increases, fluidity increases

at low temps - cholesterol increases fluidity

shorter fatty acid tails increase fluidity

unsaturated fatty acid tails increase fluidity (kinks)

saturated fatty acid tails decrease fluidity (straight)

ecothermic

cold blooded animals

increase proportions of unsaturated fatty acids in membranes at low temperatures

hibernating mammals

as body temp decreases, proportion of unsaturated fatty acids in membranes increases

simple diffusion

movement of molecules of a substance down a concentration gradient (from region where concentration is higher to region where its lower)

spontaneous

movement of molecules eventually results in equal concentration among both regions

passive transport (doesn't need energy)

osmosis

net movement of water into cell

water moves from lower solute concentration to higher solute concentration

type of diffusion, passive transport

aquaporins

type of channel/integral protein

specific to H2O

bidirectional

permit rapid movement of water in and out of cells

facilitated diffusion

movement of molecules down the concentration gradient

assisted by transport proteins

passive transport

requires help from transmembrane integral protein (channel or carrier protein)

channel proteins

transmembrane proteins

assemble to form channels for the passage of polar molecules

selectively permeable because of hydrophilic/phobic side chains inside channel

can be opened or closed (gated)

many only allow one type of ion/molecule through

ex: ion channels

carrier proteins

transmembrane proteins

play important role in facilitated diffusion, bind to solute molecules

undergoes a conformational change when molecule binds to it

transfers molecules to other side of membrane

ex: glucose transporter

active transport

comes into play when molecules need to be transported from lower concentration to higher concentration

uphill energy required, exergonic reaction

helps to take up essential nutrients, remove waste, maintain right concentrations of ions in cells

uses carrier proteins

direct active transport

where energy released by exergonic reaction is used to transport molecules across cell membrane

indirect active transport (cotransport)

movement of one solute down its concentration gradient drives movement of second solute against its concentration gradient

plays an important role in glucose absorption by the intestinal epithelial cells

membrane fluidity

depends on the fatty acid composition of the phospholipids

saturated fatty acids provide stability (because of higher melting points)

lower temperatures = lower fluidity

depends on cholesterol in animal cells (at high temperatures, reduces fluidity)

endocytosis

bulk transport mechanism by which particles are moved into the cell

cell membrane progressively invaginates and engulfs particles, pinches off to form vesicle

phagocytosis

ingestion of large solid particles

bulk transport

cellular eating

ex: white blood cells

pinocytosis

ingestion of liquids

bulk transport

smaller vesicles than phagocytosis

exocytosis

reverse of endocytosis

bulk transport of material to be secreted/excreted out of cell

via vesicles

vesicles fuse with cell membrane & contents are discharged to extracellular space

ex: secretion of glycolipids/neurotransmitters, excretion of waste

cell-adhesion molecules (CAMs)

crucial role in cell adhesion

glycoproteins

mediate the binding of cells with other cells/extracellular matrix

play a vital role in the formation of tissues

cell junctions (anchoring junctions)

connect cells to each other

allow intracellular transport and communication

important for cell proliferation and migration

prevent unregulated movement of materials between cells

adhesive junctions

present in epithelial & cardiac cells

facilitate cell adhesion

ensure stability

tight junctions

present in epithelial cells

form tight seal between neighboring cells

act as occluding junctions

barrier prevents unregulated movement of molecules across barrier

gap junctions (communicating junctions)

present in several cell types

intracellular channels connect neighboring cells for movement of molecules

help in cell-cell transfer of small molecules

desmosomes

adhesive junctions that help to anchor cells

water

universal solvent

two hydrogens covalently bonded to one oxygen atom

dipolar molecule because of differences in electronegativity

high specific heat capacity

ions

atoms that have lost/gained electrons

dissolution

separation of solute particles because of hydration shells (water molecules surrounding ions)

diffusion

general process of particle movement from an area of high concentration to an area of low concentration

passive transport

ex: air freshener

hypertonic solution

more solute concentration in this solution than other solution

water flows in

other solution is hypotonic to this solution

opposite of hypotonic

hypotonic solution

lower solute concentration in this solution than another solution

water flows out

other solution is hypertonic to this solution

opposite of hypertonic

lysis

disintegration of a cell by rupture of the cell membrane

plasmolysis

water leaving plant by osmosis

in hypertonic solution

cell membrane shrinks away from cell wall

loses turgor (internal) pressure

ectothermic

cold-blooded

higher proportioon of unsaturated fatty acids in membrane at lower temperatures

concentration gradient

difference in concentration

can be visualized as a hill

“down” = high concentration to low concentration

passive transport

does not require additional input of energy (ATP)

simple diffusion

facilitated diffusion

osmosis

active transport

does require additional input of energy (ATP)

pump proteins

bulk transport - exocytosis & endocytosis (pinocytosis and phagocytosis)

dynamic equilibrium

no net movement

equal concentration on both sides

constant movement back and forth

permeable & some mostly permeable molecules

factors that impact diffusion rate

concentration gradient (“steeper”→faster diffusion)

distance (shorter→more efficient diffusion)

temperature (higher temps, more movement→faster diffusion)

size (smaller → faster diffusion)

polarity (more polar→slower diffusion)

solvent

does the dissolving

almost always H2O

solute

what is being dissolved

ex: salt, sugar, etc

solution

solute + solvent

tonicity

ability of a solution to make water move into/out of a cell by osmosis