IB HL BIO YR 2 UNIT TWO

cellular biology

light microscope

pass light through a specime

uses lenses to magnify

alive and dead specimen (can see movement)

electron microscope

pass a beam of electrons through specimen

picked up by electron detector & used to form an image

higher resolution

only used for non-living/dead because it damages specimen

centriole

organelle in animal and fungal cells

two cylindrical organelles

help establish and organize the microtubules & help with cell division in animal cells

produce and organize cytoskeleton in fungal cells

lysosome

organelle in animal cells

specialized vesicles with hydrolytic enzymes

break down and destroy biological molecules and old organelles

vacuole

organelle in plant, fungi, and (some) animal cells

store water, nutrients, and waste products

regulate osmotic potential of plant cells

breaks down molecules in fungal cells

cilia

part of some animal cells

hair-like structures

important for movement outside of cell

cell wall (plant cells)

made of cellulose (peptidoglycan)

resists osmotic pressure, prevents cell from bursting

maintains shape of the cell

chloroplasts

organelle in some plant cells

convert light energy into chemical energy

photosynthesis

green color comes from chlorophyll

contains three membranes (outer, inner and thylakoid)

creates three distinct compartmentalized areas (intermembrane space, stroma and thylakoid space)

cell wall (fungus)

made of a polysaccharide called chitin (peptidoglycan)

protects cell

resists osmotic pressure, prevents cell from bursting

maintains shape of the cell

budding scar

fungal cells

part of reproduction

crater-like ring of tissue

forms when a daughter cell buds from a parent cell

each cell can have many

endosymbiotic theory

eukaryotic organisms evolved when LUCA engulfed a prokaryotic cell capable of generating energy from oxygen and it evolved into a mitochondria

cell differentiation

turning on of genes necessary for the function of the specialized cell

causes larger body size, more complex, and adaptable to changes in the environment

organelle

subunits of cells that perform specific functions

membrane-bound

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

Cytoskeleton

made of protein microtubules

provides shape and allows for movement of molecules around cell

not considered organelle

Cytoplasm

matrix that surrounds organelles and other structures in the cell

not an organelle

site of most metabolic processes

mostly made of water

prokaryotic and eukaryotic cells

Ribosomes

eukaryotes (80S) and prokaryotes (70S)

structures that make proteins

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

Nucleus

eukaryotic cells

double membrane (outer membrane is part of RER)

contains and protects DNA

contains chromosomes associated with histone proteins

membrane has pores in it that allow mRNA to enter cytoplasm

Post-transcriptional modification

eukaryotic cells

mRNA produced in the nucleus needs to be changed by removing pieces of it

makes a working protein

Mitochondria

produce ATP through the breakdown of molecules (glucose)

double membrane

outer membrane is permeable to many small molecules and ions

inner membrane is highly folded and forms structures called cristae

Cristae

inside mitochondria

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

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

Matrix

inside mitochondria

space between inner membrane

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

allows high concentrations of molecules to accumulate

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

Thylakoid membranes

part of chloroplasts

surround 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

part of chloroplasts

many thylakoids together in a stack

maximize the amount of sunlight absorbed

connected to thylakoid membranes called lamellae

Stroma

part of chloroplasts

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

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

proteins made are for use inside cell

RER

system of interconnected membranes that forms a series of flattened sacs and tubes

involved in protein synthesis and modification

has ribosomes

transports proteins to golgi

ER lumen

inside of flattened sacs in RER system

Golgi apparatus

stack of flattened membrane-bound sacs

organized into cis, medial and trans compartments

packages and modifies proteins for export outside of cell

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 materials, act as delivery trucks

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

transport vesicles

transport materials from one part of a cell to another

Secretory vesicles

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

Peroxisomes

similar to lysosomes

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

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, formation of lysosomes

forms cage-like structure

Morphogens

A chemical in the concentration gradient of which determines the fate of surrounding cells

cell theory

all living things are made of cells

cells are the basic units of structure and function

cells come from pre-existing cells

cryogenic electron microscopy

allows scientists to view proteins and other biomolecules that don’t readily crystalize

freeze fracture electron microscopy

technique used to examine ultrastructure of rapidly frozen biological samples (plasma membranes, etc)

membranes are rapidly frozen and fractured at an area of weakness (through phospholipid bilayer or integral proteins)

immunofluorescence

technique used to visualize a specific protein/antigen in cells/tissue by chemically binding a specific antibody to a fluorescent dye

sample is then analyzed using fluorescence microscope

can be used with living tissue

can detect molecueles at a low concentration

stains target specific targets

eye piece lens (microscope)

lens you look through

usually 10x or 15x magnification

coarse focus adjustment (microscope)

moves lens up and down

adjusts focus

fine focus adjustment (microscope)

moves lens

small adjustments

gain better focus

base (microscope)

bottom of microscope

provides stability

high power objective (microscope)

for increased magnification

usually 10x, 40x, & 100x

stage (microscope)

where the slide is held/placed

iris/diaphram (microscope)

varies intensity of light projected upwards onto slide

resolution (microscope)

ability of a microscope to distinguish details of a sample/specimen

magnification equation

measured length / actual length

cell/plasma membrane

made of phospholipids

controls what enters/exits the cell

prokaryote and eukaryote

not an organelle

nucleiod region

prokaryotic cells

contains 1 circular chromosome (DNA, genetic info for growth and development)

no membrane

flagellum

prokaryotic cells

locomotion

not all have this

pillus

prokaryotic cells

allow bacteria to stick to each other/other surfaces

allows for horizontal gene transfer

chromosomes

composed of DNA wrapped around histone proteins

SER

membrane structure without ribosomes

lipid synthesis and detoxification

phospholipid bilayer

acts as a barrier for materials entering/exiting cells

only hydrophobic/uncharged particles can pass by diffusion

large or hydrophilic/charged must pass by facilitated diffusion or active transport

phospholipid

hydrophilic phosphate head, polar

hydrophobic fatty acid tails, nonpolar

spontaneously forms bilayer

simple diffusion

passive transport of particles from high concentration to low concentration

uses no energy

moves small uncharged particles and fat soluble molecules

not a selective process

integral protein

permanently attached to the membrane

penetrate into the center of the bilayer

can be transmembrane or partial

ex: channels, protein pumps

peripheral protein

temporarily attached to one side of membrane

attached to membrane surface or integral proteins (through electrostatic interactions)

hydrophilic

ex: receptors, enzymes

osmosis

passive transport of water from low solute concentration to high solute concentration

through a semipermeable membrane

slow process

aquaporins

integral channel proteins

assist osmosis

increase membrane permeability and decrease time

facilitated diffusion

passive transport

from high concentration to low concentration

channel proteins

selective process

channel proteins

central pore that molecules move through

lined with hydrophilic amino acids for specific molecules

transmembrane proteins

active transport

movement of particles from low to high concentration

uses protein pumps and ATP

selective process

glycoprotein

membrane protein with carb chain

acts as receptors for hormones, cell to cell communication (neurotransmitters), immune response (antigens), cell to cell adhesion (forms tissues), and cell recognition

glycolipid

phosphate with a lipid attached to it

on outside of cell

cell recognition/adhesion/communication, immune response, receptors for hormones

saturated fatty acids

single bonds between carbons on hydrocarbon chain

linear and closely packed

increase melting point and viscosity

unsaturated fatty acids

1 or more double bonds between carbons on hydrocarbon chain

bend @ double bond

decrease melting point and viscosity

cholesterol

regulate membrane fluidity of animal cells

has a role in making sure which peripheral proteins are anchored to membrane

most of molecule is located within membrane between tails

OH group bonds with phosphate

at high temperatures, reduces fluidity and increases melting point

at low temperatures, maintains fluidity and prevents crystallization of phospholipids

exocytosis

release of large particles from a cell

fusion of a vesicle with the plasma membrane

active process, needs ATP

endocytosis

process by which large particles enter the cell

large particles are surrounded by the plasma membrane, which buds off inside the cell to form a vesicle

active process, needs ATP

steelhead trout

case study

as temperature decreases, concentration of unsaturated fatty acids increase in tissue

as temperature increases, concentration of saturated fatty acids increase to increase stability of membrane

Scale bar

a line drawn near the photograph

has a label showing the actual length of the bar before being magnified

Metabolism

all the physical and chemical processes in the body that convert or use energy

mostly take place in the cytoplasm

Sister chromatids

the two identical chromatids that are formed by replication of a chromosome during the S phase of the cell division

Histone protein

a protein that provides structural support for a chromosome

Cellulose

makes up plant cell walls

made of peptidoglycan

Peptidoglycan

polymer that is composed of polysaccharide and peptide chains

makes up all cell walls

Plastids

double-membrane organelles which are found in the cells of plants and algae

responsible for manufacturing and storing of food

perform photosynthesis

Fungal hyphae

have multiple nuclei

Aseptate

a cell that lacks a cell wall/membrane

Microvilli

increase the surface area in order to absorb more nutrients in the small intestine

Sap vacuole

stores food, nutrients and waste in animal cells

Scientific theory

a well-tested and widely accepted explanation for natural phenomena

Symbiosis

a relationship or interaction between two different organisms

Stem cells

undifferentiated cells

capable of self-renewal or can differentiate into specialized cells

Meristematic tissue

made up of a group of cells that divide continuously to form new cells

Specialized cells

cells that have specific structures and functions in the body

ex- red blood cells, sperm cells, neurons, etc

Cell Fractionation

separation of different parts of a cell

usually done by centrifugation in a lab

Ultrafiltration

the small molecules (water, etc) in the liquid can pass through the membrane only under a certain pressure

large molecules (proteins, etc) can’t pass through

Homogenization

process whereby different fractions of a biological sample become equal in composition

Transcription

producing mRNA using DNA as a template

only a portion of genome is copied (resource efficiency)

allows DNA to stay protected in nucleus

Translation

the process by which a cell makes proteins using the genetic information carried in mRNA