Unit 2

membrane protein functions

not all proteins are transmembrane proteins (goes from outside of cell to inside)

semipermeable membranes

not all molecules can pass through

small nonpolar get through easiest bc have to go through hydrophobic membrane

passive membrane transport

diffusion: from low → high concentration

does not require energy

active membrane transport

molecules move against concentration gradient

requires ATP (energy)

involves protein pump

facilitated diffusion

when protein is needed for ions to get across membrane

osmosis

diffusion of water across a membrane

H2O moves across membrane, not solutes

hypertonic

solution that is more concentrated

hypotonic

solution that is less concentrated

isotonic

when concentration of solute and solvent is the same

channel proteins

passive transport can be regulated by membrane channel proteins

some channels are always open

others are blocked until signal is received

bulk transport

molecules or particles too large to fit between phospholipids or through protein channels

takes energy

exocytosis

transport large molecules and/or cargo OUT of cell

endocytosis

transport large molecules and/or cargo INTO cell

eukaryotic cells

membrane-bound nucleus

membrane-bound organelles

larger size

linear DNA molecules

prokaryotic cells

no nucleus

circular DNA

nucleus

stores genetic information (DNA)

RNA produced (exists through pores in nuclear membrane)

side of ribosome synthesis

ribosomes

consist of ribosomal RNA and proteins

read RNA instructions to make proteins

puts amino acids in order to make proteins

free ribosomes

floating in cytoplasm

make proteins for immediate use in cytoplasm

bound ribosomes

attached to endoplasmic reticulum

makes membrane proteins and proteins for secretion

endoplasmic reticulum

may be continuous with nuclear membrane

lipid bilayer

lipid and carbohydrate metabolism

detoxification

synthesis of membrane and secretory proteins

membrane synthesis

golgi apparatus

shipping and receiving

receives molecules from ER

ships to cell membrane for export

modifies proteins

directional

arrive at cis space until they get to trans space, where they will be transported on

semiautonomous organelles

reproduce themselves - divide like a cell inside the cell

depends on cell for some proteins

mitochondria, chloroplasts, plastids

mitochondria

outer and inner membrane

primary role is to make ATP (gives of energy)

chloroplasts

photoshynthesis

plants and algae

outer and inner membrane

third membrane - thylakoid membrane

cytoskeleton

support cell

maintain space

anchor points for organelles and proteins

moves structures within cell

cells move by dismantling and rebuilding cytoskeleton

microtubules

largest component of cytoskeleton

tubulin polymers

grow from centrosome and centrioles (place where the cell is assembling proteins into microtubule structure)

guides movement of transport vesicles

makes sure they go from ER → cis → trans → membrane

motor proteins

energy from ATP used to change the shape of motor protein

causes motor proteins to move along microtubules

hyponatremia

medical condition for low sodium

most neurons maintain high levels of extracellular sodium ions

how might neurons adjust to maintain isotonicity

lower intracellular concentration so that the inside and outside of the cell have the same concentration

fill with other elements, but have the same total amount of concentration

what effect would very aggressive treatment of hyponatremia have?

the difference between concentrations of inside and outside the cell is huge, creates hypotonic cell → water is released outside of the cell

osmotic demyelination syndrome

caused by too rapid treatment of hyponatremia

neuron shrivels up bc water has left the cell

cilia and examples

shorter and more than flagella

tetrahymena, mucus in trachea

flagella and examples

longer and fewer than cilia

sperm, water circulation in sponges

microfilaments

smallest component of cytoskeleton

chain of actin subunits

often forms network inside cell membrane to maintain cell shape

microvillus

increases surface area for absorption to happen

microfilament goes in between microvillus to maintain shape

myosin

type of microfilament and motor protein

responsible for muscle contractions

cytoplasmic streaming

include myosin interactions

myosin connects organelles to microfilaments

myosin and actin create intracellular contractions → how chloroplasts move outside of the cell

intermediate filaments

only in cells of some animals

variety of proteins

holds nucleus in place in one part of the cell

amoeboid

cytoplasmic streaming and pseudopodia

oozing into one direction

cystic fibrosis

genetic disease caused by mutation in chloride channel (membrane protein)

cl ions not able to leave cell, allows more sodium ions to enter cell

tonicity of cystic fibrosis cells

hypertonic (because sodium ions and chlorine ions are inside at not normal amounts)

how is osmosis affected by cystic fibrosis

water will diffuse into the cell

how would cystic fibrosis affected osmosis impact the mucus layer

water diffuses out of the mucus, mucus will be thicker

how would the cilia be affected when someone has cystic fibrosis

has a harder time moving mucus, mucus will be stuck and built up

direct signaling

cytoplasmic connection → cells in direct contact

mediated by proteins → proteins can move cells without going through membrane

almost universal in multicellular tissues

contact signaling

cells touching but don’t have cytoplasmic connections

2 types of local signaling

autocrine and paracrine

autocrine signaling

cells give and receive messages, cells not touching but close

quorum sensing

bacteria senses population density, more bacteria means more chemicals released

biofilms

glues all bacteria together

sensing of density due to autocrine signaling

paracrine signaling

affects nearby target cells, nut not themselves

synaptic signaling

specialized paracrine signaline unique to nerve cells

most common in neurons

neurotransmitters: molecules that give signal from one neuron to another

endocrine signaling

travels long distance, signals between tissues and organs

hormones

three stages of cell signaling

1. signal reception

2. signal transduction

3. cellular resoonse

signaling molecule

usually a ligand (small molecule that bind to a larger molecule)

interacts not joins molecule

changes shape of receptor (receptor activation)

ligand is released and shape goes back to normal

G-protein coupled receptors

extremely widespread and diverse in their functions

activated receptor binds to G protein

G protein leaves receptor and activates downstream enzymes

kinases

class of enzymes that attach phosphate groups to other proteins

proteins that activate other proteins

phosphates

class of enzymes that remove phosphate groups from other proteins

receptor tyrosine kinases

membrane receptors that catalyze the transfer of phosphate groups from ATP to another protein

extracellular domain binds to signaling molecules, causing intracellular domain to become functional catalyst (activated)

ligated-gated ion channels

acts a a gate that opens an closes when the receptor changes shape

ligand binding causes ion channels to open and ions to flow through membrane

animals - signal between nerve and muscle cells or between 2 nerve cells

intracellular receptors

hormone receptor complex interacts directly with DNA to affect gene expression

phosphorylation cascade

usually associated with RTKs

regulated by protein phosphates

kinases turn on when hormone bonds to receptor

involves a bunch of kinases attached to phosphate groups

passes signal from receptor to response

G-protein-coupled receptor signal transduction

protein activated by G-protein

may directly trigger cellular response

may initiate signal transduction pathway into the cell

signal transduction involves production of second messengers (cAMP)

1. g-protein activates adenylyl cyclase

2. adenylyl cyclase converts ATP to cyclic AMP (cAMP)

3. cAMP activates a protein kinase

signal transduction via cAMP

a small molecule produced from ATP

one of the most widely used second messengers

g-protein activates adenylyl cyclase, which converts ATP to cAMP

phosphate groups make a ring

cholera toxin and cAMP

cholera bacterium produces a toxin that modifies a G-protein so that it is stuck in its active form

• activates adenylyl cyclase and cellular response

protein continually makes cAMP, causing intestinal cells to secrete large amounts of salt into the intestines

• makes cell hypertonic

water flows by osmosis and an untreated person can soon die from loss of water and salt

• dehydrates the cell and ultimately the person

outcomes of signal pathways (3)

quick response, quick/intermediate response, long term response

quick response from signal pathways

alter metabolism and other cell functions

changes enzymic activities

turns proteins on/off

quick/intermediate response from signal pathways

alters cell mobility and shape

changes structural proteins such as cytoskeleton

rebuilding and reconstructing

long term response

induce cell differentiation

differential gene expression

turns gene on/off to make diff set of proteins in the cell

epinephrine (arenaline)

induces quick production of glucose in the muscle cell

signal amplification

one receptor signals hundreds of g-proteins triggering lots of glucose molecules over short period of time

specificity of response

every cell doesn’t need to respond to every signal/hormone

every cell does need to respond to more than one signal/hormone

metabolism

all chemical reactions with an organism

intra or extracellular (in or out of cell)

each reaction catalyzed by different enzyme

catabolic metabolism

breakdown complex molecules into simpler molecule

associated with release of energy

anabolic metabolism

synthesis of complex molecules

usually requires input of energy

goals of metabolism

energy production or complex organic molecules

energy production (ATP)

energy from the sun (phototrophic)

energy from breaking chemical bonds (chemotrophic)

complex organic molecules (C-C bonds)

build complex molecules from single-carbon compounds (autotrophic)

ingest pre-existing C-C bonds (hetertrophic)

first law of thermodynamics

energy can be transferred and transformed, but not created or destroyed

second law of thermodynamics

some energy is going to be lost as thermal energy (heat)

biological energy conversions

starts with solar energy from cell

converted to chemical energy (photosynthesis)

simple sugars converted to molecules, eventually converted to ATP

exergonic reactions

proceed with a net release of free energy and is spontaneous (releases energy)

endothermic reactions

absorb free energy from its surroundings and is non-spontaneous (energy absorbed)

adenosine triphosphate (ATP)

hydrolysis of ATP releases energy

energy used to drive chemical reactions

ATP regenerated during cellular response

takes used phosphate group back on ADP to make ATP again to be used for energy

enzymes

macromolecular catalysts

• speeds up reactions

• not consumed in reactions

almost always a protein

lowers activation energy of reactions

reactions were going happen anyway

• happens at biologically relevant rate

• reactions can be regulated

how enzymes work

substrate binds to enzyme at active site

• creates enzyme-substrate complex

shape changes

• holds substrate in proper orientation and proximity

• pulls and stresses chemical bonds

creates favorable microenvironment (more acidic or more basic)

metabolic pathways

series of chemical reaction to reach final product

each step catalyzed and regulated by enzyme

enzymes specifically catalyzes one reaction

what determines the enzyme composition/profile of a cell?

subset by different enzymes coded in the genes

determined by signal molecules → turns gene on/off

• tells what certain enzyme the cell needs

shows evolution of mammal

phototrophic strategy

autotroph (builds complex molecules from single-carbon compounds) and phototrophic (energy from the sun)

reduction-oxidation reactions

redox reactions for short

transfer if electrons from on molecule to another

reduction

molecules gain electrons

oxidation

molecules loses electrons

glucose oxidized to _______

oxygen reduced to_________

carbon dioxide, water

metabolism and redox reactions during photosynthesis

solar energy excites electrons

high-energy electrons transferred to carbon dioxide (reducing glucose)

high-energy electrons stored in glucose

metabolism and redox during cellular respiration

glucose oxidized, releasing high-energy electrons

electrons transferred to oxygen

energy released and captured during transfer

where does photosynthesis take place

in chloroplast

membrane bound - has a thylakoid space

carbon fixation

taking single carbon atoms and fixing them together into organic sugar

chlorophyll

main photosystems in a plant

absorbs photons with certain wavelengths of energy

plants don’t absorb green → why plants appear green

photosystem 2

photon excites electrons in pigment molecules

electrons calm down and release photon

energy passed from pigment molecule to pigment molecule

electron in special chlorophyll (P680) gets excited and leaves molecules

electron “hole” in P680 filled by electron from water molecule

P680 pills water molecule apart to get electron

electrons from P680 (now in primary acceptor) passed along electron transport chain (transferred from one molecule to another)

small amount of ATP produce (releases energy)

photosystem 1

solar energy being captured and passed around

P700 loses electron

electron originally from P680 used to fill hole left by excited electron in P700

ends up in NADP+, reducing it to NADPH