Molecular and Cellular Biology Lesson 11-15 (start 16 after lunch)

Differentiation

the process of cells within a multicellular organism becoming specialized for a specific task

Stem Cell

cell that has not yet differentiated

Abiogenesis

“primordial soup hypothesis” in which simple molecules necessary for life are spontaneously created through early-earth-like conditions (simpler molecules and energy (in the form of electricity))

What does it take to make a cell?

Information, chemistry & compartments

Basic Properties of Cells

• Highly complex and organized

• Controlled by genetic program

• Can reproduce

• Assimilate & utilize energy

• Can carry out chemical reactions (enzymes)

• Engage in mechanical activities

• Respond to stimuli

• Can self-regulate

• Evolve

Central Dogma of Molecular Biology

Theory that genetic information flows in one direction DNA → RNA → protein (translation & transcription)

Enucleation

(mechanism of) removal of nuclei from developing red blood cells

Why are compartment necessary?

microenvironments for specific (tasks?) to take place

Cell Theory

1. All living organisms are composed of one or more cells

2. The cell is the most basic unit of life

3. All cells come from pre-existing cells

Prokaryotic Cells

• single cell organsims

• 1-10 μm

• no nucleus or organelles

• genetic material in nucleoid (no chromosomes, circular plasmid)

• small ribosomes

• asexual

• often have flagella and pili

Eukaryotic Cells

• single or multicellular

• 10-100 μm

• nucleus and organelles

• large ribosomes

Organelles plants have that animals do NOT

• cell wall

• vacuoles

• chloroplasts

• plasmodesmata

Organelles animals have that plants do NOT

• lysosomes

• microvilli

might elaborate on organization?

• large number of parts

• organized with respect to time and space

Why aren’t viruses alive?

• cannot reproduce without parasitism

• cannot use energy

• cannot carry out chemical reactions

• cannot engage in mechanical activities

• cannot respond to stimuli

• cannot self-regulate

What is a virion made of?

• small amount of DNA or RNA (only a few hundred genes)

• Capsid (protein capsule)

oh christ do i need to know virus families

ughhhhh (could make a baltimore virus chart. could not. who knows)

theres some structure images you could label i guess?

it would probably be a good idea but they look so different its like. wtf

Types of viral infection

• lytic

• non-lytic/integrative/lysogenic

Lytic infections

production of virus ruptures & kills cell (e.g., flu, rabies)

Non-lytic infection

Viral DNA inserted into host genome (provirus)

Infected cell is impaired but survives (e.g., HIV, chicken pox)

should i cover the examples

like do i need to know how microcephaly works

hes spending a loooong time talking abt it do i probably should

should i do something on how rna vacines work

i dont wannaaa

Functions of Biological Membranes

• Define cell boundary

• Define enclosed compartments

• Control movement of material in and out of cell

• Allow response to external stimuli

• Enable interactions between cells

• Provide scaffold for biochemical activities

how many layers in plasma membrane

3 i fucking guess

Structure of plasma membrane

• outer layers are hydrophilic, polar heads of phospholipids

• inner layer is hydrophobic, non-polar tails of phospholipids

Structure of phospholipid

im not sure which one of these images is the best to use for this

something abt the head that has stuff and then the glycerol backbone and the nthe hydrophobic tails (usually 2)

Where does phospholipid synthesis occur?

where cytosol meets outer ER membrane i guess?

How are phosphilipids synthesized i guess

• in cytosol, fatty acids are activated by coenzyme A (CoA)

• acetyl transferase inserts activated fatty acids bonded to glycerol phosplate into cytosolic side of the leaflet of the ER

• phosphate removed by phosphatase enzyme (where did the phosphate come from???

• choline already linked to phosphate is attached using choline phosphotransferase

• flippases flips some phospholipids into the inner leaflet (floppase does the reverse)

ok this makes 0 sense

something about vesicles flipping

is this still part of the prev thing

should probably copy some of the stuff hes saying on this slide

but im sure it will be elaborated on later

Fluid Mosaic Model

Fluid - stuff moves

Mosaic - diverse particles

• plasma viewed ad 2-D liquid

• proteins are embedded in phospholipid bylare

• components are mobile

  • can move easily, quickly within own leaflet

  • movement is difficult, slow between leaflets

• components can interact

• something abt proteins?????

do i need something on this one

the gist is that after fusion of cells the surface proteins like. mixed together

Properties of Membranes

• ~6 nm thick w water incorperated

• stable

• flexible

• capable of self assembly

• something abt microdomains (lipid rafts) (compartmentalizing cell processes

Three classes of Membrane Proteins

1. Integral (span entire bilayer)

2. Peripheral (associated with surface, usually attached to another protein)

3. Lipid-Anchored (attached to a lipid in the bilayer)

Functions of integral proteins

• transport nutrients/ions

• cell-cell communication

• attachment

Biological membranes are:

a. symmetrical

b. asymmetrical

b. asymmetrical

leaflets have distinct compositions, outer has glycolipids and glycoproteins

How does temperature affect fluidity of biological membranes?

a. warming increases fluidity, cooling decreases fluidity

b. cooling increases fluidity, warming decreases fluidity

c. temperature does not affect fluidity

a. warming increases fluidity, cooling decreases fluidity

[maybe insert transition temperature image with the labels and stuff]

maybe say something abt what the heat does to the lipid composution

which is more fluid? idfk

a. crystalline gel state

b. liquid crystal state

b. liquid crystal state

Which of these increases fluidity?

a. unsaturated lipids

b. saturated lipids

a. unsaturated lipids

double bonds introduce bends in the tails, so they will not be able to line up properly

[could put an image here]

something abt cholesterol doing stuff for fluidity in both directions

it fills the spaces btwn the unsaturated tails and keeps gaps between saturated ones

you could do two multiple choice questions of its addition to the two membrane states but that feels excessive. you need questions on stuff that isnt logical. like the proton chain shit

Types of transmembrane proteins

• transporter

• receptor

• enzyme

• anchor

• (huh hwta tha hell,)

• um idk if this goes here but its showing transmembrane proteins and stuff and they have non-polar sections that can go in that bilayer

What can cross the lipid bilayer?

small, uncharged molecules can pass (e.g., O₂, CO₂, NO)

large/polar/charged compounds cannot (e.g., Ca⁺, Glucose, Na⁺, K⁺)

The four basic mechanisms for moving molecules across membranes

1. Simple diffusion

2. Diffusion through a channel

3. Facilitated diffusion

4. Active transport

Passive vs. Active movement

passive relies on molecular concentration (high to low), active requires energy

Simple Diffusion key points

• passive flow down concentration gradient

• no channel, just passes through membrane

• for small, uncharged, non-polar molecules

  • polar molecules (e.g., water) cannot move through non-polar, hydrophobic inner layer

Diffusion through a channel key points

• passive flow down concentration gradient

• passes through channel (yeah duh thats the name)

• for small, charged/polar molecules (e.g., H₂O, Na⁺, K⁺, Ca²⁺, Cl^-)

• Channels are selective—only specific types of ion can pass

• formed by proteins

Ion channels (what are they)

“gated” channels that have open and closed states

Types of gated ion channels

• voltage gated

  • action potential - the passage of electric signal down a nerve potential (e.g., a neuron)

  • yeah i think the channel just opens when theres a change in electric potential across the membrane not much else to know

• ligand gates

  • e.g., acetylcholine receptor

  • channel binds to a specific molecule (a ligand)

  • binding produces conformation charge and then it opens i think

Carriers/Facilitated Diffusion key points

• passive (?) flow down concentration gradient

• substrate (?) binds to specific integral membrane protein called facilitative transportar

• change in conformation allows compound to be released on other side of membrane

Carrier/Facilitated Transport steps

1. transporter is ready to accept molecule

2. molecule is accepted by transporter

3. intracellular side of transporter opens

4. molecule is released

[image?]

Symporter (what is it)

• used when substance needs to move upstream

  • e.g., reabsorption of glucose in kidney cells - would otherwise stop when eq is reached

• relies on gradient of molecule in other direction that CANNOT reach extra/intracellular equilibrium

• gradients are in opposite directions, movement is in the same direction

example steps for symporter i think

1. binding of both molecules on outward facing binding sites

2. causes conformational change in transporter (occluded conformation)

3. transporter adopts inward facing conformation

4. molecules flowing downsteam are dissociated, pushing upstream molecule with it

5. return to outward facing (cyclic)

[image?}

Antiporter (what is it)

• used when substance needs to travel upstream

• “exchanger”—the two types of molecule are moving in opposite directions

Active Transport key points

• active flow up concentration gradient

• requires energy

  • change in conformation of transported is caused by hydrolosis of ATP

    • this is what allows it to come out the other side i guess

• these are also a type of antiporter (active antiporter)

theres examples after but it doesnt feel necessary lol. i dont remember if this is where the homework questions start but i think all the homework questions should be in here

one example of a use of active transport

fucking cell size i guess theres a picture is this really necessary. one more for today i need to stay on pace (learning half a semester in one week) aw fuck its a two parter oh well we persist

fuckin membrane proteins signal transduction what it do

lets cells respond to shit

• growth

• division

• survive (or nah)

• move

• differentiate

• up- or down-regulation

whats a ligand

small molecule that binds to a receptor (does not actually enter, just changes conformation)

three stages of signal transduction

1. binding of ligand to receptor

2. signal transduction via 2nd messenger (cAMP, calcium, G-protein, etc)

3. cellular response (growth, division, storing glucose as glycogen, etc)

what is glycogenolysis

breaking down glycogen into individial glucose units (do i need to mention the glycogenin protein in the core that the first four are attached to)

what starts glycogenolysis

epinephrine (adrenaline)

• epinephrine goes from adrenal gland thru blood to liver and triggers the thing to start

glycogenolysis steps

• epinephrine binds to receptor

• this removes GDP and replaces it with GTP

• this activates the G-protein

• part of G-protein dissociates and travels to adenyl cyclase enzyme

• this enzyme converts ATP into cAMP

• cAMP triggers a bunch of reactions i hope i dont need to know that turns glycogen into glucose

  • erm…

anchor proteins what it do

• can hold shit in place

• might be able to move sit i guess

what is the extrecellular matrix (ECM)

organized network of material produced and secreted by cells

what does the ECM do

• cell adherence

• communication between cells

• cell shape, mechanical suppord, structural integrity

• barrier, filters some stuff out

examples of ecm

• skin

• connective tissues

  • tendons, ligaments, dermis

• what if this was my final straw

• wrinkles are scarring of it and the like. fibres in it arent regenerated properly

components of the ecm

• proteins

  • collagen

• glycoproteins

  • laminin

  • fibronectin

what cells have ECM?

animals

what cells dont have ecm? what do they have instead?

bacteria, plants, and fungi

they have walls

• made of cellulose, hemicellulose, pectin, proteins

• provide structural support

• protect from damage and pathogens

should i label the cell wall

porbably you could like. label it or something

ok theres a little picture of glycogenolysis with a bunch of words underneath i think its a labelling thing? add that i guess

the things below are study questions btw

What is meant by a membrane’s transition temperature?

where it changes states i think

How will the transition temperature of a membrane be affected if the amount of unsaturated lipids is increased?

What property of transmembrane domains allows then to remain embedded in a lipid bilayer?

Thinking about the Na+/K+ pump, how many ATP molecules are required to transport 10 K+ ions into a cell?

oh lord you do need to know specific examples :-C

Endosymbiotic Theory/Symbiogenesis

the idea that eukaryotic cells evolved from consuming prokaryotes (explaining chloroplasts/mitochondria)

Evidence of Endosymbiosis

• binary fission of mitochondria & plastids

• circular DNA in these organelles

Aerobic respiration

Converts carbohydrates in the presence of oxygen into chemcial energy stored in ATP

(CH₂O) + O₂ → CO₂ + H₂O + ATP

Photosynthesis

Building carbohydrates using energy from sunlight and CO2

CO₂ + H₂O -*→ (CH₂O) + O₂

Structure of th mitochondria i guess?

inner membrane and outer membrane, aqueous compartment in between [could add image i guess]

Outer Mitochondrial Membrane (OMM)

• has enzymes in it

  • e.x. monoamine oxidases (breaks down stuff)

• has poring

  • large permeable channels

Inner Mitochondrial Membrane (IMM)

• high protein:lipid ratio (3:1)

• double layered folds called cristae

  • increased surface area increases are for ATP formation

• rich in cardiolipin

two aqueous compartments of mitochondria

1. intermembrane space

2. matrix

   • high protein content

   • gel like consistency

   • contains mitochondrial ribosomes and DNA

Substrate-level phosphorylation

• hydrolysis reaction releases enough energy to drive phosphorylation of ADP to ATP

  • e.g., glycolysis where a 1 glucose molecule is partially broken down into 2 pyruvate molecules

Oxidative phosphorylation

• chemical energy of org molecules is transferred into electron carriers to create electrochemical gradient that can power ATP synthesis

do i need to do something abt the top half of this slide

the next slide feels importatnt but i dont get it enough to put it in a flashcard

steps of cellular respiration?

• i think itll be bigger and more spread out on the next slides

reduced electron carriers:

can donate electrons when returning to oxidized state

what state does a coenzyme need to be in to accept electrons?

oxidized state

do i need to know the full names of NAD[H/+] and FAD(H2)

and do i need to know the oxidized and reduced states

steps of oxidative phosphorylation (christ hes explaining them in words im gonna cry or something idk) ????

1. Complexes I-IV

2. ATP synthase

step 1 of oxydative phosphoylation

Generate an electrochemical gradient

• electrons (and protons?) are transported thru I-IV

  • I, III, and IV directly punp protons matrix→intermembrane space

  • II does dnot directly pump but it promotes III and IV

  • they get energy from passing electrons thru

• High energy e pass from NADH & FADH2 from matrix to IMM

  • I - NADH deposits 2e, e passes thru miltiple redox centres (clustres of atoms w low→high afinity), energy is released in each centre and this is used to pump protons

    • last redox centre dontates the 2e to Co-enzyme Q (CoQ)

  • II - 2e enters from FADH2, und up at CoQ

    • energy here doesnt pump protons tho

  • III - 2e from CoQ

    • one is saved for later, one goes thru 2 redox centres to cytochrome C to IV

  • IV - 4e from cytochrome C, turns 1 molecule of O2 to 2 molecules of H2O

    • proton matrix strengthened: 4 are in new water and 4 more are pumped

    • electron transfer and ATP synthesis stops without oxygen

• series of intermediate e carriers (respiratory enzyme complexes (I-IV) = Electron Transport Chain (ETC)

  • electron carriers (the nadh stuff i think) are in oxidized form (presumably during/after bc they definitely started with H)

• energy transfer at each complex is used to pump H from matrix into intermembrane space (against gradient)

• low energy e (it loses energy moving through the complexes) is transferred to terminal e acceptor (O2) to produce H2O

should i break this into multiple slides

step 2 oxidative phosphorylation

proton movement DOWN electrochemical gradient

• F₀ subunit of F₁F₀ATP synthase forms channel that rotates as protons pass thru it

• F₁ subunit uses this energy to catalyze ATP synthesis

Parts of a chloroplast

• outer membrane

• inner membrane

• thylakoid membrane

• granum (stack of thylakoids)

• lumen (inside of thylakoid)

• stroma (around thylakoids)

Photosynthesis — Light-Dependent Reactions

• occur in thylakoid membrane

  • e^- enters ETC (in membrane)

  • H⁺ pumped into thylakoid lumen

• Chlorophyll is light harvesting complex (sunlight + H₂O → O₂ + e^- + H⁺)

[image of the chain? its different in plants]

Photosynthesis — Light-Independent Reactions

• occur in stroma

• dark reactions / calvin cycle

• ATP and NADPH from light reaction used to make carbohydrates

photophosphorylation (steps)

• light enters

• excites Photo System II

• electrons travel thru into lumen

• H2O donates electrons to make ½ O2 + 2 H

• electrons move acorss thru oxidizing centres

• to pq (plastiquinome) mobile carrier — sends it to cytosome c

• cytosome c to pc (plastocyanin) carries electrons to PS I

• lower energy e @ PS I, light excites them again, travels thruu oxidizing centres to

• Fd (ferrodoxin) passes them to NADP+

• NADP+ + H+ → NADPH (in NADP reductase)

• protons pumped from stroma to lumen

• ATP synthase uses protons to do ADP + P → ATP

[image?}

Light-independent reactions? calvin cycle???

• reduction of CO2 + ATP?, NADPH → carbohydrate???

What is apoptosis?

programmed cell death, can be due to aging, damage, illness, etc (e.g., baby mitten hands (can the duck vs chicken feet go here too?), madagascar lace plant)