bio module 2

Microtubules

Provide a framework for motor proteins to move cargo within the cell. Dimers made of a and B-tubulin monomers. 13 chains of dimers surround central cavity of microtubule (hollow). Moves chromosomes during cell division, moves cilia/flagella

Eukaryotic flagella

Made of microtubules in “9+2+ array called an axoneme. Propel cell through fluid, long, 1-2 per cell

Cilia

Move fluid over cell, short, hundreds per cell, bend during motion

Prokaryotic flagella

Rotate, propeller like motion

Dynein

Motor protein that changes conformation and causes filament to bend, moves from + end to - end, bends cilia/flagella

Kinesin

Motor protein that uses ATP to power unidirectional movement along the microtubule, goes from + end to - end

Intermediate filaments

Bear tension, maintaining the cell shape, several strands of fibrous proteins wrapped around each other to provide strength+anchor structures in place, different composition over 50

Plasma membrane/Cell membrane

Surrounds all cells, manages what enters and exits the cell, receives external signals and initiates cellular responses, adheres to neighboring cells, selectively permeable

Selectively permeable

Some substances can pass through it, but others cannot

Lipid bilayer with unsaturated hydrocarbon tails

Higher fluidity, higher permeability

Lipid bilayer with saturated hydrocarbon tails

Lower fluidity, lower permeability

Small, nonpolar molecules

Have high permeability, can pass through membrane with simple diffusion, ex: O2, CO2, N2

Small uncharged polar molecules

Second highest permeability, ex H2O, glycerol

Large, uncharged polar molecules

Less permeable, would need carrier protein to enter phospholipid bilayer, ex: Glucose, sucrose

Small ions

Low permeability, need to pass through ion gates, ex: Cl-, K+, Na+

Endocytosis

an active transport process where a cell brings external substances inside by engulfing them with its cell membrane

Three types of endocytosis

Phagocytosis, pinocytosis, receptor-mediated endocytosis

Phagocytosis

molecules or entire cells are engulfed

Pinocytosis

A vesicle forms to bring small, dissolved substances or fluids into a cell

Receptor-mediated endocytosis

Uptake of a specific substance, binds to its receptor on the outside surface of the membrane, the protein clathrin is required 95% of the time

Diffusion

The net movement of a solute from a region of higher concentration to a region of lower concentration

Equilibrium

When particles in a solution are evenly distributed, particles still move

Concentration

Number of particles in a given volume; its unit is molarity

Simple diffusion

the passive movement of particles from an area of high concentration to an area of low concentration without the help of transport proteins

Concentration gradient

The movement from a high concentration to a low concentration. Produces energy for passive transport, movement is either with cg by diffusion or against cg by active transport.

Rate of diffusion factors

concentration gradient, size and mass of the molecules or ions, temperature of the solution, density of the solution, area and distance

Osmosis

Diffusion of water across a membrane

Isotonic

Equal solute concentrations inside and outside the cell

Hypotonic

Lower solute concentration outside the cell

Hypertonic

Higher solute concentration outside the cell

Hypertonic solution

Shriveled cell, water leaves cell faster

Isotonic solution

Normal cell, equal movement in and out of water

Hypotonic solution

Swollen cell, water moves into the cell faster

Passive transport

Methods of transport in which no addition energy required, ex: simple diffusion, facilitated diffusion

Channel proteins

Help polar molecules pass through the membrane and diffuse (move down their concentration gradients to an area of lower concentration)

Facilitated diffusion

Carried out by protein channels or carriers that increase the rate of diffusion

Ion channels

Penetrate the membrane and have hydrophilic pores, most are gated can be open/closed to ion diffusion. The gate opens when the protein is stimulated to change shape by smth (a chemical signal called ligand, a mechanical signal called force, an electrical charge difference called voltage-gated)

Ligand

chemical signal, an ion, molecule, or atom that binds to a central metal atom (in chemistry) or a receiving protein receptor (in biochemistry) to form a larger complex

W/ simple and facilitated diffusion the rate is ______ as the solute concentration increases

linear

Carrier proteins

Transport polar molecules, such as glucose, across membrane in both directions, bind a specific number of their specific substance, change shape and “carry it” to the other side

With a carrier protein the rate is linear until the _____ of the carrier is reached

maximal carrying capacity

Active transport

Method of transport that requires additional energy, movement is against the concentration gradient (from area of low concentration to area of high concentration), the energy to move against its gradient comes from ATP hydrolysis

Energy is ____ when one of the phosphate groups is cleaved off ATP

Released Ex: Adenosine triphosphate (ATP), adenosine diphosphate (ADP), inorganic Phosphate (Pi)

Primary active transport

Requires direct hydrolysis of atp

Electrochemical gradient

Arises from concentration+electrical gradients

Electrical gradients

The cytoplasm contains more negatively charged molecules than the extracellular fluid

Membrane potential

The difference in electrical potential (voltage) across the membrane

Secondary active transport

Energy comes from the electrochemical gradient that was first established by primary active transport

Transport proteins for active transport

uniporter, symporter, antiporter

LPS

lipopolysaccharide, carbs covalently bond to lipids

Three types of membrane proteins

integral, peripheral, and anchored

Transmembrane protein

majority of Integral membrane proteins, extend all the way through the phospholipid bilayer, have domains (regions) that pass through the lipid bilayer, they must associate with the hydrophobic tails of phospholipids

The hydrophobic regions of integral proteins consists of amino acids with ______ R groups

hydrophobic

Integral membrane protein

Don’t always span the membrane, some ability to integrate into membrane, interact with the hydrophobic interior through noncovalent hydrophobic interactions

Peripheral protein

No hydrophobic region, no covalent attachments to the membrane, binds noncovalently w/ polar head groups

Anchored membrane proteins

Covalently attached to fatty acids or other lipids inside the membrane

cell junctions

Specialized structures comprised of many diff proteins that hold eukaryotic cells together

Tight junctions

Form a tight seal (barrier) between eukaryotic cells, which helps ensure directional movement of materials

Gap junctions

Form tunnels called channels so that adjacent eukaryotic cells can communicate by exchanging small molecules, electrical impulses, etc

Desmosomes

Hold cells together like velcro; also allows materials to move around in the intercellular space, materials can still move in the intracellular space but no direct movement between cytoplasm

Membrane association without transmembrane domains

1. Amphipathic a-helix parallel to membrane

2. Hydrophobic loop

3. Lipidation (covalently attached lipid)

4. Ionic interaction with phospholipid head

Extracellular matrix

Macromolecule-rich gel outside of cells, provides scaffold to build tissues (collagens and other fibrous proteins, glycoproteins called proteoglycans, linking proteins called integrins)

Cells can move within a tissue by binding and reattaching of adhesion receptors to the

extracellular matrix

Integrins

One type of adhesion receptor that can facilitate movement by binding and reattaching to the extracellular matrix

Cell signaling

Step 1: Ligand-receptor binding

Step 2: Transduction

Step 3: Response

Signal transduction pathway

A signal from outside the cell is relayed through a series of internal messengers that can cause short- or long- term changes in the cell

Receptor conformational change

Short-term changes: enzyme activation, cell movement Long term movement: Altered DNA, transcription

Effects of signal transduction on cell

Movement, transcription, differentiation, fight or flight response, muscle contraction, apoptosis (programmed cell death), cell divison

Signal transduction (Step 2)

spreads the response to a signal through the cell

Intercellular receptors

Respond to signals (such as light or small molecules) that can cross the cell membrane

3 kinds of eukaryotic membrane receptors

1. Ion channel linked receptors

2. Protein kinase receptors

3. G-protein couples receptors (GPCRS)

Ion channel linked receptors

Allow ions to enter/leave a cell, signal binding results in change in shape of the channel protein, and the channel opens

Protein kinase receptors

When a ligand is present at the extracellular ligand binding domain, _______ catalyze autophosphorylation and or phosphorylate other proteins to change their shapes and elicit a response

Phosphorylation

Changes the shape of a protein, alters its catalytic activity, and/or affects its interactions with other proteins

Kinase

A type of protein that adds a phosphate group to another molecule (its substrate)

3 amino acids that can be phosphorylated by protein kinase activity….

serine, threonine, and tyrosine

Protein kinase cascade

One protein activates the next, and so on. The signal is amplified at each step, info that arrived at the cell membrane is communicated to the nucleus, multiple steps provide specificity. Diff target proteins provide variation in the response

Receptor tyrosine kinase

it undergoes a conformational change after insulin binds, which leads to its autophosphorylation and activation

In a protein kinase cascade

-The signal is amplified at each

step.

• Information that arrived at the

cell membrane is communicated

to the nucleus.

• Multiple steps provide specificity.

• Different target proteins provide

variation in the response.

Ligand binding to _______ activates a special protein

called a G protein, which then activates an _______

G protein-coupled receptor, effector

G proteins are active when

they are bound to

GTP

cyclic AMP (cAMP)

is a second messenger (made from ATP by the effector

Adenylyl cyclase downstream of GPCR activation) that amplifies and

distributes a signal

Second messengers

are non-protein signaling molecules that increase in

concentration inside a cell in response to a signaling molecule that binds at

the surface, they amplify the signal in a signal transduction pathway

G-protein coupled receptors (GPCRs)

Secondary messenger is activated after ligand binds to extracellular ligand

binding domain, leading to short- and long-term cellular responses

agonist

is a chemical or drug that binds to a cell receptor and activates it to produce a biological response

Antagonists

bind to the receptor (prevents the ligand from binding) but doesn’t trigger a response

IP3 and DAG

second messengers made by Phospholipase C from the

phospholipids in the membrane

ncreased [Ca2+] (another second messenger) helps activate ______

Protein Kinase C (PKC)

Ca2+

released from cellular stores downstream of GPCR activation;

example result: helps activate PKC,

Kinases can be inactivated by ______ enzymes, which remove

phosphate groups

phosphatase

GTPases

inactivate G proteins by hydrolyzing GTP (it becomes GDP)

Second messengers can be broken down; here ________ like PDE4

degrade cAMP into AMP (or cGMP to GMP)

phosphodiesterases

Crosstalk

is when one signaling pathway influences another

Membrane receptors

large or polar ligands that cannot cross lipid bilayer Ex: Insulin, for example, is a protein hormone that cannot diffuse through the cell membrane; instead, it binds to a transmembrane receptor with an extracellular binding domain.

Intracellular receptors

Small or nonpolar ligands that can diffuse across lipid bilayer Ex: The hormone estrogen, for example, is a lipid-soluble steroid (see Figure 3.24) that can diffuse across the cell membrane; it binds to a receptor inside the cell.

Ribosome

where RNA creates protein All ______ are made of

1 small + 1 large subunit

• Made of proteins + catalytic RNA

(rRNA)

primary (1°) structure

sequence of amino acids in a

polypeptide chain

transcription

process in which the sequence of bases in DNA is read by RNA Polymerase

to make a complementary sequence of RNA

Mechanisms of antibiotic resistance

1. Enzymatic inactivation

2. Modified target

3. Resistance-conferring plasmid

4. Modified cell wall and cell membrane

5. Efflux pump over expression