Unit 3 Biochem

membranes are permeable to

small nonpolar molecules, neutral gases, water, small polar molecules, NOT ions

types of transport across membrane (3)

simple membrane diffusion, passive transport, active transport

membrane diffusion

diffusion of hydrophobic molecules down their concentration gradient through the membrane

passive transport

molecules move down their concentration gradient through a protein channel

active transport

use energy to move molecules against their concentration gradient, through some type of protein transporter

free energy of diffusion (equation)

ΔG = RTln(C2/C1) + ZFΔV with ΔV being the voltage of where the ion is going relative to where it started

facilitated diffusion

facilitating movement down concentration gradient

uniport

moving a single substance in one direction

symport

moving 2 substances in the same direction

antiport

moving 2 substances in opposite directions

contransport

movement of 2 substances across the membrane at the same time

types of passive transport proteins (3)

porins, channels, and carriers (transporters)

porins (structure)

passive membrane proteins in bacteria consisting of β-barrels

porins are permeable to

ions and small molecules

selectivity of porins

nonselective: permit passage based only on size; selective: interior permits passage of specific molecules

channels

specialized channel structures found in both eukaryotes and prokaryotes

components of channels

amphipathic 𝛼-helices come together to form a hydrophilic cavity

carriers

aka transporters; bind ligands --> conformational change from ligand binding delivers ligand to the other side

aquaporins

water specific channels found in all eukaryotes

β-barrel

channel shape made of β-sheets; hydrophobic residues on the outside interact w/ membrane, polar residues line the pore

GLUT1

glucose transporter; glucose binding causes a conformational change that opens to the other side

aquaporin structure

tetramers w/ 𝛼-helical subunits; each monomer is a channel w/ a funnel shape on either side narrowing in the middle of the channel

aquaporin vestibule

wide portion of the channel; water-accessible carbonyls lead water into the narrow middle

aquaporin landing spots

regions where water lands and hops to the next spot; 3 landing spots along the length of the channel

primary active transport

transmembrane proteins change conformation in response to ATP hydrolysis

secondary active transport

uses energy of another molecule's concentration gradient to provide energy

P-type ATPases

pumps that hydrolyze ATP; part of pump becomes phosphorylated, causing conformational change

common domains of P-type ATPases (4)

ATP/nucleotide binding domain (N), phosporyl domain (P), regulatory/actuator domain (A), and transmembrane domain (M)

SERCA

P-type Ca2+ pump in sarcoplasmic reticulum

SERCA activation steps

1) at rest, SERCA is associated w/ phospholamban 2) phospholamban is phosphorylated, dissociates from SERCA 3) SERCA opens so Ca2+ can enter 4) ATP hydrolysis phosphorylates SERCA's P-domain 5) ADP released and SERCA opens channel to inside of SR

Na+/K+ ATPase

moves 3Na+ out of cell and 2K+ into cell per ATP

ABC transporters

ATP binding casette transporters; ATP hydrolysis causes conformational change, but protein is not phosphorylated

common structures of ABC transporters (3)

nucleotide binding domains, transmembrane domains, and transient carrier proteins (sometimes)

ABC transporter mechanism

1) begins w/ ATP bound; binding of substrate carrier protein causes a conformational change that exposes the substrate binding site and holds ATP more tightly 2) ATP hydrolysis causes conformational change that releases substrate on the other side of the membrane 3) release of ADP and Pi and binding of a new ATP resets the transporter

multidrug resistance protein

export ABC transporter in eukaryotes that removes toxic compounds from cells

Na+/I- transporter

symporter; moves 1 I- per 2Na+ into thyroid cells via secondary active transport

voltage gated membrane channel structure

multiple subunits, each with 6 transmembrane helices

S5 & S6 helices of voltage gated channel

line pore and confer selectivity

S4 helix of voltage gated channel

voltage sensor; contains many charged residues

intracellular N-terminus of voltage gated channel

inactivation domain (ball and chain)

Cys-loop channels

2 Cys on extracellular N-terminus form disulfide bond (Cys loop)

Glutamate / P pore loop channels

gated by glutamate

P2X channels

gated by ATP

Cys-loop channel structure

pentamers (2𝛼, β, γ and δ) w/ 4 transmembrane segments each

nAChR is a (channel type)

Cys-loop channel

glutamate channel structure

tetramers w/ 3 transmembrane segments each

P2X channel structure

trimers w/ 2 transmembrane segments each

AChE

acetylcholine esterase; breaks down ACh in synaptic cleft

ChAT

choline acetyltransferase; synthesizes ACh from choline and acetyl CoA

NMBAs

neuromuscular blocking agents; competitive ACh antagonists

adenylyl cyclase

membrane-bound enzyme that catalyzes cyclization of ATP --> cAMP

cAMP

cyclic AMP

PKA

protein kinase A

results of PKA activation (3)

turns off glycogen synthesis, stimulates glycogen breakdown, stimulates gluconeogenesis

signaling helix on G𝛼

Gβγ binding site when inactive; when GTP binds, signaling helix changes shape & dissociates from βγ; signaling helix also binds adenylyl cyclase

β2 adrenergic receptor

7TM GPCR that binds epinephrine --> energy production

RSG2

GAP protein that stimulates GTPase activity of G𝛼

βARK

β arrestin kinase; binds to Gβγ and phosphorylates cytoplasmic tail of 7TM

β-arrestin

binds to phosphorylated tail of 7TM, tagging it for endocytosis

cAMP PDE

cAMP phosphodiesterase; breaks cAMP down into 5'-AMP

rods vs cones

rods = low light, black and white; cones = color vision

cGMP gated ion channel

sensitive to [cGMP], open at rest; selective for Na+ and Ca2+

rhodopsin

7TM light receptor

transducin

heterotrimeric G-protein associated with/ rhodopsin

retinal

chromophore in rhodopsin; sensitive to light

effect of light on retinal

changes from 11-cis-retinal to 11-trans-retinal

cGMP PDE

cGMP phosphodiesterase; breaks cGMP down into GMP

guanylyl cyclase

catalyzes GTP --> cGMP

rhodopsin kinase

phosphorylates tail of trans-rhodopsin

arrestin

binds to phosphorylated tail of trans-rhodopsin, inactivating it

PLC

phospholipase C; produces IP3

enzyme linked receptor

ligand-activated enzyme

𝛼-subunit of enzyme linked receptor

extracellular ligand binding domain

β-subunit of enzyme linked receptor

connects 𝛼 to membrane

C-terminus of enzyme linked receptor β-subunit

tyrosine kinase

tyrosine kinase

phosphorylate Tyr residues by hydrolyzing ATP

insulin

peptide hormone released in response to high glucose; stimulates glycogen synthesis, glycolysis, and cell division

Shc protein (insulin pathway)

stimulates gene expression and cell division

IRS (insulin pathway)

stimulates glucose uptake and glycogen synthesis

activation loop of RTKs

3 Tyr in β-subunit; inactive until phosphorylated

adaptor protein

proteins w/ no enzymatic activity that bind to pTyr

PI-3K

phosphoinositide-3-kinase; phosphorylates PIP2 --> PIP3

PTB domain

pTyr binding domain found on Shc and IRS

SH2 domain

binds to pTyr adjacent to Asn

PDK1

PIP3 dependent kinase

Akt

protein kinase B

serine phosphatases (insulin pathway)

dephosphorylate Akt

PTEN

lipid phosphatase; dephosphorylates PIP3 --> PIP2

tyrosine phosphatases

depohosphorylates pTyr

epidermal growth factor

peptide hormone that stimulates cell division

GRB2

growth factor receptor bound 2; SH2 domain binds to pTyr; SH3 domain binds SOS

SOS

son of sevenless; proline-rich regions bind to SOS; binds to and activates Ras

activation of EGF receptors

EGF binds to 2 separate monomers, stimulating dimerization then autophosphorylatuon

Ras

anchored monomeric G-protein like G𝛼 that causes MAP kinase signaling cascade by binding to Raf

EGF kinase cascade

Ras --> Raf --> MEK --> ERK

Raf

held at membrane by Ras so it can be phosphorylated by SRC; phosphorylates MEK

MAP

mitogen activating protein; stimulate mitogens which stimulate mitosis

MEK

MAP ERK kinase; activates ERK

ERK

extracellular related kinase; when activated, it dimerizes, enters nucleus, and phosphorylates transcription factors that stimulate cell division

Ras GAP

inactivates Ras by hydrolyzing GTP --> GDP