BCH210 (2nd Half)

cause of membrane formation

a decrease in ionic interactions with water

FRAP

Fluorescence Recovery After Photobleaching

A way to see how fast lipids and proteins diffuse laterally in a membrane. Damage fluoro phores with bleach and see how long it takes for regular fluorophores to naturally diffuse and replace white/ bleached ones.

lipid raft

Cytoskeleton part of the membrane that lipid /protein interacts with

flip-flop diffusion

Heads moving to the other side of a bilayer

Flippase

FIIppase (I for Inside) where head facing outside of cell is flipped inside

Floppase

FlOppase ( O for Outside) where head facing inside of the cell is flipped outside

Scramblase

Head moves down concentration gradient in passive transport

Flippase conformational change

begins in ATP bound closed form open slightly to the outside of the cell, then to "flip" it turns into open form with a wider opening to the inside of the cell

Lipids can be either

hydrophobic or amphipathic

Lipids are diverse

liposome

head on inside and outside forming a water filled circle

Mirelle- Inside out

heads on the inside, tails sticking out (hydrophobic env) circular

Micelle - Normal

heads on outside tails on inside (polar solvent)

Triacylglyceride function

Store carbon for energy

fatty acid charge

amphipathic

signal transduction

• cascade, amplification event throughout cell

• hormone, primary messenger

• reception of message, usually integral protein

GPCRs

g proteins coupled receptors

• 7 TM segments

• common signal receiving proteins

• conformational changes release G proteins

  • binds many ligands

GPCR ligands

• natural

  • serotonin, epinephrine, prostaglandins, dopamine, psilocin/psilocybin

• synthetic

  • morphine, histamine, LSD

ncv int.s between side chains

beta adrenergic receptor

has inactive and active states w diff structures

ligand binding changes tm5

major conf change in tm6 release GalphaGTP →activates adenylyl cyclase→secondary messenger cAMP→cAMP activates other enzymes (eg.PKA)

Ras proteins

type of g alpha proteins

structural switches (change when gtp→gdp)

signals for cell proliferation and apoptosis→issue can lead to cancer

PTMs

can turn off/on an enzyme

enzyme linked receptors

integral membrane proteins

hormone attached

conf change enzymes now work inside of cell

phospholipid mediated signalling

phospholipases hydrolyse phospholipids to produce other 2nd messengers like diacykgkycerol (dag) or ip3 → release of Ca

competing hormones example

insulin and epinephrine

act on similar metabolic pathways- one turns on and the other turns off

phosphorylation of insulin receptor substrate 1→phosphorylation of beta adrenergic receptor by PKB

degraded no epi signalling insulin is stronger and will win

GLUT transporter

facilitated diffusion

glucose binding → conf change

transport conc. dependent and saturable (at high conc.)

beta barrel proteins

facilitated diffusion

integral membrane proteins single polypeptide chains forming barrel shape

hphilic inside, hphobic outside

potassium ion channel

tetramer

v structure 

selectivity filter (TVGYG) cocntributing to K+ binding

Which glucose transporter is responsive to insulin?

GLUT 4

What is one of the molecules that inhibits glycolysis?

Alanine

Lecture 16: Carbohhydrate Structure

Carbohydrate Numbering

carbon 1 is carbonyl (CHO) carbon, proceeds from there

carbohydrate configuration

multiple carbon chiral centres, multiple isomers

L or D assigned to chiral centre furthest from carbonyl

# of structures = 2^n 

n= number of chiral centres

carbohydrate cyclization

hemiacetal aldehyde derivative

hemiketal ketone derivative

(aldehydes and ketons are very reactive, undergo nucleophilic attack)

alpha or beta based on whether hydroxl is up or down(?)

anomeric carbons are…

chiral

anomer = isomers hat differ at a new aymmetric carbon atom formed at a ring closure

haworth projections

let you see cyclic sugars in 3d

carbohydrate modification

sugar can be phosphorylated, methylated, or N-group added

hydrozyls or carbonyls may be removed

isomer

same formula differnt structure/organization

constitutional isomer

different order of functional group bonding

stereoisomers

same formula and order but can be enantionmer, diastereomer, (epimer, anomer)

enantiomer

non-superimposable mirror images

diastereomer

not mirror images.

• epimer

• anomer

epimer

differ at one asymmetric carbon

anomer

differ at a newly formed, asymmetric C in the ring
structure

why are the different positions impoertant

very specific binding in enzyme active site, may weaken interactions and fail to bind ligand

reducing sugars

sugar molcule with a (very reactive) free aldehyde or ketone group act as a reducing agent by giving e- to another molecule

to identify: 1) identify anomeric carbon (to right of ring O) 2) does it have a free OH group?

glycation

non ezymatic reaction covalent attachment of a sugar to a protein, lipid or nucleic acid molecule.

(basically glycosylation w/o an enzyme)

hemoglobin and glycation

> 6%

diagnostic tool to see if glycation “frosting” indicates diabetes

simple monosaccharides

• simplest carbohydrate (CH20)n

• aldoses or ketoses

• D form sugars are biologically relevant

• cyclization leads to 2 additional structures

• reducing sugar can reform reactive linear structure

glycosidic bonds

• forms as condensation / dehydration synthesis reaction

• cleaving these bonds is hydrolysis reaction

• monosaccharides are joined by glycosidic linkages to form disaccharides and etc

• nomenclature (1→2) carbon 1 linked to carbon 2

  • can also be alpha/beta

a or b glycodisic bond

attack from bottom→alpha conformation (point down)

attack from top → beta conformation (point up)

N or O linked glycosidic bond

intermolecular glycosisidic bonds formed b/w amine or hydroxyl and a reactive anomeric carbon

eg DNA, RNA bases, glycoproteins may be O-linked (ser/thr) or N-linked (asn)

complex carbs

mono, di, oligo, poly sacchs

oligosacch

3-20 sugars

poly sacchs

up to 1000s of sugars

• linear or branched links

• energy storage, cell strcutrue, recognition

• aka glycans

homopolymer

sme monosacchs

heteropolymer

diff monosacchs

eg lactose glucose + galactose (B- 1,4)

starch

amylose and amylopectin

amylose

• unbranched glucose units

• α(1→4)-linkages

Amylopectin

• linear glucose chains joined by α(1→4)-linkages.

• α(1→6)-linkages at branch points once every 30
  glucose units

α-amylase

• enzyme secreted by the salivary glands and pancreas to degrade starch

• Cleaves at random locations along the chains to give maltose and maltotriose

glycogen

• A storage form of long, branched
  chains of glucose

  • linear glucose chains joined by α(1→4)-
    linkages.

  • α(1→6)-linkages at branch points once
    every 8-12 glucose units.

• Contains a dimer of glycogenin at the
  centre.

• Glucose units are added and removed
  from the non-reducing ends

• Found in the liver and muscle

cellulose

• most abundant organic

• Unbranched chains of glucose units are
  joined by β(1→4) linkages with many
  hydrogen bonds

cellobiose

disaccharide of glucose linked by β(1→4).

cleavage to monosacchs

• enzymes like lactase, maltase, sucrase

• cells can only transport and use monosacchs for fuel

maltose

2 glucose alpha 1→2

lactose

glucose + galactose (B 1→4)

No. This is a B 1→4 bond. This is cellulose.

(Hydroxyl at C1 is pointing up)

challenge of sugar sequencing

• many isomers

• mass spec/visualization is hard to distinguish b/w sugars

• multiple possible sugars

  • DNA 4 possible nt, Protein 20 possible monomers, carb 100s of possible at each position

glucose transport

glucose is polar and requires facilitated transport either down or against conc. gradient

types of glucose transporters

• sodium glucose co transporters

  • 2ndary active transport

  • allow sodium to go along gradient; glucose against gradient

• glucose transporters

  • facilitated diffusion

• fructose transpoorter

  • facilitated diffusion

GLUT4

• is expressed in adipose and muscle tissues.

• insulin dependent

  • In response to insulin, this transporter is translocated to the surface of the cell, allowing glucose to enter. ‘opening a door”

GLUT1, 2, and 3

are expressed on cells that always need glucose

• glut 1 & 3 seen brain; glucose moves through glut 1 to exit neuron and glut 3 to enter another

GLUT5

is a transporter that is specific for fructose.

FASTING state blood glucose

• glucose moves most effectively in neurons and blood cells

• liver, pancreas not releasing insulin, less flow

• Km low → fast, free flowing

• no insulin for receptor in muscles→ little glucose in muscles

FED state blood glucose

• move fast in blood

• pancreas release insulin into bloodstream

• glut 3 in neurons get lots of glucose in brain

• insulin receptors GLUT 4 muslce cells use glucose and store as fats

hypoglycemia

insulin sensitivity

low blood glucose level

decreased neural activity not enough glucose in the brain , fainting not enough neurons firing

lecture 17: carb metabolism

glycogen synhesis, glycogenolysis, glycolysis, anaerobic metabolism

anabolic state

• insulin signaling increases glucose utilization

• Increases glucose transport into cells

• Increases the expression and activity of enzymes that use glucose as a
  substrate

catabolic state

• low amnt of glucose, energy

• breaking down energy, eg stored as glycogen or fats

• protein synthesis/netbreakdown might increase

• hormones epinephrine and glucagon activate this state

D-glucose strcutre"*need to know

pyruvate strcutre"*need to know

glycilysis total substrates and products of the pathway

branching and why glycolysis pathway

glycolysis regulatory enzymes and how they are regulated

glycolysis

10 step catacbolic pathway found in cytoplasm using glucose and other simple monosacchs

glycolysis starts with…

glucose (6-carbons)

stage 1 glycolysis - 

preparing

energy inputted

2 phosphorylations

Aldose

2^n stereoisomers

N=

Lecture 15: Intro to Metabolism

catabolism and anabolism are…

interrelated !

catabolism

energy yielding nutrients → energy poor products

milk the energy out of those damn nutrients

• oxidative

• exergonic (releases energy)

anabolism

precursor molecules → cell macromolecules

• reductive

• endergonic (uses energy)

catabolism is oxidative or reductive?

oxidative.

chemical energy in metabolism

includes ATP, NADPH, NADH(?), FADH2(?)

metabolism is highly …

complex !

metabolic “map” can be broken down into linear, cyclic, or branched athways

catabolism of compounds (does?)

• involved in metabolism

• releases free energy which can be stored in ATP or other high energy intermediates

anabolism of compounds (does?)

• synthesize larger macromolecules using simple building blocks and energy

what influences metabolic flux in pathways?

Gibbs free energy changes and enzymes

influence the conversion of metabolites through the pathways

determining flux through a metabolic pathway (4)

1. The presence of enzymes

2. Metabolite concentration

3. ATP availability

4. Changes in Gibbs free energy

*in order

Gibbs Free Energy Eqn

ΔG = ΔG°′+ RT ln([P]/[S])

gibbs free energy change = standard free energy change +(8.314 J/mol*K)(temperature)(ln conc. at equillibrium)