motors ii; general metabolism i

11/17/2010Motors II; Metabolism I

Motors II;General

Metabolism IAndy Howard

Introductory Biochemistry, fall 2010

17 November 2010

11/17/2010Motors II; Metabolism I of 40

Metabolism:the core of biochem All of biology 402 will concern itself with the specific pathways of metabolism

Our purpose here is to arm you with the necessary weaponry

… but first, we need to explain the role of Ca2+ in muscle contraction


What we’ll discuss

Muscle Calcium Ca2+ receptors Troponin C and I

Smooth muscle Metabolism

Definitions Pathways

Metabolism, continued Control Feedback Flux Phosphorylation

Other PTMs Evolution


Muscle Contraction Is Regulated by Ca2+Ca2+ Channels and Pumps

Release of Ca2+ from the SR triggers contraction

Reuptake of Ca2+ into SR relaxes muscle

So how is calcium released in response to nerve impulses?

Answer has come from studies of antagonist molecules that block Ca2+ channel activity


Ca2+ triggers contraction Release of Ca2+ through voltage- or Ca2+-sensitive channel activates contraction

Pumps induce relaxation


Dihydropyridine ReceptorIn t-tubules of heart and skeletal

muscle Nifedipine and other DHP-like molecules bind to the "DHP receptor" in t-tubules

In heart, DHP receptor is a voltage-gated Ca2+ channel

In skeletal muscle, DHP receptor is apparently a voltage-sensing protein and probably undergoes voltage-dependent conformational changes


Ryanodine ReceptorThe "foot structure" in terminal

cisternae of SR Foot structure is a Ca2+ channel of unusual design

Conformation change or Ca2+ -channel activity of DHP receptor apparently gates the ryanodine receptor, opening and closing Ca2+ channels

Many details are yet to be elucidated!


Ryanodine Receptor

Courtesy BBRI

QuickTime™ and a decompressor

are needed to see this picture.


Muscle Contraction Is Regulated by Ca2+

Tropomyosin and troponins mediate the effects of Ca2+

See Figure 16.24 In absence of Ca2+, TnI binds to actin to keep myosin off

TnI and TnT interact with tropomyosin to keep tropomyosin away from the groove between adjacent actins

But Ca2+ binding changes all this!


Ca2+ Turns on Contraction

Binding of Ca2+ to TnC increases binding of TnC to TnI, simultaneously decreasing the interaction of TnI with actin

This allows tropomyosin to slide down into the actin groove, exposing myosin-binding sites on actin and initiating contraction

Since troponin complex interacts only with every 7th actin, the conformational changes must be cooperative


Thin & thick filaments Changes that happen when Ca2+ binds to troponin C

Fig. 16.24


Binding of Ca2+ to Troponin C Four sites for Ca2+ on TnC - I, II, III

and IV Sites I & II are N-terminal; III and IV on C term

Sites III and IV usually have Ca2+ bound Sites I and II are empty in resting state Rise of Ca2+ levels fills sites I and II Conformation change facilitates binding of TnC to TnI


2 views of troponin C Ribbon Molecular graphic

Fig. 16.25


Smooth Muscle ContractionNo troponin complex in smooth

muscle In smooth muscle, Ca2+ activates myosin light chain kinase (MLCK) which phosphorylates LC2, the regulatory light chain of myosin

Ca2+ effect is via calmodulin - a cousin of Troponin C


Effect of hormones on smooth muscle Hormones regulate contraction - epinephrine, a smooth muscle relaxer, activates adenylyl cyclase, making cAMP, which activates protein kinase, which phosphorylates MLCK, inactivating MLCK and relaxing muscle


Smooth Muscle Effectors

Useful drugs Epinephrine (as Primatene) is an over-the-counter asthma drug, but it acts on heart as well as on lungs - a possible problem!

Albuterol is a more selective smooth muscle relaxer and acts more on lungs than heart

Albuterol is used to prevent premature labor

Oxytocin (pitocin) stimulates contraction of uterine smooth muscle, inducing labor


Oxytocin structure P.532


Metabolism Almost ready to start the specifics(chapter 18)

Define it!Metabolism is the network of chemical reactions that occur in biological systems, including the ways in which they are controlled.

So it covers most of what we do here!


Intermediary Metabolism

Metabolism involving small molecules

Describing it this way is a matter of perspective:Do the small molecules exist to give the proteins something to do, or do the proteins exist to get the metabolites interconverted?


How similar are pathways in various organisms? Enormous degree of similarity in the general metabolic approaches all the way from E.coli to elephants

Glycolysis arose prior to oxygenation of the atmosphere

This is considered strong evidence that all living organisms are derived from a common ancestor


Anabolism and catabolism Anabolism: synthesis of complex molecules from simpler ones Generally energy-requiring Involved in making small molecules and macromolecules

Catabolism: degradation of large molecules into simpler ones Generally energy-yielding All the sources had to come from somewhere


Common metabolic themes

Maintenance of internal concentrations of ions, metabolites, & (? enzymes)

Extraction of energy from external sources

Pathways specified genetically Organisms & cells interact with their environment

Constant degradation & synthesis of metabolites and macromolecules to produce steady state


Metabolism and energy


Metabolic classifications

Carbon sources Autotrophs vs. heterotrophs Atmospheric CO2 as a C source vs. otherwise-derived C sources

Energy sources Phototrophs vs. chemotrophs (Sun)light as source of energy vs. reduced organic compounds as a source of energy


Fourway divisions (table 17.2)

Energy/Carbon Phototrophs:Energy from light

Chemotrophs:Energy from reduced organic molecules

Autotrophs:Carbon from atmospheric CO2

Photoautotrophs:Green plants, cyanobacteria, …

Chemoautotrophs:Nitrifying bacteria, H, S, Fe bacteria

Heterotrophs:Carbon from other [organic] sources

Photoheterotrophs:Nonsulfur purple bacteria

Chemoheterotrophs:Animals, many microorganisms, . . .


Another distinction: the organism and oxygen Aerobes: use O2 as the ultimate electron acceptor in oxidation-reduction reactions

Anaerobes: don’t depend on O2

Obligate: poisoned by O2

Facultative: can switch hit


Flow of energy

Sun is ultimate source of energy Photoautotrophs drive synthesis of [reduced] organic compounds from atmospheric CO2 and water

Chemoheterotrophs use those compounds as energy sources & carbon; CO2 returned to atmosphere


How to anabolism & catabolism interact? Sometimes anabolism & catabolism occur simultaneously.

How do cells avoid futile cycling? Just-in-time metabolism Compartmentalization:

Anabolism often cytosolic Catabolism often mitochondrial


Pathway A sequence of reactions such that the product of one is the substrate for the next

Similar to an organic synthesis scheme(but with better yields!)

May be: Unbranched Branched Circular


Catabolism stages

Stage 1: big nutrient macromolecules hydrolyzed into their building blocks

Stage 2: Building blocks degraded into limited set of simpler intermediates, notably acetyl CoA

Stage 3: Simple intermediates are fed to TCA cycle and oxidative phosphorylation


Anabolism stages

Short list ofsimple precursors

These are elaboratedin characteristic ways to build monomerse.g.: transamination of -ketoacids to make -amino acids

Those are then polymerized to form proteins, polysaccharides, polynucleotides, etc.


Some intermediates play two roles Some metabolites play roles in both kinds of pathways

We describe them as amphibolic Just recall that:catabolism is many down to few, anabolism is few up to many


Differences between catabolic and anabolic pathways Often they share many reactions, notably the ones that are nearly isoergic (Go ~ 0)

Reactions with Go < -20 kJ mol-1 are not reversible as is

Those must be replaced by (de)coupled reactions so that the oppositely-signed reactions aren’t unfeasible


Other differences involve regulation Generally control mechanisms

influence catalysis in both directions

Therefore a controlling influence(e.g. an allosteric effector)will up- or down-regulate both directions

If that’s not what the cell needs, it will need asymmetric pathways or pathways involving different enzymes in the two directions


ATP’s role We’ve discussedits significance asan energy currency

It’s one of two energy-rich products of the conversion of light energy into chemical energy in phototrophs

ATP then provides drivers for almost everything else other than redox


NAD’s role

NAD acts as asan electronacceptor via nettransfer of hydride ions,H:-, in catabolic reactions

Reduced substrates get oxidized in the process, and their reducing power ends up in NADH

Energy implied by that is used to make ATP (2.5 ATP/NAD) in oxidative phosphorylation

QuickTime™ and a decompressor

are needed to see this picture.

Image courtesy Michigan Tech Biological Sciences


NADPH’s role

Involved inanabolic redoxreactions

Reducing power in NADPH NADP used to reduce some organic molecule

Involves hydride transfers again NADPH regenerated in phototrophs via light-dependent reactions that pull electrons from water


How do we study pathways?

Inhibitor studies Mutagenesis Isotopic traces (radio- or not) NMR Disruption of cells to examine which reactions take place in which organelle


Why multistep pathways?

Limited reaction specificity of enzymes

Control of energy input and output: Break big inputs into ATP-sized inputs

Break energy output into pieces that can be readily used elsewhere


iClicker quiz question 1

A reaction A+B C+D proceeds from left to right in the cytosol and from right to left in the mitochondrion. As written, it is probably

(a) a catabolic reaction (b) an anabolic reaction (c) an amphibolic reaction (d) we don’t have enough information to answer.

motors ii; general metabolism i

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