Notes for Chaps. 8 and 11
Jones
BSC 1010C
Chap. 8
Terms to know:
Metabolic pathways
Catabolic pathways
Anabolic pathways
Bioenergetics
Kinetic energy
Potential energy
Chemical energy
First law of thermodynamics
Second law of thermodynamics
Spontaneous process
Nonspontaneous process
Endergonic reaction
Exergonic reaction
Activation energy
Enzyme
Substrate
Active site
Enzyme-substrate complex
Cofactors
Coenzymes
Competitive inhibitors
Noncompetitive inhibitors
Allosteric regulation
Cooperativity
Feedback inhibition
Free energy
Entropy
Enthalpy
Energy coupling
A cell uses ATP as the immediate source of energy for chemical, mechanical, and transport
work. A cell regenerates ATP at a phenomenal rate. The formation of ATP from ADP and
Phosphorus is endergonic. Cellular respiration provides the energy for the regeneration of ATP.
Plants produce ATP using light energy.
Chemical reactions involve both the breaking and forming of chemical bonds. Energy must be
absorbed to contort molecules to an unstable state in which bonds can break. Energy is released
when new bonds form and molecules return to stable, lower energy states. Activation energy E
(A) is that energy that must be absorbed by reactants to reach the unstable transition state in
which bonds are likely to break and from which the reaction can proceed.
The activation energy barrier is essential to life because it prevents the energy-rich
macromolecules of the cell from decomposing spontaneously. For metabolism to proceed in a
cell, however, activation energy must be reached. Enzymes are able to lower activation energy
so that the specific reactions can proceed at cellular temperatures.
Local conditions affect enzyme activity. The speed on an enzyme-catalyzed reaction may
increase with rising temperature up to the point at which increased thermal agitation begins to
disrupt the weak bonds and interactions that stabilize protein shape. Each enzyme has optimal
conditions that include a temperature and pH that favor its most active shape.
Cofactors are small molecules that bind either permanently or reversibly with enzymes and are
necessary for enzyme function. They may be inorganic, such as various metal inons, or organic
molecules called coenzymes. Most vitamins are coenzymes or precursors of coenzymes.
Enzyme inhibitors disrupt the action of enzymes either reversibly by binding with the enzyme
with weak bonds or irreversibly by attaching with covalent bonds. Competitive inhibitors
compete with the substrate for the active site of the enzyme. Increasing the concentration of
substrate molecules may overcome this type of inhibition. Noncompetitive inhibitors bind to a
part of the enzyme separate from the active site and impede enzyme action by changing the
shape of the enzyme.
Enzymes for several steps of a metabolic pathway may be associated in a multi-enzyme
complex, facilitating the sequence of reactions. Specialized cellular compartments may contain
high concentrations of the enzymes and substrates needed for a particular pathway. Enzymes are
often incorporated into the membranes of cellular compartments. The complex internal
structures of the cell facilitate metabolic order.
*Know the difference between a nonspontaneous process and a spontaneous process.
*Know the difference between an anabolic and a catabolic pathway.
*Know the formula for the change in free energy.
*Know why metabolic disequilibrium is essential to life.
*Know the difference between exergonic and endergonic reactions and the source of energy for
endergonic reactions.
*Know the relationship between free energy, stability, and equilibrium.(section 8.2)
*Know the structure of ATP and that it can be hydrolyzed to ADP.
*Know how the hydrolysis of ATP performs work
*Know the substrate specificity of enzymes and catalysis in the enzyme’s active site.
*Know how the regulation of enzyme activity helps control metabolism especially as it relates to
allosteric regulation, cooperativity, and feedback inhibition.
Chap. 11
Terms to know:
Signal transduction pathway
Local regulators
Hormones
Ligand
G protein-coupled receptors
Receptor tyrosine kinases (RTKs)
Second messengers
Scaffolding proteins
Protein kinase
A concentration of signaling molecules allows some bacteria to sense their local density, a
process called quorum sensing. Aggregations of bacterial cells called biofilms may form in
response to signaling within the population.
Local and long-distance signaling
Chemical signals may be communicated between cells through direct cytoplasmic connections or
through contact of membrane-bound surface molecules (cell-cell recognition in animal cells).
Transmission of electrical and chemical signals within the nervous system is also a type of long
distance signaling.
The three stages of cell signaling: reception of a chemical signal by binding to a receptor protein
either inside the cell or on its surface, causing it to change shape; transduction of the signal, often
by a signal transduction pathway (a sequence of changes in relay molecules); and the specific
response of the cell.
*Know what paracrine signaling is.
*Know the difference between growth factors and synaptic signaling.
*Know the difference between paracrine signaling and endocrine signaling.
Reception: a signaling molecule binds to a receptor protein, causing it to change shape.
Malfunctions of the three major transmembrane receptors are associated with many
human diseases.
The binding of a signaling molecule to a ligand-gated ion channel opens or closes a
“gate”, thereby allowing or blocking the flow of specific ions through the receptor channel. The
resulting change in ion concentration inside the cell triggers a cellular response.
Neurotransmitters often bind to ligand-gated ion channels in the transmission of neural signals.
*Know the three major types of transmembrane receptors that bind with water-soluble signaling
molecules and transmit information into the cell and know how these receptors function and the
role they play..
*Be able to explain why G-protein coupled receptor pathways shut down rapidly in the absence
of a signal molecule.
Transduction: Cascades of molecular interactions relay signals from receptors to target
molecules in the cell.
Multistep pathways enable a small number of extracellular signals to be amplified to produce a
large cellular response and also provide opportunities for regulation and coordination.
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Know how the following are, know what their role is and how they function, and know
that they are part of the transduction process: 1)signal transduction pathways, 2) protein
phosphorylation and dephosphorylation, 3) small molecules and ions as second
messengers
Be able to name at least two second messengers
Response: cell signaling leads to regulation of transcription or cytoplasmic activities:
Signal transduction pathways may lead to the activation of transcription factors which regulate
the expression of specific genes. Signaling pathways may also activate existing cytoplasmic
enzymes, open or close protein channels in membranes, or influence overall cell activity by
orienting the growth of the cytoskeleton.
A signal transduction pathway amplifies a signal in an enzyme cascade because each successive
enzyme in the pathway can process multiple molecules which then activate the next step. As a
result of their particular set of receptor proteins, relay proteins, and response proteins, differenct
cells can respond to different signals or can exhibit different responses to the same molecular
signal. Pathways may branch to produce multiple responses or two pathways may interact
(“cross-talk”) to mediate a single response.
Scaffolding proteins that permanently attach networks of signaling-pathway proteins at synapses
have been identified in brain cells.
Apoptosis:
A type of programmed cell death in which cellular components are chopped up and packaged
into vesicles that are released as blebs and then engulfed b scavenger cells. One type of
apoptotic pathway in mammals involves proteins such as cytochrome c that are released through
pores formed by apopototic proteins in mitochondrial membranes. In other cases, binding of a
death-signaling ligand to a cell-surface receptor leads to the activation of caspases that carry out
apoptosis. Other signals can come from the nucleus when the DNA has suffered irreparable
damage or from the endoplasmic reticulum in response to extensive protein misfolding.
Programmed apoptosis is part of normal development. Faulty cell suicide programs have been
implicatedin some neurological diseases and in cancer.
In addition to the information in these notes, be familiar with the terms and concepts in sections
11.2 – 11.4.