Notes for Chaps. 8 and 11

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.

• 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.