Use Ch. 2-8 in \"Campbell Biology\" Pearson book by Urry, Cain, Wasserman, Minor

Question

Use Ch. 2-8 in "Campbell Biology" Pearson book by Urry, Cain, Wasserman, Minorsky, and Reece.

Write in multiple paragraph form. Please be detailed. Include vocabulary listed below question.

1. What controls the 3-dimensional shape of proteins in cells? What happens when proteins do not have the correct shape? How can protein folding or misfolding be related to diseases? [Hints: Your answer should include the levels of protein structure, the types of chemical bonds involved, chaperones, protein-folding diseases including Alzheimer’s and sickle cell, and prions.]

Biological Chemistry (Chapters 2-5)

In lecture, I will skip many parts of chapters 2-4; the exam will only cover those sections of the book that I talk about in lecture.

Electrons, energy levels, orbitals

Chemical bonds and intermolecular interactions: nonpolar covalent, polar covalent, ionic, hydrogen, van der Waals

Polar vs. nonpolar molecules; Hydrophobic vs. hydrophilic molecules (can you tell if a molecule is polar by looking at the structure diagram?)

Water:

Hydrogen bonding & temperature

Surface tension & hydrogen bonding

Dissociation of H20; definition of pH

Organic molecules: carbon skeletons and functional groups (understand the concepts, but don’t memorize the specific structures and groups).

Which biological molecules are polymers? Recognize molecular diagrams.

Dehydration synthesis and hydrolysis. What does it mean? What molecules does it apply to?

Nucleic acids structure & function. Recognize the structure of DNA, RNA, and nucleotides in general. You don’t need to know the individual nucleotides.

Lipids: structure & function

Saturated & unsaturated fats (recognize structures, explain why it matters)

Steroids

Carbohydrates: structure & function

Monosaccharides (recognize both ring & linear structures)

Polysaccharides

Recognize a molecular diagram of carbohydrate.

Proteins

Why do proteins do most of the work in cells? Why not polysaccharides or nucleic acids?

Amino acids. Recognize the general structure of amino acids, but not the individual amino acids. Contrast with nucleotides.

Levels of protein structure & bonds that maintain them

Prosthetic groups.

Hemoglobin: prosthetic groups, quaternary structure, sickle cell.

Macromolecule review: given a diagram of a molecule, be ready to state whether it is a lipid, carbohydrate, nucleic acid, or polypeptide. Recognize both the monomers and polymers. Also, recognize whether a structure is mostly polar or nonpolar.

Protein folding: what determines it? Why is it important?

Intrinsically disordered.

Protein domains, protein function, and introns.

Monomers, dimers & aggregates; the difference between intrachain and interchain interactions. Why do misfolded proteins form aggregates while normal proteins don’t?

Chaperone proteins

Protein quality control system: what happens to misfolded proteins and why is it important?

What does denaturation mean?

Two ways that proteins get destroyed in cells.

Prions and prion proteins. “Prion protein structure is conserved.” What does this mean?

Alzheimer’s disease. How is it like a prion disease? Why isn’t it considered a prion disease? What was the significance of the experiment with the transmission of amyloid protein in mice?

Alzheimer’s disease vs. Parkinson’s disease: compare & contrast, from the protein quality control point of view.

A Tour of the Cell (Ch. 6):

Prokaryotes vs. eukaryotes

Upper and lower limits on cell size

Origin of eukaryotic cells; why eukaryotic cells have two or more genomes.

Plasma membrane

Nucleus; nuclear envelope

Ribosomes

Endomembrane system:

Endoplasmic reticulum

Golgi apparatus

Lysosomes, vesicles, vacuoles

Mitochondria & chloroplasts

Cytoskeleton structure & function

Cell wall

Extracellular matrix

Membrane structure: lipid bilayer and fluid mosaic; proteins & carbohydrates. How is the inside of the plasma membrane different from the outside?

What controls the fluidity of the membrane?

How things cross membranes (& why):

Passive transport: simple diffusion & facilitated diffusion

Facilitated diffusion: channel & carrier proteins

Osmosis

What makes aquaporins selective?

Active transport

Sodium-Potassium pump

Electrochemical gradient

Cotransport; role of shape change in transport proteins.

Bulk transport: endocytosis & exocytosis

Metabolism (Ch. 8):

Thermodynamics:

Laws of thermodynamics

Free energy

Exergonic & endergonic

Entropy

ATP:

Phosphorylation increases free energy of reactants

Coupled reactions

Phosphorylation of proteins can cause a shape change

ATPases, kinases & phosphatases

What makes ATP suitable as the key energy transfer molecule?

Enzymes:

Catalysts lower energy of activation (study the graphs).

Active site

Induced fit between substrate & active site

Enzymes are sensitive to the local environment:

pH & temp changes

Exogenous enzyme inhibitors: Competitive & noncompetitive inhibition

Enzyme regulation in cells

Allosteric regulation

Cooperativity

Metabolic pathways:

Catabolism & anabolism

Multi-step pathways

Feedback inhibition (how does this relate to allosteric regulation?)

Explanation / Answer

1 What controls the 3-Dimentional structure of protiens in the cell

protien folding is the physical process by which a protein chain acquires its native 3- dimentional structure, a conformation that is usually biologically functional.it is the physical process by which a poly peptide folds into its characteristic and functional three dimenstional stracture from random coil,.amino acids interact with each other to produce a well defined three dimenstional structure. the process of protein folding is primary , seconadry, Tertiary and Quaternary structures by spontaneous process that is mainly guided byhydrophobic interactions , formation of intra molecular hydrogen bonds , vander waals forces, and it is opposed by conformational entropy. Molecular chaperons are also class of proteins that aid in the correct folding of other proteins in vivo.molecular chaperons operate by binding to stabilize an otherwise anstable structure of protiens in its folding pathway.

3. Incorrect protein folding and neurodegenerative diseases.

A protein is considered to be misfolding if it is connot achieve its normal native state. this can be due to mutations in the amino acid sequences or a disruption of the normal folding process by external factors.the mis folding protein typically conatins Beta sheets taht are organized in a supermolecular arrangement known as a cross-beta structure. these mis folding proteins can trigger the further misfolding and accumulation of other protiens in to aggregates or oligomers. the increased levels of aggregated protiens in the cell leads to formation of amyloid -like strutures which can causes degenerative disorders and cell death.

Aggregared protiens are associated with prion -related illnesses such as Jakob disease, Mad cow diseses and Alzheimer disese'

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