Cell Bio- Proteins: Function And Transport

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Protein function results from its structure. Levels of protein structure:

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1. Primary structure: the sequence of amino- acids
2. Secondary structure: alpha helix and beta sheet
3. Tertiary structure: Three dimensional conformation of polypeptide chain
4. Quaternary structure: a complex of more then one polypeptide chain (subunits), oligomer. hetero/homo oligomer/dimer

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Protein domain:

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part of polypeptide chain which forms independent, compact and stable structure (50- 350 amino- acids)

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Disulfide bonds:

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they are formed between adjacent cysteines and stabilize the structure of protein

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Globular proteins:

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compact shape of molecules (most of enzymes)

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Fibrous proteins:

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fibrous shape of the molecule (proteins of extracellular matrix)

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Chaperones:

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Represents proteins which bind other protein molecules and thus they help to fold and to keep the folding of the polypeptide chain in proper confirmation.

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Protein families:

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They include proteins similar in their structure and function

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Structure of protein polymers:

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1. Filaments (actin, elastin fibers)
2. Tubules (microtubules)
3. Sheets (some membrane proteins)
4. Spheres (viral capsids

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Protein complexes:

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Molecules of various proteins, including other types of molecules (e.g RNA, DNA). Can form large complexes (e.g. ribosomes and viral particles)

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Protein molecules are capable of self- organizing into more complex structures. How?

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Because of the character of the individual protein molecules

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What is a ligand?

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Protein bounded to different types of molecules (ions, small molecules, macromolecules) including molecules of other proteins. The binding of a protein to its ligand is highly selective and it is directly related to the function of the protein

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Protein bound to other molecules: (7)

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1. Binding of ion/atom (calmodulin+ calcium)
2. Binding of small nonprotein molecule (hemoglobin, heme)
3. Binding of a nonprotein macromolecule (transcription factors, DNA)
4. Binding of protein molecules (enzymes, protein substrate, antibodies)
5. Binding of a saccharide: glycosylation--> glycoprotein
6. Binding of a phosphate: phosphorylation
7. Binding of GTP: GTP- ending proteins

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Functional types of proteins: (10)

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1. Structural proteins: they form mechanical support to cells and tissues (tubulin, keratin, actin, collagen)
2. Enzymes: catalyze formation and breakage of covalent bonds (protein kinase, DNA polymerase, pepsin)
3. Motor proteins: enable movement (myosin, kinesin, dynein)
4. Transport proteins: transport ions and small molecules (hemoglobin, transferrin, albumin)
5. Storage proteins: store ions and small molecules (ferritin, casein, ovalbumin)
6. Signaling proteins: carry signal from cell to cell (insulin, EGF, NGF)
7. Receptor proteins: detect outside signals (insulin receptor)
8. Regulatory proteins: regulate function of other proteins or macromolecules by binding to them (cyclins, chaperones, transcription factors)
9. Antibodies: bind antigen in highly specific way
10. Other proteins with specific function (GFP)

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Protein sorting:

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directing and transfer of a protein to required location

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Signal sequence (signal peptide):

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A sequence of amino-acids serving as a signal for sorting proteins to required location. Proteins without signal sequence stay in cytosol.

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Mechanism of intracellular protein transport:

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1. Transport through nuclear pores
2. Transport acros the membrane
3. Transport by transport vesicles

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Transport through nuclear pores:

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Enables protein transport from the cytosol into the nucleus. Nuclear pores function as selective gates which actively transports relative proteins

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Transport across membrane:

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Enables transport of proteins into membrane bounded organelles (ER, peroxiosomes, mitochondria, chloroplast). Transport across membrane is realized by protein translocators. Transported proteins must usually unfold RER.

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Transport by transport vesicles:

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Enables transport between compartments of the endomembrane system (ER, Golgi apparatus) and transport from these compartments out of the cell. Secretory vesicles: clathrin coated pits--> endosomes

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Allosteric molecules:

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Molecules of proteins that can exist in two or more different conformations. Conformational change can be related to change in activity.

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Mechanism of protein activity regulation:

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1. Binding of ion/atom
2. Binding of small molecule
3. Regulation of enzyme activity by positive/ negative feedback
4. Binding of protein (cyclin complex/CDK)
5: Phosphorylation/ dephosphorlytaion
6. Binding of GTP--> GDP and protein inactivation
7. Proteolytic cleavage (proinsulin-> insulin, caspases)

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Degradation of proteins:

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Proteasomes degrade proteins marked for degradation by ubiwuintin (a small binding molecule)