Biochem Unit 4 (proteins)
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Created by:
kscallaway on February 23, 2012
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105 terms
Terms | Definitions |
|---|---|
 Linkage for primary protein structure | Covalent (amide, peptide) |
| Linkage for secondary protein structure | H-bonds |
| Linkage for Tertiary protein structure | Covalent (disulfide bonds/cysteine), H-bond, ionic (charged groups), hydrophobic(non-polar) |
| Linkage for Quaternary protein structure | All types except covalent |
| Molecules for primary protein structure | AA1 alpha carboxy AA2 alpha amino |
| Molecules for secondary protein structure | Between peptide bonds |
| Molecules for Tertiary protein structure | Between R groups |
| Molecules for Quaternary protein structure | Between subunits (mostly using R groups) |
| Secondary protein structure types | Alpha helix (most common) Beta conformation (sheets) Beta turns |
| Tertiary protein structure types | Super secondary structures Motifs Folds Domains |
| Quaternary protein structure types | Dimers Tetramers |
| Alpha helix H-bond almost parallel to | Peptide chain |
| Alpha helix H-bonding happens at | Residue n + 4 |
| Alpha helix R groups point | Outward |
| Alpha helix has about ____ AA/helix turn | 3.6 |
| Alpha helix pitch is about _____ | .54nm distance per a-turn or 5.4 Angstroms per a-turn |
| Alpha helix rise is about _____ | .15nm distance per AA or 1.5 Angstroms per AA |
| Alpha helix is most common | Secondary structure |
| Average alpha helix in proteins is about | 26% |
| AA that disrupt alpha helix | Proline 2 or more charged AA in a row 2 or more basic AA in a row 2 or more Glycine AA in a row 2 or more branched AA in a row |
| B-sheet antiparallel | H-Bonds almost perpendicular (90 deg) to chain Alternate between narrow and wide |
| B-sheet parallel | H-Bonds are slanted (45 deg) Evenly spaced |
| Loops & Turns are stretches of | Non-repeititve structure |
| Loops & Turns cause | Directional changes in chain |
| Loops & Turns connect a-helices and b-sheets & allow chain to | Fold on itself to produce the compact shape of globular proteins |
| Loops & Turns are normally missing | In fibrous proteins |
| Loops characteristics | Usually polar AA On surface of proteins H-bonded with water About 10% of residues |
| Turns characteristics | Loops of few AA (up to 5) B-turns most common Proline & Glycine are often present |
| AA most likely to be found in alpha helix | Glu (largest),Met(2nd largest),Ala,Leu,Lys |
| AA least likely to be found in alpha helix | Pro (2nd smallest),Gly (smallest), Tyr, Asn, Cys |
| AA most likely to be found in Beta sheets | Val (largest), Isoleucine, Tyr, Phe, Trp |
| AA least likely to be found in Beta sheets | Glu (smallest), Asp, Pro, Lys, Gly |
| AA most likely to be found in Beta turns | Asn, Gly, Pro, Asp, Ser |
| AA least likely to be found in Beta turns | Isoleucine, Val, Phe, Leu, Met |
| Globular proteins must have at least | Tertiary (simple), some up to Quaternary structure (complex) |
| Globular proteins will always have a combination of | Secondary structures |
| Globular proteins are fully | Soluble or membrane bound |
| Globular protein main function is | Mostly DYNAMIC role |
| Examples of globular proteins | Hemoglobin Myoglobin Enzymes |
| Sperm whale myoglobin | 1st protein that they showed tri dimensional shape Typical globular protein |
| Fibrous protein structure is | Mostly primary and secondary |
| Fibrous proteins are made of | Mostly one type of secondary structure |
| Fibrous proteins are practically | Insoluble |
| Main function of fibrous proteins is | Mostly STRUCTURAL role |
| Fibrous protein location is | Mostly extracellular |
| Examples of fibrous proteins | Collagen Elastin Keratin |
| Chymotrypsin residues | 247 |
| Cytochrome C residues | 104 |
| Lysozyme | Tears/saliva 1st 3D structure known |
| Cytochrome C is for ___ use | O2 |
| X-Ray diffraction AKA crystalography | Protein in crystal form |
| Nuclear Magnetic Resonance | Concentrated solution instead of crystal Can also look at tissue 3D structure |
| Troponin C | Found in muscle that binds to calcium |
| Domains are | Stable, globular units of few hundred folded amino acids |
| A protein with multiple domains may appear to | Have a distinct globular lobe for each domain (good example of troponin c) |
| Different domains often have | Distinct functions |
| Small proteins usually have only ___ domain | One (the domain is the protein) |
| 1st simple protein with 3D structure known | Myoglobin |
| 1st complex protein with 3d structure known | Hemoglobin |
| Protein Denaturation factors and conditions | High temperature Extreme pH (stomach) Mechanical shearing Detergents Heavy metals (Pb,Fe,Hg) Reducing agents (DTT, Mercaptoethanol) Chaotropic agents (Urea, Guanidine hydrochloride) |
| Chaotropic agents means | Cause chaos, cause proteins to fold inside out. |
| Renaturation means | Protein goes back to its original shape |
| Factors or conditions that increase renaturation | Low molecular weight (small) High number of disulfide bonds (4) |
| Apomyoglobin means | Incomplete |
| Removal of HEME group result is | Apomyoglobin |
| Gdn HCl | Another factor besides temperature which will turn a protein inside out Urea can also be used |
| Ribonuclease is easily | Renatured |
| Creutzfeldt-Jakob disease | Similar to alzheimers (proteins accumulated in brain cells) Caused by misfolded proteins |
| Prion | Discovered by Prussiner Smallest infection agent known (protein) |
| Chaperones are | Proteins that help other proteins |
| 2 classes of chaperones | Fixing in folding Making folding (both provide a microenvironment to help the folding or fixing the folding) |
| Digestion of proteins start in | Stomach pH 1-2 |
| Zymogen | Inactive enzyme/protease |
| Pepsinogen (zymogen) activation | [H+] (initiation) Pepsin (completion) |
| Pepsinogen source | Stomach |
| Pepsinogen specificity (target) | Mostly PHE |
| Trypsinogen (zymogen) activation | Enteropeptidase (initiation) Trypsin (completion) |
| Trypsinogen source | Pancreas |
| Trypsinogen specificity (target) | LYS & ARG |
| Chymotrypsinogen (zymogen) activation | Trypsin (initiation) Chymotrypsin (completion) |
| Chymotrypsinogen source | Pancreas |
| Chymotrypsinogen specificity (target) | Aromatic (Tyrosine, Tryptophan, Phenylalanine) Bulky AA (Leucine, Isoleucine, Valine) |
| Proelastase (zymogen) activation | Trypsin |
| Proelastase source | Pancreas |
| Proelastase specificity (target) | Small AA ALA/GLY/SER |
| Procarboxypeptidase A/B (zymogen) activation | Trypsin |
| Procarboxypeptidase A/B source | Trypsin |
| Procarboxypeptidase A/B specificity (target) | Carboxy end |
| Aminopeptidase activation | Not needed (active all the time) |
| Aminopeptidase source | Small intestine |
| Aminopeptidase specificity (target) | Amino end |
| Aminopeptidase is not a zymogen because its | Membrane bound and active all the time |
| Enteropeptidase activation | Not needed (active all the time) |
| Enteropeptidase source | Small intestine |
| Enteropeptidase specificity (target) | Trypsin C-side of Lys 6 |
| Pepsinogen, Trypsinogen and Chymotrypsin can undergo | Auto activation |
| Bonds that help form the a-helix are | H-bonds |
| Secondary active transport | Using a Na concentration gradient 4-5 of these carriers for absorption of the 20 protein amino acids |
| Liver has one of the highest | Protein turnovers |
| Cannot have globularity unless have | B-turns (always) |
| Human serum albumin | 50% plasma protein in blood Typical globular protein |
| Zymogen activation is important in | Protein digestion Lipid digestion Blood coagulation |
| Zymogen activation is | Partial hydrolysis |
| All enzymes are | Globular proteins |
| Branched AA are | Hydrophobic AA |
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