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Med’11 Biochemistry Proteins

What are peptides? Polymers of amino acids
What are oligopeptides? polypeptides? Oligopeptides: peptide chain made up of 2-10 amino acids Polypeptides: peptide chain made up of more than 10 amino acids
List the levels of protein structure, and define each. Primary: the number and sequence of amino acids. Secondary: the local spatial arrangement of the polypeptide chain without regard to the side chains Tertiary: the over all 3D structure of the chain Quaternary: organization of the subunits of the protei
What is the N-terminal of a protein? the C-terminal? N-terminal: free amino group C-terminal: free carboxyl group
What are the properties of a peptide bond? -made by a condensation reaction -strong -broken by prolonged heating in a strong acid/base OR specific enzymes -partial double bond -in trans-form -uncharged but polar
What are the 2 types of secondary structure? Alpha-Helix Beta-Pleated Sheet
What bonds are responsible for each structure level? Primary: peptide bonds Secondary: H-bonds Tertiary: R-group bonding (Van der Waal’s forces, hydrophobic bonds, ionic bonds, H-bonds, disulfide bonds) Quaternary:
Describe the alpha-helix. Coiled 1 polypeptide chain H-bonds parallel to axis; R groups protrude outwards 3.6 amino acids/turn Forms about 100% fibrous proteins and 80% globular proteins
Describe the beta-pleated sheet. Almost extended sheet, surface appears pleated 1 or more polypeptide chains H-bonds perpendicular to axis; R groups above and below plane H-bonds can be inter-chain or intra-chain bonds Found in both fibrous and globular proteins
What can disrupt an alpha-helix? Proline Large number of bulky amino acids Large number of branched amino acids Large number of acidic/basic amino acids
Differentiate between loops and turns. Loops: >5 residues Turns: =<5 residues
What are the functions of loops and turns? To allow the protein to have a more compact structure To connect alpha-helices and beta-sheets
Why is the tertiary structure important? It give the protein its characteristic shape and function.
What are domains? The functional and structural subunits of proteins. They can perform a chemical/physical task.
Describe the structure of the domain. Hydrophobic core built from super-secondary structures Connected by loops May be bound by weak inter-domain interactions
Protein folded is dictated by _____. Primary structure
What is a chaperone protein? Family of cellular proteins that bind non-covalently to the newly synthesized polypeptide chains to ensure correct folding. They don’t form part of the finished product.
What do chaperones use to work? ATP
What are the functions of chaperones? Increase the rate of correct folding of nascent polypeptide chains Aid in the assembly of multisubunit proteins Protect proteins from stress-induced damage (eg. Heat shock)
What are the 3 classifications of proteins? Simple: amino acids only Conjugated: amino acids + prosthetic group Derived: denature proteins
What is denaturation? The loss of the natural conformation of protein that gives protein its normal biological functions. It involves the loss of secondary, tertiary and quaternary structure keeping its primary structure (Keeping peptide bonds and loss of other bonds).
Denaturing agents include: Heat Changes in pH (concentrated acids or alkali) Ultraviolet rays X-ray High salt concentration Heavy metals.
How can you classify proteins according to their shape? Fibrous Globular
Describe fibrous proteins. -polypeptides arranged in strands/sheets -not soluble in water -structural -strong but flexible -e.g. keratin, collagen, elastin
Describe globular proteins. -globular -soluble in water -more than one secondary structure -e.g. hormones, enzymes, hemoproteins
What are heme proteins? Conjugated proteins with heme as the prosthetic group.
Give examples of heme proteins. Myoglobin - Hemoglobin - Cytochromes - Peroxidase - Catalase - Nitric oxide synthase - Tryptophan dioxygenase (pyrrolase)
Compare between myoglobin and hemoglobin. Myoglobin: 1 heme + 1 protein Hemoglobin: 4 heme + 4 proteins
Describe heme. Cyclic protoporphyrin IX (4 pyrrol rings) and a Ferrous atom One atom of ferrous iron (Fe2+) is at the center & forms 4 coordination bonds Fe can form 2 bonds with proximal histidine of globin & oxygen
What is the position of proximal histidine? distal histidine? His F8 His E7
Where is myoglobin found? Skeletal muscle
What is the function of myoglobin? Storage of oxygen in muscles. Oxygen transport
How many amino acid residues make up myoglobin? 153
Describe myoglobin. 153 residues polar residues on surface; nonpolar on the inside except for the 2 histidine residues compact, roughly spherical; 4.5 X 3.5 X 2.5 nm 8 helices; 80% alpha-helices
Where does heme reside in the myoglobin? between His E7 and His F8
Describe heme in the unoxygenated myoglobin. Heme lies 0.03 nm outside the plane of the ring in the direction of proximal histidine
Describe heme in the oxygenated myoglobin. an O2 molecule occupies the sixth coordination position of the iron atom, which then lies only about 0.01 nm outside the plane of the heme
Describe the conformational change in myoglobin when it becomes oxygenated. Oxygenation of Mb is accompanied by movement of the iron atom, and consequently movement of proximal histidine (His F8) and residues covalently linked to it, toward the plane of the ring.
What is the oxygen dissociation curve? What shape does it take? It is the relationship between the oxygen concentration (expressed as PO2, the partial pressure of oxygen) and the quantity of oxygen bound to Mb (Percent saturation). O2 dissociation curve for Mb is Hyperbolic.
Where is hemoglobin found? RBC
What is the function of hemoglobin? Transport of O2 from lungs to peripheral tissues Transport of CO2 and protons from peripheral tissues to the respiratory organ for subsequent excretion. Also Hb / oxy-Hb system acts as buffer in red cells for H2CO3.
Describe the structure of hemoglobin. Tetrameric proteins composed of 4 polypeptide chains attached by noncovalent bonds. -2 different polypeptide types -Has 4 heme ; can bind to 4 oxygen molecules -Has quaternary structure -Hydrophobic residues internal (except for 2 Histidines)
List the different hemoglobin types. HbA (normal adult Hb) = α2β2 (forms about 98% of adult Hb) HbA2 (a minor adult Hb) = α2(delta)2 (forms about 2% of adult Hb) HbF (fetal hemoglobin) = α2(gamma)2 (present in fetus)
How many residues make up the alpha and beta chains of HbA? alpha chain: 141 residues (7 loops) beta chain: 146 residues (8 loops)
The four polypeptide chains arranged as _______. 2 dimers
How do the 2 dimers interact with each other? Why is this significant? The α & β chains forming each dimer are held together by hydrophobic interactions (tightly) and by hydrogen & ionic bonds (less tightly). This allows movement of the 2 dimers relative to each other, and have 2 forms.
What are the 2 forms of hemoglobin (regarding oxygenation and deoxygenation)? Tense form and Relaxed form
What are the properties of the tense form? T dimers are strongly immobilized by hydrogen and ionic bonds. It has low oxygen affinity. (deoxy form)
What are the properties of the relaxed form? There is freedom of movement of dimmers due to breaking of the hydrogen and ionic bonds between them. It has high oxygen affinity. (oxygenated form)
Where does the tense form occur? Why? At the tissues where an inc CO2 & dec O2 in blood leads to increase [ H+ ] in RBCs Inc the number of ionic bonds between the 2 dimers. So, the polypeptide chains are difficult to move relative to each other. It has a lower affinity for oxy
Where does the relaxed form occur? Why? Occurs at the lungs when dec CO2 & inc O2 leads to deprotonation of Hb. So, dec charged groups & dec number of ionic bonds between the 2 dimers. So, the polypeptide chains are free to move relative to each other. It has a higher affinity to oxyge
Describe HbA2. 2- HbA2 It is formed of two alpha and two delta chains (α2 δ2). It appears 12 weeks after birth and constitutes 2% of the total hemoglobin.
Describe the shape of the oxygen dissociation curve for hemoglobin? Why does it have this shape? O2 dissociation curve for Hb is Sigmoidal Because subunits cooperate in binding oxygen. Binding of the first oxygen is difficult, but once occur, it facilitates binding of other oxygen molecules.
What are allosteric effectors? Effectors that change the affinity of hemoglobin for oxygen by binding to Hb at a site other than that of oxygen.
The allosteric properties of hemoglobin are due to _______. Quaternary structure
List the allosteric effectors of hemoglobin. Oxygen (heme – heme interaction). Partial pressure of CO2 (p CO2). Proton concentration (Bohr effect). 2,3 biphosphoglycerate (2,3BPG). Carbon monoxide.
Created by: Salma O
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