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Questions and Answers
The amino group (-NH2) of an amino acid is attached to the C-1 carbon.
The amino group (-NH2) of an amino acid is attached to the C-1 carbon.
False
Amino acids exist as enantiomers.
Amino acids exist as enantiomers.
True
Amino acids in mammalian proteins have a D configuration.
Amino acids in mammalian proteins have a D configuration.
False
Amino acids are classified based on the properties of their side chains.
Amino acids are classified based on the properties of their side chains.
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Amino acids with non-polar side chains participate in ionic bonding.
Amino acids with non-polar side chains participate in ionic bonding.
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Cys is an amino acid with an uncharged, polar side chain that contains a sulfhydryl group.
Cys is an amino acid with an uncharged, polar side chain that contains a sulfhydryl group.
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The sum of all the proteins functioning in a given cell is the cell’s genome.
The sum of all the proteins functioning in a given cell is the cell’s genome.
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Proteins constitute the largest fraction of a cell besides water.
Proteins constitute the largest fraction of a cell besides water.
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Proteomics is the study of the cell’s genome.
Proteomics is the study of the cell’s genome.
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Enzymes are an example of structural proteins.
Enzymes are an example of structural proteins.
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Myoglobin is an example of a storage protein.
Myoglobin is an example of a storage protein.
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Antibodies are an example of hormones.
Antibodies are an example of hormones.
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Collagen is an example of a protein involved in coordinated motion.
Collagen is an example of a protein involved in coordinated motion.
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Hemoglobin is an example of an enzyme.
Hemoglobin is an example of an enzyme.
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A conservative substitution involves a substitution of an amino acid with another of different character or polarity
A conservative substitution involves a substitution of an amino acid with another of different character or polarity
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In a native protein, the 3-D shape is altered
In a native protein, the 3-D shape is altered
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H-bonding between atoms of the peptide bond describes α-helix
H-bonding between atoms of the peptide bond describes α-helix
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β-sheet is stabilized by ionic bonding
β-sheet is stabilized by ionic bonding
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R groups project into the β-sheet
R groups project into the β-sheet
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Tertiary structure describes the sequence of amino acids in a polypeptide
Tertiary structure describes the sequence of amino acids in a polypeptide
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Secondary structure is stabilized by ionic bonding
Secondary structure is stabilized by ionic bonding
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Tertiary structure is stabilized by a single type of interaction
Tertiary structure is stabilized by a single type of interaction
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At a pH of 7, the amino group is deprotonated (-NH2) and the carboxyl group is protonated (COOH).
At a pH of 7, the amino group is deprotonated (-NH2) and the carboxyl group is protonated (COOH).
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Amino acids with R- charge are classified as basic.
Amino acids with R- charge are classified as basic.
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The pKa of the α-carboxyl group is typically between 8.7 and 10.7.
The pKa of the α-carboxyl group is typically between 8.7 and 10.7.
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Amino acids are strong acids.
Amino acids are strong acids.
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At a pH of 7, the side chains of acidic amino acids have a +ve charge.
At a pH of 7, the side chains of acidic amino acids have a +ve charge.
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The ionization state of amino acid in solution is constant and does not vary with pH.
The ionization state of amino acid in solution is constant and does not vary with pH.
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Amino acids with R+ charge are classified as acidic.
Amino acids with R+ charge are classified as acidic.
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Amino acids are amphoteric, meaning they can act as both acids and bases.
Amino acids are amphoteric, meaning they can act as both acids and bases.
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Hydrophobic interactions between R groups are strong and confer a certain amount of rigidity on a protein.
Hydrophobic interactions between R groups are strong and confer a certain amount of rigidity on a protein.
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Quaternary structure refers to the organization and arrangement of subunits in a protein.
Quaternary structure refers to the organization and arrangement of subunits in a protein.
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Weak interactions between subunits confer flexibility and permit conformational changes in proteins.
Weak interactions between subunits confer flexibility and permit conformational changes in proteins.
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Myoglobin is a tetrameric heme protein found mainly in red blood cells.
Myoglobin is a tetrameric heme protein found mainly in red blood cells.
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Hemoglobin is an allosteric protein that undergoes a conformational change upon binding to oxygen.
Hemoglobin is an allosteric protein that undergoes a conformational change upon binding to oxygen.
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The tertiary structures of myoglobin and hemoglobin are identical.
The tertiary structures of myoglobin and hemoglobin are identical.
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Hemoglobin reacts spontaneously with glucose to form hemoglobin A1C.
Hemoglobin reacts spontaneously with glucose to form hemoglobin A1C.
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Sickle cell anemia is caused by a mutation in the hemoglobin gene that results in a substitution of Glu for Val at position 6 on the β-chain.
Sickle cell anemia is caused by a mutation in the hemoglobin gene that results in a substitution of Glu for Val at position 6 on the β-chain.
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Hemoglobin C is a genetic disorder that causes severe anemia.
Hemoglobin C is a genetic disorder that causes severe anemia.
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Thalassemias are genetic disorders that result from mutations in the hemoglobin gene that lead to an overproduction of globin subunits.
Thalassemias are genetic disorders that result from mutations in the hemoglobin gene that lead to an overproduction of globin subunits.
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Study Notes
Biochemistry
- Proteins are long polymers of amino acids and constitute the largest fraction (besides water) of a cell.
- The sum of all the proteins functioning in a given cell is the cell's proteome, and proteomics is the systematic characterization of this protein complement under a specific set of conditions.
Functions of Proteins
- Catalysts - enzymes for metabolic pathways
- Storage and transport - e.g. myoglobin and hemoglobin
- Structural - e.g. actin, myosin
- Coordinated motion – e.g. muscle contraction
- Decoding information - translation and gene expression
- Hormones and hormone receptors
- Immune protection - e.g. antibodies
- Mechanical support – e.g. collagen
- Energy reserve
Amino Acids
- Called α-amino acids because they all have an amino (-NH2) group and a carboxyl group (-COOH) attached to C-2 carbon (α-carbon)
- α-carbon is chiral or asymmetric (4 different groups attached to the carbon; exception - Gly)
- Amino acids exist as stereoisomers (same molecular formula, but differ in arrangement of groups)
- Designated -D or -L; Amino acids in mammalian proteins: L configuration
Classification of Amino Acids
- Based on properties of their R groups
-
- Amino acids with non-polar (hydrophobic) side chains
-
- Amino acids with polar (uncharged) side chains
-
- Amino acids with polar charged side chains
Ionization of Amino Acids
- α-COOH and α-NH2 groups in amino acids are capable of ionizing (as are the R-groups of amino acids)
- Amino acids: weak acids
- At a given pH, amino acids have different net charges
- Can use titration curves for amino acids to show ionizable groups
- Amino acids: amphoteric
- At pH of 7, amino group is protonated (-NH3+) and carboxyl group is ionized (COO-). The amino acid in this form is called a zwitterion
Titration of Amino Acids
- At any given pH one should able to predict the structure of amino acid
- Able to estimate the predominant species
- Ionizable groups on amino acids carry protons at low pH (protonization). At high pH the ionizable groups on amino acids dissociate, releasing protons (deprotonization)
Protein Structure
- Primary structure: linear sequence of amino acids
- Secondary structure: describes protein folding stabilized by H- bonding
- Features: α-helix and β-sheet
- Tertiary structure: overall shape of the protein molecule (folding of a polypeptide into a closely packed three-dimensional structure)
- Quaternary structure: refers to the organization and arrangement of subunits in a protein
Protein Function-Structure Relationships
- Structure, changes in structure are crucial to the function of proteins
- Oxygen transport proteins: understanding their structure and structural changes they undergo is useful in understanding how they function
- Myoglobin (Mb) and Hemoglobin (Hb) are heme proteins that transport oxygen
Myoglobin (Mb)
- Monomeric heme protein found mainly in muscle tissue
- Function: storage and transport of oxygen
- Structure: compact, folded polypeptide chain (153 residues); 75% of Mb: α-helical (8 helices; A,..H)
- Interior: almost entirely nonpolar residues (the only polar amino acids in the interior are two Histidines, which are part of the O2 binding site)
- Contains heme; function of heme: facilitates binding of oxygen to Mb (Mb apoprotein will not bind oxygen)
Hemoglobin (Hb)
- Tetrameric heme protein
- Found in RBCs
- Binds O2 in the lungs and transport to tissues
- Transports CO2 from tissues to lungs
- Each subunit/polypeptide chain of Hb tetramer has a heme prosthetic group and O2 binding site
- Hb: allosteric protein
- Subunits: α- or -β; Hb: (α(2): β(2); α-chain (141), β-chain (146)
Hemoglobinopathies
- Genetic diseases in which the globin subunits of Hb are mutated
- Major hemoglobinopathies include:
- Sickle cell anemia
- Hemoglobin C
- Thalassemias
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Description
This quiz covers the basics of biochemistry, focusing on the human body and its functions. It is based on the recommended textbooks for the SMBM 102 course.
