NBME Biochemistry- Protein Structure and Function – Flashcards
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How many and what type of amino acids are the building blocks of human/mammalian proteins?
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20- alpha amino acids
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are there other amino acids, and if so what is their function?
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yes, they exist in free or combined states and can be non-protein associated amino acids and/or perform specialized functions
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What is the non-protein function of Tyrosine?
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precursor to thyroid hormones
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what is the non-protein function of glutamate?
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neurotransmitter
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what does an ?-amino acid consist of?
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a central carbon atoms called the ?-carbon linked to an amino group, a carboxylic acid group, a hydrogen atom, a distinctive R group
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which of the groups bound to the ?-carbon of an amino acid is known as the side chain?
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the R group
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DNA codes for how many amino acids?
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only 20
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what is the term for the 20 amino acids coded for by DNA?
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Standard amino acids
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How are the standard amino acids incorporated into proteins?
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by translation
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What are the nonessential amino acids?
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Alanine Asparagine Aspartate Cysteine Glutamate Glutamine Glycine Proline Serine Tyrosine
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What are the Essential amino acids?
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Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Trytophan Valine Arginine Histidine
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What is an aliphatic example of a hydrophobic amino acid?
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methyl group of alanine
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what is an aromatic example of a hydrophobic amino acid?
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phenyl group of phenylalanine
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neutral polar example of a hydrophilic amino acid?
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OH of serine
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what is an ionizable example of a hydrophilic amino acid?
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-COOH of aspartate
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What are the hydrophobic amino acids?
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Glycine Alanine Valine Leucine Isoleucine Methionine Proline Phenylalanine Tryptophan
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What are the hydrophilic amino acids?
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Lysine Arginine Aspartate Glutamate Asparagine Glutamine Tyrosine Serine Threonine Cysteine
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What are the aliphatic amino acids?
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Glycine Alanine Valine Leucine Isoleucine
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what are the branched chain amino acids?
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Valine Leucine Isoleucine
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What are the hydroxy amino acids?
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Serine Threonine
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What are the sulfur containing amino acids?
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cysteine methionine
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What are the acidic amino acids and amides?
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aspartic acid asparagine glutamic acid glutamine
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What are the basic amino acids?
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Arginine Lysine Histidine
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which amino acid has a guanido group?
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arginine
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which amino acid has an ? -amino group?
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Lysine
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which amino acid has an imidazole group?
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histidine
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what are the aromatic amino acids?
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phenylalanine Tyrosine tryptophan
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which amino acid has an indole ring?
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tryptophan
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which amino acid is an IMINO acid?
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proline
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Which is the smallest amino acid, the one found where peptides bend sharply?
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glycine
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where are hydrophobic amino acids typically found in a polar environment?
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in interior of proteins
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what are the 2 major functions of charged R groups in basic and acidic amino acids?
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stabilize protein conformations through salt bonds "charge relay systems" in catalysis and electron transport
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What is special about the pka of the imidazole group of histidine?
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it can be acid or base at neutral pH
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which amino acids are nucleophiles?
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Serine (-OH) Cysteine (-SH)
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the -OH of which 3 amino acids is important for regulation of enzyme activity?
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-OH of serine, tyrosine, & threonine
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which amino acid does not exhibit chirality?
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glycine
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which amino acids contain aromatic rings whose pi electrons absorb ultraviolet light?
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tryptophan tyrosine
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what are the special optical properties of tryptophan and tyrosine used for?
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quantitative estimation of proteins if their trp and tyr content is known
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what is an amphoteric molecule?
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a molecule that can act as either an acid or a base
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are amino acids amphoteric molecules?
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yes
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are a-COOH and -NH3+ weak acids or weak bases?
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weak acids
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are -COO- and -NH2 weak acids or weak bases?
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weak bases
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what is the equation used to analyze the titration curve of amino acids?
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henderson-hasselbach equation pH=pKa + log ([A-]/[HA])
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What is the net charge on an amino acid?
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the algebraic sum of all the positively and negatively charged groups present
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what does the net charge on an amino acid depend on?
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pka of its functional groups pH of the surrounding medium
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is R-COOH a stronger or weaker acid than R-NH3+?
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far stronger
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how do carboxyl and amino groups of amino acids exist at physiologic pH?
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at pH 7.4: carboxyl groups exist as COO- amino groups exist as NH3+
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what are zwitterions?
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molecules that contain both positive and negative charges on them
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what is the isoelectric species of an amino acid?
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the form of the molecule that has an equal number of positive and negative charges and thus is electrically neutral
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What is the isoelectric pH?
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the pH midway between the pKa values on either side of isoelectric species
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how does electrophoresis separate charged biomolecules?
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based on the rate of migration in a charged electrical field
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separation of plasma proteins by electrophoresis is done at what pH?
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a pH above the isoelectric pH, so the charge on proteins is negative
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in which direction does a protein move during electrophoresis?
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the protein is negatively charged so it moves toward the positive electrode
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what is isoelectric focusing?
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a specialized form of electrophoresis where proteins are separated on the basis of isoelectric pH
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What is the mechanism that creates non standard amino acid derivatives in human proteins?
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post translational modifications
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what is the only amino acid with a secondary amino group?
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proline
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Where are hydrophobic amino acids typically found in a hydrophobic environment like the cell membrane
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on the outside surface of the protein
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What change in amino acids causes the pathology of sickle cell disease?
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substitution of polar glutamate by non-polar valine in the beta-subunit of hemoglobin
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what does the unique geometry of proline contribute to?
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the formation of the fibrous structure of collagen interruptions in the alpha-helices found in globular proteins
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what is cystine?
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a dimer formed by the oxidation of the SH groups of 2 cysteines
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what does cystine contain?
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a disulfide bond
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what is a common extracellular protein that is stabilized by disulfide bonds?
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Albumin
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Which side groups of amino acids typically serve as a site of attachment for phosphate groups?
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the polar hydroxyl groups of serine, threonine, and rarely tyrosine
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which side groups of amino acids can serve as sites of attachment for oligosaccharide chains in glycoproteins?
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the amide group of asparagine, as well as the hydroxyl group of serine or threonine
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What are the abbreviations for cysteine?
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Cys=C
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What are the abbreviations for Histidine?
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His=H
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what are the abbreviations for isoleucine?
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Ile = I
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what are the abbreviations for methionine?
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Met = M
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what are the abbreviations for serine?
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Ser = S
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what are the abbreviations for Valine?
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Val = V
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what are the abbreviations for Alanine?
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Ala = A
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What are the abbreviations for Glycine?
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Gly = G
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What are the abbreviations for Leucine?
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Leu = L
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What are the abbreviations for Proline?
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Pro = P
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What are the abbreviations for threonine?
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Thr = T
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what are the abbreviations for Arginine?
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Arg = R
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What are the abbreviations for asparagine?
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Asn = N
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What are the abbreviations for Aspartate?
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Asp = D
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What are the abbreviations for Glutamate?
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Glu = E
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What are the abbreviations for glutamine?
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Gln= Q
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what are the abbreviations for phenylalanine?
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Phe = F
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what are the abbreviations for tyrosine?
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Tyr = Y
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what are the abbreviations for Tryptophan?
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Trp = W
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What is the abbreviation for aspartate or asparagine?
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Asx = B
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what are the abbreviations for glutamate or glutamine?
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Glx = Z
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what is the abbreviation for lysine?
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Lys = K
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which amino acid is optically inactive?
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glycine
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All the amino acids found in proteins are in the L or D configuration?
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L
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where are D-amino acids found?
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some antibiotics and bacterial cell walls
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What are the functions of proteins?
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Catalysis Transport Nutrient & Storage Contraction and mobility Structural Elements Defense mechanism Regulation Buffering capacity
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what determines the 3-d structure of the protein?
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amino acid sequence
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what are the levels of protein structure?
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primary secondary tertiary quarternary
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What is the primary structure of a protein?
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sequence of amino acids in its polypeptide chain
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what is the secondary structure of a protein?
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regular arrangement of amino acids within localized regions of the polypeptide
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what is the tertiary structure of a protein?
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folding of a polypeptide chain due to interactions between side chains of amino acids that lie in different regions of the primary sequence
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what is the quaternary structure of a protein?
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interactions between different polypeptide chains in proteins composed of more than one polypeptide (subunit interaction)
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what is a polypeptide chain?
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a series of amino acids joined by peptide bonds
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what is a protein residue?
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an amino acid unit
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does a polypeptide chain have polarity?
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yes
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by convention, which end is the beginning of the polypeptide chain?
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amino end (N-terminal)
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what 2 major parts make up a polypeptide chain?
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the regularly repeating part (backbone) the variable part (distinctive side chains
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how many amino acid residues does it take to make a protein?
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>50
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what is the word for chains of amino acids less than 50 residues long?
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oligopeptides
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what creates the disulfide bonds found in a polypeptide chain?
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the oxidation of a pair of cysteine residues
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what is a peptide bond?
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the linkage of ?-carboxyl of one amino acid + ? -amino group of another amino acid
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is a peptide bond a covalent or noncovalent bond?
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covalent
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what accompanies the formation of a peptide bond?
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loss of a water molecule
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what does the formation of a peptide bond require?
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input of free energy
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what is the geometry of a peptide bond?
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planar
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is there rotation about a peptide bond?
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no, its partial double bond character prevents rotation about this bond
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what is the bond length of a peptide bond?
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between the length of a single and a double bond
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what allows for proteins to fold in many different ways?
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rotation about the single bonds
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Are almost all peptide bonds cis or trans?
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trans
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where are cis peptide bonds seen?
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X-Pro linkages
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what are 3 reasons knowing amino acid sequence is important?
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essential for understanding mechanism of action amino acid sequence determines the 3-D structures of proteins alterations in amino acid sequence can produce abnormal function and disease
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what are 2 examples where alterations in amino acid sequence can produce abnormal function and disease?
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sickle-cell anemia and cystic fibrosis
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what is the 1st step in the determination of the primary structure of a protein?
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the first step is to determine the amino acid composition of the peptide
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how does one determine the amino acid composition of a peptide?
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1. the peptide is hydrolyzed into its constituent amino acids by heating it in 6 M HCl at 110 C for 24 hours 2. Amino acids in hydrosylates are separated by ion-exchange chromatography on columns of sulfonated polystyrene 3. amino acids are quantified by reaction with ninhydrin which turns all amino acids blue except proline which turns yellow
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what does Edman degradation do?
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sequentially removes one residue at a time from the amino end of a peptide
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what does phenylisothiocyanate do to the amino group of a peptide?
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reacts to form phenylthiocarbamoyl derivative
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what happens to the phenylthiocarbamoyl derivative of a peptide under mildly acidic conditions?
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a cyclic derivative phenylthiohydantoin (PTH)-amino acid is liberated and can be identified by chromatographic procedures
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what can be done once a PTH-amino acid derivative is liberated from the peptide?
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the Edman degradation can be repeated
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what has markedly decreased the time required to determine protein sequences?
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development of automated sequencers
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what is the limitation of Edman's method of determining primary structure of a protein?
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cannot be applied for peptides with more than 100 amino acids
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how is the limitation of the Edman degradation circumvented?
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by cleaving the original protein at specific amino acids into smaller peptides that can be sequenced
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what are 2 ways in which specific cleavage of peptides can be accomplished?
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chemical or enzymatic methods
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once the peptides separated by 1st chemical or enzymatic methods are sequenced by chromatography, how does one determine the order of the peptides?
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the necessary additional information is obtained from overlap peptides a second enzyme is used to split the original polypeptide chain at different linkages
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In terms of DNA sequencing, what is revealed by recombinant DNA technology?
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the amino acid sequence of the protein encoded by the gene
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when using recombinant DNA technology, the amino acid sequence of what state of the protein is obtained?
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the nascent protein, which does not include the post-translational modifications
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what are some regular periodic structures into which polypeptide chains fold?
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alpha helix beta pleated sheet beta turn omega loop
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describe the structure of an alpha helix
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rod like structure where a tightly coiled backbone forms the inner part of the rod and the side chains extend outward in a helical array
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What are the hydrogen bonds found in an alpha helix?
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the CO group of each amino acid forms a hydrogen bonds with the NH group of the amino acid that is situated four residues ahead in the sequence
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with the exception of those amino acids near the end of an alpha helix, what is true about all the main-chain CO and NH groups?
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all the main-chain CO and NH groups are hydrogen bonded
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what NH group does a CO group of residue n bond with in the hydrogen bonding scheme of an alpha helix?
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n + 4
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how many amino acid residues per turn of a helix in an alpha helix structure?
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3.6
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between right handed and left hand alpha helices, which are more energetically favorable?
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right handed
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how long are single alpha helices?
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;45 angstrom
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two or more alpha helices can entwine to form what very stable structure?
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alpha-helical coiled coils
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what are some examples of alpha helical coiled coils?
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myosin and tropomyosin, fibrin and keratin
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Ferritin is built from a bundle of what secondary structure?
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a bundle of alpha helices
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in what macroscopic structures would one expect there to be alpha helical coiled coils?
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hair, quills, claws, and horns
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what amino acid disrupts an alpha helix?
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proline
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what groups of amino acids disrupt an alpha helix?
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large numbers of: a. charged amino acids b. amino acids with bulky side chains like tryptophan c. amino acids that branch at the beta carbon like valine and isoleucine
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what is the name of a polypeptide chain in a beta sheet?
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beta strand
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how far extended are the polypeptide chains in beta sheets?
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almost fully extended
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do the side chains of adjacent amino acids in a beta sheet typically point in the same or opposite directions?
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opposite directions
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what is a beta sheet formed by?
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inter chain hydrogen bonds
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what are the 2 configuration/direction in which adjacent chains in a beta sheet can run?
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in opposite (antiparallel) directions in the same (parallel) direction
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in schematic diagrams of beta sheets, how are beta strands typically depicted?
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by broad arrows pointing in the direction of the carboxyl terminal end
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what is an example of a protein characterized by beta sheets?
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fatty acid binding proteins
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What do hydrogen bonds in a beta sheet connect?
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two parts of a polypeptide chain lying side by side
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Most proteins have compact, globular shapes, requiring reversals in the direction of their polypeptide chains. How are many of these reversals accomplished?
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reverse turn (beta turn or hairpin bend)
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what are the more elaborate (than beta turn) structures responsible for reversals?
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loops/omega loops
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do omega loops have regular, periodic structure?
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no
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where do omega loops invariably lie?
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on the surfaces of proteins
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what are the implications of having omega loops invariably lie on the surfaces of proteins?
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often participate in participate in interactions between proteins and other molecules
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What is the distribution of alhpa helices, beta strands, and turns along a protein chain often referred to as?
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its secondary structure
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what is the structure of a reverse turn?
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the CO group of residue i of the polypeptide chain is hydrogen bonded to the NH group of the residue i + 3 to stabilize the turn.
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what fraction of protein structure does nonrepetitive secondary structure account for?
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50%
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is nonrepetitive secondary structure of proteins random?
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no
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which is more difficult to describe, random or nonrandom secondary protein structure?
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nonrepetitive
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What is super-secondary protein structure?
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structural motifs that are intermediates between secondary and tertiary structure
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what is the role of super-secondary protein structure?
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may play a role in the function of the protein i.e. may bind an organic compound or substrate
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what are some of the more common types of super-secondary structure?
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??? ? loop ? ?-meander Greek key
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what is notable about the beta-alpha-beta unit of super secondary structure?
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right-handed twist
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what group of unique super secondary structures are characteristic of DNA binding proteins
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Zinc finger motif Leucine zipper motif Helix turn helix
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what is the overall course of the polypeptide chain referred to as?
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its tertiary structure
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how does the polypeptide chain, interms of its hydrophobic and hydrophilic side groups?
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hydrophobic side chains are buried and its polar, charged chains are on the surface
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many of which kinds of secondary structures are amphipathic?
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alpha-helices and beta strands
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what is the term for any of two or more compact regions that may be connected by a flexible segment of polypeptide chain?
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domains
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what is the tertiary structure of many proteins built from?
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domains
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what are some of the separate functions that a domain can perform for a protein?
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binding a small ligand spanning the plasma membrane containing the catalytic site DNA-binding providing a surface to bind specifically to another protein
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what do the 4 domains of the Src protein do?
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two of the domains form a protein kinase enzyme the SH2 and SH3 domains perform regulatory functions
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What are the major forces controlling protein structure?
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Hydrogen bonding Hydrophobic forces Ionic interactions covalent coss-linkages
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Do polypeptides contain numerous proton donors or proton acceptors both in their backbone and in the R-groups of the amino acids?
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both
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Does the environment in which proteins are found contain H-bond donors and acceptors?
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yes, water molecule
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where, in addition to within and between polypeptide chains, does hydrogen bonding occur in proteins?
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also with the surrounding aqueous medium
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what is the effect of proteins participating in hydrogen bonding with the surrounding aqueous medium?
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increases solubility
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what does the driving force of hydrophobic interactions affect the conformation of proteins?
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it stabilizes them
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what are the ionic interactions that control protein structure?
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negatively charged groups in acidic amino acids interact with positively charged groups of basic amino acids
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what are the examples of covalent cross-linkages that often stabilize extracellular proteins?
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intra chain or inter chain disulfide bonds
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where is the formation of covalent cross-linkages catalyzed?
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endoplasmic reticulum
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how do disulfide and other covalent cross-linkages behave?
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like atomic staples that reinforce the protein's most favored conformation
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do reducing agents create or break disulfide bonds?
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break
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what is the term for proteins that contain 2 or more different polypeptide chains held by non-covalent forces?
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oligomeric proteins
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what is the structure formed by a monomer-monomer interaction in an oligomeric protein known as?
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quaternary structure
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what are homooligomers?
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proteins with identical subunits
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what are heterooligomers?
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proteins containing several distinct polypeptide chains?
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How does one denature and then renature a protein?
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1. heating and treatment with reducing agents to break the disulfide bonds denatures the protein 2. returning to native conditions renatures the protein
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How do proteins fold?
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by progressive stabilization of intermediates rather than by random search
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which conformation of a protein is energetically most favored?
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the native conformation
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what are the stages of protein folding?
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1st, newly synthesized polypeptide emerges from ribosomes. Next, short segments fold into secondary structural units. These provide local regions of organized structure. 2nd, hydrophobic forces drive hydrophobic regions of the protein to the interior creating a molten globule 3rd, molecules of secondary structure rearrange to form a mature protein
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for oligomeric proteins, what happens first: individual protomers folding or protomers associating with eachother?
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individual protomers tend to fold before they associate with other subunits
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what are the three stages in unassisted protein folding?
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unfolded --> molten globule --> native
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What is the molecular chaperone that assists many proteins in folding into their proper three-dimensional structure?
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HSP 70
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in addition to HSP70, proper folding of some proteins also depends on what?
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chaperonin TCiP
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what is chaperonin TCiP?
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a complex of Hsp60 units
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What is the protein problem in the transmissible spongiform encephalopathies?
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protein misfolding
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what are the trasmissible spongiform encephalopathies/prion diseases?
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fatal neurodegenerative disorders due to deposition of insoluble protein aggregates in neural cells
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what are examples of prion diseases?
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Creutzfeldt-Jakob disease in humans, Scrapie in sheep, bovine spongiform encephalopathy in cattle
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What is the structure of human prion related protein PrPc?
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monomer, rich in alpha helix
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what is the structure of pathologic PrPsc?
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rich in beta sheet with many hydrophobic side chains exposed to solvent. These side chains associate strongly leading to insoluble protease resistant aggregates
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what is the danger of PrPsc?
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a single PrPsc can serve as a template for conformational transformation of many PrPc, a change transmitted without involvement of DNA or RNA
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What causes amyloidosis?
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accumulation of spontaneously aggregating proteins called amyloids
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what causes aggregation in amyloidoses?
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abnormal cleavage leads to change in conformation which forms long fibrillar protein assemblies of beta sheets
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what is the most important amyloid degenerative disorder?
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Alzheimer's disease
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depending on their overall morphology, how are proteins classified?
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as fibrous or globular
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what is the major function of globular proteins in the cell?
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carrying out most of the chemical work of the cell- synthesis transport metabolism
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How are the polypeptide chains of globular proteins folded?
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into compact structures
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what is one class of clinically important globular proteins?
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hemeproteins
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hemeproteins are specialized proteins with what kind of prosthetic group?
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heme
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what are some examples of heme proteins?
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cytochromes catalase myoglobin hemoglobin
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what is the function of heme in cytochromes?
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electron carrier with iron alternating between Fe2+ and Fe3+
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what is the function of heme in catalase?
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part of the active site catalyses breakdown of H2O2
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what is the function of heme in myoglobin?
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reversible binding to oxygen
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what is the structure of heme?
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complex of protoporphyrin IX and ferrous iron
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where is the Fe 2+ in the heme molecule?
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center of the molecule
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how many additional bonds can heme make?
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2
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What is myoglobin?
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intracellular protein of heart and skeletal muscle
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what is the function of myoglobin?
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reservoir of oxygen oxygen carrier
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What is the structure of Mb?
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single polypeptide chain with 8 alpha helices A-H
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how is the polypeptide chain of heme folded?
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folded into a globular structure with nonpolar amino acids inside and polar amino acids outside EXCEPT: His E7 and His F8 which lie in the interior
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how many heme groups in myoglobin and where is it?
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single heme group held in a pocket formed by E and F helices
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the Fe of Mb is coordinated by what?
answer
4 nitrogens of the porphyrin one nitrogen from a histidine side chain (F8, residue 93, proximal) Molecule of O2 interacts as 6th ligand His E7 (distal histidine) hydrogen binds O2
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what are 2 structure function relationships of Mb?
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the apoprotein structure prevents the irreversible oxidation of Fe 2+ to Fe 3+ Distal histidine creates a hindered environment so that heme cannot bind to CO easily
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Where is hemoglobin found?
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RBC
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what is the chief function of hemoglobin?
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to transport oxygen from lungs to tissues
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what is the major adult type of hemoglobin?
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HbA
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what is the structure of HbA
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Has 4 polypeptide chains -2? and 2?
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what are the secondary and tertiary structure of B globin like?
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? globin's secondary and tertiary structure are almost identical to myoglobin
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What are the secondary and tertiary structure of a-globin like?
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? globin has 7 helical regions, still closely resembles myoglobin (no D helix)
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what does the quaternary structure of Hb look like?
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Can be seen as a dimer with ?? protomers 1 & 2
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What is the geometrical arrangement of the chains of Hb?
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The chains are placed in a roughly tetrahedral arrangement
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how are alpha and beta chains of Hb held together?
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? and ? are held together by strong Hydrophobic bonds (as ?1?1 and ?2?2)
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How are Hb dimers held together by and what is their movement like?
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the two dimers can move with respect to each other as they are held together only by polar bonds
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What is possible as a result of the 2 dimers of Hb being able to move with respect to eachother?
answer
This makes it possible for 2 forms of Hb
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What are the 2 forms of Hb?
answer
T form -=taut or tense; deoxy Hb; has low O2 affinity R form = relaxed; high O2 affinity; due to breaking of bonds between ?1-?2 & ?2-?1
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What is the T form of Hb?
answer
taut or tense; deoxy Hb; has low O2 affinity
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What is the R form of Hb?
answer
relaxed; high O2 affinity; due to breaking of bonds between ?1-?2 & ?2-?1
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how does the structure of myoglobin relate to its oxygen binding?
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Single polypeptide chain with one heme group --> one oxygen binding site
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what is an oxygen dissociation curve?
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A plot of degree of saturation measured at different partial pressures of Oxygen (pO2)
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What is the shape of the oxygen dissociation curve of myoglobin?
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The curve for myoglobin is a rectangular hyperbola
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What does the rectangular hyperbola shape of the Mb O2 dissociation curve mean for O2 affinity?
answer
Indicates that Mb has higher oxygen affinity
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What are the capabilities of O2 binding by Mb in the lungs and peripheral tissues?
answer
Can bind to O2 at lungs (100 mmHg) but cannot release to tissues (20-40 mmHg)
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Is myoglobin a good transport protein?
answer
no
question
when can Mb release oxygen?
answer
When there is strenuous exercise in muscle (pO2 -5mmHg) releases O2
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What is the shape of the O2 dissociation curve of Hb?
answer
Oxygen dissociation curve of Hb is sigmoidal in shape i.e Hb shows cooperative binding
question
What is the mechanism of the cooperative binding of oxygen by Hb?
answer
binding of first O2 to deoxyHb (T) shifts Heme iron --> proximal His and other attached residues move--> breaking of salt bridges between all subunits--> rotation of one protomer with respect to another --> R conformation which has high affinity for O2( fewer salt bonds to be broken)
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How does cooperative binding affect the affinity for O2 of heme?
answer
Cooperative binding of O2(Heme -Heme interactions) --> affinity of Heme for last O2 increases by 300 fold
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What is the significance of cooperative binding of O2 by Hb?
answer
Hb is virtually saturated in lungs (pO2 -100mmHg) and unloads in peripheral tissues in response to a relatively smaller changes in pO2 (20-40mmHg)
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from what do the allosteric properties of Hb result?
answer
Result from their quarternary structure
question
what are the allosteric effectors of Hb?
answer
The allosteric effectors are -pH, pCO2 and 2,3 BPG
question
How does the Bohr effect affect the O2 binding of Hb?
answer
Under physiological conditions, decrease in pH (increased H+ concentration) results in decreased affinity of Hb for O2 and leads to its release; conversely an increase in pH increases O2 affinity
question
In what direction does the O2 dissociation curve for Hb shift when pH is lowered?
answer
Oxygen dissociation curve shifts to right when pH is lowered
question
What is the important role of the Bohr effect on Hb?
answer
Has important role in transport of O2 from lungs to tissues and CO2 from tissues to lungs
question
what is the mechanism of the Bohr effect on Hb in the lungs?
answer
In lungs: O2 binding to Hb --> disrupts salt bonds --> R state
question
what is the mechanism of the Bohr effect on Hb in the tissues?
answer
In tissues -cells respire --> release CO2 ,which enters RBC CO2 + H20 ? H+ + HCO3- H+ taken up by anionic groups ( ?-NH2, R) to form ion pairs (salt bonds) --> T state
question
What is the effect of CO2 on Hb?
answer
CO2 binds reversibly to N-terminal amino groups globin chains to form carbamate (carbamino-hemoglobin) T state is stabilised --> O2 is released H+ released --> further O2 released
question
is 2,3-BPG present in high or low concentration in RBC?
answer
high
question
Where does 2,3-BPG bind Hb?
answer
in a pocket formed by the 2 ? chains in the center of Hb
question
How does 2,3-BPG bind Hb?
answer
forms ionic bonds with positively charged amino acids lining the pocket (Val A1, Lys EF6, His H21 )
question
What does 2,3-BPG do to the T-state of Hb?
answer
stabilizes it
question
what does increase in 2,3-BPG do to the O2 dissociation curve of Hb?
answer
Increase in 2,3 BPG concentration shifts the oxygen dissociation curve to right --> more O2 is released
question
When is the concentration of 2,3-BPG increased in the RBC?
answer
Chronic Hypoxia High altitudes Chronic anemia
question
What happens to 2,3-BPG if acid-citrate-dextrose is used as a preservative in transfused blood?
answer
decreased 2,3-BPG
question
what happens to seriously ill patients who receive transfused blood preserved with acid-citrate-dextrose?
answer
may trap O2 due to high affinity compromising the status of the patient
question
what has replaced acid-citrate dextrose as a preservative for transfused blood?
answer
inosine (Hypoxanthine-ribose)
question
how does inosine affect levels of 2,3-BPG?
answer
inosine (Hypoxanthine-ribose) --> HMP --> 2,3 BPG
question
With how much affinity does CO bind Hb?
answer
Binds with a very high affinity (about 200 times that of O2)
question
What does binding of CO to Hb do to its dissociation curve and ability to deliver to tissues?
answer
Binding shifts the equilibrium to R state --> O2 binds to other 3 sites with high affinity --> cannot be released to tissues
question
What are the symptoms of CO poisoning?
answer
Symptoms : headaches and flu-like effects; larger exposures --> toxicity of the CNS and heart.
question
what are the sources of CO poisoning?
answer
house fires, furnaces or heaters, motor vehicle exhaust, exposure to methylene chloride
question
what is methylene chloride metabolized to?
answer
CO
question
what is the treatment for CO poisoning?
answer
:100% oxygen or hyperbaric oxygen therapy
question
What is the structure of HbF?
answer
Fetal Hb; ?2?2
question
From when is HbF present?
answer
From about 6th week in fetal liver
question
When and by what is HbF replaced?
answer
Replaced by HbA after birth
question
What percentage of adult Hb is HbF?
answer
Constitutes about <2% in a normal adult
question
What is the difference in structure present in HbF and what does it mean for O2 binding?
answer
as residue H21 is serine instead of His --> serine cannot form salt bonds --> 2,3 BPG binds more weakly to HbF --> has a higher affinity for O2
question
What is the purpose of the high affinity for oxygen of HbF?
answer
Helps in transfer of O2 from maternal to fetal circulation
question
Is HbF suitable in postnatal life?
answer
no
question
What diseases are associated with elevated levels of HbF?
answer
as sickle cell anemia, aplastic anemia, and leukemia
question
how much of adult Hb is HbA2?
answer
Minor component of adult Hb (2-5%)
question
What is the structure of HbA2?
answer
?2?2
question
What is HbA1C?
answer
Hemoglobin A1c :glycosylated hemoglobin, glycohemoglobin, or hemoglobin A1
question
Where is glucose attached to HbA1C?
answer
Glucose attached to amino groups of Valines at N terminal ends
question
How is glucose added to HbA1C?
answer
Non enzymatic addition
question
What is the rate of formation of HbA1C proportional to?
answer
Rate of formation proportional to average blood glucose
question
what is HbA1C used for?
answer
to monitor the glycemic control over previous 8-10 weeks
question
what is the normal range of HbA1C for healthy and diabetic individuals?
answer
normal range (that found in healthy persons) is 4%-5.9%. People with diabetes mellitus often have higher levels of HbA1c
question
what type of gene families do alpha-like and beta-like genes belong to?
answer
?-like and ?-like genes belong to clustered gene families which Include Pseudogenes
question
where are alpha like genes located?
answer
?-like genes located on chromosome 16
question
what are the alpha like genes located on chromosome 16?
answer
(?, ?1, ?2)
question
what is the proportion of a1 gene expressed to a2 gene expressed?
answer
?1, ?2 are identical; expressed equally
question
where are the beta like genes located?
answer
?-like genes located on chromosome 11
question
what are the beta like genes located on chromosome 11?
answer
(?, G g, A g, ?, ?)
question
how many introns and exons do the alpha and beta globin gene families contain?
answer
three exons separated by two noncoding introns
question
What are the 3 broad groups of disorders of human Hb?
answer
Structural variants Thalassemias Hereditary persistence of fetal hemoglobin
question
What are the variables that increase sickling in SCD?
answer
high altitudes, flying in nonpressurized plane, increased pCO2, decreased pH, increased 2,3-BPG
question
what are compound heterozygotes for SCD?
answer
Inheritance of HbS from one parent and another hemoglobinopathy from the other parent Ex: S/?0, S/ ?+, S/C
question
Is HbSC a more common or less common variant of SCD?
answer
more common
question
do HbSC patients have a greater or lesser degree of hemolytic anemia?
answer
lesser degree
question
what complications are patients with HbSC at increased risk for?
answer
retinopathy and aseptic necrosis of bones
question
how do methemoglobinemias present?
answer
Present with chocolate cyanosis, anxiety, headache and dyspnoea
question
What does decreased formation of hemoglobin in thalassemia present as?
answer
Microcytic Hypochromic anemia
question
What is the effect of inclusion bodies of alpha-globins in thalassemia?
answer
inclusion bodies of ? -globins --> "kill" proerythroblasts --> ineffective erythropoeisis
question
What is the mechanism and consequence of hemolysis in thalassemias?
answer
Surviving RBCs go through the spleen --> recognized as abnormal --> hemolysis --> severe anemia --> erythropoeitin increase
question
what is the effect of the increase in erythropoietin seen in thalassemia?
answer
marrow hyperplasia and extramedullary erythropoeisis
question
What is the level of HbA2 in beta thalassemia and why?
answer
For Beta-Thalassemias -? - gene intact --> HbA2 production continues --> elevated HbA2
question
Why is there an increase in HbF in thalassemias?
answer
selective survival and increased production
question
What are the clinical features of thalassemia that result from bone marrow expansion?
answer
chipmunk facies, frontal bossing, thinning and pathological fractures of long bones and vertebrae, (widening diploic space radiating striations: 'hair-on-end' appearance)
question
What is are the clinical features of thalassemia caused by extramedullary erythropoiesis?
answer
Hepatosplenomegaly
question
What are the clinical features of thalassemias that are the result of calorie diversion to erythropoiesis?
answer
growth retardation, inanity, increased risk of infections, endocrine dysfunction and death during first decade
question
What are the basic functions of fibrous proteins?
answer
protective connective or supportive functions
question
what are some examples of fibrous proteins?
answer
collagen and elastin
question
what is the shape of a fibrous protein molecule?
answer
elongated
question
the shapes of fibrous proteins are dominated by what?
answer
a single type of secondary structure
question
what is the general structure of collagen?
answer
long, stiff, triple stranded helical structure; comprised of 3 polypeptide chains, called alpha chains, wound around one another in a rope-like right handed superhelix
question
about how many amino acids does each polypeptide chain of collagen have?
answer
~1000
question
how many distinct alpha chains of collagen have been identified? are they coded for by the same genes?
answer
about 25 distinct collagen alpha chains have been identified, each encoded by a separate gene
question
how many types of collagen molecules have been found?
answer
19
question
what is responsible for the different types of collagens?
answer
variations in amino acid sequence
question
which collagens are Fibril forming ( fibrillar )?
answer
I, II, III
question
where is type I collagen found?
answer
bone, skin, tendons, ligaments, cornea, internal organs
question
what percentage of body collagen is type I collagen?
answer
90%
question
what is the tissue distribution of type II collagen?
answer
cartilage, intervertebral disc, notochord, vitreous humor of the eye
question
what is the tissue distribution of type III collagen?
answer
skin, blood vessels, internal organs
question
what are the Fibril-associated collagen types?
answer
IX XII
question
where is type IX collagen found ?
answer
cartilage
question
where is type XII collagen found?
answer
tendons, ligaments, some other tissues
question
what are the network forming types of collagen?
answer
IV VII
question
what is the tissue distribution of type IV collagen?
answer
basal lamina
question
what is the tissue distribution of collagen type VII?
answer
beneath stratified squamous epithelia
question
do all types of collagen have a triple helical structure?
answer
yes
question
what is the amino acid sequence of the alpha chains of collagen?
answer
Gly-X-Y X is frequently proline Y is hydroxproline or hydroxylysine
question
do the alpha chains of collagen form right or left handed helices?
answer
left handed helix
question
how many amino acids per turn in each left handed alpha chain helix of collagen?
answer
3
question
why are proline and glycine important in collagen?
answer
important in the formation of the triple stranded helix
question
how does proline affect collagen helical structure?
answer
ring structure stabilizes the helical conformation in each alpha chain--confers rigidity
question
how does glycine affect the collagen helical structure?
answer
fits into center of helix because it is the smallest amino acid
question
in what fashion are collagen fibers assembled?
answer
collagen fibers are assembled by lateral association of the triple helices in a quarter staggered fashion, which is responsible for the banded appearance of collagen
question
what do collagen fibers show within and between triple helical units?
answer
cross-links
question
what are the specialized cells which synthesize collagen?
answer
fibroblasts in connective tissue osteoblasts in bone chondroblasts in embryonic cartilage odontoblasts in teeth
question
into where is collagen secreted once it is synthesized?
answer
the extracellular matrix
question
Where and as what are individual collagen polypeptide chains synthesized?
answer
synthesized on membrane bound ribosomes as a larger precursors, called prepro-alpha-chains
question
what is at the amino terminal of the nascent collagen chain and what does it do?
answer
amino terminal signal peptide directs the nascent polypeptide to the ER
question
in addition to the signal peptide at the N-terminal end of the nascent collagen chain, what else is present at both ends?
answer
additional amino acids, called propeptides at both C- and N- terminal ends
question
What are the post translational modifications of collagen and where are they made in the cell?
answer
in the lumen of the ER, selected prolines and lysines are hydroxylated to form hydroxyproline and hydroxylysine
question
what is the cofactor required for the post-translational hydroxylation of proline and lysine on collagen alpha chains?
answer
O2 and ascorbic acid
question
what causes scurvy?
answer
a deficiency of ascorbic acid which prevents post-translational modifications of collagen alpha-chains
question
How are selected hydroxylysines modified after hydroxylation?
answer
glycosylation with glucose or glucosyl galactose
question
what are the steps of assembly of collagen fibers?
answer
1. formation of disulfide bonds at C-terminal extensions of pro-alpha chains 2. each pro-alpha chain combines with 2 others to form a hydrogen bonded, triple stranded, helical molecule known as procollagen.
question
what are the steps of the secretion of collagen?
answer
1. translocation to the Golgi 2. packaged into secretory vesicles 3. movement to the membrane 4. secretion into extracellular space
question
What happens to collagen in the extracellular space just after its secretion ?
answer
1. cleavage of N- and C- propeptides by N- and C- collagen peptidases 2. Formation of collagen fibrils by regular, staggered, spontaneous association. 3. crosslinking catalyzed by lysyl oxidase
question
by how much is each collagen overlapping its neighbor in each collagen fibril?
answer
3/4 of a molecule
question
What is the cofactor required by lysyl oxidase?
answer
copper
question
what are the reactive aldehydes created by the oxidative deamination of lysine and hydroxylysine by lysyl oxidase?
answer
allylysine and hydroxyallysine
question
what do hydroxyallysine and allyllysine do between collagen molecules
answer
condense with similar residues on neighboring chains forming covalent cross-links
question
How is collagen degraded?
answer
matrix metalloproteinases-- collagenases
question
what is the specific site where type I collagen cleavage occurs?
answer
3/4 and 1/4 length fragments
question
what are the collagen disorders?
answer
osteogenesis imperfecta Ehlers Danlos syndrome
question
What are the clinical features of osteogenesis imperfecta?
answer
brittle bones, blue sclera, hearing loss, dental deformity
question
How is ehlers danlos syndrome characterized?
answer
hyperextensible skin, hyper mobile joints, ocular fragility
question
what are the mutations involved in ehlers danlos syndrome?
answer
mutations in gene involved in metabolism of fibrillar collagen or mutations in amino acid sequences of collagens I, III, IV
question
what is the most clinically important mutation seen in ehlers danlos?
answer
mutations in gene for type III collagen- lethal vascular problems
question
what is elastin?
answer
connective tissue protein with elastic properties
question
what does elastin do?
answer
gives resilience so that tissue can recoil after transient stretch
question
where is elastin found?
answer
lungs, walls of large arteries, elastic ligaments
question
what are the chemical features of elastin?
answer
1. highly hydrophobic 2. ~750 aa long 3. unusually rich in proline and glycine 4. not glycosylated 5. contains some hydroxyproline but no hydroxylysine
question
what is the biosynthetic precursor of elastin?
answer
tropoelastin
question
into where is tropoelastin secreted?
answer
extracellular space
question
what happens to tropoelastin after it is secreted into the extracellular space?
answer
assembled onto cell surface infoldings through interactions with specific microfibril glycoproteins like fibrillin
question
how do tropoelastin fibers interact with one another after they are secreted?
answer
they becom highly cross-linked to one another, generating an extensive network of elastin fibers and sheets
question
in between which residues are elastin cross-links formed?
answer
lysines
question
what catalyzes cross linking between lysines in elastin?
answer
lysyl oxidase
question
what is a desmosine link?
answer
3 allylysine residues with one unaltered lysine
question
what is the inheritance of marfan syndrome?
answer
autosomal dominant
question
what is the mutation that causes marfan syndrome?
answer
mutation in fibrillin-1 protein
question
what is the consequence of the mutation that causes marfan syndrome?
answer
abnormal fibrillin-1 monomers from the mutated gene disrupt the multimerization of fibrillin-1 and prevent microfibril formation
question
what features characterize marfan syndrome?
answer
tall stature ectopia lentis mitral valve prolapse aortic root dilation aortic dissection
question
what is AAT?
answer
a plasma protein that inhibits a number of proteolytic enzymes, the most important of which is neutrophil elastase in alveoli and other tissues
question
where is the majority of AAT synthesized?
answer
in liver remainder by monocytes, macrophages, and other tissues
question
what happens in lungs that is opposed by AAT?
answer
alveoli are constantly exposed to low levels of neutrophil elastase from activated and degenerating neutrophils
question
why is the action of AAT in the lungs important?
answer
lung tissue cannot regenerate
question
what is the prevalence of AAT deficiency in caucasians?
answer
1/2000-1/8000
question
what is the most common mutation in AAT deficiency?
answer
GAG-->AAG Glu-->lys
question
what is the pathophysiology of AAT deficiency in the liver?
answer
mutated protein polymerizes in ER of liver cells, causing decreased secretion by liver, which leads to cirrhosis of the liver
question
what are homozygotes for AAT deficiency at risk of developing?
answer
pulmonary emphysema
question
what is the effect of smoking in AAT deficiency?
answer
oxidants inactivate a specific methionine at active site of AAT leads to accelerated destruction of lung elastic tissue why smokers have a poorer survival rate
question
what is the treatment for AAT deficiency?
answer
weekly AAT infusions
question
What are enzymes?
answer
protein biocatalysts
question
what are some RNA that have enzymatic activity?
answer
ribozymes
question
what is an example of a ribozyme?
answer
peptidyl transferase activity of 23S rRNA found in 50 S ribosomal subunit
question
what is a common function of ribozymes?
answer
participate in breaking and synthesis of phosphodiester bonds
question
under what conditions do enzymes accelerate chemical reactions>?
answer
physiological conditions 37C and neutral pH
question
what is the function of an what is an example of an oxidoreductase?
answer
oxidation/reduction Lactate dehydrogenase
question
what is the function of and what is an example of a transferase?
answer
group transfer of C-, N-, P- kinases, transaminase
question
what is the function of and what is an example of a hydrolase?
answer
cleavage of bonds by addition of water molecule protease
question
what is the function of and what is an example of a lyase?
answer
cleavage of certain bonds like C-C, C-S, C-N pyruvate decarboxylase
question
what is the function of and what is an example of an isomerase?
answer
intramolecular rearrangement racemases, mutases
question
what is the function of and what is an example of a ligase?
answer
ligation requiring ATP synthetases
question
What is a holoenzyme?
answer
apoenzyme + cofactor
question
what is an apoenzyme?
answer
the protein part of the enzyme
question
what is a cofactor?
answer
nonprotein molecule that is required for the activity of the apoenzyme i.e. Zn++, Fe++, Cu++
question
what is a coenzyme?
answer
when the additional molecule required by an apoenzyme is an organic molecule
question
what are co substrates?
answer
coenzymes that are associated with the enzyme temporarily ex: NAD+, CoA
question
what is a prosthetic group?
answer
if coenzyme is permanently associated with the enzyme ex: heme in cytochromes
question
from what are coenzymes frequently derived?
answer
vitamins
question
what is the required cofactor for carbonic anhydrase?
answer
Zn++
question
what is the required cofactor for carboxypeptidase?
answer
Zn++
question
what is the cofactor for hexokinase?
answer
Mg++
question
what is the cofactor for urease?
answer
Ni++
question
what is the cofactor for nitrate reductase?
answer
Mo
question
what is the cofactor for glutathione peroxidase?
answer
Se
question
what is the cofactor for superoxide dismutase?
answer
Mn++
question
what is the cofactor for propionyl CoA carboxylase?
answer
K+
question
what determines the specificity of the enzyme?
answer
arrangement of amino acid side chains at substrate binding site
question
what is an example of a highly specific enzyme?
answer
glucokinase
question
what is an example of an enzyme with broader specificity
answer
hexokinase
question
what occurs at the active site of an enzyme?
answer
catalysis
question
where are the residues that directly participate in the making and breaking of bonds in an enzyme contained?
answer
the active site
question
what is the active site of an enzyme?
answer
3-D cleft formed by the groups that come from different parts of the amino acid sequence
question
is the active site necessarily a part of the substrate binding site?
answer
the active site MAY BE a part of the substrate binding site
question
what is meant by "induced fit" with respect to enzyme substrate binding?
answer
active sites of enzymes assume a shape that is complementary to that of the transition state after the substrate is bound
question
what is the turnover number of an enzyme?
answer
the number of substrate molecules converted into product by an enzyme molecule in a unit time (second) when the enzyme is fully saturated with substrate
question
what is another term for turnover number of an enzyme
answer
kcat
question
by how much can an enzyme accelerate a reaction?
answer
by factors of >10^6
question
what must be overcome before reactants can be converted to products?
answer
energy of activation
question
can an enzyme cross the activation energy barrier by increasing the kinetic energy in a reaction?
answer
no, physiological temperature is tightly controlled
question
what is the reaction coordinate in an energy diagram for enzymatic reaction?
answer
the pathway in terms of bond stretching between the reactants and products
question
where on an energy diagram of an enzymatic reaction is the transition state depicted?
answer
apex of the energy barrier represents the reactants in their activated state, the activated complex, also known as the transition state
question
what does breakdown of the transition state of an enzymatic reaction form?
answer
can form the products or the reactants
question
is the transition state an intermediate in an enzymatic reaction?
answer
it is not an intermediate and cannot be isolated
question
is the energy of the reactants and products of an enzyme catalyzed reaction different than that of the uncatalyzed reaction?
answer
no
question
is the Free Energy Change of an enzyme catalyzed reaction different than that of the uncatalyzed reaction?
answer
no
question
do enzymes change the thermodynamics of reaction or the equilibrium point?
answer
no
question
what is the only thing an enzyme changes about the reaction it catalyzes?
answer
the pathway to reach the final state, allowing the energy barrier to be overcome in stages
question
what do enzymes do to the speed with which equilibrium is attained?
answer
increase it
question
what does the rate of reaction depend on?
answer
the no. of substrate molecules that have sufficient energy to cross the energy barrier
question
what do enzymes do to the energy barrier and what is the consequence of this?
answer
enzymes lower the energy barrier as a result, there is an increase in the no. of molecules that have sufficient energy to form products
question
what are 3 major mechanisms enzymes use to decrease the activation energy?
answer
acid-base catalysis substrate strain covalent catalysis
question
what happens in acid base catalysis?
answer
amino acid residues provide or accept protons
question
what are the amino acids that play a major role in acid base catalysis?
answer
histidine, tyrosine, cysteine, and lysine
question
what is substrate strain?
answer
when binding of a substrate to enzyme strains the bonds, which increases the energy level of the substrates
question
What is covalent catalysis?
answer
when a nucleophilic or electrophilic group in the active site forms a transient covalent ES complex
question
what commonly forms the covalent bonds in covalent catalysis?
answer
the coenzyme
question
what doe the mechanisms of enzymatic catalysis lead to?
answer
promotion of the substrate to enter transition state proximity effect ground state destabilization
question
what is the consequence of enzymatic promotion of the substrate to enter the transition state?
answer
transition state stabilization
question
what is the proximity effect in terms of enzymatic catalysis?
answer
the substrate being bound to the enzyme causes the proper orientation of the catalytic groups, which increases the rate of product formation
question
what is the precipitating factor leading ground state destabilization in enzymatic catalysis
answer
increasing the energy of the substrate
question
what is kinetics?
answer
a study of the rate of change of reactants to products
question
what is the rate or velocity of a reaction?
answer
number of substrate molecules converted to product per unit time micromoles of product formed per minute
question
what affects velocity in reaction kinetics?
answer
temperature pH substrate concentration
question
what is the shape of the curve when reaction velocity is plotted against temperature?
answer
bell shaped
question
what is the optimum temperature for mammalian enzymes?
answer
between 35-40C
question
what happens to enzymes at >40C?
answer
heat denaturation of enzymes
question
what happens to enzymes between 0-40C?
answer
increasing activity with an increasing temperature
question
what is the Q10 or temperature coefficient with respect to kinetics of enzyme catalysis?
answer
for every 10C increase in temperature, there is a 2fold increase in enzyme activity
question
what is the shape of pH velocity profile?
answer
bell shaped
question
what is the pH optimum in kinetics of enzymatic catalysis?
answer
the pH at which the enzyme has maximal activity
question
is the pH optimum the same between all enzymes?
answer
no, it is different for different enzymes
question
what is the pH value of the pH optimum for for most intracellular enzymes?
answer
between 5 and 9
question
in terms of the effect of pH on reaction kinetics, in what state must amino acids be at the active site for reaction to proceed?
answer
appropriate ionic state
question
in terms of the effects of pH on enzyme kinetics, binding and recognition of substrate also involves what?
answer
formation of salt bridges with the enzyme
question
what happens to an enzyme at high or low pH?
answer
denaturation
question
what is the shape of the curve plotting substrate concentration vs. enzyme activity
answer
rate of catalysis increases linearly as substrate concentration increases and then begins to level off and approach a maximum at higher substrate concentrations
question
what does the leveling off of the substrate concentration vs. enzyme activity curve indicate?
answer
all binding sites of the enzyme are occupied
question
when the initial velocity of a reaction (V0) is plotted against the substrate concentration (S) most enzymes show what?
answer
a hyperbolic curve Michelis-Menten kinetics
question
what type of curve do allosteric enzymes show when the initial velocity is plotted against the substrate concentration?
answer
sigmoidal curve
question
in the Michelis-Menten reaction model, an enzyme E combines with a substrate S to form what with a rate constant of what?
answer
ES with a rate constant of k1
question
what are the 2 possible fates of the ES complex in the Michelis-Menten reaction model?
answer
1. dissociate and form E and S with rate constant k-1 2. proceed to form product P with rate constant k2
question
since the Michelis-Menten reaction model assumes that none of the product is converted back into substrate, are holds in the initial state of a reaction before the concentration of product appreciable?
answer
yes
question
what are the assumptions made to derive the Michelis-Menten equation?
answer
ES complex is in a steady state Under saturating conditions all the enzyme is converted into ES complex If all enzyme is in the ES complex then rate of formation of product is maximal and the back reaction from P to S is negligible
question
What is Km?
answer
is the substrate concentration at which the reaction velocity is half the maximal velocity
question
what are the units of Km?
answer
units are of substrate concentration
question
is Km variable for a particular enzyme and substrate?/
answer
Km is a constant and is characteristic of an enzyme and its particular substrate
question
in general, what are Km values close to?
answer
substrate concentration found in cells
question
what is Km value used for?
answer
as a measure of the affinity of the enzyme for its substrate
question
what does small Km mean?
answer
high affinity
question
what does large Km mean?
answer
low affinity
question
does hexokinase have a higher or lower affinity for its substrate than glucokinase?
answer
hexokinase has higher affinity
question
is velocity directly or inversely proportional to enzyme concentration?
answer
directly proportional
question
when S is much less than Km, what is V0 proportional to and what is the order of reaction?
answer
V0 is proportional to S concentration, first-order reaction
question
when S is much greater than Km, what is velocity a function of and what is the order of the reaction?
answer
velocity is constant and equal to Vmax zero order reaction
question
what type of plot is a Lineweaver-Burk plot?
answer
double reciprocal plot
question
is it easy to determine Vmax on an M-M plot?
answer
no
question
what is the shape of the curve when 1/V0 is plotted against 1/S?
answer
straight line
question
what are the advantages of a Lineweaver-Burk plot?
answer
can calculate Km and Vmax can determine the action of enzyme inhibitors
question
what does the origin of a Lineweaver-Burk plot represent?
answer
infinite substrate concentration and therefore maximum velocity
question
What is an enzyme inhibitor?
answer
any substance that decreases the velocity of an enzyme catalyzed reaction
question
what is most current drug therapy based on?
answer
inhibition of enzymes
question
what is irreversible inhibition?
answer
inhibitor forms covalent bonds with the enzymes
question
what are some examples of irreversible inhibitors?
answer
Sarin-->AChE Penicillin
question
what type of interactions are associated with reversible inhibition?
answer
noncovalent interactions
question
what are the three types of reversible inhibition?
answer
competitive noncompetitive uncompetitive
question
in terms of competitive inhibition, what is substrate analogue?
answer
inhibitor is structurally similar to the substrate
question
where does a substrate analogue bind the enzyme is competitively inhibits?
answer
substrate binding site
question
how can the effect of a substrate analogue be overcome?
answer
increasing the concentration of the substrate
question
can both the substrate and substrate analogue bind the enzyme?
answer
no
question
what are examples of competitive inhibition by substrate analogue?
answer
inhibition of succinate dehydrogenase by malonate statins for HMG CoA reductase
question
what can inhibit succinate dehydrogenase?
answer
malonate
question
what is the effect on Km of competitive inhibition by substrate analogue?
answer
increase in apparent Km
question
what is noncompetitive inhibition?
answer
inhibitor binds at a site different from substrate
question
In noncompetitive inhibition does the binding of I to I have an effect on the binding of S?
answer
no
question
is noncompetitive inhibition reversible by increasing the concentration of substrate?
answer
no
question
how does noncompetitive inhibition act?
answer
as though it is removing the active enzyme from solution
question
what is the effect of noncompetitive inhibition on Km and Vmax?
answer
Km is same Vmax shows an apparent decrease
question
what are some examples of noncompetitive inhibition?
answer
ferrochelatase by lead organophosphorus compounds on AChE
question
What is uncompetitive inhibition?
answer
when inhibitor binds only to ES complex
question
what happens to Km and Vmax in uncompetitive inhibition?
answer
both vmax and km decrease
question
what is the relationship of the line affected by uncompetitive inhibition to to the unaffected line?
answer
parallel
question
why is regulation of enzyme activities essenntial?
answer
to coordinate the cellular metabolic activities
question
do most enzymes operate near to or far from equilibrium conditions?
answer
near equilibrium conditions
question
is the substrate concentration usually near to or far from Km?
answer
close to Km
question
how close the operation of an enzyme is to equilibrium and a substrate is to Km is regulated by what?
answer
availability of substrate
question
what is a specialized regulatory function of an enzyme?
answer
when it catalyzes a rate limiting reaction
question
how are enzymes that catalyze rate limiting reactions regulated?
answer
control of enzyme activity control of enzyme availability
question
what are two ways of controlling enzyme activity?
answer
allosteric regulation covalent modification
question
what is allosteric regulation?
answer
when effectors or modulators bind to a regulatory site and regulate enzyme activity
question
are most allosteric enzymes oligomeric or monomeric?
answer
oligomeric
question
what is the effect of binding of an effector to an allosteric enzyme?
answer
binding causes a conformational change in the protein which changes the affinity for the substrate or other ligands
question
what do positive allosteric effectors do?
answer
increase the affinity of the enzyme for the substrate
question
what do negative allosteric effectors do?
answer
decrease the affinity of the enzyme for subtrate
question
where does a positive allosteric effector bind?
answer
activator site
question
where does a negative allosteric effector bind?
answer
inhibitory site
question
what is a homotropic effector?
answer
when the substrate is the effector
question
how does a homotropic effector typically act?
answer
as a positive effector
question
what kind of kinetics do homotropic effectors display?
answer
sigmoidal kinetics
question
what are heterotropic effectors?
answer
ligands others than the substrate
question
heterotropic effectors, as opposed to the typical function of homotropic effectors, may act by what?
answer
feedback inhibition
question
what is a typical example of feedback inhibition by a heterotropic effector?
answer
inhibition of an early enzyme in a multistep pathway by the product of the pathway
question
can heterotropism be positive or negative?
answer
yes
question
what are examples of allosteric regulation?/
answer
PFK1 by citrate ATC by ATP(+) and CTP(-)
question
what are the allosteric regulators of aspartate transcarbamoylase?
answer
ATP (+) CTP (-)
question
what is covalent modification of an enzyme?
answer
addition or removal of phosphate groups from specific Ser, Thr, Tyr residues of an enzyme
question
what performs the reversible phosphorylation/dephosphorylation of enzymes?
answer
protein kinases and phosphatases
question
what does phosphorylation/ dephosphorylation by protein kinase/ phosphatase do to an enzyme?
answer
may enhance or inhibit the activity of enzymes
question
is glycogen phosphorylase active in phosphorylated or dephosphorylated form?
answer
phosphorylated
question
is glycogen synthase active in its phosphorylated or dephosphorlyated form?
answer
dephosphorlyated
question
how is control of enzyme availability accomplished?
answer
by changing the rate of synthesis of the enzyme- induction or repression of the corresponding genes
question
how fast is induction/repression of an enzyme to control its availability?
answer
slow process takes hours to days
question
what is an example of control of enzyme availability?
answer
dietary cholesterol decreases the hepatic synthesis of more cholesterol
question
how does dietary cholesterol decrease the hepatic synthesis of more cholesterol?
answer
cholesterol or its metabolite inhibits the expression of the gene coding for HMGCR
question
does cholesterol lead to feedback inhibition of HMGCR?
answer
no
question
what are the 2 broad classes of plasma enzymes relevant to clinical diagnosis?
answer
those secreted by cells which have a functional role in plasma enzymes released into plasma due to cell turnover which have no functional role in plasma
question
what are some examples of plasma enzymes which belong in plasma and have a functional role there?
answer
blood clotting factors lipoprotein lipase
question
what is an increase in concentration of those enzymes released into the plasma by cell turnover indicative of?
answer
tissue damage
question
what is the ideal situation for use of enzymes in clinical diagnosis?
answer
if unique enzyme for each organ can be identified this occurs only rarely
question
what is an example of an enzyme being unique to an organ and being useful in clinical diagnosis?
answer
acid phosphatase for metastatic prostate carcinoma
question
what may vary for enzymes that are not organ or tissue specific that could make them useful for clinical diagnosis?
answer
concentration in tissues
question
what factors of enzyme concentration are necessary for establishing a specific diagnosis?
answer
enzyme concentration in tissues timing of appearance and disappearance from the plasma of enzymes
question
increased ALT is useful in the diagnosis of what specific conditions?
answer
drug induced or viral hepatitis
question
elevated ALP is useful in the diagnosis of which specific conditions?
answer
cholestatic hepatitis or bone disease
question
what enzymes are elevated in pancreatitis?
answer
amylase and lipase
question
what enzymes are elevated in myocardial infarction?
answer
CK LDH
question
what are isoenzymes/isozymes?
answer
enzymes that catalyze the same reaction but migrate differently on electrophoresis
question
are the physical properties of isozymes the same?
answer
physical properties may be different
question
what are examples of iozymes that are genetic variants of each other?
answer
salivary and pancreatic isoamylase
question
how can salivary and pancreatic isoamylase be separated?
answer
by electrophoresis or ion exchange chromatography
question
what are examples of isoenzymes that are due to different subunits associating in different combinations in various tissues?
answer
CK LDH
question
between subunit rearrangement and genetic variation, which is the more common cause of isozymes?
answer
subunit rearragement
question
what are the subunits of CK1?
answer
BB
question
what are the subunits of CK2?
answer
MB
question
what are the subunits of CK3?
answer
MM
question
where is CK1 found?
answer
Brain
question
where is CK2 found?
answer
myocardium
question
where is CK3 found?
answer
skeletal muscle
question
which CK increases in myocardial infarction?
answer
CK2
question
what is the timeline for the rise and fall of CK2 levels in myocardial infarction
answer
increases within 4-8 hours reaches a peak at 24 hours returns to normal in 2-3 days
question
which is more common LDH2 or LDH1?
answer
LDH2>LDH1
question
what is the proportion of LDH1 to LDH2 in myocardial infarction?
answer
LDH1>LDH2
question
what are the subunits of LDH1?
answer
HHHH
question
what are the subunits of LDH2?
answer
HHHM
question
what are the subunits of LDH3?
answer
HHMM
question
what are the subunits of LDH4?
answer
HMMM
question
what are the subunits of LDH5?
answer
MMMM
question
where is LDH1 found?
answer
heart and RBC
question
where is LDH2 found?
answer
heart and RBC
question
where is LDH3 found?
answer
brain and kidney
question
where is LDH5 found?
answer
liver and Sk. muscle
question
what is the is timeline for the reversal of the LDH1:LDH2 ratio in myocardial infarction?
answer
peaks around 3 days and remains elevated up to 10 days
question
when is LDH5 elevated?
answer
acute hepatitis
question
What are the latest markers of MI?
answer
troponins T and I
question
what are troponins T and I?
answer
regulatory proteins involved in myocardial contractility
question
what is the most specific marker for MI?
answer
cTnI (cardiac troponin I)
question
what is the timeline for the elevation of cTnI in MI?
answer
elevated in 4-6 hours peak in 8-24 hours remains elevated for 3-10 days
question
what are the prognostic indicators in cTnI levels?
answer
prolonged and higher elevations are considered to indicate poorer prognosis, especially for unstable angina
