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134 Cards in this Set
- Front
- Back
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Objectives
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Describe structure of AA & proteins
Name different bonds involved in stabilizing protein molecule List functions of AA and proteins Name the causes of presented disorders |
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Chapters in Lippincott
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1-4, 14
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What proteins do free ribosomes make?
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Made in the cytoplasm of the cell
Cytoplasmic Mitochondrial perosixomal nuclear |
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What proteins do fixed ribosomes make?
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Proteins made on RER is further processed in Golgi
membrane secreted lysosomal |
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Specify the general structure of AA's
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Alpha carbon
Carboxyl group Amino group Hydrogen Carbon side chain |
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What structural property(s) do AA's have?
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Chiral (4 different groups attached to alpha carbon)
(mirror images, enantiomers, stereoisomers) -Always L form |
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Are AA's acidic or basic?
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Acidic
Have multiple pKa's Ionization varies with pH |
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What are the acid-base properties of AA's?
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Common main structure
Acid base characteristics Henderson-Hasselbalch equation applies side groups carry charges depending on surrounding pH - divided based on polarity and charge of side chain - 9 essential AA's - Mammalian aa's are L-form |
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What form to AA's take in the human body?
L D |
L
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What are the properties of AA side chains?
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Alipathic
Non-polar side chains Hydrophobic interactions Located inside a water soluble protein Surface for integral proteins Internal for hydrophilic/soluble proteins |
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Where do polar AA's cluster
Surface Internal |
Surface of soluble proteins
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Where do nonpolar AA's cluster?
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Surface of membrane proteins
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Name three AA's that use hydrogen bonds
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serine
Threonine Tyrosine |
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Name one AA that uses disulfide bonds
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Cysteine
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Asparagine and Glutamine use what type of bond to attach to oligosaccharides?
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sulfur-sulfur covalent bond
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Non-essential AA's are synthesized by the body
True Fales |
True
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Essential AA's are NOT synthesized by the body
True False |
True
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Name AA's that cannot be converted into fuel
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Ketogenic AA's
Convert to CoA, cannot be turned into glucose |
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What are AA's turned into
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Pyruvate, acetyl CoA, Citric cycle intermediates
Convert to other molecules as well: Nucleic acid building blocks Histidine->histamine Tyrosine->thyroxine, melanin, dopamine, epinephrine Tryptophan->serotonin and molatonin, contributes to nicotinamide ring NAD+ Polypeptide chains |
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5 summary properties of AA's
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Acid-Base properties
Essential and non-essential Act as fuel Convert to other molecules Combine to form proteins |
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Condensation produces water
True False |
True
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Hydration produces water
True False |
False
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Primary structure of protein is carboxyl group plus amine
True False |
True
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A peptide is a polar molecule
True False |
True
Somewhat, because of the electronegativity of nitrogen |
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Name 4 protein configurations
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1 - AA polypeptide chain
2 - Alpha helix, fibrous 3 - Globular (tertiary) 4 - Quaternary, 2 or more subunits together |
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Condensation reaction = dehydration reaction
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True (when water is lost)
Condensation reaction can also lose methanol or HCl These are the opposite of hydrolysis reaction, where water is absorbed and produces two parts |
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The vast majority of peptide groups in proteins are in Cis configuration
True False |
False
Vast majority are in the trans configuration |
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Name two fibrous proteins
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Elastin
Collagen |
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Which AA is present most often in collagen?
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Glycine
(Glycine-X-Y) Proline is often "X" and causes the "turns" in the molecule "Y" is frequently hydroxyproline, hydrolysine (a basic aa) Hydroxylization requires vitamin C Collagen is a triple stranded helix with hydrogen bond stabilization |
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Is elastin soluble?
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No
Polymer is from tropoelastin (700 aa's) Made primarily of small, non-polar aa's like glycine, alanine, valine. Proline (non-polar) and lysine (basic) also frequent Elastin monomers are crosslined Desmosine is the cross linker |
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Detail the structure of collagen
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Multiple repeats of Glycine-X-Y
X often proline Y often 4-hydroxyproline - 3 left handed helicies wrapped around each other in a right-handed supercoil - Glycine residues are located along central axis of a triple helix Stabilized by covalent crosslinks between lysine residues |
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Name 3 collagen associated diseases
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Scurvy
Osteogenisis imperfecta Ehlers Danlos syndrome |
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How long is the elastin molecule (in aa's)
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700 aa's
Made from tropoelastin Crosslinking between side chains (lysyl-) in tropoelastin peptides gives a network producing elasticity |
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Globular proteins tertiary structure is maintained by:
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Hydrogen bonds (including side chains)
Salt bridges (ions) Disulfide linkage (cysteine) Hydrophobic interactions (secondary), think of water soluble proteins with non-polar cores, like myoglobin |
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Protein quartenary structures are maintained by
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- multiple subunits where each is a separate polypeptide chain
- subunits may be of the same or different polypeptide - interactions are non-covalent |
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What is the characteristic of the alpha carbon
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- Adjacent to the carboxyl group
- determines whether the aa is L or D |
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How many AA's are found in mammalian cells?
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20
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What is the smallest AA
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Glycine
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What are the amino group and the hydroxyl group charges at physiological pH?
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NH3+
COO- |
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What is this type of molecule (amino acid at physiological pH) called?
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zwitterion
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Name the 9 essential amino acids
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histidine
isoleucine leucine lysine methionine valine phenylalanine threonine tryptophan |
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How are amino acids acquired?
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Made from body
Through diet Made from other AA's |
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Name the different kinds of aa's and two examples from each group
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Non-polar - glycine, proline, tryptophan
Uncharged polar - serine (form hydrogen bonds), cysteine -SH group, forms S-S crosslinks; Asparagine, glutamine - bind oligosaccharides. Only Threonine is an essential aa Tyrosine is a precursor for thyroxine, melanin, dopamine, epinephrine -Acidic side chains... aspartic acid, glutamic acid (non essential) remember glutamic acid substitution for SS anemia - Basic side chains: Histidine, essential, Lysine, essential - important in collagen, Arginine (non-essential) |
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Name characteristics associate with each type of side chain:
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Non-polar -- Hydrophobic
Polar -- hydrogen bonds, participation in active sites; Acidic -- protein donors Basic -- protein acceptors |
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Why does H:H equation apply to aa's?
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Due to acid-base properties and side chains. Differ depending on surrounding pH and the pKa for each group
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What are the different roles aa's can have?
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Fuel
Conversion to other molecules building blocks of proteins |
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Which amino acid differs from the others and causes kinks in the pp chain?
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Proline
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Which aa can form disulfide bonds?
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Cysteine
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Explain the division of amino acids into ketogenic and glucogenic amino acids?
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Division depends on where in the metabolic pathway the respective amino acids can enter and be utilized as fuel to produce cell energy glucogenic-many can be converted to glucose or puryvate or to an intermediate of the TCA cycle. Ketogenic-these enter at Acetyl-CoA either directly or through a ketone intermediate
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What causes the problems associated with sickle cell disease?
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one aa substitution glu→val in the beta hemoglobin subunit
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What causes the problems associated with alpha thalassemia?
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A variety of mutations in the genes encoding alpha hemoglobin.Severity depends on how many alpha genes that are affected
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What causes the problems associated with cystic fibrosis?
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Mutation of the CF gene. Many have been described BUT 70% of cases share the same mutation at position 508 deleting one aa and leading to complete absence of the ion transporter the gene encodes for.
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Why is anemia associated with thalassemia?
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The RBC are defective and phagocytosed faster than new cells can be produced.
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What is the theory behind the fact that sickle cell disease more commonly affects individuals of African descent?
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Because cells with sickle hemoglobin are phagocytosed faster, the RBC life span is not long enough for the Malaria parasite Plasmodium falciparium to complete the human part of its reproduction cycle so it is protective against Malaria to carry sickle cell trait.
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Name 4 characteristics of collagen
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a) triple stranded helix b)held together by hydrogen bonds, c) hydroxyproline, hydroxylysine, proline and glycine common aa, d) despite common basic structure many different forms and functions in the body-can be divided into fibril forming, network forming, fibril associated
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Name 4 characteristics of elastin:
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a) 700 aa long polypeptide-tropoelastin, b) proline, lysine rich, c) desmosine bonds d) cross links between side chains gives connective tissue its elasticity
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Why is scurvy associated with collagen malformation?
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Vitamin C is necessary for hydroxylation of proline and lysine
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Name other diseases associated with collagen.
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Brittle bone disease, Ehler-Danlos
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Name the 3 groups of collagen types:
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fibril forming, network forming, fibril associated
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Name the different levels of protein structure and how each layer is held together/stabilized
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1-peptide bonds, 2-hydrogen bonds, 3- hydrogen, disulfide, hydrophobic interactions, ionic bonds 4 as 3. Van der Waals are always present, too.
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How do the hemoglobin ratios in healthy individuals differ from ratios in individuals with homozygous hemoglobin S, hemoglobin SC and sickle trait?
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Normal: 97% hemoglobin A, 1% hemoglobin F (fetal), 2% hemoglobin A2
Trait: 49% hemoglobin A, 48% hemoglobin S 1% hemoglobin F (fetal), 2% hemoglobin A2 Hemoglobin S: 97% hemoglobin S, 1% hemoglobin F (fetal), 2% hemoglobin A2 Hemoglobin SC: 50% hemoglobin S, 49% hemoglobin C 1% hemoglobin F (fetal) |
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Why can different proteins be separated by electrophoresis?
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(Exemplify by looking at the sickle cell diagnostic slide) size and charge
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What is a desmosine bond?
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Crosslink for elastin
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What is the composition of hemoglobin
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A-alpha-beta, A2 alpha gamma, F alpha delta
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Name the essential aa's
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Phenylalanine
valine threonine tryptophan isoleucine methionine histidine arganine lysine leucine PVT TM HALL |
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Name non-polar aa's
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Glycine
Alanine Valine Leucine Isoleucine Phenylalanine Trytophan Methionine Proline GAVe LIP To My Prof |
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Name uncharged polar aa's
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Serine
Aspargine Threonine Tyrosine Cysteine SAT Thru Class |
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Which aa's have acidic side chains?
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Aspartic Acid (aspartate)
Glutamic Acid (glutamate) |
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Which aa's have basic side chains
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Histidine
Arginine Lysine HAL |
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What bonds/interactions are used to secure tertiary and quaternary folds?
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Hydrogen
Disulfide Hydrophobic interactions |
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2. Groups that dissociate in H2O have different pKa (pKa= - logKa where Ka is the acidity constant). When pH=pKa of a group that group will be
a) 100% dissociated b) neutral c) 50% dissociated d) undissociated |
50% dissociated
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3. Which of the following are true for water
a) non-polar b) hydrogen bonds capacity c) acid properties d) base properties |
B, C, D
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4. Osmosis describes the diffusion of which of the following:
a) aminoacids b) glucose c) ions d) water |
D
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5. The blood osmolality is 170 mOsm/L. This is
a) hypotonic b) hypertonic c) isotonic d) exotonic |
Hypotonic
Normal range in serum: 285-300 mOsm/L, Normal range in urine: 800-1300 mOsm/LHuman blood cells are isotonic in relation to 0.9% NaCl (308 mOsm/l). A lower plasma osmolality would mean lower concentration in the plasma relative to the cell. Water would move into the cell. |
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6. What happens to a cell in a hypertonic solution.
a) Water moves out of the cell b) Water moves into the cell c) the cell will swell d) the cell will shrink |
A & D
There is a higher concentration of salt/ions outside of the cell. Water will move out of the cell in an effort to even/balance out the osmotic pressure and the concentration difference If water was to move the opposite way i.e. into the cell, that would dilute the cell conc. even further and increase the outside inside concentration difference. |
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7. Which of the following have peptide bonds
a) carbohydrates b) lipids c) proteins d) amino acids |
D
Comment: amino acids form peptide bonds, carbohydrates are held together by glycosidic bonds between sugars, lipid have C-H bonds and fatty acids are attached to glycerol through ester linkages |
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8. A tracer would be used to
a) Diagnose vitamin B deficiency b) look for a mutation causing disease c) studying a pharmaceutical agent in vivo d) catalyze a non-competitive reaction |
C
See Gen Chem lecture |
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9. A patient has an accelerated muscle wasting condition because this amino acid was limited from the diet?
a) serine b) glycine c) cysteine d) tryptophan |
D
Serine polar, not essential, glycine, smallest aa, non-polar, non essential, cysteine- polar, forms sulfhydryl bonds between –SH groups. Tryptophan non-polar, essential. Especially important because: tryptophan is converted to serotonin and melatonin and contributes to the nicotinamide ring (NAD+). The effect that tryptophan has on both mood and sleep (for exaple after eating turkey on Thanksgiving) may be because the body naturally converts tryptophan into both serotonin and melatonin |
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10. The primary defect of sickle cell anemia relates to
a) Valine to glycine mutation in hemoglobin subunit A b) Amino acid substitution in hemoglobin subunit B c) Folic acid deficiency causing poor assembly of functional hemoglobin d) Hypoxia as a result of a CFTR deletion in the gamma gene |
B
The amino substitution is glutamic acid to valine in the beta hemoglobin unit |
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11. Isozymes
a) differ in structure but have the same enzymatic function in different tissues b) are identical in structure but the enzymatic function differs between tissues c) are identical in structure and enzymatic function but have different substrate specificity d) cannot be used to localize disease e) none of the above |
A
Review the use of isozymes in disease |
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12. An allosteric modulator influences enzyme activity by
a) competing with the substrate for the substrate-binding site b) binding to a site on the enzyme molecule distinct from the substrate-binding site c) altering the configuration of the substrate d) changing the ideal operative pH of the enzyme e) covalently modifying the structure and function of the enzyme |
B
Comment: Alleosteric modulator can function either as positive (upregulators/activators) or negative (down regulators/inhibitors). |
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13. Inhibitor-drugs may
a) target enzymes localized in certain tissues b) target enzymes specialized for bacteria or viruses c) competitively bind to an enzyme d) irreversibly bind to an enzyme e) all of the above |
E
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14. Pellagra can manifest as
a) impaired eye vision b) poor collagen crosslinking c) dementia d) Anemia |
C
Comment: the 3 Ds- Dermatitis, Diarrhea, Dementia. This is a deficiency of niacin. High doses of niacin will cause ”niacin flush” : indigestion or heartburn, headaches, and flushing (which is not in your book or the powerpoint). Niacin is important because the active form is NAD+, an important electron carrier (tryptophan is important in the formation of NAD+). We discussed the use of niacin in treatment of certain kinds of hyperlipidemia and will get back to this when we discuss amino acid metabolism. A recent combination treatment study was stopped early by the NIH because it found that adding high dose, extended-release niacin to statin treatment in people with heart and vascular disease, did not reduce the risk of cardiovascular events, including heart attacks and stroke. |
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15. The relatively high boiling point and high freezing point characterizing water is mainly caused by:
a) pH b) tissue type c) hydrophobic interactions d) van der Waals interactions e) hydrogen bonds |
E
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16. The configuration about one of the following atoms will determine whether an amino acid is in the D or L form. Which one?
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Alpha Carbon (attached to the carboxyl group)
The alpha carbon is adjacent to the carboxyl group COOH. The configuration of 4 different groups situated around the alpha is what will determine the form. In humans aa are in the L-form. |
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17. Marfan syndrome is an inborn error disorder that affects eyes, causes disproportionally long arms and fingers, heart symptoms, among other symptoms. Which of the following proteins/mechanisms do you expect is affected?
a) Collagen b) Elastin c) Microtubules d) Fibrillin e) Laminin |
D
This is an extra difficult question, that was only briefly discussed in class. Marfan syndrome is a connective tissue disorder, that I mentioned in class but only briefly relating to fibrillin-1. It could be a board question later on, though so I thought it worth mentioning. |
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18. Between which of the following functional groups could a hydrogen bond be formed?
a) R-CH3 b) R-OH c) R-CH2-NH2 d) Carboxyl |
B & D (have polar side groups - hydroxyl)
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19. Seafarers frequently included limes as part of the crew’s diet to prevent sore and bleeding gums among other symptoms. Which biochemical step was affected specifically?
a) Crosslinking of peptide bonds between polar amino acids b) Hydroxylation of proline residues in collagen c) Formation of desmosine bonds in elastin d) Hydrogen bonds formation under reduced pH conditions |
B
Comment: Vitamin C is necessary for the formation of hydroxyproline |
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20. Microcytic anemia most commonly is caused by a deficiency of ______________ in the erythrocyte
a) Vitamin B12 b) Beta hemoglobin c) Iron d) Alpha hemoglobin |
C
Comment: The most common cause of microcytic anemia is iron deficiency. Folate and vitamin B12 are both associated with macrocytic or megaloblastic anemia. |
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21. The kinetic analysis of an enzyme in the presence and absence of a drug shows a delayed response to substrate concentration but a matching Vmax at some point. Which best describes the drug?
a) Non-competitive inhibition b) Competitive inhibition c) Irreversible inhibition d) Increased enzyme production e) Rapid enzyme breakdown |
B
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24. Which of the following is true for alpha thalassemia
a) It affects the production of beta hemoglobin b) Patients carrying the trait are always asymptomatic c) It is caused by a specific mutation in position 508 of the alpha globin gene d) Hemolytic anemia can be mild to severe |
D
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A world traveler and humanitarian presents to the clinic with cholera after his latest mission trip. What would his acid base condition be?
a) Metabolic acidosis b) Metabolic alkalosis c) Respiratory acidosis d) Respiratory alkalosis |
A
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Name characteristics of vitamins
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Small organic molecules
Required in small amounts Not produced by the body Found in various food types Active and inactive form Excess intake might be toxic |
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Proteins, Carbs and fats (triglycerides) end up in what common cycle
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Citric Acid Cycle
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ATP is produced by the CA cycle in what mechanism?
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Oxidative phosphorylation
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What are the functions of vitamins?
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Cofactors for enzymes
Growth and cell differentiation Antioxidants Blood formation and function |
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Name water soluble vitamins
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B complex
C |
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Name fat soluble vitamins
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A,D,E,K
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Name B vitamins
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Thiamine (B1)
Riboflavin (B2) Niacin (B3) Pantothenic acid (B5) B6 Biotin (B7) Folate (B9) B12 Note that a deficiency in one B vitamin usually indicates a deficiency in all B's |
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B vitamins function in what capacity for enzymes?
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Cofactor
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Name the vitamin that does the following:
Becomes TPP Functions in decarboxylation rxn's Polished rice (beriberi) as a major food source Wernicke-Korsakoff syndrome |
B1 (Thiamine)
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Thiamine interacts with what food/energy source?
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Helps in Pyruvate->Acetyl CoA
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Riboflavin transforms to which two compounds
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Flavin mononucleotide (FMN)
Flavin adenine nucleotide (FAD) |
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Niacin deficiency is known as
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Pellagra
Has skin, GI & CNS impact (Dermatitis, diarrhea, dementia) |
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Niacin is known as nicotinic acid. What vital compound does niacin become?
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NAD+
NADP+ |
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Vit B6 comes from the following sources:
Plant Animal Both |
Both
Active form is pyridoxal phosphate (PLP) |
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Vitamin B6 (as PLP) is involved in the metabolism of:
Proteins Carbs Fats All of the above |
Proteins
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Biotin (B7) is involved in which metabolic pathways?
Glucose Fatty acid synthesis Protein metabolism |
Glucose & FA
Deficiency does not occur naturally |
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Pantothenic acid (B5) active form is:
Arginine Lysine Coenzyme A Glutamic acid |
CoA
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Pantothenic acid (B5/CoA) is involved in which metabolic pathway(s)
Protein Carbs Fats (triglycerides) Citric acid cycle |
All
No deficiency is noted |
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Vitamin B group deficiencies are
Rare Common |
Rare and usually associated with protein deficiencies
Symptoms include: Nausea, depression, anemia, loss of appetite, impaired immune system, severe exhaustion, neurologic disorders, skin problems, weight loss |
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Name two other nutrients that are coenzymes
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Coenzyme Q (electron transport)
Lipoic acid (prosthetic group of an enzyme) |
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Name the functions of Vitamin A
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Eye sight (part of rhodopsin)
Cell growth Resistance to infection Reproduction Retinoids Carotenoids |
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Deficiency in Vitamin A can lead to which of the following:
Night blindness Eye damage risk of infection Keratinization mucosal changes |
all except mucosal changes
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Vitamin A toxicity - list symptoms
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Loss of appetite
Blurred vision Dry flaky skin Teratogenic Brain damage in infants whose mothers consume high doses |
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Vitamin D is made by body?
True False |
True, after sun exposure
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Vitamin D's most important role is
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Regulate calcium and phosphorous concentrations in blood
Fatty fish and fortified cereal are sources |
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Vitamin D deficiency leads to?
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decreased calcium in bones
rickets in children osteomalacia in adults |
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Which two water soluble vitamins function as antioxidants?
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None
Vitamin E & C are major antioxidants |
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Vitamin E deficiency is
Common Rare |
Rare
Mainly in newborns, seen as hemolytic anemia |
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Vitamin C can be stored in a cool environment for long periods of time
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False
Air exposure & temperature also destroy Vit C |
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Major role of Vitamin C
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Collagen formation
Brain & nerve function Iron absorption Scurvy is a result of deficiency |
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As antioxidants, Vit E&C prevent formation of what?
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Free radicals...
Free radicals change the formation of lipids (non-polar tails) |
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Microcytic anemia causes?
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Deficiency in iron, copper, pyridoxine
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Normocytic anemia (MCV 80-100) causes?
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Protein / calorie malnutrition
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Macrocytic anemia causes
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Vitamin B12 deficiency
Folate deficiency |
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Folate (Vitamin B9) active form?
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THFA (tetrahydrofolate)
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THFA major function?
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Amino acid & nucleotide metabolism
DNA synthesis |
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Pernicious anemia is the result of?
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Vitamin B12 deficiency.
Anemia and nerve damage |
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Where is Vitamin K stored in the body?
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Not stored
Two forms, K-1 & K-2 |
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Where is Vitamin K produced?
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Bacteria in intestines
Deficiency is rare |
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Name minerals important in body function
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Calcium
Potassium Chloride Phosphorus Sodium Magnesium Iron Zinc Copper Iodine Flouride Selenium Manganese Chromium |
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What are the functions of minerals?
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Maintain osmotic pressure
Strong bones Nerve signaling Hormone signaling Cofactors for enzymes O2 Transport |
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Match vitamins with their active form:
1 - Folate (B9) 2 - Pantothenic acid (B5) 3 - Vitamin (B6) A - CoA B - NADH C - THFA D - PLP (Pyridoxal Phosphate) |
Folate - THFA
Pantothenic Acid - (CoA) B6 - PLP |
