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140 Cards in this Set
- Front
- Back
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What percentage of adults are water? children?
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Adults 60%
children 75% |
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What decreases the amount of H20 in our bodies?
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age and fatness
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What is the percentage of water inside vs outside our cells?
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60% inside
40% outside |
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What is the breakdown of extracellular fluid?
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10L interstital
5L blood |
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What is the strength of H bonds? What is that related to the strength of a covalent bond/
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-2 - -4 kcal/mol in strength
1/20th the strength of a covalent bond |
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What acts a H bond acceptor? donor?
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Acceptor = O
Donor - H |
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What is largely responsible for the properties of water?
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H bonding
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What properties of water allows it to readily dissolve solutes?
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H bonding and dipolar nature
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What causes hydrophobicity?
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the increase in entropy in the water
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How does entropy decrease with hydrophobic groups mixing with hydrophillic?
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Water forms a cage around the nonpolar group and forms a cage - making it more ordered
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What does a high heat of fusion mean?
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it takes a lot of energy to make it freeze
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Why is it important for water to be a good thermal conductor?
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to exchange heat - you have to exchange heat from the brain to the blood
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What does a high heat of vaporization mean?
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energy required to evaporate - why sweating is cooling
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Electrolyte-
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a collection of inorganic anions and cations and bicarbonate found in body fluids
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What are the electrolytes in extracellular vs intracellular?
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extracellular - Na and Cl
intracellular -Po4 and K |
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Where is HCO3- found in higher concentrations - intra or extracellular?
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Extracelluar
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Osmolality-
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the concentration of solutes in each compartment
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osmotic pressure-
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the force requried to maintain the same amount of WATER on each side of the membrane
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If water is passed from blood to urine, where is it replinished from? when does this occur?
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From the interstitial fluid -- hyperglycemia
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What is the concentration of H20 in water?
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a constant 55.5M
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What does the Ka tell you?
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the tendency for an acid to dissociate
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What happens at the pKa?
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HALF the acid is dissociated -- where it is the best buffer
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What are buffers made out of?
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weak acids and their conjugate base
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Where is the pKa the best buffer?
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+/- 1 pH unit
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How much CO2 does the body normally produce each day?
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13 moles
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What is the pKa of carbonic acid?
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3.8
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What is the pH of blood?
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7.4
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What percentage of gaseous CO2 is dissolved in blood?
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3%
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What is the healthy range of PaCO2?
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37-43 mmHg
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What is the healthy range of HCO3-?
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24-28 mEq/ml
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What happens to pH during hyperventilation? wHy?
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Increases pH because you are decreasing CO2 which leads to a decrease in HCO3
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What buffers intracellular pH?
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phosphate anions and proteins and organic phosphates anions can also act as buffers (glucose -6-phosphate)
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What amino acids allow proteins to buffer intracellular pH?
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His Asp and Glu
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How is intracellular osmolarity maintained while maintaining pH?
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Too acidic - H is pumped out in exchange for an NA
Too basic - HCO3- is pumped out in exchange for Cl- |
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How are non-volatile acids excreted?
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excreted through the urine
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What is urinary pH? what is the minimum pH?
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5.5-7 -- min 5
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What acids are excreted through the urine?
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phosphate, ammonium ions, uric acid, dicarboxylic acid, tricarboxylic acid (citric acid)
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What is a major buffer of urine?
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ammonium
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What is the concentration of ammonium in blood? Why?
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Very low - because it is toxic to neural tissues
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How do the kidneys help regulate blood pH?
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At high pH kidneys produce NH4, which signals HCO3- to be returned to the blood
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What is HCl secreted by?
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Parital cells
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What is HCl used for?
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to denature ingested proteins
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How is HCl neutralized?
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by bicarbonate secreted by pancreatic cells and cells in the intestinal lining
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What is the normal range of blood pH?
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7.37-7.43
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What is the order of strength of covalent and non covalent forces of individual forces?
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Covalent, ion pairs, H bonding, van der waalss
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What force is the strongest when you consider the entire protein?
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van der Waals
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What is the relationship between the dielectric constant and electric forces?
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As the dielectric constant increases the force decreases
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What does the dielectric constant describe?
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the dipolar nature of the environment
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Where are the electrostatic interactions on protein the strongest?
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Inside the protein
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What has a van der waal force?
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it is between ALL atoms
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How many of the amino acids have the regular amino acid structure?
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19 - all except pro
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What isomer form of amino acids is in mammals?
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L-isomer
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Which amino acid does not have a chiral C?
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Gly
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What is a zwitterion?
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When the amino acid has both postive and negiative charges - not necessary in equal amounts
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Primary Oxaluria Type 1-
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Defects in glycine degradation - causes a buildup of oxalate
- oxalate forms precipitates with Ca and forms renal stones - can cause renal faiure |
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What are the non polar aliphatic amino acids?
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Valine, Leucine, Isoleucine, Alanine, Methinoine
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What are the aromatic amino acids? in order from nonpolar to polar
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F, (W and Y)
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What are the small polar uncharged amino acids?
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Serine, and Threonine
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What charge do acids have? bases?
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Acids - negative
bases - positive |
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What is proline called?
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NOT an AMINO ACID - called a imino acid
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Under what conditions can 2 cysteines form? - what does the name change to?
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under oxidative conditions
cysteines ----> cystines |
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What is a cystine?
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a PAIR of 2 cysteines bonded together
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Cysteinuria-
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a autosomal recessive disorder (effects 1/10,000)
- a mutation in the transport protein that aids in reabsorption from urine of cystine, lysine, and arginine - cystine isnt very soluble- forms renal stones in kidney ureter and bladder |
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What amino acid is considered both essential and non essential?
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Arg - because we can make it - but cant make enough
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What are the essential amino acids?
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WITHRKFLVM
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Why do different amino acids have different properties?
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because of the side chain
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At physiologic pH 7.4 what amino acids have a charge?
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Lys, Arg, Asp, Glu,
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pI-
how do you find it? |
Where the amino acid carries NO NET charge
-average the pKa- different if more acidic or basic groups |
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How do you find the pI for a basic amino acid?
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average the 2 bases
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What is the driving force of hydrophobicity?
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the nonpolar groups mixed in h20
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Hydropathy-
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a measure of how hydrophobic an amino acid is - (negative values= polar Positive - nonpolar)
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What causes PKU?
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In classic PKU there are mutations in the PAH gene that impairs the enzyme that converts Phe to Tyr (so you get more Phe)
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What is the effect is PKU is untreated? what is the treatment?
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severe metal retardation
limit Phe at birth |
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What is one breakdown product of aspartame?
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Phe
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What end of a protein is listed first?
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The amino end (NH2)
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What is a residue?
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An amino acid connected with a peptide bond
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What is the regular repeating part of the amino acid? variable?
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regular - the backbone
variable - the side chain |
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What is the backbone rich in potential for?
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Hydrogen bonding
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Primary Structure-
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The list of amino acids (n-term to C-term)
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What are the molecular weights of amino acids measured in?
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Da -daltons of kDa
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How many amino acids do typical natural proteins have?
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between 50-2000 residues
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Oligopeptides-
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proteins with less that 50 residues
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How many residues are different in bovine and human insulin?
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5 residues
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Isoforms/isozymes-
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Typically have the same function but somewhat different property and sequence
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How many different isoforms does hemoglobin have?
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3 -embryonic, fetal, and adult
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What are the 3 isoforms of calcineurin and where are they expressed?
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alpha- brain
beta- everywhere gamma- testis |
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Where is the isomers of Creatine Kinase?
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M isomers- MM in skeletal muscle
B isomers- BB in brain MB, BB, MM in the heart |
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What isomer of Creatine Kinase is a test for myocardial infractions?
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MB - leaks from the heart from damaged heart cells into the blood
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homologous family of proteins-
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proteins related to the same ancestral protein - not necessarily in the same species
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paralogs-
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WITHIN a SPECIES- groups of proteins with similar but not idential sequences
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What arises from divergent evolution?
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paralogs
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Divergent evolution-
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A gene is duplicated - one copy keeps performing the old function and the other one gets a new function
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What forms protein crosslinks?
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disulfide bonds - the oxidation of a pair of cysteines -cystine
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What part of the polypeptide is planar? Why?
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the peptide bond - due to the C-N bond having partial double bond -prevents rotation about the bond
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What are the 2 different configurations possible for the peptide bond?
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trans and cis
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What amino acid can also be found in cis?
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Pro
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What part of the amino acid is free to rotate?
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the backbone bonds on either side of each alpha C
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What are each of the angles called?
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phi- between the N and alpha C
psi - alpha C- C |
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What is the angle of rotation about phi and psi called?
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dihedral or torsion
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When does a steric clash occur?
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When 2 or more atoms overlap each other
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What does the Rramachandran plot assume that isnt true?
what does this change? |
Assumed the bond lengths and angles were fixed -- They're not
-makes the allowable values a little bit bigger |
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What forms most of the steric clash in the Ramachandran plot?
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The beta C
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What two amino acids have different R plots?
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Glycine -no beta C - freer rotation
Proline- more restricted - less rotation |
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What 2 things play a big role in the backbone structure?
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1. dihedrals lie in allowable reagions of the H plot
2. Form the max number of H bonds |
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What are the 4 major types of secondary structure?
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Regular- alpha helix beta sheets
Irregular - loops and turns |
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Name the properties of an alpha helix-
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1. phi and psi have regular repeating values (-60 and -40)
2. L isomers = right handed helix 3. 3.6 residues per turn 4. H bond between n and n+4 residues 5. ALL CO and NH groups within the helix are H bonded |
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Name 2 reasons alpha helices are right handed
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1. L isomers
2. If left handed there would be a steric clash |
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What are the phi and psi values for right handed helix?
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-60 and -60
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Keratin formation
protofilament- protofibril- |
protofilament- pairs of coiled-coils wrap around each other
protofibril-prrtofilaments wrapped around each other |
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What do keratinopathies mostly effect? How?
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the skin and liver - usually by mutations in the formation of protofibrils and protofilaments
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What are the values of phi and psi in a beta sheet?
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neg phi and positive psi
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Where are H bonds in a beta sheet?
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between 2 beta strands in the backbone's CO and NH
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What is the more common orientation for beta sheets
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anti-parallel
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In what shape are beta sheets often found?
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twisted - beta barrel
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How can a beta strand change direction?
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only by a loop or a turn
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Where do turns H bond? Loops?
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Turns- In the middle
Loops- the 2 ends |
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How many residues are typical in loops and turns
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loops- more than 4 residues
turns - less than 4 |
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What is more flexible - a loop or a turn?
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A loop
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How many beta strands does it take to make a beta sheet?
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2
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Secondary structure propensitities-
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the tendency for a residue to be found in a given secondary structure
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What is the reason behind different secondary structure propensities?
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The side chains
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What are the repeating values for loops and turns?
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Dont have one - unlike alpha and beta
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What do numbers mean in secondary structure propensities?
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Greater than 1- found more often than expected
Less than 1 - less often than accepted |
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Tertiary structure-
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the overall fold of a protein
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What is tertiary structure stabilized by?
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hydrophobicity, h bonds, electrostatic forces, van der waals
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What is the percentage of the different secondary structures that make up myoglobin?
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70% alpha helix
30% turns and loops |
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What is protein folding driven by
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hydrophobic collapse - the placing of hydrophobic groups inside a protein
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Where is the backbone found in a protein?
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On the outside - its polar
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Porins-
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channels that allow small molecules through the membrane
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How can tertiary structure be classified?
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classified by the secondary structure
all alpha proteins - predominately consist of alpha helix beta proteins - mostly beta sheets |
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domains-
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two or more compact regions - each of which resemble small proteins range from 30-400 residues
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Quaternary structure-
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more than 1 polypeptide chain together - subunits can be the same or different
Cro-DNA binding protein (same subunits) Calcineurin - different subunits |
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What is the most abundant protein in the body?
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collagen
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What is the conformation of collagen?
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left handed polyproine II helix
made of 3 strands rod shaped - |
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What amino acid is largely in collagen? why?
what is every 3rd residue? why? |
Proline the most common amino acid in collagen - to stabilize the polyproline II helix
Glycine - every 3rd residue - needed for the 3 chains to pack against each other |
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What happens when glycine isnt the 3rd residue in collagen?
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Osteogeneisis imperfecta (brittle bone disease)
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What needs to be done to denature proteins?
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Break disulfide bonds if there
and make all other interactions unfavorable |
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What can break disulfide bonds?
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beta-mercaptoethanol
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What chemicals can denature a protein? How?
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urea and guanidinium chloride -- unfold by interacting with the backbone more strongly than the backbone interacts with itself
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Random coils-
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unfolded proteins - with no structure or activity
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