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47 Cards in this Set
- Front
- Back
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Why is water a suitable substance for being a catalyst for life as opposed to other molecules?
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Water has a high melting point and boiling point than any other low-molecular weight compounds. Moreover, it remains liquid at a wider range of temperatures. It has a high dielectric constant, it’s cohesive, it’s awesome.
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Why does water have high surface tension?
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It is cohesive
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What is the dielectric constant?
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80
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Why do we say that covalent interactions are stronger than ionic interactions?
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Most life uses significant amounts of water. Water reduces electrostatic interactions.
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How do you calculate the attraction between atoms in water?
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You find the dielectric constant of the atoms in the air, and divide that number by 80.
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Is a hydrophobic interaction a chemical interaction?
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No.
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Where do hydrophobic interactions exist?
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Only in h2o
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How do hydrophobic interactions it work?
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The water molecules will attract each other and will push out anything that isn’t a polar molecule
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What are the three structures of amphibathic molecules?
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Monolayers, micelle, and liposome
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What is a monolayer?
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A layer of amphipatic molecules where all of the h-phobic tails are pointed away from the water. |
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What is a micelle?
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A bubble formed by amphipatic molecules. All of the h-phobic tails are pointed inwards.
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What is a liposome?
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A vessicle formed by amphipatic molecules. There is a bilayer formed with a center has water in it, the outside has water in it. The h-phobic tails are facing eachother.
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What are the ions that H2O dissociates into?
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H+ and OH-
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How many different amino acids are there?
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20
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What are the four classes of amino acid side chains?
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Non-polar, polar, acidic, basic
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What are the non-polar side chains?
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Ala, val, Leu, Ile, Pro, Phe, Met, Trp, Gly, Cys
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What are the polar side chains?
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Ser, Thr, Tyr, Asn, Gln
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What are the basic side chains?
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Arg, Hys, Lys
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What are the acidic side chains?
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Asp, Glu
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What side of a protein chain is the N terminus located on, and what is the charge?
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On the left and + because NH3+
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What side of a protein chain is the C-Terminus located on, and what is the charge?
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Right and – because Coo-
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What is the standard size of a protein?
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Between 100-000
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How do you know you are reading a protein in the correct direction if there are no C or N terminuses?
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Read in the direction: CONH.
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What is the polypeptide backbone made of?
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HCONHCCONHCCONHCCONH…
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L or D isomer, which is the majority of amino acids?
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L
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What do the L and D isomer look like?
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L: NH3 on the left. Coo- on the right.D: Coo on the right, NH3 on the left.
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What are zeitterions?
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Amino acids at physiological pH. It has a NH3+ and a COO-, therefore there is no net charge.
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How do you calculate pH?
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pH=-log[H+]
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How do you calculate pka?
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pka= -logka = -(log[H+]+log[A-]/[HA])
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What is the Henderson-Hasselbalch equation?
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pH=pKa + log[A-]/[HA]
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What does the Henderson hasselbalch equation give you?
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The relationship between the pH of solution, pKa value, and the ration of ionized/not ionized forms of acid
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What does it mean when pH=pKa?
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Any given group with that pKa value is 50% disassociated
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The terminals have a typical pKa value at?
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2 and 9 (when it isn’t in water)
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What are side chains differed by?
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Size, shape, charge, h-bonds, hydrophobicity, chemical reactivity
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Why is cysteine considered non-polar?
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The electronegativity is less in S than in O. The hydrophobic side chain isn’t exposed to water.
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What amino acid produces a disulfide bond?
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Cys
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Where are SS bonds normally produced?
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Extracellular proteins
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Where are basic amino acids normally found?
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The exterior surface of proteins, so they can be hydrated by the surrounding environment
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Where are peptide bonds formed? |
Between the C=O carbon and the N of the next amino |
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How do you judge between L and D amino acids? |
You put hydrogen in the back and go from NH3+ Coo- R |
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What form are all amino acids in proteins? |
L |
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pKa of amino? |
9-10 Yes it is lessened by the surrounding proteins. |
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pKa of Carboxyl? Does it change in a protein? |
2. Yes it is affected by the surrounding amino acids. |
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On the typical pKa table, if you have a pKa that is greater than typical, do you favor acid or base? |
Base |
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On the typical pKa table, if you have a pKa that is less than typical, do you favor acid or base? |
Acid |
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On the typical pKa table, if you have a pKa that is equal to typical, do you favor acid or base? |
50-50 |
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What occurs to pH near pKa? |
pH is buffered |
