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Biochemistry PMY-3 > Amino Acids,structure and organization > Flashcards

Amino Acids,structure and organization Flashcards

1
Q

Where do polar amino acids cluster?

A

On the surface of soluble proteins

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2
Q

Where do nonpolar amino cluster?

A

On the surface of membrane proteins

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3
Q

Describe amino acids at physiological pH

A

At pH 7.4, the alpha amino group and the alpha carboxyl group are both ionized, so no net charge exists (many amino acids take their zwitterionic form at neutral pH form at neutral pH; positive NH3+ and negative COO- charges)

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4
Q

What are the properties of amino acids with non-polar side chains?

A
  • The R group does not bind nor give protons (no acid/ base chemistry)
  • do not form hydrogen bonds
  • have hydrophobic interactions
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5
Q

Describe the Location of non-polar (hydrophobic) amino acids in proteins

A
  • In soluble proteins (aqeous environment), found in the interior of proteins(shielded from environment)
  • In membrane or other hydrophobic environments, found on protein surface
  • Proline: side chains forms an imino group
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6
Q

Describe the amino acids with uncharged polar side chains

A
  • Not charged at neutral pH
  • Cys and Tyr can be proton donors at alkaline pH
  • Ser, Thr and Tyr- polar -OH can form hydrogen bonds
  • Asn and Gln contain -COOH (carboxy) and -CONH2 (carboxyamine) groups - can form hydrogen bonds
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7
Q

Describe the disulfide bonds(covalent) of amino acids

A
  • Side chain ofCys contains a sulfylhydryl (SH group)- important active site of many enzymes
  • Proteins with 2- SH groups can form a disulfide bridge or cystine dimer ( -S-S-, intermolecular or intramolecular)
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8
Q

Describe Amino acids with uncharged polar side chains

A
  • Side chains of amino acids as sites of attachments for other compounds:
  • Ser, Thr and Tyr contain a polar -OH (hydroxyl group)
  • Ser side-chain is an important active site component in some enzymes
  • Also, the -OH group can be a site of attachment for PO4(phosphate)
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9
Q

What is a function of the CONH2 of Asn?

A

May serve as site of attachment of oligosaccharides chains in glycoproteins (N-linked glycosation)

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10
Q

What is the function of the -OH group of Ser and Thr?

A

May serve as site of attachment of oligosaccharide chains in glycoproteins (O-linked glycosation)

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11
Q

Give 2 examples amino acids with acidic side chains

A

Aspartate (aspartic acid)

Glutamate (glutamic acid)

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12
Q

Give the properties of amino acids with acidic side chains

A
  • Asp and Glu are proton donors
  • At neutral pH (physiological), side chains almost fully ionized or dissociated (COO-) and carry a negative net charge
  • These contribute negative charges to proteins
  • R groups typically have a pk< 7
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13
Q

Give the properties of the amino acids with basic side chains

A
  • the side chains of a basic amino acids may accept a proton
  • At physiological pH, side chains of Lys and Arg are fully ionized and therefore carry a positive charge
  • Contribute a positive charge to proteins that contain them
  • Have a pk > 7
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14
Q

Why do histones have appositive charge?

A

Due to the abundance of Arginine and lysine

-DNA has a negative charge which histone bind to

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15
Q

What is one function of histidine?

A

To exert physiological buffering capacity

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16
Q

How can histidine exert physiological buffering?

A

It is weakly basic and partially positively charged at physiologic pH

In proteins, it can be positive or uncharged, depending on environment of protein, and pH(important role in proteins like hemoglobin and myoglobin)

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17
Q

What is the abbreviation and symbol for Cysteine ?

A

Cys and C

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18
Q

What is the abbreviation and unique first letter/symbol of Histidine?

A

His and H

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19
Q

What is the abbreviation and symbol of isoleucine?

A

Ile and I

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20
Q

What are the abbreviation and symbol of methionine?

A

Met and M

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21
Q

What are the abbreviation and symb of serine?

A

Ser and S

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22
Q

What are the abbreviation and unique first letter/symbol of valine?

A

Val and V

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23
Q

The most commonly occurring amino acids have priority for…

A

The 1 letter code

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24
Q

What are the abbreviation and symbol of alanine ?

A

Ala and A

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25
Q

What are the the abbreviation and one letter code for glycine ?

A

Gly and G

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26
Q

What are the abbreviation and one letter code for leucine?

A

Leu and L

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27
Q

What are the abbreviations and one letter code for proline?

A

Pro and P

28
Q

What are the abbreviation and one letter code for threonine ?

A

Thr and T

29
Q

What are the abbreviation and one letter code for arginine?

A

Arg and R

30
Q

What are the abbreviation and 1-letter code for asparagine?

A

Asn and N

31
Q

What are the abbreviation and 1-letter code for asp Aspartate?

A

Asp and D

32
Q

What are the abbreviation and 1-letter code for Glutamate?

A

Glu and E

33
Q

What are the abbreviation and 1-letter code for Glutamine?

A

Gln and Q

34
Q

What are the abbreviation and 1-letter code for phenylalanine ?

A

Phe and F

35
Q

What are the abbreviation and 1-letter code for tryptophan?

A

Trp and W

36
Q

What is a chiral molecule?

A

Rotated molecule cannot be superimposed on its mirror image

37
Q

What are the abbreviation and 1-letter code for for letters close to initial letters of Aspartate or asparagines

A

Asx and B

38
Q

What are the abbreviation and 1-letter code for letters close to initial letters of Glutamine or glutamate

A

Glx and Z

39
Q

What are the abbreviation and 1-letter code for letters close to the initial letters of lysine?

A

Lys and K

40
Q

What is the letter of an undetermined amino acid?

A

X

41
Q

Why is glycine special?

A

The alpha C of glycine is not joined to4 different groups so it has no optical activity

42
Q

Describe optical activity of amino acids

A
  • The alpha C of each amino acid(except glycine) has 4 different groups attached so it is chiral/optically active
  • the number of optical isomers is 2n, where n is the number of chiral atoms in the molecules
43
Q

What is created by a chiral center?

A

A chiral center in a molecule creates 2, optical isomers or enantiomers :

-D - and L- forms are mirror images of one another

44
Q

What are stereoisomers?

A

Molecules with the same bonding structure but different arrangements in space

- Optical isomers
- Geometrical isomers
45
Q

What are optical isomers?

A

They have D and L form because they can rotate plane polarized light

46
Q

What are geometrical isomers?

A

Have different arrangements around double bonds in the molecule: cis and trans arrangements (same face, or different sides of the face)

47
Q

How can L-Amino acids and D-amino acids be distinguished?

A

L-Amino acids are those with alpha amino group on the left and D-amino acid have the alpha amino groups on the right

48
Q

How are optical isomers(enantiomers) named(D- and L-)?

A
  • Done by lining up the carbon atoms of the molecules vertically with the chiral atom in the center.
  • The carbons are numbered beginning with the aldehyde or carboxyl carbons on the end.
  • With this presentation, the R group is always below the alpha carbon
49
Q

How much amino acids are known? How much are coded for by DNA ?

A

300 known, 20 coded for by DNA

50
Q

What are the 3 branched chain amino acids?

A

Valine, leucine and isoleucine

51
Q

What amino acid connects the carbon to the amino nitrogen?

A

Proline

52
Q

How can cystine be formed?

A

Taking away the w hydrogens of -SH on cysteine and having the sulfur’s form a cysteine bond

53
Q

Differentiate aspartic acid and glutamic acid

A

Aspartic acid has one less CH2 than glutamic acid

54
Q

Differentiate aspartic acid/glutamic acid from Aspartate and glutamate

A

Glutamate/ Aspartate R group has COO- not COOH

55
Q

Name the amino acids with non-planar side chains

A

Glycine

Alanine

Valine

Leucine

Isoleucine

Phenylalanine

Tryptophan

Methionine

Proline

56
Q

Give examples go uncharged polar side chains

A
  • Serine
  • Threonine
  • Tyrosine
  • Asparagine
  • Cysteine
  • Glutamine
57
Q

Give examples of amino acids with basic side chains

A
  • Histidine
  • Lysine
  • Arginine
58
Q

Explain Acetyl CoA formation in cytosol

A
  1. Acetyl CoA formed in mitochondria cannot leave the mitochondria
  2. Citrate leaves the mitochondria only at very high citrate levels in mitochondria and is transported into the cytosol.

This prevents predict inhibition of citrate synthase by high mitochondrial citrate levels

  1. In the cytosol, citrate is cleaved by ATP-citrate lyase to Acetyl CoA and oxaloacetate
59
Q

What is the regulated enzyme of fatty acid synthesis?

A

Acetyl CoA carboxylase is the regulated enzyme and provides fuel for fatty acid synthase

60
Q

How can you describe the reaction of Acetyl CoA carboxylase?

A

acetyl CoA carboxylase (active polymer) contains biotin

Acetyl CoA carboxylase uses cytosolic Acetyl CoA, carbon dioxide and ATP for formation of malonyl CoA

Note: cytosolic Acetyl CoA is available in hepatocytes only after a carbohydrate-rich meal and at high insulin levels. It is formed by citrate levels

61
Q

Describe allosteric regulation of Acetyl CoA carboxylase

A

Cytosolic citrate leads to the active polymer-activates Acetyl CoA active polymer

Accumulation of fatty acyl CoA leads to the inactive protomers
-long chain fatty acyl CoA inhibits Acetyl CoA carboxylase active polymer

62
Q

Why is Acetyl CoA carboxylase allosterically activated by cytosolic citrate?

A

Only at very high mitochondrial levels, citrate leaves into cytosol and is cleaved by citrate lyase to Acetyl CoA which provides substrate for Acetyl CoA carboxylase

Note: cytosoliccitrate shall not accumulate as it would allosterically inhibit PFK-1

63
Q

Why is Acetyl CoA carboxylase inhibited by accumulation of long-chain fatty acyl CoA and not by palmitate?(state points)

A
  1. Palmitate is the end product ofFA synthase but shall never accumulate as free palmitate damages the cell.
  2. The free CoA pool in cytosol is limited
  3. An accumulation of long-chain fatty acyl CoAs indicates a slow turnover of FA-CoAs and that soon free CoA may not be available for newly synthesized FA
  4. That is why fatty acid synthesis is not inhibited by its end product free palmitate but instead inhibited by high levels of long-chain fatty acyl CoAs
64
Q

The free CoA pool in cytosol is limited. How does this lead to fatty acyl CoA inhibiting Acetyl CoA carboxylase but not palmitate?

A

The free CoA pool in cytosol is limited. Usually, free CoA is used for fatty acid activation to fatty acyl CoA and this bound CoA is released again as free CoA during synthesis of TAGs or phospholipids

65
Q

Palmitate is the end product of fatty acid synthase. Why doesn’t this accumulate?

A

Palmitate is the end product FA synthase but shall never accumulate as free palmitate damages the cell. The fatty acid needs to be activated by the separate enzyme fatty acyl CoA synthetase to palmitoyl CoA which is then used for synthesis

Biochemistry PMY-3 (37 decks)

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