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KEMBIO1: Biochemistry 1 > LONG EXAM 2 > Flashcards

LONG EXAM 2 Flashcards

1
Q

Amino acid is a compound that contains _____ and _____

A

amino group (H3N+) and carboxyl group (COO-)

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2
Q

Alpha amino acid has

A

amino group attached to the carbon adjacent to the carboxyl group

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3
Q

R gives what?

A

identity to the amino acid

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4
Q

Most of the amino acids have L configuration except for one

A

Proline

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5
Q

Tryptophan contains

A

an indole group (heterocyclic structure) bonded to the alpha carbon

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6
Q

structure of glycine

A

Alpha carbon (of carboxy group) bonded to H and amino group with H as the R group.

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7
Q

R group of alanine

A

CH3

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8
Q

structure of phenylalanine

A

contains phenyl group on the alpha carbon

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9
Q

R group of tyrosine

A

alpha carbon (CH2) bonded to phenol

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10
Q

amino acid that contains a thiol group

A

cysteine

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11
Q

methionine contains

A

sulfide group

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12
Q

Group A amino acids have? What are these amino acids

A

nonpolar side chains

Alanine - aliphatic
Valine - aliphatic
Leucine - aliphatic
Isoleucine - aliphatic
Proline - cyclic structure
Phenylalanine - aromatic
Tryptophan - indole
Methionine - sulfide

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13
Q

Group B amino acids have? Enumerate the amino acids

A

neutral polar side chain

Serine - contains an OH
Threonine - contains an OH
Tyrosine - contains a phenol
Cysteine - contains thiol
Glutamine - contains an amide
Asparagine - contains an amide

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14
Q

Group C contains? What are the amino acids? What are the properties?

A

acidic side chains

Glutamic Acid (Glu)
Aspartic Acid (Asp)

properties
1. can lose a proton
2. negatively charged at neutral pH

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15
Q

Why are aspartic acid and glutamic acid negatively-charged at neutral pH?

A

pH > pI

excess OH- in the solution deprotonates the amino group, making it neutral and leaving the carboxy group negatively charged and therefore the whole molecule itself

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16
Q

Group D contains? What are the amino acids? Properties?

A

basic side chains

Histidine - contains an imidazole group
Arginine - contains a guanidino group
Lysine - contains an aliphatic chain

Properties:
1. Positively charged at neutral pH

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17
Q

The only secondary alpha amino group

A

Proline

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18
Q

What differs isoleucine and threonine from the other amino acids?

A

They contain 2 stereogenic centers

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19
Q

uncommon amino acids that are found in few connective tissues like collagen

A

hydroxyproline and hydroxylysine

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20
Q

uncommon amino acid found in the thyroid gland

A

thyroxine

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21
Q

overarching principles that links 3D structures of proteins and their biological functions

A
  1. function depends on structure
  2. structure depends on sequence and on weak, noncovalent forces
  3. the number of protein folding patterns is large but finite
  4. structures of globular protein folding patterns is large but finite
  5. marginal stability facilitates motion
  6. motion enables function
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22
Q

Primary protein structure

A
  1. determines the 3D conformation of protein
  2. includes covalent interactions in the linear chain and is stabilized by resonance
  3. results of amino acid substitutions may range from negligible effects to complete loss of activity depending on the protein and the nature of the altered residue
  4. Changes in just one aa sequence can alter biological function
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23
Q

What stabilizes the secondary, tertiary, and quaternary protein structure

A

weak forces

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24
Q

what type of interaction enables protein folding?

A

hydrophobic interaction

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25
Q

a type of interaction that occurs on the protein surface

A

ionic interactions

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26
Q

this type of interaction can be found everywhere

A

van der Waals interaction

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27
Q

what are the several factors that can disrupt an alpha helix?

A
  1. proline that creates a bend because of the restricted rotation due to its cyclic structure and it has no available N-H for H-bonding
  2. strong electrostatic repulsion caused by the proximity of several side chains of the like charge
  3. steric crowding caused by the proximity of bulky side chains
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28
Q

why proline can disrupt an alpha helix?

A
  1. restricted rotation due to its cyclic structure
  2. its amino group has no N-H for hydrogen bonding
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29
Q

What do you know about the alpha helix secondary structure of proteins?

A
  1. the coil is right-handed
  2. there are 3.6 amino acids per turn
  3. the pitch or repeat distance or the distance between turns is 5.4 Å.
  4. C=O of each peptide is hydrogen bonded to the N-H of the fourth amino acid away
  5. C=O — H-N bonds are parallel to the axis of the helix
  6. R groups point outward from helix
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30
Q

What do you know about Beta-pleated sheets?

A
  1. polypeptide chains lie ADJACENT to one another having parallel of antiparallel configuration
  2. R groups alternate - above and below the plane
  3. each peptide bond is s-trans and planar
  4. C=O and N-H groups of each peptide bond are perpendicular to the axis of the sheet
  5. C=O — H-N hydrogen bonds are between adjacent sheets and perpendicular to the direction of the sheet
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31
Q

which is more stable parallel or antiparallel beta pleated sheet?

A

antiparallel because the hydrogen bonds are aligned directly opposite each other, making stronger and more stable interaction

32
Q

two parallel strands of B sheet connected by a stretch of alpha helix

A

BaB unit

33
Q

two antiparallel alpha helices

A

aa unit

34
Q

antiparallel sheet formed by a series of tight reverse turns connecting stretches of a polypeptide chain

A

Beta meander

35
Q

a repetitive supersecondary structure formed when an antiparallel sheet doubles back on itself

A

Greek key

36
Q

created when beta sheets are extensive enough to fold back on themselves

A

beta barrel

37
Q

How does anti parallel beta sheet occurs?

A

when a polypeptide chain sharply reverses direction. it occurs in the presence of two consecutive proline residues which creates an an angled kink

38
Q

what are motifs?

A

-certain groups of secondary structural elements
-interaction of secondary elements with each other
-building blocks of 3D protein structure
-a supersecondary structure
-they do the same purpose
- found in protein domains

39
Q

what are domains?

A

portion of protein that does a specific function

40
Q

give an example of domain

A

kinase domain (where phosphorylation takes place)

41
Q

what are leucine zippers?

A

they recognize DNA and are normally found in DNA polymerases

42
Q

proteins fold to form these stable structures

A
  1. large numbers of intramolecular hydrogen bonds
  2. reduction in the surface area accessible to solvent upon folding
43
Q

two factors that lie at heart of the principle of the secondary structure of proteins

A
  1. proteins are typically a mixture of hydrophilic and hydrophobic amino acids
  2. the hydrophobic groups tend to cluster together in the folded interior of the protein
44
Q

this is what we get after being synthesized by the ribosome

A

tertiary structure

45
Q

what do u know about tertiary structures of proteins

A
  • 3D arrangement of atoms in a molecule
  • allows for the determination of the way helical and pleated sheet sections fold back on each other
46
Q

difference between fibrous and globular proteins

A

fibrous proteins
-the arrangement of atoms in the side chains is not specified by the secondary structure
- the backbone does not fold back on itself

globular proteins
-fold back on each other

47
Q

what are fibrous proteins?

A

contain polypeptide chains that are organized approximately parallel along a single axis.

  • consists of long fibers or long sheets
    -tend to be mechanically strong
    —insoluble in water and dilute salt solutions
    -play structural roles in nature
48
Q

examples of fibrous proteins

A
  • keratin of hair and wool
    -collagen of connective tissue of animals including cartilage, bones, teeth, skin, and blood vessels
49
Q

proteins which are folded to a more or less spherical shape

A

globular proteins

50
Q

characteristics of globular proteins

A

-tend to be soluble in water and salt solutions
-most polar side chains are on the outside and interact with the aqueous environment by h bonding and ion dipole interactions
-nonpolar side chains are burried inside
-all have substantial sections of alpha helix and beta sheet

51
Q

what differentiates tertiary structure from others?

A

R groups of amino acids interact such that they fold properly, minimizing unnecessary interactions

52
Q

in the cell environment, explain why and how proteins fold?

A

ribosomes synthesize proteins and these proteins are directed into the cytosol. but since the environment of the cytosol is aqueous, interaction between the water and the protein occurs. the protein will fold in such a way that the hydrophobic residues are shielded from the aqueous environment. the hydrophobic portion goes inside the cell whereas the hydrophilic portion stays outside, interacting with water.

53
Q

what are the interactions that govern the tertiary structure of protein?

A
  1. noncovalent interactions
    - H bonding between polar side chains
    - hydrophobic interaction between nonpolar side chains
    -electrostatic interaction between side chains of opposite charge
    -electrostatic repulsion between side chains of like charge
  2. Covalent interactions
    -disulfide bonds between side chains of two cysteine molecules
54
Q

what makes up the core of most globular proteins

A

helices and sheets

55
Q

the surface of the proteins is made up of ____ that connect the helices and sheets of the core

A

loops and tight turns

56
Q

these are nature’s modular strategy for protein design

A

protein domains

57
Q

proteins are composed of about how many amino acids?

A

250 amino acids which are simple, compact globular shape

58
Q

two or more recognizable and distinct structures that are compact, folded protein segments that have specific functions. they make up larger globular proteins. they may consist of a single continuous portion of the protein single sequence

A

domains or modules

59
Q

these are proteins that help other proteins to fold

A

molecular chaperones

60
Q

how do molecular chaperones help proteins fold?

A

they protect nascent proteins from the concentrated protein matrix in the cell and accelerates slow steps

61
Q

this is the classification of proteins that contains all information necessary to produce the tertiary structure

A

primary structure

62
Q

the association of polypeptide chains into aggregations. those that exist as multiple subunits. these are oligomeric proteins that interact to have their function

A

quaternary structure

63
Q

quaternary structure is the association of ____ into _____. example: dimers, trimers, tetramers

A

polypeptide monomers inti multisubunit proteins

64
Q

what is a heme group?

A

a porfirin ring with an iron bonded to it. this is the portion where the oxygen binds.

65
Q

what are the structural and functional advantages driving quaternary association?

A
  • stability: reduction of surface to volume ratio
  • genetic economy and efficency
  • bringing catalytic sites together
  • cooperativity
66
Q

what is protein denaturation

A

the disruption of the protein’s structural order wherein the protein loses its biological activity/function

67
Q

denaturation can be brought about by

A

-heat
-large changes in the pH
-detergents such as sds that dirupts hydrophobic interactions
-urea or guanidine which disrupts h bonds
-mercaptoethanol which disrupts disulfide bonds

68
Q

the consensus amino acid sequence that is a repeating heptamer of (-a-b-c-d-e-f-g-) where residues a and d are nonpolar

how many residues are there capped with non helical N- and C-termini?

this protein is rich in?

A

alpha keratin

311-314 residues

cysteine residues and disulfide bridges

69
Q

properties of alpha keratin

A

-strong
-insoluble
-inextensible
-chemically inert

70
Q

What is myoglobin?

A
  • a single polypeptide chain of 153 amino acods
  • a single heme group in a hydrophobic pocket
  • 8 regions of alpha helix and no regions of beta sheet
  • polar portion - surface
  • non polar portion - interior
  • two histidine side chains are in the interior, involved with interaction with the heme group
71
Q

Fe (II) of heme has how many coordinates? How many interacts to what?

A

6 coordinates
4 interact with N atoms of heme
1 with N of a Histidine side chain
1 with either an O2 molecule or an N of the second Histidine side chain

72
Q

hemoglobin is a tetramer made up of

A

two alpha chains having 141 amino acids each and
two beta chains having 153 amino acids each

73
Q

how many heme group does hemoglobin have?

A

4

2 in alpha chain and 2 in beta chain

74
Q

purpose of hemoglobin

A

transports oxygen

75
Q

binding of o2 in hemoglobin is exhibited by positive cooperativity. what is positive cooperativity?

A

when one O2 is bound it becomes easier for the next O2 to bind

76
Q

molecules that affect the ability of the hemoglobin to bind and transport oxygen

A

H+
CO2
Cl-
2,3-bisohosphoglycerate (BPG)

KEMBIO1: Biochemistry 1 (4 decks)

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