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anatomy > BIOCHEM - Protein & Amino acid chemistry > Flashcards

BIOCHEM - Protein & Amino acid chemistry Flashcards

1
Q

characteristics of proteins

A
  1. organic nitrogenous substances (CHON)
  2. high molecular weight (a big macromolecule)
  3. found in all plant and animal cells
  4. consist of alpha-amino acids
  5. linked by peptide bonds
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2
Q

FUNCTIONS OF PROTEINS:

A
  1. Catalyst of chemical reactions - enzymes
  2. Transport and storage - hemoglobin
  3. Coordinated motion - actin and myosin
  4. Mechanical support - collagen and keratin (structural proteins)
  5. Immune protection - gamma globulins
  6. Transmission of nerve impulses -neurotransmitters
  7. Cell signaling - membrane receptors
  8. Hormones – insulin, thyrotropin, somatotropin
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3
Q

another example of transport protein.

Example of a substance stored by our
proteins is iron

A

Albumin

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4
Q

These serve as a communication, along
with hormones.

that are derived from amino acids

A

neurotransmitters

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5
Q

SIMPLE PROTEINS:

A
  1. Albumin
  2. Globulin
  3. Glutelin
  4. Prolamine
  5. Albuminoid
  6. Histone
  7. Protamine
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6
Q

soluble in water and dilute aqueous salt solution; heat coagulable

a plasma protein that acts as a transporter. It transports a lot of things in our blood.

A

Albumin

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7
Q

insoluble in water; soluble in aqueous salt soln; heat coagulable

A

Globulin

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8
Q

soluble in dilute acids and alkalies; heat coagulable

ex. plant proteins – glutenin (wheat), oryzenin (rice)

A

Glutelin

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9
Q

alcohol-soluble protein

ex: seed proteins – zein (corn), gliadin
(wheat)

A

Prolamine

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10
Q

least soluble

ex: animal proteins – keratin, collagen

A

Albuminoid

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11
Q

basic protein; soluble in water, dilute acid and alkali; found in combination with DNA

A

Histone

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12
Q

simplest; basic; soluble in water, dilute ammonia, acid and alkali; found in spermatozoa

A

Protamine

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13
Q

CONJUGATED PROTEINS (proteins that
contain other functional groups or other
macromolecules):

A
  1. Nucleoproteins
  2. Glycoproteins and proteoglycans
  3. Chromoproteins
  4. Lipoproteins
  5. Metalloproteins
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14
Q

contain nucleic acid (DNA, RNA) as the prosthetic group

Ex. histones

A

Nucleoproteins

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15
Q

contain carbohydrates

____________ have more carb content than proteins.

___________ have more protein content than carbs.

A

proteoglycans

Glycoproteins

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16
Q

contain prosthetic groups that give color

ex. hemoglobin
- Iron is the prosthetic group

A

Chromoproteins

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17
Q

have groups
other than our macromolecules

A

Prosthetic group

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18
Q

associated with lipids
ex. VLDL chylomicron, LDL, HDL

  • Transporters of lipids in the body
A

Lipoproteins

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19
Q

contain minerals

ex. iron in cytochromes

A

Metalloproteins

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20
Q

Somewhat similar to chromoproteins except that in chromoproteins, their prosthetic group would give them color

_________ would contain metal as their prosthetic group like iron, copper, or magnesium

A

Metalloproteins

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21
Q

CLASSIFICATION BASED ON THE SHAPE AND CERTAIN PHYSICAL CHARACTERISTICS:

A

A. FIBROUS PROTEINS
B. GLOBULAR PROTEINS

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22
Q
  • tough
  • involved in structural functions
  • ex. collagen, keratin
A

FIBROUS PROTEINS

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23
Q

(has more functions as transport proteins or enzymes)

  • involved in mobile and dynamic functions
  • ex. enzymes, plasma proteins, hemoglobin
A

GLOBULAR PROTEINS

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24
Q

FUNCTIONS OF AMINO ACIDS:

A
  1. Building blocks of proteins
  2. Precursor of various substances
  3. Source of energy
  4. Special amino acids as components of certain types of proteins
  5. Phosphorylation and dephosphorylation
  6. Chemical messengers
  7. Metabolic intermediates
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25
Q

proteins as Precursor of various substances

A

a. Glycine
b. Glutamic acid
c. Phe and Tyrosine
d. Tryptophan

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26
Q

the precursor of heme, purine, creatine

A

Glycine

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27
Q

the precursor of GABA

A

Glutamic acid

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28
Q

the precursor of thyroxine, & epinephrine

A

Phe and Tyrosine

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29
Q

the precursor of niacin, serotonin,
melatonin

A

Tryptophan

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30
Q

If our glucose and fat storage is already
depleted, the next thing that is used for
energy would be_________.

A

amino acids

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31
Q

substrate for the building blocks of our proteins

A

amino acids

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32
Q

during prolonged cases of low blood glucose or starvation, the _________ is used as a source of energy

A

amino acids

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33
Q

Special amino acids as components of certain types of proteins:

A

a. Hydroxyproline & hydroxylysine
b. Gamma-carboxyglutamic acid
c. Desmosine (derivative of lysine)

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34
Q

component of collagen

A

Hydroxyproline & hydroxylysine

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35
Q

component of prothrombin

A

Gamma-carboxyglutamic acid

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36
Q

component of elastin

A

Desmosine (derivative of lysine)

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37
Q

Phosphorylation and dephosphorylation of
amino acids with rings such as _____________.

__________ play a major role in activation and inactivation (or inhibition) of enzymes

A

serine

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38
Q

In cell signaling, there are other amino
acid residues found on receptors that are
important in communication such as
_________, ___________, & ____________

A

serine, threonine, and tyrosine

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39
Q

amino acids or their derivatives act as
chemical messengers example:

A

GABA, serotonin

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40
Q

amino acids act as metabolic intermediates:

A

a. Arg, citrulline, ornithine
b. amino acids that are converted to the intermediates of the Krebs cycle

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41
Q

amino acids metabolic intermediates in urea cycle:

A

Arg, citrulline, ornithine

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42
Q

Each amino acid has a central carbon, called the _________, to which four different groups are attached (chiral carbon):

A

alpha carbon

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43
Q

4 groups of amino acids:

A
  1. basic amino group (-NH2)
  2. acidic carboxyl group (-COOH)
  3. hydrogen atom (-H)
  4. distinctive side chain (-R)
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44
Q

its distinct side chain is a hydrogen atom hence it is not chiral anymore

A

Glycine

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45
Q

DIFFERENT FORMS OF AN AMINO ACID:

A
  1. Unionized form
  2. Ionized form
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46
Q

Ala or A

A

Alanine

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47
Q

Arg or R

A

Arginine

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48
Q

Asn or N

A

Asparagine

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49
Q

Asp or D

A

Aspartic acid

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50
Q

Cys or C

A

Cysteine

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51
Q

Glu or E

A

Glutamic acid

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52
Q

Gln or Q

A

Glutamine

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53
Q

Gly or G

A

Glycine

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54
Q

His or H

A

Histidine

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55
Q

Ile or I

A

Isoleucine

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56
Q

Leu or L

A

Leucine

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57
Q

Lys or K

A

Lysine

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58
Q

Met or M

A

Methionine

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59
Q

Phe or F

A

Phenylalanine

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60
Q

Pro or P

A

Proline

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61
Q

Ser or S

A

serine

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62
Q

Trp or W

A

Tryptophan

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63
Q

Thr or T

A

Threonine

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64
Q

Tyr or Y

A

Tyrosine

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65
Q

Val or V

A

Valine

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66
Q

CLASSIFICATION OF AMINO ACID
BASED ON R-GROUP (overview only)

A
  1. Amino acids with nonpolar or hydrophobic R groups
  2. Amino acids with uncharged polar R groups
  3. Amino acids with positively charged R groups
  4. Amino acids with negatively charged R groups
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67
Q

Amino acids with nonpolar or hydrophobic R groups:

A

a. Amino acids with aliphatic side chains
b. Amino acid with aromatic side chains

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68
Q

Amino acids with aliphatic side chains:

A
  1. Glycine
  2. Alanine
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69
Q

Branched-chain amino acids (aliphatic):

A
  1. Valine
  2. Leucine
  3. Isoleucine
  4. Methionine
  5. Proline
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70
Q

Amino acid with aromatic side chains:

A
  1. Phenylalanine
  2. Tryptophan
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71
Q

Amino acids with uncharged polar R groups:

A

a. Hydroxyl-containing amino acids
b. Amide derivatives of Glu and Asp

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72
Q

Hydroxyl-containing amino acids:

A
  1. Serine
  2. Tyrosine
  3. Threonine
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73
Q

Amide derivatives of Glu and Asp:

A
  1. Glutamine
  2. Asparagine
  3. Cysteine (Thiol Group)
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74
Q

Amino acids with positively charged R groups
a. Basic amino acids

A
  1. Lysine
  2. Arginine
  3. Histidine
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75
Q

Amino acids with negatively charged R groups
a. Acidic amino acids

A
  1. Glutamic acid
  2. Aspartic Acid
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76
Q

● Neutral amino acids
● R groups do not bear (+) or (-) charges
● Interact poorly with water
● Play an important role in maintaining the
conformation or 3-dimensional structure of proteins

A

AMINO ACIDS WITH NONPOLAR OR
HYDROPHOBIC R GROUPS

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77
Q

Within nonpolar groups, there could be
interactions (bonding / ___________
force on non-polar).

Due to this force, they could play a role in maintaining the stability of the protein conformation.

A

Van der Waals

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78
Q

Amino acids with aliphatic (straight
hydrocarbon) side chains

A
  1. Glycine
  2. Alanine
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79
Q

simplest amino acid.

its R group: Hydrogen only; the only amino acid that is NOT CHIRAL

A

Glycine

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80
Q

Alanine R group:

A

Methyl group (CH3)

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81
Q

Branched because there is tree-like branching in their R group

Differs in hydrocarbon length

A

Branched-chain amino acids

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82
Q

Branched-chain amino acids:

A
  1. Valine
  2. Leucine
  3. Isoleucine
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83
Q

these amino acids are the ones affected by metabolic errors for branched chain amino acid metabolism

A

LIV - branched chain

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84
Q

Other examples of branched-chain amino acids, but belongs to another group

A
  1. Proline
  2. Methionine
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85
Q

R group is a distinct closed ring

Secondary amino acid or an imino acid

Nitrogen is bonded to the α-carbon and the side-chain group

A

Proline

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86
Q

what do you call when amino group is NH2 instead of NH3

A

imino acid

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87
Q

what do you call when NH is unable to
bond because it is part of the R group

A

helix-breaker

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88
Q

Sulfur-containing, non-polar amino acid

A

Methionine

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89
Q

Methionine is converted to ___________, an
important methyl group donor in methylation reactions,

since it is able to donate the CH3 in its R group

A

S-adenosylmethionine (SAM)

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90
Q

Amino acid with aromatic side chains:

A
  1. Phenylalanine (benzene ring)
  2. Tryptophan (indole ring)
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91
Q

contain unsaturations or double
bonds

A

aromatic

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92
Q

has CH2 in its R group which would contain the phenyl group (“piattos”)

A

Phenylalanine

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93
Q

Alanine R group is CH3, while here, instead
of additional hydrogen, phenyl group is
attached

A

Phenylalanine

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94
Q

the largest of all twenty amino acids

side chain is indole, which is aromatic with a binuclear ring structure

has phenyl group and attached to that phenyl ring is a 5-membered ring

A

Tryptophan; indole

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95
Q

have functional groups capable of hydrogen bonding

-OH groups serve other functions in proteins

A

AMINO ACID W/ UNCHARGED POLAR R GROUP

96
Q

AMINO ACID W/ UNCHARGED POLAR R GROUP:

A

A. Hydroxyl (-OH) -containing amino acids
B. Amide derivatives of Glutamine and Asparagine

97
Q

OH groups serve other functions in proteins:

Formation of the phosphate ester of
____________is a common regulatory mechanism

Formation of hydrogen bonds with other
macromolecules that would contain covalent bonds

OH groups of ___________& ___________ are
points for attaching carbohydrates

A

Tyrosine

Serine and Tyrosine

98
Q

Hydroxyl (-OH) -containing amino acids

A
  1. Serine
  2. Threonine
  3. Tyrosine
99
Q

Important in cell-to-cell communication, because these are sites of phosphorylation reaction;

-OH can be used as attachment for phosphate groups, which in turn can either activate or inhibit the enzymes - important in regulation of enzyme activity

site of glycosylation reaction - important in
formation of mucin

A

Hydroxyl (-OH) -containing amino acids

100
Q

Simplest amino acid that contains the -OH group

A

Serine

101
Q

Has branching but still contain -OH

A

Threonine

102
Q

Closely related to Phenylalanine;

difference: additional -OH group

A

Tyrosine

103
Q

Glutamine is derived from _________

Asparagine is derived from _________

A

Glutamic acid

Aspartic acid

104
Q

Glutamine and Asparagine Contains -NH2 instead of ________

A

-OH

105
Q

Important in detoxification of ammonia

Able to get extra ammonia from the body
system.

Ammonia will be taken up by _________ & ___________ to form Glutamine and Asparagine

A

Glutamate and Aspartate

106
Q

lower down our ammonia level, such
that __________is the primary source of urinary ammonia

A

Glutamine

107
Q

Instead of -OH, it contains a sulfhydryl (-SH) group (a.k.a. thiol group)

● Important in maintenance of protein
structure (e.g. insulin, immunoglobulins)

A

Cysteine

108
Q

Two cysteine residues combine and form a strong disulfide bond, and _______ is the resulting product.

A

cystine

109
Q

Principle behind hair rebonding is that the
chemicals used break the disulfide linkages between _______ residues, and by doing so, protein structure is lost.

A

cysteine

110
Q

the 21st L-α-Amino Acid

➢ Found in peroxidases and reductases

A

Selenocysteine

111
Q

Selenium (Se) atom replaces the sulfur of its structural analog __________

A

cysteine

112
Q

There is no codon for this amino acid

➢ Inserted into the polypeptide during translation

A

selenocysteine

113
Q

Selenocysteine is not inherently introduced by your sense from your DNA, RNA

what happens is that during the synthesis of your cysteine, it is modified, hence ____________ forms selenocysteine

A

posttranslational modification

114
Q

AMINO ACID W/ POSITIVELY CHARGED R GROUP:

A

Basic amino acids - have a net positive charge

  1. Lysine
  2. Arginine
  3. Histidine
115
Q

contains the guanido group

A

Arginine

116
Q

contains the imidazole group

A

Histidine

117
Q

responsible for the buffering capacity of hemoglobin

A

Histidine

118
Q

AMINO ACID W/ NEGATIVELY CHARGED R GROUP:

A

Acidic amino acids
1. Glutamic acid or Glutamate
2. Aspartic acid or aspartate

119
Q

interactions between acidic and basic amino acids results in the formation of ionic bond aka ________________

A

salt bond, electrostatic bond

120
Q

Important in maintaining protein structure:

A
  1. Glutamic acid or Glutamate
  2. Aspartic acid or aspartate
121
Q

Types of interactions entered into by the different R groups of amino acids:

A

1.Hydrogen bonding
2. Ionic interaction
3. Hydrophobic interactions of nonpolar R grps
4. Disulfide bond

122
Q

Hydrogen is attracted to other electron rich areas

A

Hydrogen bonding

123
Q

examples of Hydrogen bonding

A

a. -O-H …….. O=C
b. -O-H …….. O
c. -S-H ……… O

124
Q

usually involved in the carboxyl grp and amino grp of another amino acid

-COO- ……..NH3+

A

Ionic interaction

125
Q

Hydrophobic interactions of nonpolar R grps :

A

Van der Waals interaction

126
Q

PHYSICAL PROPERTIES OF AMINO ACID:

A
  1. Solubility
  2. Melting points
  3. Taste
  4. Appearance
  5. Optical property
  6. Ultraviolet absorption spectrum of aromatic amino acids
  7. Acid-base properties
127
Q

For all the standard amino acids, except _____________, the & carbon is asymmetric , bonded to four different substituent groups.

In this case the &-carbon is a chiral center

A

glycine

128
Q

All molecules with a chiral center are _____________

ex. they can rotate the plane-polarized light either to the right (dextrorotatory) or to the left (levorotatory).

A

optically active

129
Q

D and L amino acids
- due also to the presence of chiral center

A

Stereoisomerism

130
Q

Ultraviolet absorption properties of proteins are determined solely by __________, ___________, & _____________(Aromatic AA)

A

Phe, Tyr and Trp

131
Q

The amino (NH3) and carboxylic acid (COOH) groups readily ionize

A

Acid-base properties

132
Q

Amino will give off its H and will be ______________charged (NH3 -> NH2+)

A

positively

133
Q

Carboxylic acid will donate H and will be
______________charged (COOH -> COO-)

A

negatively

134
Q

pK (&-COOH)

A

around pH 2.2

135
Q

pK (&-NH2)

A

around pH 9.4

136
Q

is a constant that determines that R grp is able to give off or receive protons.

A

pK

137
Q

COOH will be COO- at pH 2.2 but at pH 1
which is below ph 2.2 , what will happen?

A

it will not give off H and will remain as COOH

138
Q

Amino grp will not donate proton at lower pH (less than pH 9.4) like pH 7 (neutral) - it will remain as NH3 but at higher pH beyond pH 9.4 , what will happen?

A

the amino grp will become NH2+

139
Q

An amino acid can act as a base or proton
recipient and an acid or proton donor
(amphoteric).

T or F?

A

True

140
Q

Different Forms of an Amino Acid:

A
  1. Unionized form
  2. Dipolar ion or zwitterion form
  3. Fully protonated form (pH 1)
  4. Fully ionized form (pH 11)
141
Q

electrically neutral; zero charge

number of positive charge equal to number of negative charge

A

Zwitterion

142
Q

remain stationary in an electrical field

A

Dipolar ion or zwitterion form

143
Q

Form of an Amino Acid that has net
positive charge (+)

A

Fully protonated form (pH 1)

144
Q

Form of an Amino Acid that is negatively charge at higher pH

A

Fully ionized form (pH 11)

145
Q

is the step-by-step dissociation of the amino acid starting from the fully protonated or positive form up to the fully ionized or negative form.

A

Protonic equilibria (Titration of Amino Acids)

146
Q

can predict the charge of the amino acid in a given solution with known pH

can devise a procedure of separating amino acids based on their charge

A

uses of Protonic equilibria (Titration of Amino Acids)

147
Q

That pH at which an amino acid bears no net charge and hence does not move in an electrical field.

  • That pH exactly at the midpoint between the pK values on either side of the zwitterion species.
A

Isoelectric Point (pHI, pI, IpH)

148
Q

The pI of neutral amino acids are in the neighborhood of 6.0;

acidic amino acids – very much below 6.0;

basic amino acids – very much above 6.0.

A

true

149
Q

titration: At lower pH, if the pKa is 2.34 for the COOH, lower than that (example pH 1) there will be no donation of hydrogen.

So the overall net charge of the whole
amino structure is +1

what will happen if the pH already exceeded the pKa of the carboxyl group (example pH 7.4)?

A

the carboxyl group can now readily donate the proton and the net charge of this Alanine is now 0 because the negative
charge cancels out the positive charge in the amino group

150
Q

in the isoelectric zwitterion of Alanine with carboxyl group COO- has pKa of 9.69, what will happen to it in pH 10?

A

it now exceed the pKa of the Amino group so the amino group donates the
proton, the positive charge disappears and what is left behind is the negative charge.

So if we calculate the net charge, it will be -1

151
Q

how to compute for the isoelectric point ?

A

by getting the average of the pKa of the different groups

pI = pK 1 + pK 2 / 2

152
Q

where the amino acid is electrically neutral

A

isoelectric point

153
Q

dissociation constant of &-COOH (most acidic)

A

pK1

154
Q

If the R group is able to donate or receive H+.

how are you gonna determine the pI?

A

The basic and acidic amino acids have an additional dissociation constant so there will be an additional pKa that will help you determine the isoelectric point of that amino acid.

155
Q

amino acid polymers with low molecular
weights, typically consisting of less than 50 amino acids.

A

Peptides

156
Q

more than 50 amino acids

A

Proteins

157
Q

consisting of 2 to 10 amino acids

A

Oligopeptides

158
Q

have more than 10 amino acid residues

A

Polypeptides

159
Q

PEPTIDES WITH SIGNIFICANT BIOLOGIC ACTIVITIES

A

1.Glutathione
2. Oxytocin and vasopressin
3. Met-enkephalin and Leu-enkephalin
4. Atrial natriuretic factor
5. Substance P and bradykinin
6. Glucagon
7. Corticotropin
8. Aspartame

160
Q

(gamma-glutamyl-L-cysteinylglycine)

reducing agent; due to –SH group

A

Glutathione

161
Q

It is the cysteine group esp. the Sulfhydryl group that is important in its activity.

It has to be in an -SH form to be a good reducing agent/ antioxidant (reduced form)

A

Glutathione

162
Q
  • protects the cell from the destructive effects of oxidation by peroxides
  • works hand in hand with glutathione peroxidase
A

Glutathione

163
Q

Glutathione is Composed of 3 amino acids:

A

Glutamate, Cysteine, Glycine

164
Q

contain nine amino acid residues

A

Oxytocin and vasopressin

165
Q

stimulates contraction of uterine muscle during childbirth

A

oxytocin

166
Q

is an antidiuretic hormone; stimulates water reabsorption in the kidney

A

vasopressin

167
Q

pentapeptide; opioid peptides

  • relieve pain; bind to receptors in the brain and induce analgesia
A

Met-enkephalin and Leu-enkephalin

168
Q
  • has 28 amino acid residues
  • stimulates the production of a dilute urine.
A

Atrial natriuretic factor

169
Q

The effect is opposite of that Vasopressin.

A

Atrial natriuretic factor

170
Q

stimulate the perception of pain

A

Substance P and bradykinin

171
Q

has 29 amino acid residues

  • opposes the action of insulin
A

Glucagon

172
Q

with 39 amino acid residues;

stimulates adrenal cortex

A

Corticotropin

173
Q

artificial sweetener

A

Aspartame (L-aspartyl phenylalanine methyl ester)

174
Q

The formation of your peptide bond is
very similar to Glycosidic bond, it is a condensation reaction or a dehydration reaction but the interaction is between the ______________

A

carboxyl group of Amino Acid 1 and the
Amino group of Amino Acid 2

175
Q

LEVELS OF STRUCTURAL ORGANIZATION OF PROTEINS:

A

a. Primary Structure
b. Secondary Structure
c. Tertiary Structure
d. Quaternary Structure

176
Q
  • quantitative amino acid composition
  • sequence of amino acids
  • number of peptide chains
A

PRIMARY STRUCTURE

177
Q

Most abundant amino acid in proteins:

A

Leu,
Ala,
Gly,
Ser,
Val
Glu

178
Q

Rarest in proteins are

A

Trp,
Cys,
Met
His

179
Q

The backbone of a protein refers to the

A

atoms that participate in the formation of peptide bonds

180
Q

The 3-dimensional shape of a folded polypeptide is result of the interactions among the ____________

A

R groups

181
Q

Due to the formation of hydrogen bonds between peptide bonds

A

SECONDARY STRUCTURE

182
Q

Two types of secondary structure:

A
  1. Coils or helices
  2. Sheets or pleats
183
Q

intrachain hydrogen bonding

A

Coils or helices

184
Q

interchain hydrogen bonding

A

Sheets or pleats

185
Q

discovered by Linus Pauling in 1951

A

Alpha-helix

186
Q

Stabilized by INTER-residue hydrogen bonds formed bet.

the H atom attached to a peptide N and the carbonyl O of the residue 4th in line behind in the primary structure

Each peptide bond participates in hydrogen bonding

A

Alpha-helix

187
Q

forms spontaneously as it is the lowest energy, most stable conformation for a polypeptide chain.

A

alpha-helix

188
Q

There are ___________________amino acid residues per turn with a pitch of .54 nm (5.4 A); spacing per residue is .15 nm (1.5 A)

  • Amino acid R groups extend outward from the helix
A

3.6

189
Q

distance bet. corresponding points per turn

A

pitch

190
Q

FACTORS THAT DESTABILIZE (destroy) THE ALPHA HELIX:

A
  1. Presence of adjacent similarly charged
    amino acids (like charges repel)
  2. Presence of adjacent bulky R groups. (groups with aromatic ring)
  3. Presence of proline
191
Q

Why presence of proline destabilize the alpha helix?

A
  • contains rigid ring that prevents the N-C bond from rotating
  • no N-H group available to form intrachain
    hydrogen bonds

(helix breaker; incapable of forming
hydrogen bonding)

192
Q

destabilize = ________

A

destroy

193
Q

second most commonly occurring protein 2 degree structure

A

BETA-PLEATED SHEET

194
Q

Formed when 2 or more almost fully extended polypeptide chains lie side by side such that hydrogen bonding occurs between adjacent peptide chains

A

BETA-PLEATED SHEET

195
Q

Hydrogen bonds in beta-pleated sheets are ______________

A

interchain

196
Q

Amino acids with less bulky R groups are
present

A

BPS

197
Q

BETA-SHEETS OCCUR IN TWO DIFFERENT
ARRANGEMENTS:

A
  1. ANTIPARALLEL BETA-SHEET
  2. PARALLEL BETA-SHEETS
198
Q
  • neighboring H bonded polypeptide
    chains run in opposite directions
  • more stable because the H bond in between is somewhat perpendicular to the plane
A

ANTIPARALLEL BETA-SHEET

199
Q

hydrogen bonded chains extend in the
same direction.

A

PARALLEL BETA-SHEETS

200
Q

FACTORS THAT DESTABILIZE THE BETA-PLEATED SHEETS:

A
  1. Bulky R groups.
  2. R groups with like charges
201
Q

SUPERSECONDARY STRUCTURES OR MOTIFS:

A

● Combinations of 2 degree structure
● Occur as part of a larger functional unit
● Have a particular function
● Have different functions in different proteins
● Have roughly 10 to 40 amino acid residues each

202
Q

COMMON SUPERSECONDARY STRUCTURES:

A
  1. Helix-loop-helix
  2. Coiled-coil motif
  3. Beta-alpha-beta unit
  4. Hairpin
  5. Zinc finger
  6. Leucine zipper
  7. Greek key

in picture:
8. Beta-meander
9. alpha-alpha units
10. beta-barrel

  1. EF hand - E helix and F helix
  2. Leucine zipper
  3. Zinc finger
203
Q

3-dimensional structure

● Protein conformation

● Results from further folding of a poly-peptide with regions of α-helix and/or beta-sheet, into a closely packed, nearly spherical shape

A

TERTIARY STRUCTURE

204
Q

Indicates how 2 degree structural features – helices, sheets, bends, turns and loops assemble to form domains.

A

TERTIARY STRUCTURE

205
Q

Amino acid residues that are distant from each other in the 1 degree structure come into close proximity when the polypeptide folds

A

tertiary structure

206
Q

When polypeptide folds, proteins become more compact; most water molecules are excluded from the proteins’ interior making possible the interactions between

A

polar and nonpolar Amino Acids

207
Q

Large globular proteins (> 200 AA) often
contain several compact units called ________

A

domains

208
Q

are structurally independent segments
that have specific functions (e.g. binding an ion)

A

Domains

209
Q

TYPES OF INTERACTIONS THAT STABILIZE
TERTIARY STRUCTURE:

A

● Hydrophobic interactions [R leu] [CH3] [aromatic rings]
● Electrostatic interactions (salt bridges) [NH3+]

● Hydrogen bonds [O…H]
● Covalent bonds (disulfide bridges) [SH - SH]

210
Q

PROTEIN FOLDING IS ASSISTED BY :

A

MOLECULAR CHAPERONES AND ENZYMES

211
Q

– proteins that have the net effect of increasing the rate of correct folding by binding newly synthesized polypeptides before they are completely folded.

  • assist in the translocation of polypeptide
    chains across membranes
A

Molecular chaperones

212
Q

examples of molecular chaperons

A

heat-shock proteins, chaperonins

213
Q

Enzymes involved in protein folding:

A
  1. Peptidyl prolyl cis-trans isomerase
  2. Protein-disulfide isomerase
214
Q

they are discrete, independent folding units within the 30 structure that perform a particular task such as binding of a substrate or other ligand

A

DOMAINS OR LOBES

215
Q

they consist of combinations of several units of supersecondary structures.

A

DOMAINS OR LOBES

216
Q

Size of domains varies from 25-30 to about 300 amino acid residues, with an average of about _____ amino acids.

A

100

217
Q

Exhibited only by proteins containing more than one polypeptide chain.

● Most proteins with molecular masses above 100 kD, consist of more than one polypeptide chain

A

QUATERNARY STRUCTURE

218
Q

Each polypeptide component is called a
______________

maybe identical or different

A

subunit

219
Q

proteins are those with more than one subunit

A

Oligomeric

220
Q

are identical subunits.

A

Protomers

221
Q

describes the characteristic manner in which the individual , folded polypeptide chains fit each other or interact with one another so that they can act as one single molecule.

A

Quaternary structure

222
Q

When you have more than 1 tertiary structure, you have a _________

A

Quaternary structure

223
Q

a classic example of a quaternary
structure, has 4 subunits. Each subunit has a tertiary structure.

When you combine them together, you have the quaternary structure of
the ————

A

Hemoglobin

224
Q

INTERACTIONS THAT HOLD SUBUNITS TOGETHER:

A

● Hydrophobic interactions
● Electrostatic interactions
● Hydrogen bonds
● Interpolypeptide disulfide bonds

225
Q

are the principal forces that hold the subunits together

A

Hydrophobic interactions

226
Q

contribute to the proper alignment of the subunits

A

Electrostatic forces

227
Q

occurs when a protein loses its native
secondary, tertiary and/or quaternary structure;

there is cleavage of noncovalent bonds

always correlated with the loss of a protein’s function

A

DENATURATION OF PROTEINS

228
Q

DENATURING AGENTS:

A

A. PHYSICAL AGENTS
B. CHEMICAL AGENTS

229
Q

examples of PHYSICAL AGENTS

A

● extremes of pH and temperature
● high pressure
● ultraviolet light
● ultrasound

230
Q

examples of CHEMICAL AGENTS

A

● organic solvents – acids, alkali, urea, guanidine
● Detergents

231
Q

substances that would disrupt ionic bridges (electrostatic bonds) in between proteins (e.g. soap, lysol)

A

Detergents

232
Q

CHEMICAL ALTERATIONS

A
  1. Decrease in solubility – most visible effect in globular proteins
  2. Many chemical groups which were inactive become exposed and more readily detectable
233
Q

Whenever there is decrease in solubility, it can also signify a loss of _________

A

function

234
Q

PHYSICAL ALTERATIONS:

A

● increased viscosity
● decreased rate of diffusion
● increased levorotation
● cannot be crystallized

All of these would result in the loss of function of the proteins.

235
Q

BIOLOGICAL ALTERATIONS:

A

● increased digestibility
● enzymatic or hormonal activity is destroyed
● antibody functions are altered

236
Q
A

anatomy (15 decks)

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