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Botany > peptide formation + structure > Flashcards

peptide formation + structure Flashcards

1
Q

stereochemistry of peptide bond

A

trans

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2
Q

true structure of peptide bond

A

resonance hybrid

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3
Q

which is stronger, peptide or single bond

A

peptide

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4
Q

which is longer, peptide or single bond

A

single

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5
Q

protein function

proteins accelerate thousands of biochemical reactions in the cell

A

catalysis

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6
Q

examples of proteins involved in catalysis

A

rubisco (photosynthesis)

hexokinase (first enzyme in glycolysis)

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7
Q

most abundant protein in earth

A

rubisco

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8
Q

first enzyme in glycolysis

A

hexokinase

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9
Q

protein function

some proteins provide protection and support

A

structure

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10
Q

ex of proteins for structure

A

collagen (connective tissue), elastin (elastic fibers), keratin (hair)

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11
Q

protein function

proteins are involved in all cell movements and muscle contraction

A

movement

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12
Q

– movement of sperm and protozoa

A

*dynein

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13
Q

protein function

various proteins have protective functions

A

Defense -

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14
Q

ex proteins for defense

A

keratin

immunoglobulins

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15
Q

protein function

various proteins regulate cellular processes

A
  1. Regulation –
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16
Q

ex proteins for transport

A

glucose transporter
hemoglobin
LDL and HDL
transferrin

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17
Q

storage proteins containing 20 AA

A

Casein and ovalbumin

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18
Q

example of proteins for toxin

A

plant lectins, venom of snake

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19
Q

protein structure
the order or sequence of amino acids in the polypeptide chains
*Peptide bond is a covalent bond

A

primary

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20
Q

protein structure

conformation of the polypeptide backbone

A

2ndary

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21
Q

protein structure

arrangement in space of all atoms in the polypeptide chain

A

tertiary

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22
Q

protein structure
describes the interaction of the subunits in an oligomeric protein
*stabilized by both covalent & non-covalent forces

A

quaternary

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23
Q

levels of protein structure stabilized by covalent and non-covalent forces

A

quaternary and tertiary

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24
Q

has *intersubunit interaction

A

quaternary

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25
Q

has intrasubunit interaction

A

tertiary

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26
Q

what proteins have quaternary structure

A

only oligomericproteinswith ≥ 2 subunits

e.g. dimer

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27
Q

stabilizing force of secondary structure

A

H-bonding between the amide proton and carboxyl oxygen

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28
Q

the sequence of amino acids linked by peptide bonds.

▪ The backbone of a peptide chain or protein.

A

primary structure

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29
Q

Proteins are composed of ___ only

A

L-amino acids

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30
Q

conformation of the polypeptide backbone (stabilized by H-bonding) without side chains

A

secondary

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31
Q

which is stronger? H bond or peptide

A

Peptide bonds

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32
Q

– combination of α-helix & β-pleated sheet

A

random coil

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33
Q

The backbone can change direction by making __

A

reverse turn and loops.

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34
Q

type of secondary structure

Backbone coils into a periodic/repeating, compact structure (rigid)

A

alpha-helix

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35
Q

H-bonds of alpha helix are typically ____ (olarity)

A

amphiphilic

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36
Q

is alpha helix left-handed or right handed

A

right handed

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37
Q

is a “helix-breaker”

  • no more H in Nitrogen of _____; no more H-bonding
  • cannot rotate freely at ф
A

proline

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38
Q

a helix breaker

due to too much flexibility of H atom in _ H atom is too small

A

glycine

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39
Q
  • Polypeptide backbone is almost fully extended.
A

β-pleated sheet (Zigzag)

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40
Q

≥ 2 backbones aligned for H-bonding

A

β-pleated sheet (Zigzag)

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41
Q

Backbones are aligned side by side leading to formation of H-bonds between carbonyl O of one chain & -NH group of the adjacent chain

A

β-pleated sheet (Zigzag)

42
Q

maybe parallel or antiparallel orientation

- more stable than α-helix

A

β-pleated sheet (Zigzag)

43
Q

these AA make reverse turns

A

Proline & glycine

44
Q

this type of 2 structure is typical of fibrous proteins such as silk

A

β-pleated sheet (Zigzag)

45
Q

– combination of coils; higher form of secondary structure

A

SUPERSECONDARY STRUCTURE

46
Q

bonding with the side chain creates a specific overall shape (3-D structure) of the protein
“arrangement of all the atoms”

A

tertiary structure

47
Q

type of conformation wherein Polypeptides fold into its 3-D structure

A

(native conformation)

48
Q

Covalent & Non-covalent Interactions in the 30 Structure

A

H-bonding

  • hydrophobic interaction
  • π- π complexation reaction (specifically for aromatic rings)
  • salt bridge/ionic/electrostatic
  • metal-ion coordination bond (hemoglobin, myoglobin) for transition metal (Fe)
  • oxidation of two cysteine to form cystine
49
Q
  • combination of large number of βαβ motifs
A

*β-barrelor superbarrel

50
Q

– composed of 4 amino acids; due to glycine & proline

A

bends

51
Q

– they do not have regular, periodic structures

A

loop

52
Q

– denaturation of proteins

A

unfolding

53
Q

types of tertiary structure

A

globular
disordered
fibrous

54
Q

type of tertiary structure

interacts well with water and takes a random config

A

disordered

55
Q

type of tertiary structure
many insoluble amino acids
proteins tend to minimize surface to volume ratio

A

globular

56
Q

type of tertiary structure

strong secondary structure allows protein to retain a nonspherical shape

A

fibrous

57
Q

type of protein structure

aggregates of two or more protein chains connected by weak non-covalent interactions

A

quaternary

58
Q

examples of tetramers

A

alcohol dehydrogenase

hemoglobin

59
Q

example of dodecamer

A

glutamine synthetase

60
Q

– has only 10, 20 & 30 structures

A

*MONOMERIC PROTEINS

61
Q

– has 10, 20, 30 & 40 structures

A

*OLIGOMERIC PROTEINS

62
Q

▪ rod-like forming fibers; elongated
▪ insoluble in H2O (because they are structural proteins)
▪ usually has structural functions
▪ e.g. keratin, collagen, elastin

A

Fibrous Proteins

63
Q

▪ spherical shaped
▪ soluble in H2O
▪ mostly functions as enzymes; for catalysis (non-structural functions)
▪ the interior is highly hydrophobic; amino acids are nonpolar inside
▪ the surface of the globular protein has polar amino acids
▪ e.g. casein, albumin, hormones

A

Globular Proteins

64
Q

approximately spherical in shape; consist of several different lobes called domains
◦ hydrophobic core; hydrophilic external surface that reacts with water
◦ highest level maybe 30 or 40

A

Globular Proteins`

65
Q

◦ elongated molecules in which the 20 structure (either α-helices or β-pleated sheets) is the dominant structure.
◦ muscle movement and cilliary proteins
◦ insoluble in water; structural functions
◦ often have repeating structures
◦ generally have 10 and 20 structures only

A

FIBROUS PROTEINS

66
Q

amide linkages between the α-carboxyl group of one amino acid and the α-amino group of another
-not broken by conditions that denature proteins, such as heating or high concentrations of urea

A

peptide bonds

67
Q

each component amino acid in a polypeptide
-named as such because it is the portion of the amino acid remaining after the atoms of water are lost in the formation of peptide bond.

A

Residue –

68
Q

Bonds between ___ can be freely rotated (which allows the polypeptide chain to assume a variety of configurations

A

α-carbons and the α-amino or α-carboxyl groups

69
Q

_____ of the peptide bond are uncharged, polar, and involved in hydrogen bonds

A

-C=O and –NH groups

70
Q

– sequence of amino acids

  • order in which amino acids are covalently linked by peptide bonds; one dimensional
  • important to understand because many genetic diseases result in proteins with abnormal amino acid sequences
  • dictates the secondary structure
A

primary structue

71
Q
  • folding of the backbone
  • regular folding
  • have repetitive interactions resulting from hydrogen bonding
  • conformations of the side chain are not part of —– structure
A

SECONDARY STRUCTURE

72
Q
  • spatial arrangement of the atoms in a polypeptide chain

- interaction: H-bond between the amide proton and carbonyl oxygen

A

SECONDARY STRUCTURE

73
Q
  • spiral structure consisting of a tightly packed, coiled polypeptide backbone core
  • side chains extend outward to avoid steric interference
A

alpha helix

74
Q

• stabilized by extensive hydrogen bonding between peptide-bond carboxyl oxygens and amide hydrogens

  • hydrogen bonds extend up and are parallel to the spiral
  • intramolecular H-bonds
A

alpha helix

75
Q

disrupts the helix because its secondary amino group is not geometrically compatible with the right-handed spiral of the helix
-inserts a kink in the chain

A

Proline –

76
Q

disrupt the helix by forming ionic bonds or by repelling each other

A

Charged amino acids

77
Q

all of the peptide bond components are involved In the hydrogen bonding
-surfaces appear pleated

A

β-sheet

78
Q

have hydrogen bonds perpendicular to the polypeptide backbone, instead of parallel.

A

β-sheet

79
Q

– when hydrogen bonds are formed between the polypeptide backbones of separate polypeptide chains

A

Interchain bonds

80
Q

when a β-sheet is formed by a single polypeptide chain folding back on itself

A

Intrachain bonds

81
Q

– usually produced by packing side chains from adjacent secondary structural elements close to each other
-combinations of alpha and beta strands

A

Supersecondary Structures

82
Q

– repetitive supersecondary structure

A

Motif

83
Q

Other secondary structures (3)

A
  • Other helix structures
  • Random coils
  • Reverse turns or β-bends
84
Q

– almost similar with β-pleated sheet but there are bends

-glycine and proline are frequently encountered in reverse turns

A

Reverse turns or β-bends

85
Q

– refers to both folding of domains and final arrangement of domains in the polypeptide

  • three-dimensional arrangement
  • important aspect: arrangement of side chains as AA residues
A

Tertiary

86
Q

– covalent linkage formed from the sulfhydryl group of each of two cysteine residues

A

Disulfide bond

87
Q
  • spatial arrangement of polypeptide subunits

- interactions: same with tertiary structure

A

quaternary

88
Q
  • unfolding of a protein

- loss of high-level of structural organization of protein except for primary structure

A

DENATURATION

89
Q

-denaturing agents (6)

A
  1. Heat – increase in temp
  2. Change in Ph – high or low extremes of ph
  3. Organic solvents (alcohol, urea) – urea may form stronger H-bonds and can disrupt hydrophobic interactions
  4. Detergents (SDS) – disrupt hydrophobic interactions
  5. Salts of heavy metals
  6. Performic acid and 2-mercaptoethanol
    Β-mercaptoethanol – reduce disulfide bridges to two sulfhydrryl groups
90
Q
  • may be acid, base, neutral hydrolysis

- breakdown of peptide bond or the primary structure

A

HYDROLYSIS

91
Q

leads to unfolding of protein and subsequent loss of biological function

A

denaturation

92
Q

remains of hydrolysis

A

individual aa

93
Q

remains of denaturation

A

group of aa

94
Q

physical agents of protein denaturation

A

Heat or temperature

Mechanical agitation or stress

95
Q

by applying __, bubbles will form (foam) which signifies denaturation
e.g. Bradford assay

A

stress

96
Q

a chemical agent which targets the salt bridges in the protein.

A

Strong acid

97
Q

Chemical agents

target ionic interactions with protein

A

Strong acids and bases

98
Q

Most common reducing agents are for breaking ____ bonds

A

disulfide

99
Q

reducing agents

A
  1. β-mercaptoethanol

2. Dithiothreitol (DTT)

100
Q

▪ target proteins in the body particularly the enzymes
▪ target cysteine side chain (-SH) which is very important in protein
-SH + Hg → -SHg
▪ target charged interaction

A

heavy metal ions

Botany (324 decks)

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