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Flashcards in peptide formation + structure Deck (100):
1

stereochemistry of peptide bond

trans

2

true structure of peptide bond

resonance hybrid

3

which is stronger, peptide or single bond

peptide

4

which is longer, peptide or single bond

single

5

protein function
proteins accelerate thousands of biochemical reactions in the cell

catalysis

6

examples of proteins involved in catalysis

rubisco (photosynthesis)
hexokinase (first enzyme in glycolysis)

7

most abundant protein in earth

rubisco

8

first enzyme in glycolysis

hexokinase

9

protein function
some proteins provide protection and support

structure

10

ex of proteins for structure

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

11

protein function
proteins are involved in all cell movements and muscle contraction

movement

12

– movement of sperm and protozoa

*dynein

13

protein function
various proteins have protective functions

Defense -

14

ex proteins for defense

keratin
immunoglobulins

15

protein function
various proteins regulate cellular processes

5. Regulation –

16

ex proteins for transport

glucose transporter
hemoglobin
LDL and HDL
transferrin

17

storage proteins containing 20 AA

Casein and ovalbumin

18

example of proteins for toxin

plant lectins, venom of snake

19

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

primary

20

protein structure
conformation of the polypeptide backbone

2ndary

21

protein structure
arrangement in space of all atoms in the polypeptide chain

tertiary

22

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

quaternary

23

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

quaternary and tertiary

24

has *intersubunit interaction

quaternary

25

has intrasubunit interaction

tertiary

26

what proteins have quaternary structure

only oligomericproteinswith ≥ 2 subunits
e.g. dimer

27

stabilizing force of secondary structure

H-bonding between the amide proton and carboxyl oxygen

28

the sequence of amino acids linked by peptide bonds.
▪ The backbone of a peptide chain or protein.

primary structure

29

Proteins are composed of ___ only

L-amino acids

30

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

secondary

31

which is stronger? H bond or peptide

Peptide bonds

32

– combination of α-helix & β-pleated sheet

random coil

33

The backbone can change direction by making __

reverse turn and loops.

34

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

alpha-helix

35

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

amphiphilic

36

is alpha helix left-handed or right handed

right handed

37

is a “helix-breaker”
- no more H in Nitrogen of _____; no more H-bonding
- cannot rotate freely at ф

proline

38

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

glycine

39

- Polypeptide backbone is almost fully extended.

β-pleated sheet (Zigzag)

40

≥ 2 backbones aligned for H-bonding

β-pleated sheet (Zigzag)

41

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

β-pleated sheet (Zigzag)

42

maybe parallel or antiparallel orientation
- more stable than α-helix

β-pleated sheet (Zigzag)

43

these AA make reverse turns

Proline & glycine

44

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

β-pleated sheet (Zigzag)

45

– combination of coils; higher form of secondary structure

SUPERSECONDARY STRUCTURE

46

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

tertiary structure

47

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

(native conformation)

48

Covalent & Non-covalent Interactions in the 30 Structure

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

- combination of large number of βαβ motifs

*β-barrelor superbarrel

50

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

bends

51

– they do not have regular, periodic structures

loop

52

– denaturation of proteins

unfolding

53

types of tertiary structure

globular
disordered
fibrous

54

type of tertiary structure
interacts well with water and takes a random config

disordered

55

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

globular

56

type of tertiary structure
strong secondary structure allows protein to retain a nonspherical shape

fibrous

57

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

quaternary

58

examples of tetramers

alcohol dehydrogenase
hemoglobin

59

example of dodecamer

glutamine synthetase

60

– has only 10, 20 & 30 structures

*MONOMERIC PROTEINS

61

– has 10, 20, 30 & 40 structures

*OLIGOMERIC PROTEINS

62


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

Fibrous Proteins

63

▪ 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

Globular Proteins

64

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

Globular Proteins`

65


◦ 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

FIBROUS PROTEINS

66

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

peptide bonds

67

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.

Residue –

68

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

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

69

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

-C=O and –NH groups

70

– 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

primary structue

71

-folding of the backbone
-regular folding
-have repetitive interactions resulting from hydrogen bonding
-conformations of the side chain are not part of ----- structure

SECONDARY STRUCTURE

72

-spatial arrangement of the atoms in a polypeptide chain
-interaction: H-bond between the amide proton and carbonyl oxygen

SECONDARY STRUCTURE

73

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

alpha helix

74

• 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

alpha helix

75

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

Proline –

76

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

Charged amino acids

77

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

β-sheet

78

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

β-sheet

79

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

Interchain bonds

80

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

Intrachain bonds

81

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

Supersecondary Structures

82

– repetitive supersecondary structure

Motif

83

Other secondary structures (3)

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

84

– almost similar with β-pleated sheet but there are bends
-glycine and proline are frequently encountered in reverse turns

Reverse turns or β-bends

85

– 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

Tertiary

86

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

Disulfide bond

87

-spatial arrangement of polypeptide subunits
-interactions: same with tertiary structure

quaternary

88


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

DENATURATION

89

-denaturing agents (6)

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

-may be acid, base, neutral hydrolysis
-breakdown of peptide bond or the primary structure

HYDROLYSIS

91

leads to unfolding of protein and subsequent loss of biological function

denaturation

92

remains of hydrolysis

individual aa

93

remains of denaturation

group of aa

94

physical agents of protein denaturation

Heat or temperature
Mechanical agitation or stress

95

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

stress

96

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

Strong acid

97

Chemical agents
target ionic interactions with protein

Strong acids and bases

98

Most common reducing agents are for breaking ____ bonds

disulfide

99

reducing agents

1. β-mercaptoethanol
2. Dithiothreitol (DTT)

100

▪ 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

heavy metal ions

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