Chapter 20 Flashcards
(124 cards)
1
Q
amino acid with a polar but neutral R group
7 amino acids
no charges, not completely C and H
A
polar neutral amino acid
1
Q
several proteins
A
>10,000 amino acid residues are known
2
Q
polar acidic amino acid
A
amino acid with with carboxyl R group
2 amino acids
2
Q
type of secondary structure
A single protein chain adopts a shape that resembles a coiled spring (helix):
–H-bonding between amino acids with in the same chain –intramolecular H-bonding
–Coiled helical spring
–R-groups stay outside of the helix – not enough room for them to stay inside
A
alpha-helix
2
Q
membrane proteins
A
proteins associated with cell membranes
–Insoluble in water – hydrophobic amino acid residues on the surface
–Help in transport of molecules across the membrane
2
Q
type of tertiary structure interaction
•Salt Bridge between charged side chains of acidic and basic amino acids
–-OH, -NH2, -COOH, -CONH2
A
electrostatic interaction
2
Q
type of tertiary structure interaction
occurs between non-polar side chains
A
hydrophobic interactions
3
Q
>10,000 amino acid residues are known
A
several proteins
4
Q
alpha-helix
A
type of secondary structure
A single protein chain adopts a shape that resembles a coiled spring (helix):
–H-bonding between amino acids with in the same chain –intramolecular H-bonding
–Coiled helical spring
–R-groups stay outside of the helix – not enough room for them to stay inside
5
Q
A protein that has one or more non-amino acid entities (prosthetic groups) present in its structure
e.g. lipoproteins, glycoproteins, metalloproteins
A
Conjugated (complex) proteins
5
Q
contractile proteins
A
proteins necessary for movement
e.g. actin and myosin
6
Q
20+ amino acids
A
polypeptide
7
Q
peptide bonds
A
covalent bond between amino acids
caused by reaction between amino group of one amino acid and carboxyl group of another amino acid.
every bond has an N-terminal end and a C-terminal end
7
Q
structural protein
A
protein related to stiffness and rigidity
e.g. keratin and collagen
8
Q
oxytocin
A
small peptide hormone
regulates uterine contractions and lactation.
8
Q
proteins associated with cell membranes
–Insoluble in water – hydrophobic amino acid residues on the surface
–Help in transport of molecules across the membrane
A
membrane proteins
9
Q
amino acid
A
building blocks of proteins
an organic compound that contains both an amino (-NH2) and a carboxyl (-COOH) group attached to same carbon atom
they all differ from each other by their R-groups
9
Q
zwitterion
A
how amino acids exist in physiological conditions
ions with a positive and negative charge on the same molecule for a net charge of 0
carboxyl groups give up proton to get neg charge
amino groups accept protons to get pos charge
10
Q
proteins that transmit signals to coordinate biochemical processes between different cells, tissues, and organs.
e.g. hormones like insulin or glucagon
A
messenger proteins
11
Q
naturally-occurring, unbranched polymer in which the monomer units are amino acids
most abundant molecules in the cells after water
Elemental composition - Contain Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), and Sulfur (S)
A
protein
13
Q
polar neutral amino acid
A
amino acid with a polar but neutral R group
7 amino acids
no charges, not completely C and H
13
Q
Asn, N
A
Asparagine
13
Q
Gln, Q
A
Glutamine
13
Q
Beta-pleated sheets
A
type of secondary structure
•Completely extended amino acid chains
•H-bonding between two different chains – inter and/or intramolecular
•Side chains below or above the axis
14
amino acid with amino group in R group
3 amino acids
polar basic amino acid
15
protein that help control the movement of small molecules and ions across membrane
transport is very selective
transmembrane proteins
17
isomeric peptides
Peptides that contain the same amino acids but present in different order are different molecules with different properties
–For example, two different dipeptides can be formed between alanine and glycine
•The number of these increase rapidly as the length of the peptide chain increases
18
* refers to the order in which amino acids are linked together in a protein
* Every protein has its own unique amino acid sequence
* Proteins of the same organism always same sequence.
* Same protein from different sources:, e.g., Insulin from pigs, cows, sheep, humans, are similar but not identical.
primary structure of proteins
20
Tryptophan
Trp, W
21
type of secondary structure
•Completely extended amino acid chains
•H-bonding between two different chains – inter and/or intramolecular
•Side chains below or above the axis
Beta-pleated sheets
22
fibrous proteins
Simple, regular, linear structures (elongated shape)
insoluble in water
aggregate together to form macromolecule strucutes (hair, nails, etc)
e.g. keratin and collagen
24
dipeptide
2 amino acids
26
how amino acids exist in physiological conditions
ions with a positive and negative charge on the same molecule for a net charge of 0
carboxyl groups give up proton to get neg charge
amino groups accept protons to get pos charge
zwitterion
26
arrangement in space adopted by the backbone portion of a protein
2 common types:
•alpha-helix and beta-pleated sheet
The peptide linkages are essentially planar thus allows only two possible arrangements for the peptide backbone for the following reasons:
.
secondary structure of proteins
26
Simple, regular, linear structures (elongated shape)
insoluble in water
aggregate together to form macromolecule strucutes (hair, nails, etc)
e.g. keratin and collagen
fibrous proteins
27
non-polar amino acids
amino acid with nonpolar R group
R group is made of only C and H (with 2 exceptions)
hydrophobic (insoluble in water)
9 amino acids
in proteins they are inferior where there is no polarity
27
cysteine
only standard amino acid with a sulfhydryl group ( — SH group).
sulfhydryl group give it a unique chemical property
in the presence of mild oxidizing agents dimerizes to form a cystine molecule.
linked via covalent disulfide bond
28
Glutathione
small peptide antioxidant
a tripeptide
regulates oxidation-reduction reactions
protects cellular contents from oxidizing agents such as peroxides and superoxides
•Unusual structural feature – Glu (glutamic acid) is bonded to Cys through the side-chain carboxyl group.
29
oligopeptide
10-20 amino acids
29
collagen
type of fibrous protein
•Most abundant proteins in humans (30% of total body protein)
•Major structural material in tendons, ligaments, blood vessels, and skin
•Organic component of bones and teeth
•Predominant structure - triple helix
•Rich in proline (up to 20%) – important to maintain structure
29
protein that bind and store molecules
e.g. ferritin store iron and myoglobin store oxygen
storage protein
30
small peptide antioxidant
a tripeptide
regulates oxidation-reduction reactions
protects cellular contents from oxidizing agents such as peroxides and superoxides
•Unusual structural feature – Glu (glutamic acid) is bonded to Cys through the side-chain carboxyl group.
Glutathione
30
proteins that fight bacterial infections
e.g. immunoglobins or antibodies
defense proteins
31
Alpha (a) carbon
C in amino acid that connects to the NH2 and COOH groups
31
caused by cooking – Makes it easy for enzymes in our body to hydrolyze/digest protein
•but does not change protein nutritional value
Denatured proteins
33
small peptide hormone
regulates uterine contractions and lactation.
oxytocin
34
type of globular protein
–An oxygen storage molecule in muscles.
–Monomer - single peptide chain with one heme unit
–Binds one O2 molecule
–Has a higher affinity for oxygen than hemoglobin.
–Oxygen stored in myoglobin molecules serves as a reserve oxygen source for working muscles
myoglobin
35
Conjugated (complex) proteins
A protein that has one or more non-amino acid entities (prosthetic groups) present in its structure
e.g. lipoproteins, glycoproteins, metalloproteins
35
protein embedded in exterior surface of cell membrane, bind to enzymes and turn them on or off
regulatory protein
36
storage protein
protein that bind and store molecules
e.g. ferritin store iron and myoglobin store oxygen
38
only standard amino acid with a sulfhydryl group ( — SH group).
sulfhydryl group give it a unique chemical property
in the presence of mild oxidizing agents dimerizes to form a cystine molecule.
linked via covalent disulfide bond
cysteine
38
tertiary structure of proteins
•The overall three-dimensional shape of a protein
•Results from the interactions between amino acid side chains (R groups) that are widely separated from each other.
•In general 4 types of interactions are observed.
–Disulfide bonding
–Electrostatic interactions
–H-Bonding
–Hydrophobic interactions
39
type of protein that transports. bind small biomolecules
e.g. hemoglobin carries oxygen and transferrin carries iron from liver to bone marrow
transport proteins
40
protein that speeds up reactions but are not consumed by reactions.
e.g. enzymes, globular proteins
catalytic protein
41
messenger proteins
proteins that transmit signals to coordinate biochemical processes between different cells, tissues, and organs.
e.g. hormones like insulin or glucagon
42
pH at which concentration of zwitterion complex is maximum
net charge is 0
isoelectric point
43
polar basic amino acid
amino acid with amino group in R group
3 amino acids
43
A standard amino acid needed for protein synthesis that must be obtained from dietary sources – adequate amounts cannot be synthesized in human body.
arginine (for children, not adults), histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine
these ten valuable amino acids have long preserved life in man
essential amino acid
44
small peptide hormone
also called antidiuretic hormone (ADH) regulates excretion of water by the kidneys, also effects blood pressure.
Vasopressin
46
polar amino acids
amino acid with polar R group
hydrophillic
3 types: polar neutral, polar acidic and polar basic
47
transport proteins
type of protein that transports. bind small biomolecules
e.g. hemoglobin carries oxygen and transferrin carries iron from liver to bone marrow
48
Vasopressin
small peptide hormone
also called antidiuretic hormone (ADH) regulates excretion of water by the kidneys, also effects blood pressure.
49
building blocks of proteins
an organic compound that contains both an amino (-NH2) and a carboxyl (-COOH) group attached to same carbon atom
they all differ from each other by their R-groups
amino acid
50
covalent bond between amino acids
caused by reaction between amino group of one amino acid and carboxyl group of another amino acid.
every bond has an N-terminal end and a C-terminal end
peptide bonds
52
C in amino acid that connects to the NH2 and COOH groups
Alpha (a) carbon
52
•Conjugated proteins with carbohydrates linked to them:
–Many of plasma membrane proteins are these
–Blood group markers of the ABO system are also these
–Collagen and immunoglobulins are examples
glycoprotein
53
type of globular protein
* An oxygen carrier molecule in blood
* Transports oxygen from lungs to tissues
* Tetramer (four polypeptide chains) - each subunit has a heme group
* Can transport up to 4 oxygen molecules at time
* Iron atom in heme interacts with oxygen
hemoglobin
54
protein classification based on function
catalytic protein, defense proteins, transport proteins, messenger proteins, contractile proteins, structural proteins, transmembrane proteins, storage proteins, regulatory proteins, nutrient proteins
55
transmembrane proteins
protein that help control the movement of small molecules and ions across membrane
transport is very selective
57
a small peptide NT
pentapeptide neurotransmitters produced by the brain and bind receptors within the brain
Help reduce pain
Enkephalins
58
protein that is particularly important to early stages of life
e.g. casein (milk protein) and ovalbumin (egg white)
nutrient proteins
59
catalytic protein
protein that speeds up reactions but are not consumed by reactions.
e.g. enzymes, globular proteins
61
polypeptide
20+ amino acids
63
common proteins
–contain 400–500 amino acid residues
65
secondary structure of proteins
arrangement in space adopted by the backbone portion of a protein
2 common types:
•alpha-helix and beta-pleated sheet
The peptide linkages are essentially planar thus allows only two possible arrangements for the peptide backbone for the following reasons:
.
66
protein classification based on shape
fibrous proteins, globular proteins and membrane proteins
68
protein
naturally-occurring, unbranched polymer in which the monomer units are amino acids
most abundant molecules in the cells after water
Elemental composition - Contain Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), and Sulfur (S)
69
hemoglobin
type of globular protein
* An oxygen carrier molecule in blood
* Transports oxygen from lungs to tissues
* Tetramer (four polypeptide chains) - each subunit has a heme group
* Can transport up to 4 oxygen molecules at time
* Iron atom in heme interacts with oxygen
71
–contain 400–500 amino acid residues
common proteins
72
globular protein
protein molecules with peptide chains folded into spherical or globular shapes:
–Generally water soluble – which enables them to travel through the blood and other body fluids to sites where their activity is needed.
–hydrophobic amino acid residues are in the protein core
–Function as enzymes and intracellular signaling molecules
e.g. myoglobin and hemoglobin
73
A protein in which only amino acid residues are present:
simple proteins
74
a conjugated protein that contains lipids in addition to amino acids
•Major function - help suspend lipids and transport them through the bloodstream
•Four major classes:
– Chylomicrons: Transport dietary triacylglycerols from intestine to liver.
–Very-low-density lipoproteins (VLDL): Transport triacylglycerols synthesized in the liver to adipose tissue.
–Low-density lipoproteins (LDL): Transport cholesterol synthesized in the liver to cells throughout the body.–High-density lipoproteins (HDL): Collect excess cholesterol from body tissues and transport it back to the liver for degradation to bile acids.
lipoproteins
75
refers to the organization among the various polypeptide chains in a multimeric protein
•Highest level of protein organization
•Present only in proteins that have 2 or more polypeptide chains (subunits)
•Subunits are generally independent of each other - not covalently bonded
•Proteins with quaternary structure are often referred to as oligomeric proteins
Contain even number of subunits
quaternary structure of proteins
76
–The — COOH group is put at the top,
–The R group is place at the bottom position of the carbon chain vertically
–The — NH2 group is placed in a horizontal position.
–Positioning — NH2 on the left (H on the right) - L isomer
–Positioning — NH2 on the right - D isomer.
Fischer projection formulas for amino acid structures
77
quaternary structure of proteins
refers to the organization among the various polypeptide chains in a multimeric protein
•Highest level of protein organization
•Present only in proteins that have 2 or more polypeptide chains (subunits)
•Subunits are generally independent of each other - not covalently bonded
•Proteins with quaternary structure are often referred to as oligomeric proteins
Contain even number of subunits
78
electrostatic interaction
type of tertiary structure interaction
•Salt Bridge between charged side chains of acidic and basic amino acids
–-OH, -NH2, -COOH, -CONH2
79
amino acid with with carboxyl R group
2 amino acids
polar acidic amino acid
79
catalytic protein, defense proteins, transport proteins, messenger proteins, contractile proteins, structural proteins, transmembrane proteins, storage proteins, regulatory proteins, nutrient proteins
protein classification based on function
80
2 amino acids
dipeptide
82
Asparagine
Asn, N
84
Glutamine
Gln, Q
85
hydrogen bonding
type of tertiary structure interaction
occurs between between polar, acidic and/or basic R groups
, the H must be attached to O, N or F
87
simple proteins
A protein in which only amino acid residues are present:
88
•The overall three-dimensional shape of a protein
•Results from the interactions between amino acid side chains (R groups) that are widely separated from each other.
•In general 4 types of interactions are observed.
–Disulfide bonding
–Electrostatic interactions
–H-Bonding
–Hydrophobic interactions
tertiary structure of proteins
90
Trp, W
Tryptophan
90
small proteins
–contain 40–100 amino acid residues
91
fibrous proteins, globular proteins and membrane proteins
protein classification based on shape
93
regulatory protein
protein embedded in exterior surface of cell membrane, bind to enzymes and turn them on or off
94
Fischer projection formulas for amino acid structures
–The — COOH group is put at the top,
–The R group is place at the bottom position of the carbon chain vertically
–The — NH2 group is placed in a horizontal position.
–Positioning — NH2 on the left (H on the right) - L isomer
–Positioning — NH2 on the right - D isomer.
95
lipoproteins
a conjugated protein that contains lipids in addition to amino acids
•Major function - help suspend lipids and transport them through the bloodstream
•Four major classes:
– Chylomicrons: Transport dietary triacylglycerols from intestine to liver.
–Very-low-density lipoproteins (VLDL): Transport triacylglycerols synthesized in the liver to adipose tissue.
–Low-density lipoproteins (LDL): Transport cholesterol synthesized in the liver to cells throughout the body.–High-density lipoproteins (HDL): Collect excess cholesterol from body tissues and transport it back to the liver for degradation to bile acids.
97
10-20 amino acids
oligopeptide
98
myoglobin
type of globular protein
–An oxygen storage molecule in muscles.
–Monomer - single peptide chain with one heme unit
–Binds one O2 molecule
–Has a higher affinity for oxygen than hemoglobin.
–Oxygen stored in myoglobin molecules serves as a reserve oxygen source for working muscles
98
proteins necessary for movement
e.g. actin and myosin
contractile proteins
99
nutrient proteins
protein that is particularly important to early stages of life
e.g. casein (milk protein) and ovalbumin (egg white)
100
Peptides that contain the same amino acids but present in different order are different molecules with different properties
–For example, two different dipeptides can be formed between alanine and glycine
•The number of these increase rapidly as the length of the peptide chain increases
isomeric peptides
101
hydrophobic interactions
type of tertiary structure interaction
occurs between non-polar side chains
103
isoelectric point
pH at which concentration of zwitterion complex is maximum
net charge is 0
104
Denatured proteins
caused by cooking – Makes it easy for enzymes in our body to hydrolyze/digest protein
•but does not change protein nutritional value
106
disulfide bond
type of tertiary structure interaction
•covalent, strong, between two cysteine groups
108
type of tertiary structure interaction
•covalent, strong, between two cysteine groups
disulfide bond
109
glycoprotein
•Conjugated proteins with carbohydrates linked to them:
–Many of plasma membrane proteins are these
–Blood group markers of the ABO system are also these
–Collagen and immunoglobulins are examples
110
protein molecules with peptide chains folded into spherical or globular shapes:
–Generally water soluble – which enables them to travel through the blood and other body fluids to sites where their activity is needed.
–hydrophobic amino acid residues are in the protein core
–Function as enzymes and intracellular signaling molecules
e.g. myoglobin and hemoglobin
globular protein
112
alpha keratin
type of fibrous protein
•Provide protective coating for organs
•Major protein constituent of hair, feather, nails, horns and turtle shells
•Mainly made of hydrophobic amino acid residues
•Hardness of keratin depends upon -S-S- bonds
–More –S-S– bonds make nail and bones hard and hair brittle
114
essential amino acid
A standard amino acid needed for protein synthesis that must be obtained from dietary sources – adequate amounts cannot be synthesized in human body.
arginine (for children, not adults), histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine
these ten valuable amino acids have long preserved life in man
115
type of fibrous protein
•Provide protective coating for organs
•Major protein constituent of hair, feather, nails, horns and turtle shells
•Mainly made of hydrophobic amino acid residues
•Hardness of keratin depends upon -S-S- bonds
–More –S-S– bonds make nail and bones hard and hair brittle
alpha keratin
116
protein related to stiffness and rigidity
e.g. keratin and collagen
structural protein
117
amino acid with nonpolar R group
R group is made of only C and H (with 2 exceptions)
hydrophobic (insoluble in water)
9 amino acids
in proteins they are inferior where there is no polarity
non-polar amino acids
118
Enkephalins
a small peptide NT
pentapeptide neurotransmitters produced by the brain and bind receptors within the brain
Help reduce pain
119
type of fibrous protein
•Most abundant proteins in humans (30% of total body protein)
•Major structural material in tendons, ligaments, blood vessels, and skin
•Organic component of bones and teeth
•Predominant structure - triple helix
•Rich in proline (up to 20%) – important to maintain structure
collagen
120
–contain 40–100 amino acid residues
small proteins
121
type of tertiary structure interaction
occurs between between polar, acidic and/or basic R groups
, the H must be attached to O, N or F
hydrogen bonding
122
amino acid with polar R group
hydrophillic
3 types: polar neutral, polar acidic and polar basic
polar amino acids
123
primary structure of proteins
* refers to the order in which amino acids are linked together in a protein
* Every protein has its own unique amino acid sequence
* Proteins of the same organism always same sequence.
* Same protein from different sources:, e.g., Insulin from pigs, cows, sheep, humans, are similar but not identical.
124
defense proteins
proteins that fight bacterial infections
e.g. immunoglobins or antibodies
