Proteins Flashcards
(115 cards)
1
Q
true or false: proteins are very small biomolecules
A
false
2
Q
true or false: proteins have an amino acid polymer chain
A
true
3
Q
proteins are essential for life because..
A
– Cell structure
– Cellular communication • Receptors
– Metabolism • Enzymes
– Transport, storage
4
Q
in nature, proteins are synthesized…
A
from RNA- translation
5
Q
man made protein creation includes…
A
chemical synthesis, genetic engineering, directed evolution techniques
6
Q
What is a protein?
A
A protein is a naturally-occurring, unbranched polymer in which the monomer units are amino acids
7
Q
true or false: Proteins are most abundant molecules in the cells after water – account for about 15% of a cell’s overall mass
A
true
8
Q
Explain the elemental composition of proteins
A
Contain Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), and Sulfur (S)
9
Q
true or false: in some specialized proteins, iron and phosphorus are present
A
true
10
Q
Amino acid
A
An organic compound that contains both an amino (- NH2) and a carboxyl (-COOH) group attached to same carbon atom
11
Q
he position of carbon atom is the
A
Alpha (a) Carbon
12
Q
what two groups are attached to the Alpha (a) Carbon
A
NH2 and -COOH groups are attached
13
Q
the R chain of an amino acid…
A
vary in size, shape, charge, acidity, functional groups present, hydrogen-bonding ability, and chemical reactivity.
14
Q
true or false: Based on common “R” groups, there are 13 standard amino acids
A
false- there are 20
15
Q
Standard amino acids are divided into four groups based on the properties of R-groups
A
- Non-polar amino acids
- Polar neutral amino acids
- Polar acidic amino acids
- Basic amino amino acids
16
Q
Non-polar amino acids
A
R-groups are non-polar
– Such amino acids are hydrophobic (lipophilic) -
(insoluble in water)
– Nine (9) of the 20 standard amino acids are non polar
– When present in proteins, they are located in the interior of protein – hydrophobic (lipophilic
17
Q
Polar amino acids:
A
R-groups are polar (hydrophilic)
– Three types: Polar neutral; Polar acidic; and Polar
basic
18
Q
Polar-neutral:
A
contains polar but neutral side chains • Six (6) amino acids belong to this category
19
Q
Polar acidic:
A
Contain carboxyl group as part of the side chains
Two (2) amino acids belong to this category
20
Q
Polar basic:
A
Contain amino group as part of the side chain
• Three (3) amino acids belong to this category
21
Q
Essential Amino acid:
A
A standard amino acid needed for protein synthesis that must be obtained from dietary sources – adequate amounts cannot be synthesized in human body
22
Q
True or false: half of the 20 standard amino acids are considered
essential
A
false- 9
23
Q
true or false : Four different groups are attached to the a-carbon atom in all of the standard amino acids
A
true
24
Q
true or false: Molecules with chiral centers exhibit enantiomerism (left- and right-handed forms)
A
true
25
Chirality of Amino Acids
The amino acids found in nature as well as in proteins are L isomers.
– Bacteria do have some D-amino acids
– With monosaccharides nature favors
D-isomers
26
*Rules for drawing fischer projection formulas
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 - L isomer. Example: Alanine
– Positioning — NH2 on the right - D isomer.
27
Acid-base properties of amino acids
In pure form amino acids are white crystalline solids
• Most amino acids decompose before they melt
• Not very soluble in water
28
*Zwitterions:
An ion with + (positive) and – (Negative) charges on the same molecule with a net zero charge
– Carboxyl groups give-up a proton to get negative charge
– Amino groups accept a proton to become positive
29
Amino acids in solution exist in three different species
(zwitterions, positive ion, and negative ion) - Equilibrium shifts with change in pH
30
*Isoelectric point (pI)
pH at which the concentration of Zwitterion is maximum -- net charge is zero
– Different amino acids have different isoelectric points
– At isoelectric point - amino acids are not attracted towards an applied electric field because they carry net zero charge
31
Cysteine:
amino acid with a thiol (sulfhydryl) group (-SH group).
| • The -SH group gives cysteine unique chemical properties among the standard amino acids.
32
Cysteine in the presence of mild oxidizing agents dimerizes to form a
Cystine molecule
33
Cystine
two cysteine residues linked via a covalent disulfide bond.
34
Cysteine is important for
Important for peptide and protein structures, shapes
35
*Nature of Peptide Bond
• Under proper conditions, amino acids can bond together to produce an unbranched chain of amino acids.
– The reactions is between amino group of one amino acid and carboxyl group of another amino acid.
• The length of the amino acid chain can vary from a few amino acids to hundreds of amino acids.
• Such a chain of covalently-linked amino acids is called a peptide.
• The covalent bonds between amino acids in a peptide are called peptide bonds (amide).
36
*Dipeptide:
bond between two amino acids
37
*Oligopeptide:
bond between ~ 10 - 20 amino acids
38
*Polypeptide:
bond between large number of amino acids
39
true or false: Every peptide has an N-terminal end (on the right) and a C-terminal end (on the left)
false- other way around
40
*Isomeric Peptides
Peptides that contain the same amino acids but present in different order are different molecules (constitutional isomers) with different properties
– For example, two different dipeptides can be formed between alanine and glycine
• The number of isomeric peptides possible increases rapidly as the length of the peptide chain increases
41
*Many relatively small peptides are biochemically active:
– Hormones, Neurotransmitters, Antioxidants
42
*Small Peptide Hormones:
– Best-known peptide hormones: oxytocin and vasopressin
| – Produced by the pituitary gland
43
*Oxytocin
regulates uterine contractions and lactation; also involved in stress or anxiety; also involved in empathy: “love hormone”
44
*Vasopressin
regulates retention/excretion of water by the kidneys, blood pressure
45
*Oxytocin and Vasopressin receptors:
GPCRs
46
Nonapeptide (nine amino acid residues)
6 residues form a loop by a
| disulfide bond formed between two cysteine residues
47
*Enkephalins
are pentapeptide neurotransmitters produced by the brain and bind receptors within the brain
– Same receptors that pain drugs Morphine, Heroin, Fentanyl, Oxycodone target
Help reduce pain
• Best-known enkephalins:
– Met-enkephalin: Tyr–Gly–Gly–Phe–Met – Leu-enkephalin: Tyr–Gly–Gly–Phe–Leu
48
Opioid receptors:
G-Protein Coupled Receptors (GPCRs)
49
NarcanTM Naloxone – Opioid Antagonist:
Blocks effects of Agonists
50
*Glutathione (Glu–Cys–Gly)
a tripeptide – is present is in high levels in most cells – very high levels in liver
• Regulator of oxidation–reduction reactions.
• Glutathione is an antioxidant and protects cellular contents from oxidizing agents such as peroxides and superoxides
– Protects against highly reactive forms of oxygen often generated within the cell in response to bacterial invasion
• Often used in biochemical experiments as an antioxidant
• Unusual structural feature – Glu is bonded to Cys through the side-chain carboxyl group.
51
Special definition of protein
A protein is a peptide in which at least 40 amino acid residues are present
52
true or false: The terms polypeptide and protein are often used interchangeably to describe a protein
true
53
More than one polypeptide chain may be present in a protein:
Monomeric : Contains one polypeptide chain
| – Multimeric: Contains 2 or polypeptide chains
54
Many drugs these days are proteins:
Insulin, (Diabetes); Avastin - Generic name: Bevacizumab (cancer), Humira - Generic name: Adalimumab (antiinflammatory). Mab – monoclonal antibody
55
Simple proteins:
protein in which only amino acid residues are present:
| – More than one protein subunit may be present but all subunits contain only amino acids
56
Conjugated (complex) proteins:
A protein that has one or more non- amino acid entities (prosthetic groups) present in its structure:
– One or more polypeptide chains may be present
– Non-amino acid components - may be organic or inorganic - prosthetic groups
57
Lipoproteins
contain lipid prosthetic groups
58
*Glycoproteins
contain carbohydrate groups
| • Immunoglobins or Antibodies
59
Metalloproteins
contain a specific metal as prosthetic group
60
*The four types of protein structure
– Primary Structure
– Secondary Structure
– Tertiary Structure
– Quaternary
61
*Primary Structure:
Primary structure of protein refers to the order in which amino acids are linked together in a protein – amino acid sequence
• Every protein has its own unique amino acid sequence
62
true or false:Proteins of the same organism always same sequence.
true
63
Amino terminus-
beginning of sequence
64
Carboxyl terminus
end of sequence
65
*Secondary structure
arrangement of atoms of backbone in space
66
*two types of secondary structure:
alpha-helix (a-helix) and the
| beta-pleated sheet (b-pleated sheet)
67
The peptide linkages are essentially planar thus allows only two possible arrangements for the peptide backbone for the following reasons:
For two amino acids linked through a peptide bond six atoms lie in the same plane
– The planar peptide linkage structure has considerable rigidity, therefore rotation of groups about the C–N bond is hindered
– Cis–trans isomerism is possible about C–N bond.
– Thetransisomeristhepreferredorientation
68
*Alpha-helix (a-helix)
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
69
*Beta-Pleated Sheets
* Completely extended amino acid chains
* H-bonding between two different chains – inter and/or intramolecular
* Side chains below or above the axis
70
*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.
71
*In general 4 types of interactions are observed in tertiary structure:
– Disulfide bonding
– Electrostatic interactions
– H-Bonding
– Hydrophobic (Lipophilic) interactions
72
*Disulfide bond:
covalent, strong, between two cysteine groups
73
*Electrostatic interactions:
Salt Bridge between charged side chains of acidic and basic amino acids
74
*H-Bonding between polar, acidic and/or basic R groups
– For H-bonding to occur, the H must be attached to O,
| N or F
75
*Hydrophobic interactions:
Between non-polar side chains
76
*Quaternary Structure of Proteins
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
77
Hydrolysis of proteins
reverse of peptide bond formation:
– Results in the generation of an amine and a carboxylic acid functional groups.
– Digestion of ingested protein – usually an enzyme- catalyzed hydrolysis
– Free amino acids produced are absorbed into the bloodstream and transported to the liver for the synthesis of new proteins.
– Hydrolysis of cellular proteins and their resynthesis is a continuous process.
78
Digestive enzymes:
Chymotrypsin – Cleaves near large hydrophobic aa – Phe, Tyr, Trp Trypsin – Cleaves near Lys, Arg
79
*Protein Denaturation –
Partial or complete disorganization of protein’s tertiary structure
Heat, microwaves, UV radiation, strong acids, bases, heavy metals, detergents, strong whipping, reducing agents, etc.
80
*Coagulation: Precipitation (denaturation of proteins)
Egg white - a concentrated solution of protein albumin - forms a
jelly when heated because the albumin is denatured
81
*Cooking:
Denatures proteins – Makes it easy for enzymes in our body to hydrolyze/digest protein
– Kills microorganisms by denaturation of proteins
– Fever: >104oF – the critical enzymes of the body start getting denatured
82
*Denaturation process can be reversible:
Hair permanent – p. 734 in text.
83
*Protein Classification Based on Shape
fibrous, globular, and membrane
84
*Fibrous proteins:
protein molecules with elongated shape:
– Generally insoluble in water
– Single type of secondary structure
– Tend to have simple, regular, linear structures
– Tend to aggregate together to form macromolecular structures, e.g., hair, nails, etc
85
*Globular proteins:
protein molecules with peptide chains folded into spherical or globular shapes:
– Generally water soluble – hydrophobic amino acid residues are in the protein core
– Function as enzymes and intracellular signaling molecules
86
*Membrane proteins:
associated with cell membranes
– Insoluble in water – hydrophobic amino acid residues on the surface
– Help in transport of molecules across the membrane
87
*Fibrous Proteins: Alpha-Keratin
Provide protective coating for organs
• Major protein constituent of hair, feather, nails, horns and turtle shells
• Mainly made of hydrophobic amino acid residues
• Form a double helix
• Hardness of keratin depends upon -S-S- bonds
– More –S-S– bonds make nail and bones hard and hair brittle
88
*Fibrous Proteins: Collagen
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 (Pro - up to 20%) and hydroxyproline (Hyp) – important to maintain structure
89
*Globular Proteins: Myoglobin
– An oxygen storage molecule in muscles.
– Monomer - single peptide chain with one heme unit
– Oxygen stored in myoglobin molecules serves as a reserve oxygen source for working muscles
90
*Globular Proteins: Hemoglobin
* 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
91
The functional versatility of proteins stems from:
– Ability to bind small molecules and peptides specifically and strongly
– Ability to bind other proteins and form fiber-like structures, and
– Ability integrated into cell membranes
92
*Catalytic proteins:
Enzymes are best known for their catalytic role.
– Almost every chemical reaction in the body is driven by an
enzyme
93
*Defense proteins:
Immunoglobulins or antibodies are central to
| functioning of the body’s immune system.
94
*Transport proteins:
Bind small biomolecules, e.g., oxygen and other ligands, and transport them to other locations in the body and release them on demand.
95
*Messenger proteins:
transmit signals to coordinate biochemical processes between different cells, tissues, and organs.
– Insulin and glucagon - regulate carbohydrate metabolism
– Human growth hormone – regulate body growth
96
*Contractile proteins:
Necessary for all forms of movement.
– Muscles contain filament-like contractile proteins (actin and myosin).
– Human reproduction depends on the movement of sperm – possible because of contractile proteins.
97
*Structural proteins:
Confer stiffness and rigidity
– Collagen is a component of cartilage a
– Keratin gives mechanical strength as well as protective covering to hair, fingernails, feathers, hooves, etc.
98
*Transmembrane proteins:
Span a cell membrane and help control the movement of small molecules and ions. Ex. GPCRs, Channels
– GPCRs – Conformational change causes downstream biochemical change
– Channels – How molecules enter and exist cell - Very selective - allow passage of one type of molecule or ion.
99
*Storage proteins:
| list the two examples
Bind (and store) small molecules.
– Ferritin - an iron-storage protein - saves iron for use in the biosynthesis of new hemoglobin molecules.
– Myoglobin - an oxygen-storage protein present in muscle
100
*Regulatory proteins:
Often found “embedded” in the exterior surface of cell membranes - act as sites for receptor molecules
– Often the molecules that bind to enzymes (catalytic proteins), thereby turning them “on” and “off,” and thus controlling enzymatic action.
101
*Nutrient proteins:
Particularly important in the early stages of life - from embryo to infant.
– Casein (milk) and ovalalbumin (egg white) are nutrient proteins
– Milk also provides immunological protection for mammalian young.
102
Casein
(milk) and ovalalbumin (egg white) are nutrient proteins
103
Conjugated proteins with carbohydrates linked to them:
– Many of plasma membrane proteins are glycoproteins
– Blood group markers of the ABO system are also glycoproteins
– Collagen and immunoglobulins are glycoproteins
104
*Collagen -- glycoprotein
Most abundant protein in human body (30% of total body protein)
Triple helix structure
Rich in 4-hydroxyproline (5%) and 5-hydroxylysine (1%) — derivatives
Some hydroxylysines are linked to glucose, galactose, and their disaccharides – help in aggregation of collagen fibrils.
105
*Immunoglobulins
lycoproteins produced as a protective response to the invasion of microorganisms or foreign molecules - antibodies against antigens.
106
*Immunoglobulin bonding to an antigen via variable region of an immunoglobulin occurs through
hydrophobic interactions, dipole – dipole interactions, and hydrogen bonds.
107
*Antibody Drugs – Avastin (Bevacizumab)
Developed by Genentech to treat cancers (colon, non-small cell lung cancer (NSCLC) and others. FDA did not approve for breast cancer.
• Vascular Endothelial Growth Factor (VEGF) receptors promote the formation of blood vessels in tumors (angiogenesis)
• Avastin blocks the binding of VEGF to its receptors
108
*Lipoprotein:
a conjugated protein that contains lipids in addition to amino acids
109
*major function of lipoprotein
help suspend lipids and transport them through the bloodstream
110
*4 main classes of lipoproteins
Chylomicrons
Very-low-density lipoproteins
Low-density lipoproteins
High-density lipoproteins
111
*Chylomicrons:
Transport dietary triacylglycerols from intestine to liver and to adipose tissue.
112
*Very-low-density lipoproteins (VLDL):
Transport triacylglycerols synthesized in the liver to adipose tissue.
113
*Low-density lipoproteins (LDL):
Transport cholesterol synthesized in the liver to cells throughout the body.
114
*High-density lipoproteins (HDL):
Collect excess cholesterol from body tissues and transport it back to the liver for degradation to bile acids.
115
Aequorea victoria, (aka: crystal jelly)
A. bioluminescent hydrozoan jellyfish. GFP first isolated from this jellyfish.
