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Proteins > Proteins > Flashcards

Proteins Flashcards

1
Q

true or false: proteins are very small biomolecules

A

false

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2
Q

true or false: proteins have an amino acid polymer chain

A

true

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3
Q

proteins are essential for life because..

A

– Cell structure
– Cellular communication • Receptors
– Metabolism • Enzymes
– Transport, storage

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4
Q

in nature, proteins are synthesized…

A

from RNA- translation

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5
Q

man made protein creation includes…

A

chemical synthesis, genetic engineering, directed evolution techniques

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6
Q

What is a protein?

A

A protein is a naturally-occurring, unbranched polymer in which the monomer units are amino acids

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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

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8
Q

Explain the elemental composition of proteins

A

Contain Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), and Sulfur (S)

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9
Q

true or false: in some specialized proteins, iron and phosphorus are present

A

true

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10
Q

Amino acid

A

An organic compound that contains both an amino (- NH2) and a carboxyl (-COOH) group attached to same carbon atom

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11
Q

he position of carbon atom is the

A

Alpha (a) Carbon

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12
Q

what two groups are attached to the Alpha (a) Carbon

A

NH2 and -COOH groups are attached

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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.

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14
Q

true or false: Based on common “R” groups, there are 13 standard amino acids

A

false- there are 20

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15
Q

Standard amino acids are divided into four groups based on the properties of R-groups

A
  1. Non-polar amino acids
  2. Polar neutral amino acids
  3. Polar acidic amino acids
  4. Basic amino amino acids
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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

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17
Q

Polar amino acids:

A

R-groups are polar (hydrophilic)
– Three types: Polar neutral; Polar acidic; and Polar
basic

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18
Q

Polar-neutral:

A

contains polar but neutral side chains • Six (6) amino acids belong to this category

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19
Q

Polar acidic:

A

Contain carboxyl group as part of the side chains

Two (2) amino acids belong to this category

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20
Q

Polar basic:

A

Contain amino group as part of the side chain

• Three (3) amino acids belong to this category

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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

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22
Q

True or false: half of the 20 standard amino acids are considered
essential

A

false- 9

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23
Q

true or false : Four different groups are attached to the a-carbon atom in all of the standard amino acids

A

true

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24
Q

true or false: Molecules with chiral centers exhibit enantiomerism (left- and right-handed forms)

A

true

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25
Q

Chirality of Amino Acids

A

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

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26
Q

*Rules for drawing fischer projection formulas

A

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.

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27
Q

Acid-base properties of amino acids

A

In pure form amino acids are white crystalline solids
• Most amino acids decompose before they melt
• Not very soluble in water

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28
Q

*Zwitterions:

A

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

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29
Q

Amino acids in solution exist in three different species

A

(zwitterions, positive ion, and negative ion) - Equilibrium shifts with change in pH

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30
Q

*Isoelectric point (pI)

A

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

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31
Q

Cysteine:

A

amino acid with a thiol (sulfhydryl) group (-SH group).

• The -SH group gives cysteine unique chemical properties among the standard amino acids.

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32
Q

Cysteine in the presence of mild oxidizing agents dimerizes to form a

A

Cystine molecule

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33
Q

Cystine

A

two cysteine residues linked via a covalent disulfide bond.

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34
Q

Cysteine is important for

A

Important for peptide and protein structures, shapes

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35
Q

*Nature of Peptide Bond

A

• 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).

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36
Q

*Dipeptide:

A

bond between two amino acids

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37
Q

*Oligopeptide:

A

bond between ~ 10 - 20 amino acids

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38
Q

*Polypeptide:

A

bond between large number of amino acids

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39
Q

true or false: Every peptide has an N-terminal end (on the right) and a C-terminal end (on the left)

A

false- other way around

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40
Q

*Isomeric Peptides

A

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

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41
Q

*Many relatively small peptides are biochemically active:

A

– Hormones, Neurotransmitters, Antioxidants

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42
Q

*Small Peptide Hormones:

A

– Best-known peptide hormones: oxytocin and vasopressin

– Produced by the pituitary gland

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43
Q

*Oxytocin

A

regulates uterine contractions and lactation; also involved in stress or anxiety; also involved in empathy: “love hormone”

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44
Q

*Vasopressin

A

regulates retention/excretion of water by the kidneys, blood pressure

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45
Q

*Oxytocin and Vasopressin receptors:

A

GPCRs

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46
Q

Nonapeptide (nine amino acid residues)

A

6 residues form a loop by a

disulfide bond formed between two cysteine residues

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47
Q

*Enkephalins

A

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
Q

Opioid receptors:

A

G-Protein Coupled Receptors (GPCRs)

49
Q

NarcanTM Naloxone – Opioid Antagonist:

A

Blocks effects of Agonists

50
Q

*Glutathione (Glu–Cys–Gly)

A

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
Q

Special definition of protein

A

A protein is a peptide in which at least 40 amino acid residues are present

52
Q

true or false: The terms polypeptide and protein are often used interchangeably to describe a protein

A

true

53
Q

More than one polypeptide chain may be present in a protein:

A

Monomeric : Contains one polypeptide chain

– Multimeric: Contains 2 or polypeptide chains

54
Q

Many drugs these days are proteins:

A

Insulin, (Diabetes); Avastin - Generic name: Bevacizumab (cancer), Humira - Generic name: Adalimumab (antiinflammatory). Mab – monoclonal antibody

55
Q

Simple proteins:

A

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
Q

Conjugated (complex) proteins:

A

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
Q

Lipoproteins

A

contain lipid prosthetic groups

58
Q

*Glycoproteins

A

contain carbohydrate groups

• Immunoglobins or Antibodies

59
Q

Metalloproteins

A

contain a specific metal as prosthetic group

60
Q

*The four types of protein structure

A

– Primary Structure
– Secondary Structure
– Tertiary Structure
– Quaternary

61
Q

*Primary Structure:

A

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
Q

true or false:Proteins of the same organism always same sequence.

A

true

63
Q

Amino terminus-

A

beginning of sequence

64
Q

Carboxyl terminus

A

end of sequence

65
Q

*Secondary structure

A

arrangement of atoms of backbone in space

66
Q

*two types of secondary structure:

A

alpha-helix (a-helix) and the

beta-pleated sheet (b-pleated sheet)

67
Q

The peptide linkages are essentially planar thus allows only two possible arrangements for the peptide backbone for the following reasons:

A

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
Q

*Alpha-helix (a-helix)

A

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
Q

*Beta-Pleated Sheets

A
  • Completely extended amino acid chains
  • H-bonding between two different chains – inter and/or intramolecular
  • Side chains below or above the axis
70
Q

*Tertiary Structure of Proteins

A

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
Q

*In general 4 types of interactions are observed in tertiary structure:

A

– Disulfide bonding
– Electrostatic interactions
– H-Bonding
– Hydrophobic (Lipophilic) interactions

72
Q

*Disulfide bond:

A

covalent, strong, between two cysteine groups

73
Q

*Electrostatic interactions:

A

Salt Bridge between charged side chains of acidic and basic amino acids

74
Q

*H-Bonding between polar, acidic and/or basic R groups

A

– For H-bonding to occur, the H must be attached to O,

N or F

75
Q

*Hydrophobic interactions:

A

Between non-polar side chains

76
Q

*Quaternary Structure of Proteins

A

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
Q

Hydrolysis of proteins

A

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
Q

Digestive enzymes:

A

Chymotrypsin – Cleaves near large hydrophobic aa – Phe, Tyr, Trp Trypsin – Cleaves near Lys, Arg

79
Q

*Protein Denaturation –

A

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
Q

*Coagulation: Precipitation (denaturation of proteins)

A

Egg white - a concentrated solution of protein albumin - forms a
jelly when heated because the albumin is denatured

81
Q

*Cooking:

A

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
Q

*Denaturation process can be reversible:

A

Hair permanent – p. 734 in text.

83
Q

*Protein Classification Based on Shape

A

fibrous, globular, and membrane

84
Q

*Fibrous proteins:

A

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
Q

*Globular proteins:

A

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
Q

*Membrane proteins:

A

associated with cell membranes
– Insoluble in water – hydrophobic amino acid residues on the surface
– Help in transport of molecules across the membrane

87
Q

*Fibrous Proteins: Alpha-Keratin

A

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
Q

*Fibrous Proteins: Collagen

A

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
Q

*Globular Proteins: Myoglobin

A

– 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
Q

*Globular Proteins: Hemoglobin

A
  • 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
Q

The functional versatility of proteins stems from:

A

– 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
Q

*Catalytic proteins:

A

Enzymes are best known for their catalytic role.
– Almost every chemical reaction in the body is driven by an
enzyme

93
Q

*Defense proteins:

A

Immunoglobulins or antibodies are central to

functioning of the body’s immune system.

94
Q

*Transport proteins:

A

Bind small biomolecules, e.g., oxygen and other ligands, and transport them to other locations in the body and release them on demand.

95
Q

*Messenger proteins:

A

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
Q

*Contractile proteins:

A

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
Q

*Structural proteins:

A

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
Q

*Transmembrane proteins:

A

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
Q

*Storage proteins:

list the two examples

A

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
Q

*Regulatory proteins:

A

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
Q

*Nutrient proteins:

A

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
Q

Casein

A

(milk) and ovalalbumin (egg white) are nutrient proteins

103
Q

Conjugated proteins with carbohydrates linked to them:

A

– Many of plasma membrane proteins are glycoproteins
– Blood group markers of the ABO system are also glycoproteins
– Collagen and immunoglobulins are glycoproteins

104
Q

*Collagen – glycoprotein

A

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
Q

*Immunoglobulins

A

lycoproteins produced as a protective response to the invasion of microorganisms or foreign molecules - antibodies against antigens.

106
Q

*Immunoglobulin bonding to an antigen via variable region of an immunoglobulin occurs through

A

hydrophobic interactions, dipole – dipole interactions, and hydrogen bonds.

107
Q

*Antibody Drugs – Avastin (Bevacizumab)

A

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
Q

*Lipoprotein:

A

a conjugated protein that contains lipids in addition to amino acids

109
Q

*major function of lipoprotein

A

help suspend lipids and transport them through the bloodstream

110
Q

*4 main classes of lipoproteins

A

Chylomicrons
Very-low-density lipoproteins
Low-density lipoproteins
High-density lipoproteins

111
Q

*Chylomicrons:

A

Transport dietary triacylglycerols from intestine to liver and to adipose tissue.

112
Q

*Very-low-density lipoproteins (VLDL):

A

Transport triacylglycerols synthesized in the liver to adipose tissue.

113
Q

*Low-density lipoproteins (LDL):

A

Transport cholesterol synthesized in the liver to cells throughout the body.

114
Q

*High-density lipoproteins (HDL):

A

Collect excess cholesterol from body tissues and transport it back to the liver for degradation to bile acids.

115
Q

Aequorea victoria, (aka: crystal jelly)

A

A. bioluminescent hydrozoan jellyfish. GFP first isolated from this jellyfish.

Proteins (1 decks)

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