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Proteins Flashcards

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1
Q

What is COPD?

A

Chronic obstructive pulmonary disease (COPD) is a common lung disease. Having COPD makes it hard to breathe. There are two main forms of COPD: Chronic bronchitis, which involves a long-term cough with mucus. Emphysema, which involves damage to the lungs over time (The enlargement of the alveoli accompanied by destruction of cell walls

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2
Q

What is the cause of COPD?

A
  • Absence of normal inhibition of human neutrophil (leukocyte) elastase, a proteolytic enzyme in our bodies
  • Elastase breaks down elastin, a normal structural component of lung tissue, but the inhibitor α-1-antitrypsin (AAT) protects the lung from the enzyme
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3
Q

What are the three main proteolytic enzymes in the body?

A

three main proteolytic enzymes produced naturally in your digestive system are pepsin, trypsin and chymotrypsin.

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4
Q

What are proteolytic enzymes?

A

enzymes involved in the breakdown of proteins into smaller polypeptides or amino acids

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5
Q

What is the number one reason for uncontrolled levels of circulating elastase?

A 
Cigarette smoke 
(also hereditary - familial emphysema, hereditary deficiency of AAT)
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6
Q

What is elastase?

A

A serine protease (breaks down proteins and peptides)

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7
Q

What is the inhibitor of elastase?

A

α-1-antitrypsin

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8
Q

What is drug design?

A

Utilizing atomic-level 3D structural information to screen/synthesize tighter-binding (computer-aided drug design)

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9
Q

What are drugs?

A

chemical or biological substances that have some kind of physiological? or biochemical? effect on our bodies.

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10
Q

What are the targets of drugs mainly?

A

Drug targets are usually proteins, but are in some cases small regions of DNA or RNA

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11
Q

What are the three stages in drug development

A

Stage 1 : Drug discovery
Stage 2 : Pre-clinical development
Stage 3 :Clinical development

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12
Q

What is the approach taken for drug discovery?

A
  1. high-throughput screening: which allows scientists to test thousands of potential targets with thousands of diverse chemical compounds to identify a new drug-target combination.
  2. rational drug design: which involves designing and synthesising compounds based on the known structure of a specific target molecule
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13
Q

What is the aim of pre-clinical testing?

A

used to determine how best to develop the drug for its intended use.
It aims to establish how drugs are absorbed and distributed in the body, and how they are broken down and removed from the body.

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14
Q

What will the results of the pre-clinical testing be used to determine?

A

how to best formulate the drug for its intended clinical use, whether it would be most effective as a cream, a pill, an injection or a spray.

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15
Q

When is the compound ready for stage three of drug design?

A

These few drugs will then be submitted to the appropriate regulatory authorities and, if accepted, the compound can be taken on to clinical development

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16
Q

What is stage 3 of drug design, Clinical Development?

A

involves testing the drug on human volunteers to provide more information about its safety and effectiveness.By the end of the clinical development phase, most of the investigational new drugs will have been eliminated on the grounds of safety and effectiveness

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17
Q

What is the drug development funnel?

A

As drugs travel through the funnel, their number decreases as studies indicate problems with safety and/or effectiveness

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18
Q

How much of dry mass do proteins account for?

A

More than 50%

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19
Q

What is the range of protein functions?

A

Some proteins speed up chemical reactions whilst other protein functions include defense, storage, transport, cellular communication, movement and structural support

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20
Q

What is the function of enzymatic proteins and give an example

A

Function : Selective acceleration of chemical reactions

Example : Digestive enzymes catalyze the hydrolysis of bonds in food molecules

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21
Q

Why do we need Elastin?

A

you need elastin for integrity of cell) – but elastase chops it down because of the cells in our lungs cannot be rigid, they need to be supple. If you let elastase to do it too much, then COPD

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22
Q

What is the function of defensive proteins and give an example

A

Function : Protection against disease

Example : Antibodies inactivate and help destroy viruses and bacteria

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23
Q

What is the function of storage proteins and give examples

A

Function : Storage of amino aicds
Examples : -Casein, the protein of milk, is the major source of amino acids for baby mammals. -Plants have storage proteins in their seeds. -Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo.

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24
Q

What is the function of transport proteins and give an example

A

Function : Transport of substances
Examples : Haemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body.

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25
Q

What is the function of hormonal proteins and give an example

A

Function : Coordination of an organism’s activities
Example : Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose and thus regulating blood sugar levels

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26
Q

What is the function of receptor proteins and give a example

A

Function : Response of cell to chemical stimuli

Example : Receptors built into the membrane of a nerve cell detect signalling molecules released by other nerve cells

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27
Q

What is the function of contractile and motor proteins and give examples

A

Function : movement
Examples : Motor proteins are responsible for the undulations (flowing, up-and-down movement ) of cilia and flagella
Actin and myosin proteins are responsible for the contraction of muscles

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28
Q

What is the function of structural proteins and give examples

A

Function : Support
Examples : Keratin is the protein of hair, horns, feathers and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively.
Collagen and elastin proteins provide a fibrous framework in animal connective tissues

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29
Q

What protein functions as a workhorse that carries out the processes of life?

A

Enzymes

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30
Q

What are proteins made up of?

A

are all constructed from the same set of 20 amino acids

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31
Q

What are polypeptides?

A

unbranched polymers built from amino acids

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32
Q

What is a protein?

A

biologically functional molecule that consists of one or more polypeptides

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33
Q

What is an amino acid?

A

Amino acids are organic molecules with amino and carboxyl groups.

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34
Q

How do amino acids differ in their properties?

A

Due to differing side chains, called R groups

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35
Q

Give the structure of a typical protein

A

H R =O
N - C - C -
H H OH

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36
Q

Keratin has a lot of a certain element which helps with crosslinking molecules which make up hair. What is this element?

A

sulfur

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37
Q

What are the four types of amino acids you can have, based on properties

A
  1. Nonpolar side chains
  2. Polar side chains
  3. (Electrically charged)
    Acidic (negatively charged)
  4. Basic (positively charged)
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38
Q

Give examples of amino acids with non-polar side chains (hydrophobic)

A

Glycine, Alanine Valine, Luecine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline

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39
Q

Give examples of amino acids with polar side chains (hydrophilic)

A

Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine

40
Q

Give examples of amino acids with Acid (negatively charged) side chains (hydrophilic)

A

Aspartic acid

Glutamic acid

41
Q

Give examples of amino acids with Acid (positively charged) side chains (hydrophilic)

A

Lysine, Arginine, Histidine

42
Q

How are amino acids linked?

A

Covalent bonds called peptide bonds

43
Q

What is a polypeptide?

A

Polymer of amino acids

44
Q

What does each polypeptide consist of?

A

A unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus)

45
Q

What are the two types of hydrophilic amino acids that you have?

A

Uncharged (polar) and Charged (acidic and basic)

46
Q

What is the N-terminus?

A

Left most amino acid

47
Q

What is the C-terminus?

A

Right most-amino acid

48
Q

How is a peptide bond formed?

A

A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). This is a dehydration synthesis reaction (also known as a condensation reaction)

49
Q

The specific activities of proteins result from what?

A

Their intricate three-dimensional architecture

50
Q

What is a functional protein and what does it consist of?

A

Functional proteins carry out a function in the body unlike structual proteins which produce structures (eg bones and muscles)
Consists of : one or more polypeptides precisely twisted, folded, and coiled into a unique shape

51
Q

How is a protein made hydrophilic?

A

Add hydroxyl

52
Q

What are the three structral models used?

A

1) Space filling model
2) Ribbon model
3) Wire-frame model

53
Q

What determines a protein’s three dimensional structure?

A

Sequence of amino acids

54
Q

What does the function of a protein depend on?

A

It’s ability to recognise and bind to some other molecule

55
Q

What are the four levels of protein structure/four levels of protein folding?

A

Proteins are macromolecules and have four different levels of structure

1) Primary structure
2) Secondary structure
3) Tertiary Structure
4) Quaternary Structure

56
Q

What is the primary structure of a protein?

A

Its unique sequence of amino acids (polypeptide chain)

57
Q

What is the secondary structure of proteins?

A

Within the long protein chains there are regions in which the chains are organised into regular structures known as alpha-helices (alpha-helixes) and beta-pleated sheets.

58
Q

How is the tertiary structure of proteins determined?

A

determined by interactions among various side chains (R groups)

59
Q

What is the Quaternary structure of proteins?

A

Quaternary structure is the only one, which involves multiple protein subunits. It involves clustering of several individual peptide or protein chains into a final specific shape

60
Q

What holds the together the primary structures?

A

Peptide bonds hold the adjacent amino acids together in the polypeptide chain

61
Q

What holds together the secondary structures?

A

These secondary structures are held together by hydrogen bonds

62
Q

What is the tertiary structure of a protein?

A

Protein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain “backbone” with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways.

63
Q

Give examples of proteins with quaternary structure

A

hemoglobin (globular protein consisting of four polypeptides, to alpha and two beta subunits), DNA polymerase

64
Q

How is the primary structure of a protein determined?

A

Inherited genetic information

65
Q

What is the coil and folded structure of a typical secondary structures?

A

Coil : alpha helix

Folded Structure : B pleated sheet

66
Q

What is the typical secondary structure of a protein?

A

Coil called an alpha helix and a folded structure called a beta pleated sheet

67
Q

What do the coils and folds of a secondary structure result from?

A

Hydrogen bonds between repeating constituents of the polypeptide backbone

68
Q

What interactions are involved in the tertiary structure?

A

Hydrogen bonds, Ionic bonds, hydrophobic interactions and van der Waals
Strong covalent bonds called disulfide bridges may reinforce the protein’s structure

69
Q

What does a Quaternary Structure result from?

A

Two or more polypeptide chains to form one macromolecule

70
Q

If there is a slight change in the protein’s primary structure, what is the effect it has?

A

It can affect a protein’s structure and ability to function

71
Q

How does sickle cell disease occur?

A 
Conformational diseases (misfolding diseases)
An inherited blood disorder which results from a single amino acid substitution in the protein hemoglobin.
The abnormal hemoglobin molecules cause the red blood cells to aggregate into chains (a fibre) and to deform into a sickle shape
72
Q

What is the secondary and Tertiary structure of haemoglobin?

A

Normal Beta subunit

73
Q

What is the primary structure of haemoglobin?

A

Val,His,Leu,Thr,Pro,Glu,Glu

74
Q

What is the quaternary structure of haemoglobin?

A

Two beta and two alpha

75
Q

What is the typical tertiary structure of a protein?

A

mix of alpha helix, beta pleated sheet and Transytherin

76
Q

What are the subunits of a protein?

A

A protein subunit is a single protein molecule that assembles (or “coassembles”) with other protein molecules to form a protein complex.Many protein molecules are composed of more than one subunit, where each subunit is a separate polypeptide chain and can form a stable folded structure by itself

77
Q

How is each subunit formed in a protein?

A

Ribosome will synthesis each subunit separately

78
Q

What determines Protein’s Structure?

A

Primary Structure, Physical and Chemical conditions

79
Q

What physical and chemical conditions can change the structure of a protein?

A
  • alterations in PH
  • salt concentration
  • temperatyre
  • other environmental factors
80
Q

What is the loss of a protein’s native structure known as?

A

Denaturation

81
Q

What do scientists use to determine a protein’s structure?

A

X-ray Crystallography and nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallisation
Bioinformatics is another approach to predict protein structure from amino acid sequence (hard to predict)

82
Q

What is X-ray Crystallography?

A

the study of crystals and their structure by means of the diffraction of X-rays by the regularly spaced atoms of crystalline materials

83
Q

What is NMR?

A

-High-resolution, atomic-level methodology for the determination of chemical and biochemical structures of molecules

84
Q

Why are peptide bonds strong?

A

While a relatively stable bond, peptide bonds are merely a condensation reaction that links a carbon from one amino acid with the nitrogen of another, there is not a strong electronegativity difference between these two atoms. This creates a non-polar covalent bond, in which the electrons are shared equally

85
Q

What is considered the most abundant type of protein?

A

Structural proteins are the most abundant class of proteins in nature.

86
Q

What is recognized as the most abundant mammalian protein?

A

Collagen

87
Q

What does collagen consist of?

A

Three polypeptide chains (cartilage, teeth). It doesn’t have in one of the amino acids it has hydroxine proline (instead of proline), due to enzyme which attaches hydroxyl group.

88
Q

Why is it possible to stretch silk (protein)?

A

due to beta pleat sheets (Pleat is flexible, however it will always go back to energetically stable state)

89
Q

How are red blood cells designed?

A

Red blood cells (no nuclei) – have proteins known as haemoglobin (4 different subunits, 2 of alpha, 2 of beta) – it is designed that there is preferable interactions between unlike subunits. Middle, axis of symmetry known as twofold screw axis

90
Q

When a protein is denatured, why does it lose its functionality?

A

Denaturation breaks the intramolecular bonds, such as hydrogen bonds and van der Waals interactions, that hold the protein in its three-dimensional shape. Without the proper shape, the protein cannot function. It disrupts secondary, tertiary, and quaternary protein structure, causing the protein to lose its form, and thus its function.

91
Q

The α helix and β pleated sheet represent which level of protein structure?

A

Secondary structure

92
Q

What is the peptide bond ?

A

a covalent bond joining amino acids together to form a polypeptide

93
Q

What do Alzheimer’s, Parkinson’s, and mad cow disease have in common?

A

All are associated with the buildup of misfolded proteins in cells.

94
Q

A shortage of phosphorus in the soil would make it especially difficult for a plant to manufacture __________.

a) fatty acids
b) proteins
c) cellulose
d) DNA
e) sucrose

A

d) DNA

The backbone of a nucleic acid consists of alternating sugar and phosphate groups.

95
Q 
Which functional group(s) shown below is (are) present in all amino acids?
a) -OH
b) =O
     C-O-H
c) -NH2
d) -SH
A

B and C - An amino acid has an amino group (-NH2) and a carboxyl group (-COOH)

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