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Alia - Biology > Lecture 4-Proteins > Flashcards

Lecture 4-Proteins Flashcards

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1
Q

The human body can generate .. ……. different types of proteins from —— genes?

A

2 million

20,000 genes

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2
Q

What’s a polypeptide?

A

Amino acid monomers linked together by peptide bonds

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3
Q

Polypeptides >40 AA can what?

A

Fold into a defined shape

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4
Q

What determines the shape + function of a protein?

A

Protein sequence of AA

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5
Q

Structural protein

A

Support

Collagen

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6
Q

Storage protein

A

Storage

Casein

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7
Q

Transport protein

A

O2 transport

Haemoglobin

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8
Q

Hormonal protein

A

Metabolism

Insulin

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9
Q

Receptor protein

A

Cellular response

Beta-Adrenergic receptor

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10
Q

Contractile protein

A

Movement

Actin, Myosin

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11
Q

Defensive protein

A

Protection

Antibodies

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12
Q

Enzymatic protein

A

Catalysis

Digestive enzymes

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13
Q

Proteinogenic AA

A

All proteins are composed of 20 standard AA

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14
Q

Apart from ……. , the C in all AA is a …. …..

A

GLYCINE

chiral centre

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15
Q

What’s a chiral centre?

A

An atom in a molecule that is bonded to 4 different chemical species

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16
Q

AA can exist as 2 …………?

A

Enantiomers

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17
Q

What are enantiomers?

A

Mirror images (L + D) = non-superimposable

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18
Q

What form of enantiomers dominates amino acids?

A

L

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19
Q

Physicochemical properties of an AA is determined by what?

A

R group

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20
Q

R groups can be:

A

Nonpolar
Polar
Acidic
Basic

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21
Q

Which R groups are hydrophobic?

A

Nonpolar

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22
Q

Which R groups are hydrophilic?

A

Polar
Acidic
Basic

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23
Q

Which AA is a secondary amino group + why?

A

PROLINE , because its attached to 2 carbons

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24
Q

What AA have non-polar R groups?

A 
Glycine
Alanine
Valine
Leucine
Isoleucine
Methionine
Phenylalanine
Tryptophan
Proline
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25
Q

What AA have basic R groups?

A

Lysine
Arginine
Histidine

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26
Q

What AA have polar R groups?

A 
Tyrosine
Asparagine
Glutamine
Serine
Threonine
Cysteine
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27
Q

What can polar R groups do?

A

form H bonds with similar side chains + peptide bonds

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28
Q

What can CYS residues form?

A

Disulphide bridges

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29
Q

How does polypeptide chains form?

A

Achieved via linkage of -COOH + -NH2 groups via dehydration synthesis

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30
Q

What are peptide bonds?

A

Rigid + planar

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31
Q

Why are peptide bonds rigid + planar?

A

Because of bond resonance

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32
Q

Are peptide bonds trans or cis?

A

Trans

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33
Q

Except for glycine, why is rotation at C usually limited in cis form?

A

Because of STERIC CLASHES between bulky R groups

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34
Q

Primary structure

A

AA sequence

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35
Q

Secondary structure

A
  • Interactions between adjacent AA ,so parts of polypeptide chains to take on regular patterns of H bonding:
  • Alpha helices
  • Beta pleated sheets
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36
Q

Tertiary structure

A

3D folding of a single polypeptide chain

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37
Q

Quaternary structure

A

Assembly of multiple proteins into a complex

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38
Q

AA sequence from …….. to ……..

A

N-terminus to C-terminus

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39
Q

What is the primary structure determined by?

A

The DNA sequence of the gene for each protein

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40
Q

Why do primary structures of proteins dictate the final protein structure?

A

Because the sequential arrangement of R groups influencing subsequent structures

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41
Q

Describe the alpha helix secondary structure?

A
  • Coiled rod-like structure
  • Most common secondary structure
  • Flexible + elastic
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42
Q

What can disrupt alpha helix structure?

A

Proline

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43
Q

Where is alpha helices abundant in?

A

Haemoglobin

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44
Q

Where is alpha helices absent in?

A

Chymotrypsin

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45
Q

How is the alpha helix stabilised?

A

The extensive intra-chain hydrogen bonding

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46
Q

How many AA are in the alpha helix per turn?

A

3.6

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47
Q

What bond forms the backbone of alpha helices?

A

Peptide bonds

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48
Q

Why do R groups project outwards in alpha helices?

A

To avoid steric hindrance

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49
Q

C=O is the . ……..

N-H is the . ………..

A

H acceptor

H donor

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50
Q

Describe the beta plated sheet?

A
  • Flat sheets
  • Pleated
  • short runs of 5-10 AA
  • Can be parallel / anti-parallel / mixed
  • Strands are = almost fully extended
  • Strong
  • Resilient
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51
Q

What are multiple sheets connected by in beta pleated sheet?

A

Short turns / hairpin loops

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52
Q

Side chains of beta sheets are arranged?

A

ALTERNATELY ON OPPOSITE SIDES of the strand

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53
Q

Are beta sheets more flexible than alpha helices?

A

YES

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54
Q

Length of beta sheets in a protein ranges from ……….. residues?

A

2-22 residues

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55
Q

What is the function of loops/random coils?

A

Connect secondary structural elements

56
Q

Where are loops/random coils normally located?

A

On the surface

57
Q

Describe loops/random coils?

A

Rich in polar + charged residues

58
Q

Loops/random coils lengths?

A

2-20 residues

59
Q

What are loops/random coils frequently part of?

A

Enzyme active sites

60
Q

How are loops/random coils different to other secondary structures?

A

LESS CONSERVED

61
Q

Differences between structurally similar proteins typically occur in …

A

loops

62
Q

Beta hairpin motif

A

2 adjacent anti-parallel beta strands joined by a hairpin loop

63
Q

What is the simplest supersecondary structure?

A

the beta hairpin motif

64
Q

Where are beta hairpin motifs most common in ?

A

Globular proteins

65
Q

What is the specific function of beta hairpin motif?

A

No specific function

66
Q

Helix loop helix motif

A

2 alpha helices connected by a loop

67
Q

What are the functions of helix loop helix motif?

A

1) DNA binding e.g. c-Myc

2) Ca2+ binding motif e.g. Calmodulin

68
Q

Where are helix loop helix motif common in ?

A
  • transcription factors (helix-basic- loop-helix)

- cell signalling proteins that bind Ca2+ (EF-hand)

69
Q

Greek key motif

A

3 anti-parallel beta strands connected by hairpins plus a 4th strand which is adjacent to the 1st + linked to the 3rd by a longer loop

70
Q

What are greek key motifs common in?

A

A range of proteins

  • proteases (trypsin)
  • cytokines (TNF alpha)
71
Q

What function do greek key motives have?

A

NO specific function

72
Q

Coiled coil motif

A

Contain repeats of a 7 RESIDUE PATTERN (hxxhcxc)

73
Q

In coiled coil motifs, resulting amphipathic alpha helices have a …..

A

a “stripe” of hydrophobic residues that coil around similar stripes in other helices such that hydrophilic residues project outwards

74
Q

Examples of coiled coil motif?

A

Leu zippers in transcription factors e.g. c-Fos

Structural proteins e.g. Myosins

75
Q

Zinc finger motif

A

2 antiparallel beta sheets followed by 1 alpha helix , stabilised by a zinc iron

76
Q

What can zinc finger motifs bond to?

A

Fe, Zn / no metal at all

77
Q

What is metal bonding in zinc finger motifs mediated by?

A

Cys (in beta sheets) + His (in alpha helix)

78
Q

Can zinc finger motifs be present frequently within the same polypeptide chain?

A

YES

79
Q

Functions of zinc finger motifs?

A

Binding of DNA , RNA , lipid + protein substrates

80
Q

Zinc finger motifs are common motifs in many proteins including ……

A

Transcription factors e.g. Kruppel-like factor 4 (KLF4)

81
Q

Beta barrel motif

A

Multiple anti-parallel beta-sheets that twist + to form a closed structure

82
Q

The first strand in a beta barrel motif is …….

A

H bonded to the last

83
Q

Types of beta barrel motifs

A

Greek key barrel
Up-and-down barrel
Jelly roll barrel (complex)
Beta-helix barrel

84
Q

Why are beta barrel motifs pore-forming?

A

Can form water channels (aquaporins)

85
Q

Up-and-down barrel

A

8 anti-parallel beta-sheets connected by hairpin loops e.g. retinol-binding protein

86
Q

Jelly roll barrel (complex)

A

8 beta strands arranged as 2x 4 stranded antiparallel beta sheets which wrap around a hydrophobic interface
e.g. major capsid protein P2 from bacteriophage PM2

87
Q

Pore forming barrel

A

Complexes of protein subunits each with 2x 4 stranded antiparallel beta sheets

  • Polar side chains form channel for hydrophilic molecules
    e. g. Porin 1
88
Q

Domains

A

A polypeptide chain that folds independendentLY into a stable structure WITH ITS OWN HYDROPHOBIC CORE

89
Q

What are domains formed from?

A

Several simple motifs + secondary structure elements

90
Q

How many domains can proteins have?

A

One to several tens of domains

91
Q

What is each domain associated with?

A

A distinct biological function

92
Q

Examples of domains

A

Src homology 2 (SH2) domain
-binds phospho-Tyr residues
(important in insulin signalling)

93
Q

Tertiary structure

A

Overall 3D shape of the entire polypeptide

94
Q

What are tertiary structures held together by?

A

1) H bonds
(between R groups)

2) Ionic bonds (ELECTROSTATIC ATTRACTION)
(between CO2- + NH3 of R groups)

3)Disulphide bridges (COVALENT CROSSLINKS)
(between cysteine -SH groups )

4)Hydrophobic interactions
(hydrophobic R groups cluster inside proteins to shield themselves from H20)

95
Q

What do can secondary structures form form?

A

Long parallel fibres + sheets

96
Q

How do long parallel fibres + sheets react with water?

A

Normally insoluble in H20

97
Q

What are the functions of long parallel fibres + sheets?

A

Providing strength + support

98
Q

Where are alpha keratins found?

A

Mammalian hair + nails

99
Q

Where are beta keratins found?

A
  • Invertebrates
  • Silks
  • Reptile scales
  • Claws
  • Avia feathers
  • Beaks
  • Claws
100
Q

Collagen structure?

A

Super-helices of Gly-rich triple alpha helices (=tropocollagen) that assemble into fibrils

101
Q

What is collagen the main protein in and what is its function?

A

connective tissue

-supports , connects / separates tissues + organs

102
Q

Is collagen abundant?

A

VERY (25% of total protein)

103
Q

Collagen is …. + …..?

A

Strong + elastic

104
Q 
Bone
Cartilage
Teeth
Ligaments
Tendons
Skin
Blood vessels
Eyes (cornea + lens)
A

collagen

105
Q

What happens when collagen goes wrong?

A

Ehlers Danlos Syndrome (EDS)

106
Q

What is Ehlers Danlos Syndrome?

A

-A genetic connective tissue disorder
-Multiple mutations possible in multiple genes
Can affects :
Skin
Musculoskeletal
Cardiovascular

107
Q

Alpha keratins : Hair+Nails

A
  • Composed of coiled-coils of 2 alpha helices that assemble together into larger fibres
  • Strong
  • Inextensible
  • Insoluble + chemically inert
  • Disulphide bridges cross link coiled-coils
108
Q

Beta keratins : Fibroin

A

Found in silk+spider webs

-Layers of anti-parallel beta sheets in Ala + Gly residues

109
Q

How do beta keratins fibroin allow close packing of beta sheets?

A

Small side chains interdigitate

110
Q

How are the beta sheets joined in beta keratins fibroin?

A

Via amorphous stretches (confer elasticity + strength)

111
Q

Globular proteins

A

Mixture of irregularly folded secondary elements to form a compact 3D shape

112
Q

Why are globular proteins easily transported in body fluids?

A

Usually soluble in H20 (with inner hydrophobic core)

113
Q

What are globular proteins a common structure for?

A

Enzymes

114
Q

Examples of globular proteins?

A

Myoglobin
Haemoglobin
Immunoglobin

115
Q

What is haemoglobin?

A

A tetramer

116
Q

Describe haemoglobin structure?

A

-4 polypeptide subunits
-4 haem molecules
(haem= porphyrin + Fe2+ , O2)

117
Q

Myoglobin

A

Related to haemoglobin exists as single polypeptide

118
Q

Function of heamoglobin

A
  • TRANSPORTS 02 from lungs to the rest of the body

- RELEASING 02 to permit aerobic respiration to provide energy

119
Q

Specific mutations in DNA encoding Hb genes can cause what diseases?

A
  • Sickle cell disease

- Thalassaemias

120
Q

Describe carbon monoxide poisoning?

A

Carbon monoxide bonds haemoglobin more readily than oxygen + is released more slowly

121
Q

What is sickle cell disease?

A

Disease cause by single gene defect in DNA coding region within beta globin gene

122
Q

What type of mutation is in sickle cell disease?

A

Missense mutation + changes primary sequence

123
Q

Symptoms of sickle cell disease

A
  • Changes in RBC shape (sickle)
  • RBCs rigid , become blocked in capillaries (ischaemia / organ damage / pain)
  • Increased haemolysis (RBC destruction)
124
Q

Being a carrier (heterozygous) for the sickle cell gene is protective against what?

A

Malaria

125
Q

What are immunoglobulins?

A

Y-shaped proteins of the immune system which identifies + combats invading foreign organisms

126
Q

Describe the structure of immunoglobulins?

A
  • 4 chains linked by disulphide bridges
  • -2 large Heavy chains
  • -2 short Light chains
127
Q

Where are the variable structures in immunoglobulins?

A

H + L chains

-Form specific binding sites for non-self targets “antigens”

128
Q

Antigen recognition by an antibody does what?

A

MARKS IT FOR ATTACK by other components of the immune system engaged by CONSTANT PORTIONS OF THE H CHAINS

129
Q

Denaturation

A

Process in which proteins lose quaternary , tertiary + secondary structure present in their native state due to a change in environment

130
Q

Denaturation factors

A

Extreme temp
Extreme pH
Organic solvent

131
Q

What bonds are sensitive to pH and why?

A

iONIC BONDS
,because it disrupts the tertiary structure
-renders protein insoluble in H20 + precipitate out of solution

132
Q

How does heat denature proteins?

A

Increase in temp = bonds VIBRATE + H / ionic bonds break

133
Q

How does the extremophile thermus aquaticus grow at temps above 70c?

A

By producing a DNA polymerase that is stable at high temps (This is essentail for PCR)

134
Q

List ORGANIC SOLVENTS?

A

Ethanol , acetone , phenol

135
Q

How do organic solvents denature proteins?

A

By disrupting intra- + inter- H bonds , by forming new H bonds with protein side chains +backbone SO THE PROTEIN UNFOLDS

Alia - Biology (10 decks)

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