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proteins Flashcards

1
Q

what can proteins function as

A
  • catalysts (for chemical reactions and carry out vital reactions in living systems as enzymes)
  • transporters (channel proteins or more complex transmembrane proteins with multiple sub-units in impermeable lipid membranes)
  • mechanical support
  • immune protection
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2
Q

what do proteins control

A
  • movement
  • growth
  • development
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3
Q

what proteins can transmit nerve impulses

A

signal receptors

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4
Q

what are proteins

A
  • linear polymers built from monomer units called amino acids
  • contain a wide range of functional groups (mostly governed by side chains of amino acids)
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5
Q

what do proteins interact with one another and with other biological molecules to form

A

complex assemblies

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6
Q

what types of structures can proteins display

A
  • all different
  • can be v rigid
  • can display flexibility (ie structural proteins)
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7
Q

what are amino acids

A

building blocks of all proteins
20 proteinogenic amino acids (encoded as codons in the genetic code + linked together during translation to form a protein

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8
Q

what do the variable r side chain groups give amino acids

A
  • different properties which influence folding

- 20 different r side chains = 20 different amino acids

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9
Q

what can happen to the amine and carboxyl groups of amino acids

A

can be protonated and deprotonated (work like acids and bases =
its why theyre called amino acids mostly bc of the carboxyl group)

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10
Q

what are the properties of the amine and carboxyl groups of amino acids at physiological (pH 7)

A

BOTH IONISED
- amine group = protonated ie +vely charged (-NH3^+)

  • carboxyl group = deprotonated ie -vely charged (COO-)
  • gives each amino acid a net charge of 0
  • this is the zwitterionic form
  • each amino acid has zwitterionic possibility in terms of their charge
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11
Q

what are the properties of amino acids at low pH

A
  • protonated (as many H+/protons)
  • amine group = protonated so +ve charge
  • carboxyl group = protonated so no charge
  • net charge = POSITIVE
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12
Q

what are the properties of amino acids moving towards neutral / physiological pH

A
  • amount of zwitterionic (neutral) form is increasing
  • amine group is protonated (+ve)
  • carboxyl group deprotonated (-ve)
  • net charge = 0
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13
Q

what are the properties of amino acids at high pH

A
  • less H+/protons in solution
  • moves to more basic environment
  • amine group = deprotonated so no charge
  • carboxyl group = deprotonated so -ve charge
  • net charge = NEGATIVE
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14
Q

what does the asymmetric alpha carbon atom allow for

A

OPTICAL ISOMMERY

  • 2 optical isomers of the molecule can be formed
  • contain same atoms but the way the atoms are bound around the C-alpha atom differs
  • 2 mirror images (or stereoisomers) that cant be superimposed
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15
Q

what can the optical/stereo isomers exist as in amino acids

what is the only one found in proteins in living systems

A
  • L- or D- isomers
  • the L-form
  • ribosomes and tRNAs work as catalysts in terms of only incorporating the L forms of amino acids
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16
Q

how do side chains in amino acids and the backbone in the protein contribute to protein folding

A
  • charge interaction

- hydrogen bonding

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17
Q

how does polarity occur in uncharged water molecules

A

because electrons between oxygen and hydrogen are differentially distributed and more skewed toward the oxygen atom

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18
Q

what does polarity mean in water molecules

A
  • shift of overall electron distribution in the molecule is more towards the electronegative oxygen atom
  • this moves -ve charge more towards the oxygen atom
  • giving polarity (indicated by delta ie delta positive on H atoms and delta negative on O atom) which acts somewhat like a charge
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19
Q

what does polarity mean for water molecules

A

water forms hydrogen bonds with water molecules or other polar molecules

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20
Q

what do hydrogen bonds form between

A
  • oxygen atom of 1 H2O
  • hydrogen atom of 2nd
  • demonstrated as small vertical lines between the two
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21
Q

what does polarity dictate

A

if a molecule is miscible w water / associates with it or NOT
- assume a molecule is miscible if it is considered polar + has a shift in its electron distribution

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22
Q

explain why methane is not easily miscible with water under normal conditions

A
  • CH4
  • no difference in electron charge distribution across the molecule = its APOLAR
  • electron distribution is equal between all atoms
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23
Q

so why is it important to look at amino acid side chains?

what are all proteins in our bodies made up of

A

see if on inside or outside of the protein depending on their miscibility with h2o OR if they are hydrophilic or hydrophobic

the same 20 proteinogenic amino acids

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24
Q

what can side chain groups be grouped into

A

side chain types

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25
Q

what can we group amino acids into at the top most level split

A

1) polar amino acids (contain a charge or unequal distribution of electrons across the molecule )
2) nonpolar amino acids (uncharged side chains, equal electron distribution)

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26
Q

what names do we have for each amino acid

A

1) long name
2) short 3 letter abbreviation for that name
3) assign a letter to an amino acid (used to abbreviate sequences)

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27
Q

how can polar amino acids be further classified

A
  • by their side chains
    a) negative = side chains have -ve charge
    b) positive = side chains have +ve charge
    c) uncharged polar
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28
Q

which amino acids are polar (what is the charge on their side chains)

A 
aspartic acid (negative)
glutamic acid (negative)
arginine (positive)
lysine (positive)
histidine (positive)
asparagine (uncharged polar)
glutamine (uncharged polar)
serine (uncharged polar)
threonine (uncharged polar)
tyrosine (uncharged polar)
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29
Q

where are polar amino acids placed in proteins

A
  • on outside

- facing aqueous environment bc are hydrophilic + miscible with h2o

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30
Q

what property makes amino acids non polar

A
  • uncharged side chains

- equal distribution of electrons in the side chains so not miscible with water

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31
Q

where are non polar amino acids placed in proteins

A

towards the inside of the protein when it folds as they are hydrophobic

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32
Q

which amino acids are non-polar with uncharged side chains

A 
alanine
glycine
valine
leucine
isoleucine
proline
phenylalanine
methionine
tryptophan
cysteine
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33
Q

what other class of amino acids exists and related to nutrition and what are these

A

essential amino acids

  • cannot be synthesised by our bodies
  • we dont have the biochemistry to synthesise these from simple building blocks
  • take them in in diet (ingest nutrients containing them)
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34
Q

what are the essential amino acids

A 
threonine
methionine
lysine
valine
leucine
isoleucine
histidine
phenylalanine
tryptophan
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35
Q

what are conditionally essential amino acids

A
  • only become essential under certain special conditions (ie in infants, if have a disease)
  • supplied by nutrition as cannot be synthesised in high amnts in the body
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36
Q

what are the conditionally essential amino acids

A 
arginine 
cysteine
glutamine
glycine
proline
tyrosine
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37
Q

what are non-essential amino acids

A

all of these can be synthesised by the body

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38
Q

which amino acids are non-essential

A 
alanine
aspartic acid
asparagine
glutamic acid
serine
selenocysteine
pyrrolysine
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39
Q

in a single letter abbreviation amino acid code what is the a) stop codon
b) a start codon

A

a) an asterisk

b) M = methionine (= coded by the start codon)

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40
Q

what is the side chain of histidine

A

a cyclic moiety linked to itself (complex side chain)

41
Q

amino acids considered basic (with basic side chains) are what 4 things

A

1) charged
2) polar
3) hydrophilic
4) usual charge of side chain is +ve at physiologic pH (can take up a H which makes them into a base)

42
Q

amino acids considered acidic (with acidic side chains) are what

A

1) contain an extra carboxyl group in the side chain
2) functional side chains have a carboxyl group deprotonated in physiologic pH (O- on single bonded O atom)
3) so -vely charged polar side chain
4) hydrophilic
5) side chain can be protonated AND deprotonated (usually deprotonated at physiologic pH so can release protons into solutions that turns it into an acidic side chain group)

43
Q

amino acids considered non-polar (with non-polar side chains) are what

A

1) no charge
2) no groups with unequal electron distribution
3) so polar and non-miscible with water
4) usually hydrophobic

44
Q

why is cysteine a special case

A
  • SULFHYDRYL GROUP in its side chain (SH)

- so can link to another cysteine side group by covalent bonding and form a DISULPHIDE BOND (imp for protein structures)

45
Q

amino acids with uncharged polar (hydrophilic and miscible w h2o) side chains are what

A
  • asparagine and glutamine are variants of aspartic + glutamic acid where 2nd oxygen in R group is substituted by an amino group. although amide N isnt charged at neutral pH it is polar
  • in serine, threonine and tyrosine the -OH group is polar
  • amine not charged at physiologic pH BUT is considered polar (unequal distribution of electrons)
46
Q

what are amino acid side chain responsible for

A
  • mediating protein folding

- 3d structure of proteins

47
Q

what does the 3d structure of proteins confer

A

structural or functional properties as enzymes

48
Q

what is essential for proteins to acquire

A

a 3d folded state (inherently governing their properties)

49
Q

how is protein folding mediated by amino acid side chains

A
  • protein is many amino acids linked (polymer of peptide bond linked amino acids)
  • amine + carboxyl groups participate in the peptide backbone of protein
  • side chains just stick out from this backbone
  • due to different chemical properties of side chain, this unfolded protein polypeptide chain starts to fold in an aqueous solution
  • gives EVERY protein a distinct 3d structure which determines its function
50
Q

what is the primary structure

A

unfolded protein / polypeptide where side chains are stuck out from polypeptide backbone

51
Q

what causes the unfolded protein polypeptide chain to fold in an aqueous solution

A
  • some amino acid side chains interact w
    1) aqueous environment directly
    2) each other
  • apolar amino acid side chains cluster on the inside of globular proteins as they are hydrophobic
52
Q

what forces are involved in protein folding

A

1) ELECTROSTATIC ATTRACTIONS
2) ELECTRON CLOUD INTERACTIONS / VAN DER WAALS ATTRACTIONS
3) HYDROGEN BONDS

53
Q

how do electrostatic bonds + electrostatic interactions form

A
  • most basic
  • charged amino acids interact directly w the opposite charge
  • ie +vely charged side chain forms electrostatic interactions with a -vely charged one (ie between +vely charged N and -vely charged O)
54
Q

how do electron cloud interactions/van der waals attractions form

A
  • weaker than electrostatic attractions
  • lead to apolar side chains associating with each other (on top of hydrophobic forces working on them)
  • as they fold into the inside to get away from water then when close enough to each other can attract each other by van der waals
55
Q

where are hydrogen bonds involved

A

in secondary structure folding of proteins

56
Q

what is the property of the disulfide bond formed by 2 cysteine side chains’ -SH groups

A
  • goes through oxidation (to form disulfide bond) + reduction (to break it) reactions so is a reversible interaction
57
Q

where can cysteine side chains interact with themselves

A
  • within the same protein = INTRAmolecular reaction forming intrachain disulfide bond
  • in 2 independent proteins = INTERmolecular reaction (interchain disulfide bond between 2 independent proteins) forming interchain disulfide bond
  • in subunits of proteins
58
Q

how is the disulfide bond formed by 2 cysteine side chains

A
  • oxidise sulfhydryl groups
  • removes hydrogens
  • the 2 sulfur groups bond w each other (covalent bond)
59
Q

where does disulfide bond formation between cysteines occur in the body

A

INSULIN FORMATION (protein synthesised as 1 long protein precursor)

60
Q

how is insulin formed

A

1) synthesised as a long pro insulin molecule which folds
2) folding stabilised by linking it in place through formation of 2 INTRAchain / intramolecular disulphide bonds
3) connecting peptide is cleaved and removed (post translationally processed) leaving complete 2 chain insulin molecule (2 independent proteins linked by INTERchain / intermolecular disulphide bonding between independent subunits)
4) this is reduced to irreversibly separate the 2 chains into 2 separate sub-units

61
Q

what are primary structure proteins

A

linear polymers

62
Q

how do primary structure proteins form

A

1) peptide bonding between alpha-carboxyl group of one amino acid and alpha-amino group of another (condensation reaction)
2) seq of amino acids joined by peptide bonds form a polypeptide chain (a protein)

63
Q

what gives a polypeptide chain polarity

A
  • its ends are different
    1) amino or N-terminal end
    2) carboxyl or C-terminal end
64
Q

what is the N terminal end of the polypeptide chain

A
  • amine group of 1st amino acid of protein
  • taken as beginning of chain (toward the left)
  • so each protein starts w an N-terminal end
65
Q

how is a peptide bond formed

A
  • 2 amino acids react together (ie during translation)
  • condensation reaction
  • carboxyl group of one joined together w amino group of other
  • H2O removed
  • covalent peptide bond formed (old cats need houses)
66
Q

what is important to note about the peptide bond

A

IT CANNOT BE ROTATED

  • peptide bond forms a rigid planar unit with no free rotation about the C-N bond
  • bc of resonance
67
Q

where is there free rotation of all groups

A

on the central alpha carbon atom

  • means long chains of amino acids are very flexible
  • allows protein folding
68
Q

what is resonance in the peptide bond and what does it mean we must assume

A
  • double bond between the carbon + oxygen can also be considered to be occurring between the carbon and nitrogen atom and then alternating between those states
  • assume it is partially double bonded (means it cannot rotate) so it cannot be defined / fixed in place
69
Q

where is the rigid, planar, non rotational nature of the peptide bond important

A
  • for secondary structure where polypeptide chain folds in a specific way to form alpha helices + beta pleated sheets
70
Q

what do the N terminus (NH3+) and C terminus (carboxyl free terminus -COO) ends demonstrate

A

EVERY PROTEIN HAS DIRECTIONALITY

N —> C

71
Q

how do we show different 3d structural elements of proteins that may repeat or fulfil certain subfunctions (domains)

A
  • list with specific domains / subfolding or 3d structures in diff simple shapes + colours
  • shows which proteins share similar subunit folding and structural units in the protein seq/domains
72
Q

what regular structures does the polypeptide fold into during secondary structure

A
  • ALPHA HELIX
  • BETA SHEETS
  • form turns and loops to connect these
73
Q

what different models can we use to illustrate 3d structure of the same protein

A
  • the polypeptide chain (most simple)
  • cartoon model = indicates position of helices and beta sheets
  • ball and stick model = indicates position of all atoms except hydrogen
  • space filling spherical model (most complex) = usually used when looking at catalytic pockets or sites (to model binding of other chemicals into certain proteins to design inhibitors)
74
Q

what is an alpha helix

A
  • oxygen groups of peptide bond + nitrogen / hydrogen groups bound to the nitrogen form H bonds
  • SO protein backbone folds on itself in a helix as a spiral
  • every 4th or 3rd amino acid binds back to the hydrogen of the amino acid that was free before
75
Q

where does the bonding occur in alpha helices

A

Every backbone N−H group hydrogen bonds to the backbone oxygen of the C=O group of the amino acid located three or four residues earlier along the protein sequence

76
Q

what type of conformation 3d structure is alpha helix

A

right handed spiral

77
Q

which depiction is usually used to show protein secondary structure containing helices and loops

A

cartoon like schematics (DO NOT have all structural formulas and atoms labelled)

  • depicts how this protein folds in 3d space
  • and how some sub-regions of this protein is folded into an alpha helices
78
Q

what is formed when 2 alpha helices wind around one another

A

alpha helical coiled coils (coiled-coil superhelix)

79
Q

where are alpha helical coiled coils (coiled-coil superhelix) found

A

many proteins

1) keratin (hair)
2) quills
3) claws
4) horns

collagen forms a TRIPLE helix (important extracellular matrix protein)

80
Q

why do alpha helical coiled coils (coiled-coil superhelix) form

A
  • apolar amino acid side chains want to point away from water (on inside of the protein)
  • induces a twisting of 2 helices against each other to minimise exposure to aqueous environment
81
Q

what do alpha helical coiled coils (coiled-coil superhelix) give us possibilities for

A
  • designing structurally rigid or flexible structural proteins that can form fibrils (v imp organisational pattern of protein folding)
82
Q

how do beta sheets form

A
  • induced by H bonding between components of the peptide bonds the
    same as alpha helix but forms a sheet instead
83
Q

what stabilises beta sheets

A

hydrogen bonding between polypeptide strands

84
Q

what 2 ways can beta sheets be

A

1) antiparallel = adjacent beta strands run in opposite directions
2) parallel = run in same direction (both N-C terminus)
- if can identify directionality of a stretch of a protein backbone involved in beta sheet formation we can look at directionality of the other strand its H bonding to to determine if beta sheet is parallel or antiparallel

85
Q

how does beta sheet folding work

A
  • multiple strands of polypeptide backbones h bond with each other
  • O interacts with H of amine
86
Q

what pattern is formed in a beta pleated sheet

A
  • alternating ziz zag 3D planarity pattern (not all in 1 planar area)
  • due to geometric alignment and flexibility of the backbone sequence and peptide bond
87
Q

what does the alternating zig zig pattern of beta sheets represent

A
  • distance between each involved amino acid side chain + peptide bond group in the beta sheet
88
Q

what can be seen in the secondary structure

A
  • first time the protein folds from its primary sequences into the 3d structure
  • complex combinations of helices, turns, loops and beta sheets
  • turns connect helices and beta sheets in the protein sequence
  • forms distinct structural subunits
89
Q

what is the tertiary structure of proteins

A
  • final 3D folding
  • devoid of symmetry
  • globular proteins (ie myoglobin) = interior almost entirely nonpolar side chains, hydrophilic side chains containing amino acid backbone are on outside of protein
90
Q

where are charged amino acid residues found on a fully folded protein

A

on surface

91
Q

what is the quarternary structure of proteins

A
  • final level of protein folding
  • different proteins fold together / associate to form larger protein complex
  • so some proteins contain >1 polypeptide chain OR >1 protein encoded by a gene
92
Q

what is the name for polypeptide chains in quaternary proteins and what can polypeptide chains can assemble into

A
  • sub-units

- multisubunit structures (may contain many of same subunit or different subunits)

93
Q

what is an example of a multisubunit structure assembled by protein quaternary structure assemblies of the same repeating sub-ubits

A

virus capsid/coat proteins

  • multiple globular sub-units sat on 1 repeating circular sub unit (central core protein)
  • these independent polypeptides (protein quaternary structure assemblies of same repeating sub-unit) associate together to form large macromolecular complex capsid structure (100nm)
94
Q

how is the formation of a viral capsid protein different to insulin formation

A

insulin = 2 independent polypeptide chains linked by disulphide bond BUT insulin protein encoded by 1 gene and synthesised as 1 protein + only afterwards cleaved into 2 independent protein sub-units

viral capsid = different proteins encoded by different genes associate to form multiprotein sub-unit complexes

95
Q

what mediates association of 2 independent protein sub-units to form a multi-subunit

A

charge interactions on the side chains available on the surface of the 3D folded structure of each sub-unit

96
Q

what is an example of a quaternary protein in the body

A

human haemoglobin

  • complex
  • transports O2 in blood
97
Q

how did Max Perutz decipher the 3d model of human haemoglobin in 1959

A
  • based on x-ray diffraction pattern
  • 1st model hand drawn back and produced as built model based on xray diffraction
  • major achievement
98
Q

what does the complex computer model of haemoglobin contain

A

ball and stick simulation superimposed with cartoon depiction of secondary structure

IOE (22 decks)

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