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ANAT 212 > Lecture 3 > Flashcards

Lecture 3 Flashcards

1
Q

what is the most abundant macromolecule in the cell

A

proteins
have functions
most abundant groups

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2
Q

are protein structures mostly the same

A

no incredible diversity between protein structures
diff protein = diff structure

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3
Q

what does structure conformation mean

A

function

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4
Q

diverse strcutures of proteins lead to

A

Multiple functions

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5
Q

what do cell building blocks do - proteins

A

Provide shape and structure

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6
Q

what functions do proteins undertake

A

enzymes catalyze cell chemical reactions
membrane proteins form communication channels = transmembrane proteins, communication (er to golgi, nucleus to cytoplasm)
transport of cargo and mechanical forces

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7
Q

how important are proteins

A

very

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8
Q

what are the main functional components in cells

A

proteins

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9
Q

how do proteins acquire function

A

by folding into a 3d conformation

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10
Q

what does folding of proteins provide

A

physical stability and functional surfaces

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11
Q

what does sequence of aas determine

A

sequence of aas of a protein determine its structure, function and localization
allows proteins to interact with other macromolecules

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12
Q

describe central dogma - proteins

A

nucleic acids function as linear polymers
nucleic acid – DNA –> transcription –> RNA –> translation by ribosomes= all in a line, no function yet, must get 3d conformation state

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13
Q

what are proteins

A

sequence of aas
polymers made of 20 different amino acids - monomers

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14
Q

what is a polymer

A

peptide chain

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15
Q

describe amino acid general formula

A

alpha carbon with covalent bonds
amino group
carboxyl group (acidic)
Hydrogen
side chain or functional group = R
at ph 7, both amino and carboxyl groups are ionized (NH3+ and COO-)

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16
Q

describe R

A

Commonly one of 20 diff side chains

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17
Q

name the chemical characteristics of the side chains

A

hydrophobic, polar or charged (acidic or basic - neg or pos)
small or large
Covalently linked into polypeptides, - alpha carbon

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18
Q

name polar aas

A

asparagine
glutamine
serine
threonine
tyrosine

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19
Q

describe peculiarities of polar aas

A

r groups form h bonds
glutamine = extra methylene group, amide chain
asparagine = amide chain
serine = hydroxide group
threonine = hydroxide group
tyrosine = ring, not as hydrophilic so this one is the least polar, hydroxide group *H bonding

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20
Q

name the 5 charged aas to ph 7 and a feature of the R groups

A

3 basic R = pos charged = lysine, arginine, histidine
2 acidic R = neg charged = aspartate, glutamate

r groups allows for electrostatic/ionic interactions between basic and acidic aas, if pos and neg together

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21
Q

describe peculiarities of charged aas

A

lys vs arg vs his = his has ring, pos charge of chemical group not as big, not as easy to form polar and ionic interactions, his nitrogens have a weak affinity for an H and are only partly pos at neutral ph

asp vs glutamate = glu has extra methylene

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22
Q

name 10 hydrophobic nonpolar aas

A

alanine
valine
proline
phenylalanine
glycine
cysteine
leucine
isoleucine
methionine
tryptophan

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23
Q

describe peculiarities of hydrophobic aas

A

proline = conformations
glycine = smaller, hydrophobic aa = inside, fits everywhere,
cysteine = covalent bonds with other cysteine= disulfide bond, covalent v strong, sulfhydryl group
tryptophan = hydrophobic aas, some noncovalent, not perfect, not as nonpolar as others, bc nh group, H little bit polar= some H bonding

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24
Q

describe hydrophobic aas - features

A

interact through the hydrophobic interactions - exclusion of water molecules
disulfide bonds can form between 2 cysteine side chains in proteins - NEVER in cytosol since reducing environment - low nadp+ and nadph, only in er lumen and exterior of cells

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25
what are polypeptides made by
covalent bonds
26
what are aas joined by
joined together by amide linkage = peptide bond
27
describe peptide bonds
peptide bonds in backbone of polypeptide = uncharged but polar
28
what do the side chains of a polypeptide determine
charge and hydrophobicity of a polypeptide
29
what can side chains and backbone do
both side chains and backbone can form noncovalent contacts with other aas polypeptide bond = polar condensation reaction
30
describe polypeptide backbone
planar cannot rotate rotation around bonds to central carbon (alpha) is possible polypeptide backbone has limited freedom of rotation some rotation angles between aas (residues) in a polypeptide are preferred
31
is there flexibility in aa chain
yes, 2 single bonds allow rapid rotation so long aa chains are v flexible not part of polypeptide backbone tho partial double bond character = not able to rotate
32
what do proteins contain
only L amino acids can have L or D = optical isomers but only L in aas
33
describe what configuration peptide bonds occur in
trans configuration always for all aas EXCEPT P (PROLINE) trans highly favoured for all other aas, cis configuration highly disfavoured since steric clash
34
DESCribe why proline peptide bonds not in trans formation
closed ring structure so doesnt matter much if trans or cis configuration trans = slightly favoured cis = slightly disfavoured both still steric clash a bit
35
what participates in noncovalent bonding
side chains and backbone
36
what stabilizes structure
interactions between residues of a polypeptide
37
name non covalent interactions and describe a bit
Hydrogen bonds van der waals interactions - transient dipoles between all atoms, all have these, sometimes e- move and make small interactions ionic bonds - between pos and neg charge hydrophobic interactions - exclusion of water
38
describe hydrophobic interactions
no h bonds, forced to interact with water= among themselves, make cages since inside aa = hydrophobic so cannot make h bonds with hydrophobic, so water interacts with itself becomes one big salvation cage, entropically favourable in one cage = ΔS >0
39
what is covalent interaction between cysteines
disulfide bonds
40
which proteins have disulfide bonds
secretory proteins often have covalent disulfide bonds between cysteine side chains Extracellular proteins inside secretory organelles disulfides reinforce structure
41
which proteins do not have disulfide bonds
cytosolic proteins normally do not have disulfide bonds cytosol, nucleus, mitochondria
42
what interactions happen between disulfide cysteine bonds
intramolecular and intermolecular interactions
43
what is order of how proteins fold
linear aa sequence = primary structure --> polypeptide backbone --> folding --> 2d confirmation: tertiary structure, very diverse
44
how many levels of organization contribute to protein structure
4
45
describe secondary structure
local conformation patterns polypeptide bonds important results from h bonding between N-H and C=O groups in polypeptide backbone many diff aas can form them stretches of polypeptides adopts regular and repeating arrangements of the polypeptide backbone and position of side chains common structures = alpha helices and beta sheets
46
describe secondary structure - alpha helix
single polypeptide chain twist around on itself backbone is coiled h bonds between carbonyl and amine hydrogen formed every 4 peptide bonds in each turn of helix backbone = stabilizes side chains point outwards always face out
47
describe secondary structure - beta sheets
Neighbouring segments of the polypeptide backbone backbone is extended almost straight - parallel and antiparallel backbones several strands pack sideways into a beta sheet h bonds between backbone strands side chains on alternate sides v rigid structure 2 types = anti parallel - to c and n terminals, parallel - all towards c terminals
48
describe tertiary structure
complete 3 d arrangement of the polypeptide secondary structure elements packed against each other to form the tertiary structure hydrophobic contacts between secondary elements = into cages and aa that are polar/charged noncovalent bonding and gives it structure long range contacts between residues that are far apart in the primary sequence
49
describe loops of tertiary structure
flexible loops = not all proteins engaged in secondary structure, intrinsically disordered regions loops have no regular secondary structure and can be flexible important for post trans mods
50
describe quaternary structure
assembly of multiple polypeptides (subunits) into a final protein interactions between subunits very stable dimer = 2 polypeptide subunits timer, tetramer, 5-mer, 6-mer etc oligomer = many subunits ex = nuclear pore complex
51
name ways to visualize proteins
polypeptide backbone ribbon diagram = polypeptide backbone only but with secondary structure stick diagram = includes AA R chains, side chains space filling model = with mass of atoms
52
what are domains
independently folded unit within a protein proteins can have multiple domains diff domains in protein often have diff functions independent function maintains tertiary structure on its own
53
give examples of domains or things with domains
hsp 70 = 2 domains transcription factor transcription activation domain dna binding domain
54
what are domain combos
some conserved domains are found in many diff proteins in combo with other domains
55
describe modular domains
modular domains form reversible, specific, non covalent contacts with other molecules other proteins - diff from quaternary structure lipids, carbs, rna, dna, other cofactors
56
describe polypeptide length - most human polypeptides
100-800 aas long or from 12kda - 90 kda molecular weight
57
describe polypeptide length - domains
50-200 aas long
58
what do long proteins have
multiple domains rich in domains
59
what do many biological functions require
noncovalent protein interactions
60
describe specific protein interactions
only Certain molecular surfaces are bound lock and key - noncovalent bonding
61
describe transient protein interactions
often transient interactions = form and break apart quickly thermal motion means all molecules are constantly moving, tumbling and colliding inside = transient interactions, depends on concentration and equilibrium, less abundant = less interactions depends on binding equilibria
62
describe sequence similarity
sequences of diff polypeptides can be compared with each other to align identical (same aa, sequence) and similar amino acids (same properties, characteristics)
63
what does sequence similarity indicate
homology (serves a function) indicated evolutionary conservation
64
what does homology suggest
common structure or function
65
what happens when polypeptides do not have any sequence similarity
they are considered to be divergent
66
give ex of sequence similarity
homo vs apis Valine vs alanine = both hydrophobic so similar sequence, so weak similarity tyrosine vs phenylalanine =same structure but tyrosine has hydroxyl, so strong similarity
67
what are protein families
family is a set of proteins or domains which have homologous sequences and structures
68
describe protein families
often have related functions - similar domain structure function Organism can have several proteins from same family proteins from a family can be found in diff organisms - conserved by evolution
69
describe homologous domains and not homologous
human hsp 70 atpase domain, temp depends on protein, survival VS e coli hsp 70 atpase domain = homologous, very important and conserved function. z domains almost identical ecoli hsp70 vs ecoli arsenite transport atpase subunit = not homologous since diff functions
70
what are proteins - summary
polymers made of 20 diff aas
71
what are the types of aas and why - summary
4 types = hydrophobic, polar, basic, acidic based on chemical properties - functional group of their side chain
72
what do aas bind through - summary
a peptide bond sequence of aa determines the folding of the protein into functional 3d structures
73
what do the aa peptide bond and side chain engage in - summary
both engage in non covalent interactions to form the secondary, tertiary and quaternary structures
74
what does side chain determine - summary
R determines the proteins charge, polarity, hydrophobicity and interactions with other molecules/function
75
are some aas similar - summary
some aas are similar and provide homology among protein members of the same family or proteins conserved through evolution

ANAT 212 (34 decks)

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