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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
Q

what are polypeptides made by

A

covalent bonds

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26
Q

what are aas joined by

A

joined together by amide linkage = peptide bond

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27
Q

describe peptide bonds

A

peptide bonds in backbone of polypeptide = uncharged but polar

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28
Q

what do the side chains of a polypeptide determine

A

charge and hydrophobicity of a polypeptide

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29
Q

what can side chains and backbone do

A

both side chains and backbone can form noncovalent contacts with other aas
polypeptide bond = polar
condensation reaction

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30
Q

describe polypeptide backbone

A

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

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31
Q

is there flexibility in aa chain

A

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
Q

what do proteins contain

A

only L amino acids
can have L or D = optical isomers but only L in aas

33
Q

describe what configuration peptide bonds occur in

A

trans configuration always for all aas EXCEPT P (PROLINE)
trans highly favoured for all other aas, cis configuration highly disfavoured since steric clash

34
Q

DESCribe why proline peptide bonds not in trans formation

A

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
Q

what participates in noncovalent bonding

A

side chains and backbone

36
Q

what stabilizes structure

A

interactions between residues of a polypeptide

37
Q

name non covalent interactions and describe a bit

A

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
Q

describe hydrophobic interactions

A

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
Q

what is covalent interaction between cysteines

A

disulfide bonds

40
Q

which proteins have disulfide bonds

A

secretory proteins often have covalent disulfide bonds between cysteine side chains
Extracellular proteins inside secretory organelles
disulfides reinforce structure

41
Q

which proteins do not have disulfide bonds

A

cytosolic proteins normally do not have disulfide bonds
cytosol, nucleus, mitochondria

42
Q

what interactions happen between disulfide cysteine bonds

A

intramolecular and intermolecular interactions

43
Q

what is order of how proteins fold

A

linear aa sequence = primary structure –> polypeptide backbone –> folding –> 2d confirmation: tertiary structure, very diverse

44
Q

how many levels of organization contribute to protein structure

A

4

45
Q

describe secondary structure

A

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
Q

describe secondary structure - alpha helix

A

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
Q

describe secondary structure - beta sheets

A

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
Q

describe tertiary structure

A

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
Q

describe loops of tertiary structure

A

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
Q

describe quaternary structure

A

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
Q

name ways to visualize proteins

A

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
Q

what are domains

A

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
Q

give examples of domains or things with domains

A

hsp 70 = 2 domains
transcription factor
transcription activation domain
dna binding domain

54
Q

what are domain combos

A

some conserved domains are found in many diff proteins in combo with other domains

55
Q

describe modular domains

A

modular domains form reversible, specific, non covalent contacts with other molecules
other proteins - diff from quaternary structure
lipids, carbs, rna, dna, other cofactors

56
Q

describe polypeptide length - most human polypeptides

A

100-800 aas long or from 12kda - 90 kda molecular weight

57
Q

describe polypeptide length - domains

A

50-200 aas long

58
Q

what do long proteins have

A

multiple domains
rich in domains

59
Q

what do many biological functions require

A

noncovalent protein interactions

60
Q

describe specific protein interactions

A

only Certain molecular surfaces are bound
lock and key - noncovalent bonding

61
Q

describe transient protein interactions

A

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
Q

describe sequence similarity

A

sequences of diff polypeptides can be compared with each other to align identical (same aa, sequence) and similar amino acids (same properties, characteristics)

63
Q

what does sequence similarity indicate

A

homology (serves a function) indicated evolutionary conservation

64
Q

what does homology suggest

A

common structure or function

65
Q

what happens when polypeptides do not have any sequence similarity

A

they are considered to be divergent

66
Q

give ex of sequence similarity

A

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
Q

what are protein families

A

family is a set of proteins or domains which have homologous sequences and structures

68
Q

describe protein families

A

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
Q

describe homologous domains and not homologous

A

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
Q

what are proteins - summary

A

polymers made of 20 diff aas

71
Q

what are the types of aas and why - summary

A

4 types = hydrophobic, polar, basic, acidic
based on chemical properties - functional group of their side chain

72
Q

what do aas bind through - summary

A

a peptide bond
sequence of aa determines the folding of the protein into functional 3d structures

73
Q

what do the aa peptide bond and side chain engage in - summary

A

both engage in non covalent interactions to form the secondary, tertiary and quaternary structures

74
Q

what does side chain determine - summary

A

R determines the proteins charge, polarity, hydrophobicity and interactions with other molecules/function

75
Q

are some aas similar - summary

A

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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