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Biochemistry > Amino Acids and Proteins L3 > Flashcards

Amino Acids and Proteins L3 Flashcards

1
Q

what does DNA make

A

RNA

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2
Q

what does RNA make

A

protein

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3
Q

what RNA is transcribed from DNA

A
  • tRNA
  • rRNA
  • mRNA
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4
Q

what happens in the nucleolus

A

rRNA combines with proteins imported in from cytoplasm

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5
Q

how do RNA leave nucleus

A

nuclear pores

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6
Q

why do RNA leave nucleus

A

can perform their task - manufacture protein

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7
Q

what happens in cytoplasm

A

all RNAs together synthesize amino acid strings, primary structure of proteins

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8
Q

how are proteins formed

A

tRNAs attract their amino acid partners
two subunits of rRNA lock onto the 5’ end of mRNA
In ribosome, sequence of mRNA nucleotides recognized three at a time
tRNAs with their attached amino acids wait
Releasing factor allows protein chain to break from ribosomes
Proteins fold in precise tertiary structure

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9
Q

where are some ribosomes

A

embedded in endoplasmic reticulum

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10
Q

what happens in golgi apparatus

A

protein molecules assembled for other cell components or as secretion from cell

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11
Q

what happens at smooth regions of endoplasmic reticulum,

A

launch vesicles containing protein and other large biomolecules

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12
Q

what is exocytosis

A

vesicles move towards cell membrane where their membranes fuse, send their contents across membrane. May be several golgi’s in an active cell

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13
Q

what is endocytosis

A

at same time, nutrients entering cell by reverse route. Vesicles bud inward to carry large biomolecule across cell membrane into cytoplasm

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14
Q

what is the initiation complex formation made of

A

30S ribosomal subunit, formyl-methionyl (f-Met) tRNA and mRNA

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15
Q

what happens in protein synthesis in prokaryotic cell

A

translation initiated by initiation complex formation
50S ribosomal subunit joins complex
70S ribosome has two sires that tRNA-carrying amino acids can bind
- P site
- A site
fMet carried by tRNA in P site joined to amino acid carried by tRNA that just entered A site by peptide bond
ribosome moves one codon along and tRNA that carried fMet released from E site
tRNA carrying next amino acid moves into A site where anticodon on tRNA matches mRNA codon
ribosome shifts down one codon, two amino acids on tRNA in P site transfer to new amino acid and second tRNA released from E site
ribosome continues to move along mRNA and new amino acids added to growing polypeptide chain
polypeptide elongation terminated when stop codon moves into A site
ribosome dissociates into 30S and 50S subunits and mRNA and protein released

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16
Q

what is P site

A

peptide site

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17
Q

what is A site

A

acceptor site

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18
Q

what is E site

A

exit site

where tRNA released

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19
Q

what are non-essential amino acids

A

made from common metabolic intermediates directly

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20
Q

what are essential amino acids

A

Can’t make all amino acids need to consume them

Protein not made unless all essential amino acids are present

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21
Q

why is it essential to consume ’pool of amino acids’

A

don’t have essential amino acids

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22
Q

what are aromatics

A

amino acids are made from complex

metabolic pathways

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23
Q

what sort of organisms can make all of the amino acids

A

bacteria
yeast
plants

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24
Q

what is the problem with Phenylketonuric subjects

A

don’t have enzyme phenyl alanine hydrolase can’t make tyrosine
phenylalanine accumulates in brain and urine
tyrosine is an essential amino acid to phenylketonuric subjects

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25
Q

what diets do Phenylketonuric subjects need

A

low phenylalanine diet

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26
Q

how is tyrosine formed from phenylalanine

A

Phenyl alanine hydrolase adds OH

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27
Q

example of lack of essential amino acids

A

kwashiorkor

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28
Q

what does Glyphosate inhibit

A

EPSP synthase an essential enzyme for production of aromatic amino acid

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29
Q

how does weed killer work

A

Glyphosate inhibit part of pathway to prevent growth as cannot synthesis any aromatic amino acids
Amino acids become essential as cannot make them
Can’t make the amino acids so proteins not made so they die

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30
Q

what are the amino acids used for building blocks

A

L enantiomers

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31
Q

what is NH2

A

amino group

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32
Q

what is the first carbon in amino acids

A

alpha-carbon

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33
Q

what is the second carbon in amino acids

A

beta-carbon

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34
Q

what is the third carbon in amino acids

A

gamma-carbon

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35
Q

what are zwitterions

A

physiological pH zwitterions - positive molecule

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36
Q

what is chiral

A

not superimposable on its mirror image

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37
Q

what are optically active amino acids

A

some rotate light one side, whereas some forms of same amino acid rotate it another way

38
Q

why is chirality important in drug design

A

one enantiomer is more effective

other may be potentially dangerous

39
Q

what are the amino acids that exist

A

D and L amino acids exist in nature

40
Q

which amino acid is used in building blocks of proteins

A

only L-amino acids

41
Q

where are D-amino acids found

A

in few rare bacteria

42
Q

what can occur to amino acids in ageing

A

may include the isomerization of amino acid aspartic acid from L to D in teeth and eye proteins

43
Q

what are isomerised proteins

A

less biologically active

44
Q

what dictates the amino acids properties

A

R chain attached to alpha carbon

45
Q

what are the three groups of amino acids

A
  1. Non-polar side chains (hydrophobic)
  2. Polar, uncharged side chains
  3. Polar charged acidic and basic side chains
46
Q

what are amino acids importance

A

Amino acids are important physiological buffers

47
Q

what is a buffer

A

aqueous solution containing a weak acid and a weak base that are a conjugate-acid base pair

48
Q

what is a buffers job

A

resist changes in pH upon addition of acid or base

49
Q

what can pH imbalance of blood cause

A

alkalosis or

acidosis

50
Q

what acidity are amino acids

A

weak acids and possess at least 2 titratable protons

51
Q

what are amino acids covalently linked by

A

peptide bonds

52
Q

what shape is peptide bond

A

planar

53
Q

what is a peptide bond like

A

double-bond

restricted rotation

54
Q

what are the two configurations pf amino acids

A

planar conformation there are Cis and Trans

55
Q

what are polypeptide chains like

A

flexible yet conformationally restricted

56
Q

what is a phi angle

A

angle of rotation about the bond between the nitrogen and the α-carbon atoms

57
Q

what degree is a Phi angle

A

-80

58
Q

what is a psi angle

A

angle of rotation about bond between alpha-carbon and carbonyl carbon atoms

59
Q

what degree is psi angle

A

+85

60
Q

what does a Ramachandran Diagram show

A

showing values of ϕ and ψ
Proteins have area where prefer to be
As soon as amino acids produced start folding into a particular shape
Don’t have freedom we think they have, they’re restricted

61
Q

what does the peptide rigidity do

A

rigidity of peptide unit limits the structures accessible to unfolded form sufficiently to allow protein folding to occur

62
Q

what is an alpha helix

A

3.6 amino acids per complete turn with hydrogen bonding between every fourth amino acid to maintain helical shape

63
Q

what is a beta sheet

A

formed from largely extended polypeptide strands that make hydrogen bonds between backbone group of neighboring strands

64
Q

what does a beta sheet consist of

A

multiple sequences in same protein that are arranged adjacently and anti-parallel, let each amino acid form hydrogen bond

65
Q

what are the forces during protein folding

A 
hydrophobic interaction
hydrogen bonds
electrostatic attraction
metal ion coordination
covalent bridges
66
Q

example of proteins needing metal

A

haemoglobin

67
Q

why do we need small amount of ‘metal’ in diet

A

essential proteins to work

68
Q

what are the steps of enzyme-catalysed protein disulfide isomerisation reaction (disulfide interchange)

A

-SH group from reduced PDI attacks non-native disulfide bond in partially folded polypeptide
Non-native disulfide bond breaks, new disulfide bond forms between PDI and one of the original partners from non-native bond
Other partner become reduced to –SH group, can attack another non-native disulfide bond in polypeptide
New native disulfide forms in polypeptide, allows folding into native state
PDI released in reduced state, catalyse additional disulfide interchange reactions

69
Q

where are proteins formed and internalized

A

endoplasmic reticulum

70
Q

what is PDI

A

protein disulfide isomerase

71
Q

benefit of the native state

A

Native state more resistant to further PDI attack

72
Q

dynamics of proteins

A

structure of proteins is divided into four different levels

73
Q

what is primary structure

A

amino acid sequence, which is translated from RNA

74
Q

what are the two variations in secondary structure

A

alpha helix and beta sheet

75
Q

what is the tertiary structure

A

overall shape of one chain of amino acids, take alpha helices into account, and four different types of interactions between amino acids

76
Q

where are ionic bonds

A

present between oppositely charged particles, usually found in nonpolar centre

77
Q

where are hydrophilic acidic molecules

A

on outside

78
Q

where are the basic amino acids

A

on outside

79
Q

where are hydrophobic molecules located

A

central parts of chains

80
Q

what does cysteine forms disulfide bonds

A

–SH on end of its chain

81
Q

what happens when -SH group oxidized

A

let sulfur atoms form covalent bond

82
Q

what does the quaternary structure involve

A

combination of multiple chains of amino acids, alpha helices, beta sheet, hydrogen bonding, ionic bonding, disulfide bonds, hydrophobic/hydrophilic interactions

83
Q

what happens if polypeptide chain put into water

A

will naturally fold self – not sufficient, need machinery

84
Q

what is a chaperonin

A

requires ATP, end polypeptide bound to chaperonin and proteins are expelled from complex

85
Q

what is folding like

A

a highly cooperative process

86
Q

how are proteins classified on biological role basis

A
  • Structural proteins (mechanical support
  • Enzymes (biological catalysts)
  • Transport and storage (Carrier of small molecules)
  • Muscle contraction and mobility
  • Protective proteins (Immune system)
  • Regulatory and receptor proteins
87
Q

what drives biochemical pathways

A

most driven by enzymes

88
Q

what is needed to break molecules

A

Need energy to break molecules

89
Q

what happens if add a regulatory molecule

A

enzyme stops working – allosteric effect

90
Q

what does the catalytic activity of enzymes might depend on

A

presence of cofactors

Biochemistry (13 decks)

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