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1014 Biological Chemistry > protein structure > Flashcards

protein structure Flashcards

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1
Q

what are the four groups present in a amino acid?

> be specific about their properties

A

amino = acid so proton donor
carboxyl = base so proton acceptor
R side group = this is variable so can change
Hydrogen

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2
Q

what does chiral mean?

A

it cannot be superimposed (mirror image)

each vairent is called an enanitomers

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3
Q

what is a zwitterion?

A

dipolar ion with 0 charge
only exisits at the isoelectric point at which pH is 7
where the amino acid is protonated

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4
Q

SIDE CHAINS
Gly
Ala
Ser

A

Hydrogen
CH3 = methyl
CH2OH = some polarity due to electronegative Oxygen

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5
Q

SIDE CHAINS
Cys
His

A

CH2SH

aromatic ring = potentially be acharged molecule

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6
Q

whats the difference between an aa and amino residue

A

residue does not have a free amino/carboxyl group

but esentially the same thing

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7
Q

what is cool about double bonds?

A

they cannot rotate

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8
Q

are sidechain interaction involved in secondary structures of proteins?

A

NO. it only involves the backbone

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9
Q

facts about ALPHA HELIX

A

> held by hydrogen bonding
right handed helix (so turns towards the right)
side chains project out at 100° so have 3.6 residues a turn
n to n+4 linkage so Carboxyl2 to amine6

it can stretch ———– longitudinally
but it is rigid | laterally
> like a slinky

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10
Q

why is Proline /P considered a helix breaker?

A

it cannot rotate as its sidechain is connected to its amino group (loop)
irregular geometry interrupting the backbone

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11
Q

why is Tyrosine/Y considered a helix destabiliser?

A

it has a large bulky side group

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12
Q

common aa found to create alpha helix

A 
Alanine
Arginine
Histidine
Leucine
Lycine
Glutamate
Glutamine
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13
Q

facts about beta sheets

A

can be parallel or antiparallel

> anti parallel is flexible laterally but NOT longituidnally as its already extended

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14
Q

Amino acids can have two isomeric forms, L or D. Which form(s) is found as constituents of proteins?
A L-isomer
B D- isomer
C Both isomers

A

YAAAY Only L isomers can form proteins

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15
Q

What are the key features of an alpha-helix?

> but drill it into your mind!

A

Right-handed
3.6 residues/turn
n to n+4 linkage
Side chains project out at 100° to each other

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16
Q

What is the difference between parallel and anti-parallel beta sheets?

A

parallel has weaker hydrogen bonding and had R groups that are available to interact

17
Q

What makes an amino acid a zwitterion?
A No charges on any atom
B Negative charge on amino group only
C Positive charge on carboxyl group and negative charge on amino group
D Positive charge on amino group and negative charge on carboxyl group

A

OPTION D

In solution under neutral conditions, an amino acid residue will exist as a dipolar zwitterion. The COOH looses the H to from COO-, and the NH2 gains the H+ to form NH3+.

18
Q 
What method of purification of proteins involves the unfolding of a protein by coating it with a detergent?
A Size Exclusion Chromatography
B Affinity Chromatography
C Precipitation by ammonium sulphate
D Isoelectric focusing
E SDS-PAGE
A

OPTION E
> charged and hydrophobiC which allows protein to be dragged through gel
> smaller protein moves faster
> protein can be stained afterwards

> > protein is denatured

19
Q 
What protein is created from 2 identical subunits which is more efficient to create?
A Haemoglobin
B Albumin	
C Collagen
D HIV protease dimer
E Myosin
A

OPTION D
dimer - clues in the name
> efficient and less chance of an error
as its assmeble at the quaternary levle

20
Q 
Which amino acid is a helix breaker?
A Lysine
B Histidine
C Cysteine
D Proline
E Tyrosine
A

OPTION D
proline cannot rotate as side chain is bonded back to amino gorup

> tyrosine is detabliser as it has a big bulky side group

21
Q

What are some key features of the protein structure of collagen?

A

Every 3rd a.a. = glycine
High proportion of proline (less flexibility, enforces KINKS in chain)
High proportion of hydroxyproline (proline modified after incorporation into protein)

22
Q 
in competitive inhibition what happens
A V-max increases, Km constant
B V-max constant, Km increases
C V-max constant, Km decreases
D V-max decreases, Km constant
A

OPTION B
v max the same but km increaes as you need more substrate to overcome inhibitor
> km/ km apparant for enzyme-inhibitor

> > enzymes are still functional so have the same vmax

23
Q

in irreversible inhibition

what happens to Vmax + Km?

A

different vmax as there are LESS fucntional enymes

> functional enzymes work witht eh same affinitiy thoug

24
Q

name some hydrophobic and hydrophilic aa (side chains)

A

Val, Leu, Phe - hydrophobic
Asp, Lys, Ser - hydrophilic
> they stay together in their groups during the ‘‘hydrophobic effect’’

25
Q

decribe ‘‘hydrophobic effect’’ what occurs? when thinking about teritary structure (protein folding)

A
  1. hydrophobic collapse as water surrounds the hydrophobic molecules making them immobile = less entropy
  2. if water becomes free then energy becomes available for protien to fold
26
Q

If the specificity constant of an enzyme is high…
It is a ‘good’ enzyme
kcat is high
km is high

It is a ‘good’ enzyme
kcat is high
km is low

It is a ‘good’ enzyme
kcat is low
km is high

A

OPTION B

hihg turnover rate and uses not a lot of substrate to do it

27
Q 
a plot of substrate concentration against reaction velocity generates what type of curve?
A horizontal line 
B sigmoid
C hyperbolic / curved
D directly proportional 
E inversely proportional
A

OPTION C - is a nice curved line that plateaus

28
Q

for competitive inhibition, which statement is incorrect?
A irreversible
B an inhibitor with the same shape as the substrate blocks the active site
C Vmax stays the same
D Km increased
E the amount of substrate available will be increased

A

OPTION A
competitve is reversible

substrate accumualtes so Km also increases

29
Q 
Which of the following sidechains is hydrophobic? 
A Aspartate
B Valine
C Lysine
D Serine
A

OPTION B

Valine has two methyl groups and a H group attached, these are non-polar hence the sidechain is hydrophobic

30
Q 
the central carbon in an amino acid is called what?
alpha
beta
omega
gamma
delta
A

ALPHA CARBON

1014 Biological Chemistry (8 decks)

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