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MBB proteins
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1what
- Aindole
2what
- Aimidazole
3[blank_start]Proline[blank_end] reduces structural flexibility of regions in the polypeptide as it has a saturated ring linking Ca and Na atoms, preventing rotation around the N-C bond. The ring is [blank_start]puckered[blank_end].
[blank_start]Methionine[blank_end] contains sulfur.
Aromatic residues absorb UV light at [blank_start]280nm[blank_end]
Cysteine forms [blank_start]disulphide[blank_end] bridges.
[blank_start]Histidine[blank_end] can be positively or neutrally charged at pH 7 as its pKa is near neutral. It can act as a proton donor or acceptor.- AProline
- Bpuckered
- CMethionine
- D280nm
- Edisulphide
- FHistidine
4The sequence of am acids in the protein is its [blank_start]primary[blank_end] structure. Polypeptides are linear polymers with polarity- they have an N and a C terminal end. [blank_start]Ionisable[blank_end] R groups in the polypeptide dominate charge status. The amide bond is essentially planar and it [blank_start]resonates[blank_end] between single and double bond character.
N-Ca and Ca-C bonds are pure single. Rotation about these bonds allows conformational flexibility in the backbone. There are 3 dihedral angles.
[blank_start]Phi[blank_end] is rotation about N-Ca
[blank_start]Psi[blank_end] is rotation about Ca-C
Omega is rotation about N-C, it is O if the two residues are in [blank_start]cis[blank_end] conformation, and 180 if they are trans which they usually are to reduce steric clashes. Phi and Psi can be [blank_start]any[blank_end] value between -180 and +180, allowing proteins to fold in many ways. Most combinations are prohibited due to [blank_start]steric[blank_end] clashes. Gly has a broad range. [blank_start]Pro[blank_end] has a very narrow range.- Aprimary
- BIonisable
- Cresonates
- DPhi
- EPsi
- Fcis
- Gany
- Hsteric
- IPro
5Cysteine contains an SH group. Pairs of cysteine if close enough can [blank_start]oxidise[blank_end] to produce a [blank_start]disulfide[blank_end] bond. (intra and intermolecular). This releases 2[blank_start]H[blank_end]+ +2[blank_start]e[blank_end]-
- AH
- Be
- Cdisulfide
- Doxidise
6Keratins form hair, [blank_start]horns[blank_end], nails, feathers. a keratins are in mammals and provide protection. Polypep chains form a [blank_start]helices[blank_end] and a helices wrap around one another to form a [blank_start]coiled[blank_end] coil. Chains that are rich in [blank_start]cysteine[blank_end] residues can be [blank_start]oxidised[blank_end] to form intermolecular disulphide bonds. The number of disulfide bonds determines the protein [blank_start]properties[blank_end].
Proteins can also associate to form large [blank_start]complexes[blank_end].- Ahorns
- Bhelices
- Ccoiled
- Dcysteine
- Eoxidised
- Fproperties
- Gcomplexes
7[blank_start]Conformation[blank_end] is the spatial arrangement of a molecule's atoms. This includes any structure it can adopt [blank_start]without[blank_end] breaking [blank_start]covalent[blank_end] bonds. Even a small polyps has a huge number of allowed conformations although most are not allowed due to [blank_start]steric[blank_end] clashes. Only 1 or a few conformations are found for most proteins in nature as those which are most [blank_start]thermodynamically[blank_end] stable are adopted. These energetic conditions drive protein folding to a particular [blank_start]subset[blank_end] of conformations which could be adopted.
Segments of a protein usually fold to characteristic secondary structures where a phi and psi values are [blank_start]the same[blank_end] along the segment due to a repeating pattern of [blank_start]hydrogen[blank_end] bonds. These structures then interact to form [blank_start]tertiary[blank_end] structure. Structures can be monomeric or multimeric. [blank_start]Quaternary[blank_end] structure describes how multiple polypeps are arranged in the complex- AConformation
- Bwithout
- Ccovalent
- Dsteric
- Ethermodynamically
- Fsubset
- Gthe same
- Hhydrogen
- Itertiary
- JQuaternary
8A [blank_start]denaturant[blank_end] is an agent that results in the loss of folding in a protein. Secondary structures fold and [blank_start]test[blank_end] out different conformations until they find an energy [blank_start]minimum[blank_end] as they form weak bonds between different polypep components.
Covalent bonds e.g. disulfide bonds
Salt bridges are [blank_start]strong[blank_end]
VdW interactions are weak but there are [blank_start]many[blank_end]
H bonds [blank_start]weak[blank_end] but there are many
Hydrophobic effect- hydrophobic chains are folded on the [blank_start]interior[blank_end] of a protein away from water.- Adenaturant
- Btest
- Cminimum
- Dstrong
- Einterior
- Fmany
- Gweak
9[blank_start]Salt[blank_end] bridges are thermodynamically favourable but create [blank_start]ordered[blank_end] water molecules nearby. [blank_start]Entropy[blank_end] decreases as order increases, offsetting favourability of salt bridge. Salt bridges contribute little to protein stability. en of association proportional to 1/[blank_start]r[blank_end] so they can be fairly long range. En of ass of 2 electric charges separated by dist r:
U=kq1q2/[blank_start]Dr[blank_end] q1+q2 = charges on atoms r= hist between atoms in A D=Dielectric constant, accounting for effects of intervening medium
An attractive interaction has a [blank_start]negative[blank_end] value.
Inside a protein there are [blank_start]fewer[blank_end] H2O molecules to intervene
Dipole Dipole
1/r3 they are [blank_start]short[blank_end] range and en decreases rapidly.- ASalt
- BEntropy
- Cordered
- Dr
- EDr
- Fnegative
- Gfewer
- Hshort
10H bonds only [blank_start]weakly[blank_end] stabilise proteins but provide a structural basis for folding. The strongest H bonds are [blank_start]linear[blank_end]. There are lots of them.
Hydrophobic side chains cluster together in the [blank_start]interior[blank_end] of proteins to increase entropy.- Aweakly
- Binterior
- Clinear
11An a helix is [blank_start]right[blank_end] handed. Side chains are orientated [blank_start]away[blank_end] from the helix centre as they are bulky. There's a pitch of [blank_start]5.4[blank_end]A and [blank_start]3.6[blank_end] residues per turn. The a helix optimises internal H bonds within the backbone, but some residues' R groups affect the backbone's ability to adopt necessary phi and psi angles. A residue's position relative to its neighbours is also important- a long block of residues with the [blank_start]same charge[blank_end] will repel. The bulk and shape of some will destabilise a helix. positive residues are often 3 away from negative residues so a salt bridge can form.
[blank_start]Gly[blank_end] residues are too flexible.
Pro residues are rigid so the N-Ca bond cannot rotate. they are [blank_start]helix breakers[blank_end]- Aright
- B5.4
- C3.6
- Daway
- Esame charge
- FGly
- Ghelix breakers
12The b sheet is composed of b [blank_start]strands[blank_end]. H bonds form between NH and CO groups in the [blank_start]backbone[blank_end] of adjacent strands. B sheets are more extended than helices. There are 2 types of b sheet. Parallel and [blank_start]antiparallel[blank_end], they differ in relative directions of N-C terminus. Side chain orientation alternates above and below the sheet plane. They can be [blank_start]flat[blank_end] or [blank_start]twisted[blank_end] in shape.
Proteins can be primarily a helical, primarily b sheet or a [blank_start]mix[blank_end].- Astrands
- Bbackbone
- Cflat
- Dtwisted
- Eantiparallel
- Fmix
13Which direction does the b sheet arrow point in
- Ac terminus
- Bn terminus
14[blank_start]Quaternary[blank_end] structure describes spatial arrangement of subunits in a protein complex. VdW interactions, salt bridges, H bonds, disulfide bonds and hydrophobic effect allow subunits to interact. Hb has a quat structure. We can see the relative position of atoms in proteins by [blank_start]X ray crystallography[blank_end] and NMR.
Proteins are also present in [blank_start]membranes[blank_end]. They are used for transport, photosynthesis and oxidative phosphorylation and cell-cell recognition. 20-30% of proteins encoded are [blank_start]integral[blank_end] membrane proteins. Membrane proteins can be [blank_start]peripheral[blank_end] or integral. Integral proteins interact [blank_start]extensively[blank_end] with the very hydrophobic part of the lipid bilayer. a helices most commonly span the membrane, and these proteins are often enriched in [blank_start]hydrophobic[blank_end] residues- the absence of water prevents meeting H bond potential of hydrophilic residues.
An example is [blank_start]bacteriorhodopsin[blank_end]- it uses light to generate a proton gradient and is made of [blank_start]7[blank_end] very hydrophobic transmembrane a helices.- AQuaternary
- BX ray crystallography
- Cmembranes
- Dintegral
- Eperipheral
- Fextensively
- Ghydrophobic
- Hbacteriorhodopsin
- I7
15Some integral membrane proteins act as [blank_start]channels[blank_end] through the membrane. Channels are exposed to [blank_start]water[blank_end] so contain polar and [blank_start]charged[blank_end] residues. The presence of [blank_start]polar[blank_end]/charged residues in membrane spanning a helices is an indicator of possible exposure to the [blank_start]aqueous[blank_end] environment by channel formation.
Denatured proteins have [blank_start]no activity[blank_end] as function is dictated by [blank_start]structure[blank_end]. [blank_start]Urea[blank_end] and [blank_start]guanidium[blank_end] chloride act as denaturing reagents. They increase [blank_start]non-polar[blank_end] residue [blank_start]solubility[blank_end] and reduce hydrophobic effect. Unfolding occurs and can be observed by monitoring conformationally sensitive protein properties.
shape can be changed by [blank_start]heat[blank_end] pH solvents or ionic strength.- Achannels
- Bwater
- Ccharged
- Dpolar
- Eaqueous
- Fno activity
- Gstructure
- HUrea
- Iguanidium
- Jnon-polar
- Ksolubility
- Lheat
16If we [blank_start]dialyse[blank_end] out the denaturant, the protein can refold spontaneously.
[blank_start]Ribonuclease[blank_end] cleaves RNA. Enzyme activity was assayed- activity indicates native fold. He purified.
Added [blank_start]urea[blank_end] a denaturant and [blank_start]b-mercaptoethanol[blank_end] which reduced all disulfide bonds.
Enzyme activity was lost
He removed urea and b-mercaptoethanol by [blank_start]dialysis[blank_end]
enzyme activity was recovered so all the info needed is in the [blank_start]primary[blank_end] sequence.
Proteins fold by progressive [blank_start]intermediates[blank_end]. Local [blank_start]sec[blank_end] structures with high stability form first. these are [blank_start]nucleation[blank_end] points and aid folding of less stable sec structures. [blank_start]Chaperonins[blank_end] reduce misfolding but it may still occur. protein aggregates form [blank_start]amyloid[blank_end] fibrils. Alzheimers, Parkinsons and C-J caused by this.- Adialyse
- BRibonuclease
- Curea
- Db-mercaptoethanol
- Edialysis
- Fprimary
- Gintermediates
- Hnucleation
- Isec
- JChaperonins
- Kamyloid
17[blank_start]Cofactors[blank_end] increase the repertoire of reactions that proteins can perform. They are either metals or [blank_start]small[blank_end] organic coenzymes.
Proenzyme+coenzyme=[blank_start]holoenzyme[blank_end]
A metal ion or coenzyme which is tightly bound to an enzyme is a [blank_start]prosthetic[blank_end] group.
Coenzymes are [blank_start]transient[blank_end] carriers of a functional group. The use of the same coenzyme by 2 diff enzymes usually indicates similar catalytic mechanisms.
Metal ions give important structural features to enzymes- [blank_start]zinc fingers[blank_end] bind to DNA and regulate gene transcription.- ACofactors
- Bsmall
- Choloenzyme
- Dprosthetic
- Etransient
- Fzinc fingers
18COVALENT MODIFICATION
[blank_start]Glycosylation[blank_end] is adding 1 or more carbohydrate groups to residues on a protein to form a glycoprotein. Sugar is hydrophilic so protein [blank_start]solubility[blank_end] increases, important as prots are often secreted into [blank_start]aqueous[blank_end] environments. Stability increases, helping shape and function. This can also shield [blank_start]pathogens[blank_end]' surface proteins from recognition by the host immune system.
O-linked- glycosyl bond formed with o of [blank_start]serine[blank_end]
N-linked- glycosyl formed with n of [blank_start]asparagine[blank_end]
HYDROXYLATION is where proline and [blank_start]lysine[blank_end] residues are hydroxylated. Some prolines are hydroxylated in collagen to [blank_start]stabilise[blank_end] it as OH group locks the proline to one conformation. Prolyl hydroxylase needs [blank_start]vitC[blank_end] as a cofactor.- AGlycosylation
- Baqueous
- Csolubility
- Dpathogens
- Eserine
- Fasparagine
- Glysine
- HvitC
- Istabilise
19Phosphorylation is where [blank_start]local[blank_end] charge is added to part of a protein that is only moderately polar. They can alter conformation and function of the whole protein. It is readily reversible by protein [blank_start]kinases[blank_end]. and protein phosphates.
[blank_start]acetylation[blank_end] is where [blank_start]lysines[blank_end] are acetylated by [blank_start]acetyl coenzyme A[blank_end]. This is important in lysine residues in [blank_start]histones[blank_end] for regulating gene transcription. It creates a more open form of chromatin. This is reversible.- Alocal
- Bkinases
- Cacetylation
- Dlysines
- Eacetyl coenzyme A
- Fhistones
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- idk Biochemistry Quiz on MBB proteins, created by Mara Sampsyn on 13/12/2015.
- Author
- Mara Sampsyn
- Language
- English
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