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biological chemistry 2 > bimolecular structure > Flashcards

bimolecular structure Flashcards

1
Q

amino acids

A

free floating amino acids in aqueous solutions, a zwitterion forms - + and - charge, neutral overall

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2
Q

chirality and S/R config

A

four different groups bound to central carbon

to identify S/R

  1. assign priorities to 4 groups based on atomic number. higher atomic number = higher priority
  2. orient molecule so that the lowest priority group is pointing away, into the plane
  3. trace path of 1,2,3,4
    if clockwise = R config
    if counter clockwise = s config
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3
Q

amino acids in nature

A

S/L is most common

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4
Q

aliphatic side chains - amino

A

R= simple hydrocarbon side chains
chemically inert
hydrophobic - non polar

as size of side chain increases, more bulky, more hydrophobic and less flexible

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5
Q

proline

A

cyclin side chain - unusual

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6
Q

acidic amino acids

A

COOH group in R chain
negatively charged
hydrophilic, form hydrogen bonds
role in enzyme active sites

can deprontate, donate H+

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7
Q

amide amino acide

A

-CONH2 group
stable and lacks ionisable properties
polar but neutral
involved in H bonding

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8
Q

basic amino acids

A

-NH2 or -NH group
become protonated - receive a H+

hydrophilic
plays a big role in salt bridges

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9
Q

aromatic amino acids

A

have aromatic rings
hydrophobic
quite bulky

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10
Q

alcohol amino acids

A

-OH group
POLAR and hydrophilic

PTMs

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11
Q

thiol/thioether amino acids

A

thiol - contains sulphur - makes reactive under oxidative conditions, can form disulphide bonds
- polar, reactive

thioether - non polar, hydrophobic

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12
Q

peptide bond formation

A

condensation reaction between C + N terminus, nucleophilic attack using protease enzyme

amino acids join to form polypeptide

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13
Q

primary structure

A

sequence of amino acids, forming a polypeptide chain

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14
Q

secondary structure

A

alpha helix or beta pleated sheets (parallel or anti parallel, seen by arrows in ribbon diagram)

due to folding of primary structure held together by hydrogen bonding

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15
Q

alpha helix

A

n to n+4 is where the hydrogen bonding occurs to form this helix, between backbone of amide N donors and carbonyl O acceptors

  • intrahelical hydrogen bonding between the two to hold helix together.
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16
Q

beta pleated sheets

A

hydrogen bonding in same way:

  • amide NH as donor
  • carbonyl O as acceptor
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17
Q

tertiary structure

A

3d folding of secondary structure into a specific shape , held together by hydrogen bonds, disulphide bridge, ionic bonding, van Der Waals forces

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18
Q

domains

A

independent folded part of bigger polypeptide

stable on their own

could split up domains and rearrange to form new proteins

multiple domains are held together by
- intermolecular forces
H bonding
sulphide
electrostatic bondign

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19
Q

subunit

A

independent polypeptide made up of domains

  • proteins with more than one subunit have cooperative behaviour
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20
Q

post translation modifications

A

these are used to regulate function of protein for when and where it is needed in cell

e.g. if needed to be near cell membrane, it would decrease hydrophicity in carbon chain

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21
Q

heteroproteins

A

type of protein that contain non protein elements - prosthetic groups or cofactors, like metal ions, organic molecules

examples - glycoproteins, metal contain proteins, phosphoproteins

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22
Q

protein folding

A

negative entropy process - becomes more ordered as it folds into the protein which isnt good

random process where an unfolded high entropy protein folds into a specific 3D low entropy protein

however, interactions with the protein help contribute to a large negative enthalpy to ensure that gibbs is negative

23
Q

gibbs free energy

A

delta G. = delta H - Temperature (k) x delta entropy

24
Q

golf course model

A

protein remains unfolded until falls into an energetic well and folds instantly

  • hole is the lowest energy state - native conformation of protein where it is most stable and functional
25
Q

pathway model

A

describes protein folding as steps or pathways, something happens at a certain point to stabilise the protein and travel down a path of intermediates to native conformation

26
Q

funnel model

A

energy collapses at every point making it more favourable for reactions to occur that are contributing to a more stable native state

27
Q

driving force of protein folding

A

take the hydrophobic parts of protein and fold away from solvent

28
Q

rugged landscape

A

shows the thermodynamic and kinetic path of protein folding and intermediates need to give energy, get over energy barrier to reach native

29
Q

protein folding summary

A
  • a negative enthalpy process
  • needs a pathway, guidance
  • involves chaperon proteins to help fold or protect protein
30
Q

nucleic acids

A

pyrimidines - cytosine, thymine, uracil
purines - adenine and guanine

31
Q

oh in RNA c2

A

this OH makes RNA less stable than DNA due to the interaction between OH and phosphate that can cause backbone to break

  • DNA not have as needs to be much more stable
32
Q

DNA pi stacking

A

non covalent interactions between aromatic rings and nitrogenous bases

form van der Waals forces involving the pi electrons delocalising to form planar interactions
- these increase stability and structure, allowing DNA to be helical

33
Q

grooves in DNA

A

major groove- wider , exposing more base pairs, more accessible to proteins, interact with TFs

minor groover - narrower, less accessible

10 bases per turn

B DNA

34
Q

forming a new backbone

A

condensation reaction between C3 and C5

nucleophilic attack 3’ OH end to 5’ phosphate end

uses energy of disphosphates leaving - they are good leaving group as quite stable

35
Q

ribosome structure

A

70S ribosome in bacteria
- 30s subunit
- 50s subunit

70s = measure of sedimentation
together 50+30, faster than the sum of their parts alone

36
Q

ribosome sites

A

E - releases tRNA from chain to go get another one
P - elongation of the polypeptide , with tRNA still attached to hold growing chain in place as it shfits
A - tRNA comes in, bringing new amino acid as recognises the anticodon and attaches, and adds to the chain, moves to P

37
Q

unsaturated and saturated

A

if a larger molecule, = stronger IMF = higher BP
if unsaturated = less strong IMF as steric conditions preventing, lower BP

saturated non c=c, likely to be a fat
unsatuarated c=c, likely to be an oil

38
Q

trans fats

A

uncommon in nature

39
Q

recombination proteins

A
  1. use specific restriction enzymes to cut DNA at desired sequence
  2. use same enzyme to cut vector - plasmid
  3. ligate the gene in vector
  4. transform into e.coli
  5. culture of e.coli produce copies of vector
  6. purify using chromatography
40
Q

PCR components

A

DNA sample
primers - limited
nucleotides - limited
tag polymerase
mix buffer
per tube

41
Q

PCR process

A

denaturing - increase temp to 95 to break H bonds
annealing - lower temp to 55 to allow hydrogen bonds to form with primers
extension - increase temp to 72 to synthesis new strand with taq

42
Q

agarose gel electrophoresis

A

DNA = agarose

43
Q

restriction enzymes

A

endonuclease target specific DNA sequence to cleave
produce protruding ends to join the gene

44
Q

chemical transformation

A

incubate
heat shock to open pores
plasmids enter
recovery, lower temp to close pores and plasmids stay inside

45
Q

electroporation

A

start with electro-competent cell and incubate
- electric shock to open cells and then recover
same process as chemical one but just with electric shock

46
Q

bacterial expression

A
  • cheap and easy
  • good for bacterial soluble proteins - simple proteins
  • no PTMs, not good for eukaryotic cells
47
Q

yeast expression

A
  • harder to grow
  • good for glycosylation
    includes PTMs
48
Q

insect/mammalian expression

A

used for more difficult proteins
good for PTMs, antibody drugs

49
Q

uses of recombinant proteins

A

drugs, vaccines, insulin
research
industrial enzymes, laundry
argiculture
biocatalyst in biotech

50
Q

SDS-PAGE

A

sodium dodecyl sulfate polyacrylamide gel electrophoresis

denaturing agent for larger proteins to be denatured into subunits

can do a native -page, no denaturing to see whole protein

51
Q

how to get re combo proteins

A

dialysis - cellulose tubing to only allow small proteins out, trapping desired protein in tubing

ammonium sulfate precipitation - each protein precipitates at different cones of this so titrate desired protein

chromatography - ion exchange or size exclusion

52
Q

affinity chromatography

A

introduce hex-histidine to tag protein of interest in cloning stage

histidine has a higer affinity for metals and will hold in column

collect and this remove his-tag by cleaving off with protease, then run through again just to get protein without tag

53
Q

resolution of cryo-em structure

A

image alignment
particle image contrast/resolution
number of images covering all orientations
computing power
conformational and compositional homogeneity

biological chemistry 2 (5 decks)

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