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(1) Biochemistry: Cellular Composition > Proteins and Ligands > Flashcards

Proteins and Ligands Flashcards

1
Q

What is the central dogma?

A

The information flow from DNA to RNA to Proteins

replication, transcription, translation

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2
Q

Protein function is determined by its shape, what is its shape determined by?

A

Its amino acid sequence

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3
Q

How many standard amino acids are there?

A

20 plus some post-transcriptionally modified ones

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4
Q

What is chirality?

A

When two molecules are optical isomers. They’re asymmetric and cannot be superimposed into one another

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5
Q

What are the two stereoisomers of amino acids and which ones form peptide bonds with ribosomes?

A

L + D

Ribosomes only form peptide bonds with L amino acids

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6
Q

What is the primary sequence?

A

The sequence of amino acids in the polypeptide chain

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7
Q

What part of an amino acid chain is the N-terminus?

A

NH3+

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8
Q

What part of the amino acid chain is the alpha carbon?

A

The carbon before each C=O bond

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9
Q

What part of the amino acid chain is the peptide bond?

A

O=C-N-H-

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10
Q

What part of the amino acid chain is the C terminus?

A

O=CO-

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11
Q

What is resonance and what does it do for the peptide bond?

A

The electron in the C=O can jump between C=O and C=N

This gives the peptide bond double bond properties

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12
Q

What are phi and psi angles?

A

They describe the protein backbone shape, some are more favoured than others. The angles for an alpha carbon can be plotted on a Ramachandran plot

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13
Q

Are peptide bonds usually in trans or cis? What does this mean?

A

Trans.

This means the alpha carbons are further apart. This conformation is more stable due to steric hinderance

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14
Q

What is steric hindrance?

A

Where molecules bump into each other, making the conformation less stable and less favourable

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15
Q

What does urea do to purified proteins? What does this show?

A

High concentrations of urea denature and unfold proteins. When the urea is removed, the protein folds back into its original shape. This shows that the shape of a protein is determined by its amino acid sequence.

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16
Q

What physiochemical interactions are involved in the folding of a.acid chains? (6)

A 
Ionic interactions
Van der waals interactions
Hydrophobic/hydrophilic interactions
Disulfide bonds
Covalent bonds
Hydrogen Bonds
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17
Q

What are some examples of amino acids with charged side chains (at neutral pH)?

A

Glutamate + Aspartate are negative

Lysine and Histidine are positive

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18
Q

How does pKa affect the form of an acid?

A

When above its pKa, an acid is in its base form

When below its pKa, an acid is in its acid form

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19
Q

What are Van der Waals interactions?

A

When brought close together, atoms not sharing electrons experience VDW interactions. They will attract as they become closer until they become too close and repel instead.

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20
Q

How do hydrophobic interactions dominate protein structure?

A

Non-polar side chains tend to be buried in the core of the protein.
Polar side chains stay outside to form hydrogen bonds to water

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21
Q

How are covalent bonds made and broken?

A

Made through oxidation. Lost through reduction

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22
Q

What is the secondary structure?

A

Regular, repeated structures like alpha-helices and beta-sheets, formed out of the amino acid chain.

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23
Q

What is the tertiary structure?

A

The 3D shape of a single polypeptide chain

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24
Q

What is a quaternary structure?

A

The 3D shape of a protein that consists of more than one polypeptide chain.

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25
Q

What is the general structure of an alpha helix? 4

A

Tight with no free space inside,
Usually twists right,
Sidechains can point out of the helix,
Every carbonyl oxygen forms a hydrogen bond with the amide hydrogen

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26
Q

Why are alpha helices very common?

A

They are very stable structures. Every backbone atom that can form a hydrogen bond is forming one.

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27
Q

Why are other helices important?

A

They are usually short and can come in between an alpha helix to allow kinks and bends.

28
Q

What is the structure of a collagen triple helix?

A

Three polypeptide chains with very condensed sequences. Every third R-group is a Glycine to allow structure and hydrogen bonds.

29
Q

What is the basic structure of a beta-sheet?

A

Hydrogen bonds between adjacent backbones.

30
Q

Whats the difference between anti-parallel and parallel beta-sheets?

A

Antiparallel: N-C and C-N, perpendicular H-bonds, more stable
Parallel: N-C and N-C, not perpendicular, less stable.

31
Q

How does retinol-binding protein use hydrophobic and hydrophilic side chains?

A

Hydrophobic chains allow it to interact with the hydrophobic retinol.
Hydrophilic chains on the outside allow it to dissolve in the blood.

32
Q

What is the importance of loops and turns?

A

Form variable and biologically active parts of proteins. Loops can interact with other molecules and form their active sites.

33
Q

What is a coiled coil?

A

When two alpha-helices assemble together. This is very common in nature.

34
Q

What are motifs and domains?

A

The building blocks of many proteins. Inbetween secondary and tertiary structure. These are made of more than one polypeptide chain but are not the completed protein. The same domains are found in many different proteins all with different functions.

35
Q

What does Levinthal’s paradox state?

A

That for a protein to try every possible composition before finding the correct, most energetically favourable one, it would take millions of years. Therefore it can be said that proteins do not find the correct structure by random.

36
Q

What are Vf and Vr and what do they rely on?

A

Vf = velocity of forward reaction
Vr = velocity of reverse reaction
They depend on reactant concentration

37
Q

How can ligand binding be observed?

A

Using a signal (i.e colour change) to show the fraction of the protein bound to the ligand (Y)

38
Q

What happens when ligand concentration is equal to Kd? What about when it is much higher than Kd?

A

When equal, half the binding sites are occupied.

When much higher, most of the binding sites are occupied.

39
Q

What happens to affinity as Kd increases?

A

Affinity decreases as it binds ligands more weakly.

40
Q

What is Kd?

A

The ligand concentration required to occupy half the binding sites

41
Q

What are the two forms of haemoglobin?

A

Deoxyhaemoglobin (T) : tense form with a low affinity for O2

Oxyhaemoglobin (R) : relaxed form with a high affinity for O2.

42
Q

What changes haemoglobin structure between R and T form?

A

The proximal histidine on heame is bound to Fe2+ + part of an alpha helix. This increases the specificity of Hb to bind to O2 to become oxyhaemoglobin.

43
Q

what does a sigmoidal binding curve of O2 to haemoglobin show?

A

The binding of the first O2is much harder.

Once the first one has bound, the others bind much more easily

44
Q

What are allosteric effectors in Hb?

A

Substances that bind to Hb at a site other than the O2 binding site

45
Q

What does BPG do when bound to Hb?

A

Stabilises the t-state Hb to increase the p50 at higher altitudes or in response to airway obstruction

46
Q

What is the role of serine histidines in fetal Hb (HbF)?

A
  • makes BPG bind less tightly
  • gives it a smaller p50
  • binds O2 more tightly so it can be taken from the mothers normal Hb
47
Q

What is the Bohr effect? What is an example of where this happens?

A

H+ can bind to deoxy-Hb when pH is low, releasing the O2.

E.g in the production of lactic acid

48
Q

Describe the path of CO2 from the tissues to the lungs.

A
  • CO2 produced by tissues
  • Converted into HCO3- and H+ in RBC
  • H+ binds to Hb, releasing O2 which diffuses into the tissues.
  • HCO3 diffuses into the plasma and is transported to the lungs
  • converted back into CO2 and H2O where CO2 diffuses into the lungs and is expelled
49
Q

How and where do salt bridges help stabilise Hb?

A
  • only in the T-state
    O2 binds to the amino terminal groups of Hb by forming carbamate
    -carbamate helps to build these salt bridges
50
Q

Does CO2 or drop in pH reduce O2 affinity in Hb more?

A

CO2

51
Q

What effects can mutations on the surface of Hb have?

What about mutations on the inside?

A

Mutations on the surface often have no phenotype

Mutations on the inside can cause hemolytic anemia

52
Q

How does sickle cell anaemia affect red blood cells?

A
  • sickle shape
  • broken down more easily
  • molecules interact in ways they shouldn’t and can form fibres
  • can block capillaries
53
Q

How does antibody specificity arise through combinational rearrangement?

A

Many different types of random antibodies are produced by B cells. Some of these will happen to bind to the antigen. The ones that bind to the antigen will be specific and can replicate to produce clonal antibodies.

54
Q

What is cross-reactivity? What is an example of this?

A

When one antibody binds to more than one antigen.

E.g antibodies against cowpox can also bind to smallpox antigens due to their similar structure

55
Q

How do vaccines work?

A

Stimulate B cell proliferation, including memory B cells.

The body can then generate clonal B cells rapidly in the event of future infection.

56
Q

How can antibodies be produced using an animal?

A
  • inject animal with protein
  • collect serum a few weeks later
  • serum will contain specific antibodies which can then be easily purified
57
Q

What are reporter molecules?

A

Enzymes, radioisotopes or fluorescent molecules that bind covalently to the antibody and report the binding event

58
Q

What do the Fab and Fc regions do in antibody technology?

A

Fab region gives specitivity

Fc region allows binding to be detected

59
Q

What is a western blot?

A
  • mixture of proteins containing antigen is separated by gel electrophoresis (weight)
  • antibody is added to the gel
  • antibody binds to the antigen of interest and a reporter molecule shows which protein is the antigen
60
Q

What is the globin fold?

A

a recurring structure of a set of αlpha helices in myoglobin and hemoglobin

61
Q

What is the functional role of the “distal histidine”?

A

It donates a hydrogen bond the bound oxygen molecule to stabilize the complex between iron and oxygen.

62
Q

How does the Bohr effect change the oxygen binding curve?

A

Moves it to the right

63
Q

What fragment of the antibody is responsible for effector function

A

Fc

64
Q

What parts of the antibody bind to the antigen?

A

Fab and variable regions

65
Q

What fragments determine antibody specificity?

A

variable regions of both light and heavy chains

(1) Biochemistry: Cellular Composition (8 decks)

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