Proteins Flashcards

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1
Q

What is the main sequence of events during translation?

A
  1. Amino acid activation / tRNA charging, amino acids are linked to tRNA.
  2. Initiation where a small ribosomal subunit bought together with an mRNA and the first amino acid is bound to the AUG start codon. This is followed by the large subunit binding.
  3. Elongation the next tRNA binds to the next codon and the initial amino acid transfers from the tRNA to the second amino acid starting the chain. The ribosome translocates along the mRNA
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2
Q
A
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3
Q

What’s the difference between the smooth and rough endoplasmic reticulum?

A

The rough ER is where protein synthesis takes place as it has ribosomes. The smooth ER produces lipids, phospholipids (membranes) and steroids.

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4
Q

What is different about cells that produce lots of proteins?

A

Large quantities of ribosomes and prominent nuclei.

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5
Q

What are lysosomes?

A

Organelles that are membrane bound vesicles containing digestive enzymes that degrade proteins. Enzymes are active at low pH and are adapted to be active in white blood cells for example.

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6
Q

What is the Greek derivative of protein

A

“proteios” which means of the first rank

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7
Q

What is the central dogma of biology?

A

The central dogma of molecular biology is a theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein.

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8
Q

What is the start codon and its corresponding amino acid?

A

AUG -> methionine

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9
Q

What direction does transcription and protein synthesis occur?

A

5’ -> 3’
N terminus -> C terminus

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10
Q

What is the generic structure of an amino acid?

A

Zwitterion
An alpha carbon with an amine group (NH3+), a carboxyl group (CO2-), a functional R group / residue and usually a H.

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11
Q

How is protein folding variation facilitated?

A

Varying properties of R groups dictate the folding of proteins. For example a hydrophobic R group will be pushed into the centre of a protein away from H2O.

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12
Q

What are the types of protein structure?

A

Fibrous
Transmembrane
Globular
Natively unfolded

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13
Q

What are the types of fibrous proteins?

A

Cytoskeletal such as actin, myosin and troponin.
Extracellular matrix proteins such as collagen and elastin.
(self assembly)

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14
Q

What do globular proteins do?

A

Largest category of proteins but some common examples:
Enzymes
Immune system proteins
Cell adhesion proteins

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15
Q

What are natively unfolded proteins for?

A

Generally signalling peptides.

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16
Q

What is the Shine-Dalgarno box?

A

A consensus sequence that can initiate translation. 16S RNA in the small ribosomal subunit will bind to the box attaching the mRNA to the small subunit to the mRNA. The Shine-Dalgrano boxes allows for prokaryotes to express polycistronic genes as it allows ribosomes to bind throughout the transcript and initiate transcription. these boxes are also important for allowing translation and transcription to occur simultaneously as the ribosomal subunits are only seeking out the Shine-Dalgrano boxes.

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17
Q

What are the initiation factors in bacteria and their roles?

A

IF1 blocks tRNA from entering the ribosome subunit too early.
IF2 binds specifically to the initiator fMet tRNA to bring it to the start codon
IF3 ensures that there is a match between codon and anticodon for the fMet.
Together these ensure correct translation and stops it occurring prematurely.
These all dissociate when the large subunit binds and are critical for ensuring translation starts correctly.

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18
Q

What is different about what AUG codes in bacteria compared to eukaryotes?

A

AUG is the start codon that codes for methionine but in bacteria, it codes for methionine with a formyl group (fMet) on a specialised tRNA. This specialisation allows it to bind in the middle p-site of the ribosome instead of the a-site. Once this binds it recruits the large subunit completing the ribosome. (reminder: in a ribosome amino acids are added like so E <- P <- A )

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19
Q

What are the main differences between eukaryotic and bacterial translation?

A

Eukaryotes do not have Shine-Dalgarno boxes, instead, a small ribosome subunit binds to the guanosine 5’ cap and moves along the mRNA until it reads an AUG and initiates translation.
In eukaryotes, a normal methionine on an initiator tRNA is recruited before the assembly of the large ribosomal subunit.

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20
Q

What two eukaryotic initiation factors are required to ensure the mRNA transcript is complete and how?

A

eIF4E replaces the 5’ cap on the transcript
eIF4G binds to the poly(A) binding proteins and eIF4E.
The binding of these two transcription factors acts as a proof read to signal that the transcript is in intact and in good condition.
Once the first AUG is read the transcription factors dissociate allowing the large subunit to bind.
There are many other eukaryotic transcription factors with important roles.

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21
Q

In eukaryotes why are translation and transcription separated

A

Transcription occurs in the nucleus and translation in the cytoplasm.
The 5’ cap and poly A tail modifications are required to initiate translation and these only happen once the mRNA is exported from the nucleus.

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22
Q

How, in eukaryotes, are multiple copies of a protein made?

A

Polyribosomes will bind. This is enabled by the mRNA forming a spiral due to the 3’ and 5’ mdoifications joining via the eFIG and eFIE allowing the initiation factors and ribosomal subunits can leave and rejoin the transcript in close proximity.

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23
Q

What is the function of micro RNA and how do they work?

A

Micro RNA transcripts are normally negative regulators of gene expression. They block expression either by
-binding to the mRNA and blocking initiation, elongation or termination.
- or degrading the mRNA transcript so no translation can occur.

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24
Q

How is the peptide bond formation between amino acids facilitated during elongation?

A

The joining of an amino acid to the peptide chain is mediated by the RNA enzyme, peptidyl transferase, which is part of the large subunit.
The enzyme mediates the nucleophilic attack from the nitrogen terminal of the new amino acid onto the ester bond between the polypeptide chain and its tRNA breaking the bond and creating a new peptide bond between the chain and the amino acid on the aminoacyl-tRNA.

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25
Q

How does aminoacyl tRNA become polypeptidyl-tRNA?

A

When the amino acid attached to the aminoacyl tRNA (in the A site) is added to the chain and the chain is transferred to this tRNA from the one in the P site. This is followed by the large subunit translocating then the small putting the unbound tRNA in the exit site, the peptidyl tRNA in the P site and leaving the A site free for a new aminoacyl tRNA

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26
Q

What direction does polypeptide chain elongation propagate in?

A

N - terminal (amine group) to C - terminal (ester group).
Amino acids are always added to the c terminus of a chain.

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27
Q

Describe the four steps of elongation.

A
  1. tRNA ejected from E site, peptide chain bound to tRNA in p site, tRNA enters A site and amino acid joins chain.
  2. Chain is transferred to tRNA in A site.
  3. Large subunit translocates moving unbound tRNA into e-site and peptidyl tRNA into p-site.
  4. The small ribosomal subunit translocates to pair up with the large subunit. A site is empty ready for the next aminoacyl tRNA and the e-site ready to eject the used tRNA.
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28
Q

What are elongation factors?

A

GTPases that improve translation efficiency by increasing the translocation speed of ribosomal subunits and they also have a role in proofreading. Without these translation would be hella slow stylllll.

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29
Q

What is EF-Tu and its function?

A

An elongation factor that helps load the A site.
It is bound to an aminoacyl-tRNA and helps bring it to the A site. If the codon and anticodon match the ribosome will cause the EF-Tu to hydrolyse the GTP bound to it into GDP causing a conformational change to occur in EF-Tu. This leads to it dissociating allowing the amino acid to join the peptide chain. The hydrolysis of GTP acts as a proof reading mechanism as it only occurs with correct anticodon-codon matching, so the aminoacyl will not bind to the A site unless if there’s not a match

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30
Q

What is the function of EF-G?

A

This elongation factor will help move tRNAs during translocation. Each ribosomal binding site has an affinity for a tRNA in the appropriate site (E: unbound, P: peptidyl, A: aminoacyl) but at one point the A site amino acid becomes peptidyl instead of aminoacyl and is in a hybrid state and therefore prefers the P site and the unbound P site tRNA prefers the E site. EF-G bound to GTP will enter the A site and bind to hybrid state to stabilise it. The GTP is then hydrolysed causing a conformational change in the protein that forces the hybrid A/P site tRNA into the P site only which in turn forces the unbound tRNA into the exit site. This followed by the tRNA being ejected and EF-G dissociating.

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31
Q

How is translation terminated?

A

Stop codons end translation (termination sites are for transcription). The general three stop codons are UAA, UAG and UGA. Stop codons are not recognised by tRNA but by a release factor. Release factors are protein that have molecular properties that mimic an aminoacyl-tRNA which allow them to enter the ribosome. They release the polypeptide by adding a water molecule to the end of the chain instead of an amino acid. This causes the protein to be released from the P site followed by the disassembly of the ribosome by the action of other release factors.

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32
Q

How are distant regions of polypeptide chains linked?

A

Often two cystine amino acids will covalently bond via disulfide linkages.

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33
Q

Where does an amino acids negative and positive charge come from, how do these groups interact at different pHs?

A

The amine group provides a negative charge and the carboxyl group a positive charge.
At acid pH the amino group the amino group is protonated and becomes slightly positive.
At basic pH the carboxyl group is ionised giving a slight negative charge.

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34
Q

What happens at neutral pH (physiological pH) to amino acid and how is this defined?

A

The carboxyl group is ionised and the amino group is protonated giving the molecule an overall neutral charge and so can act as both a negative and positive molecule. This is called a zwitterion. (can be altered by the properties of the R group).

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35
Q

What is the 3D structure of an amino acid generally?

A

They have an asymmetric chiral structure. Most are L:laevis which means they are left handed asymmetric. A chiral structure cannot be superimposed on its counterparts (think hands). The CORN acronym can be used to check this: going clockwise around the alpha carbon it goes CO group, R group then the H group.

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36
Q

How are peptide bonds formed between amino acids?

A

This occurs via a linkage forming between the carboxyl group and the amnio group of another amnio acid with the removal of water in a condensation reaction. For example glycine’s carboxyl group will bond to the amine group of alanine.

37
Q

What is the difference between hydrolysis and condensation?

A

Hydrolysis is the addition of water and condensation is the loss of water.

38
Q

What is the structure of a peptide bond its properties?

A

The bond is planar and allows for no rotation between the C=O and N-H but there is still rotation around the alpha carbon.

39
Q

Why do peptide bonds have their shape?

A

The planar shape is due to the sharing of electrons which creates a resonance (localised negative charge) meaning no movement is capable around that bond.

40
Q

What is a trans-peptide bond and cis-peptide bond?

A

The standard formation of peptide bonds in a chain creating the zig zag shape /\/\ (trans)
A cis peptide bond creates a zig zig shape
_/ placing the R groups near each other. This occurs less and is formed by special enzymes.

41
Q

Why are cis-peptide bonds uncommon?

A

Only certain amino acids can accommodate a cis-peptide bond as the R groups may clash stereo chemically.

42
Q

What are the 4 common groupings used to classify amino acids?

A

Whether the side chains are either:
Acidic (negative R group)
Basic (positive R group)
Polar (hydrophilic)
Non-polar (hydrophobic)

43
Q

Which groups commonly used for classifying amino acids overlap with each other?

A

Charged side groups (negative or positive) make an amino acid polarised and therefore hydrophilic.

44
Q

What is common among non-polar amino acids? How is their hydrophobic quality related to this common feature?

A

Their side chains consist of hydrocarbons. The longer the hydrocarbon structure the more hydrophobic they are, with the side chains containing rings being the most hydrophobic. Methionine is the exception with a sulfur in the chain.

45
Q

What is common among non-charged polar amino acids?

A

They are all able to hydrogen bond with water most commonly through an OH group or NH2 group except for cysteine which has a disulfide bond.

46
Q

What is special about cysteine?

A

Among many interesting properties it is capable of displaying hydrophobic or hydrophilic properties depending on present conditions.

47
Q

What is common among acidic amino acids?

A

They have carboxyl groups at the end of their side chains.

48
Q

What is common among basic amino acids?

A

They have amine groups at the end of their side chains.

49
Q

What is special about glycine?

A

It only has a hydrogen as its R group and so it is often found in very tightly in very tightly packed regions of proteins. This allows for very tight bends.

50
Q

What is special about proline?

A

It is called a cyclic amino acid or an imino as its side chain loops back round and bonds to the alpha carbon. This creates a kink like structure and is very common is cis peptide bonds creating a kink in the protein structure. Although it can’t be clearly classified is slightly hydrophobic.

51
Q

What are aliphatic amino acids?

A

Aliphatic = denoting organic compounds in which carbon atoms form open chains not aromatic rings.
Aliphatic amino acids are a subdivision of hydrophobic amino acids without aromatic rings.

52
Q

What are the aromatic amino acids?

A

A subdivision of amino acids with aromatic rings. Aromatic refers to their ability to absorb UV light. By using absorbance measurement these amino acids help to study the structure and properties of a protein. Two of the three aromatic amino acids are hydrophobic except for tyrosine that can be either hydrophobic or hydrophilic but is often found on the outside of proteins where it can H bond to water.

53
Q

How do disulfide bonds form between different regions of a protein?

A

The thiol groups (R-SH) of two amino acids covalently bond forming a disulfide bridge.

54
Q

What is a normal haemoglobin structure and what happens to individuals diseased with sickle cell anaemia?

A

Normal: Heme iron surrounded by 4 globin proteins.
Infected: defective haemoglobins that stick together damaging red blood cells

55
Q

What is genetic explanation for sickle cell anaemia?

A

Normal DNA double strand sequence: GAG/CTC -> mutated GTG/CAC
This instead of a glutamic acid (hydrophilic) being coded a valine (hydrophobic) in the protein. These amino acids have very different properties meaning the mutated protein structure will be greatly effected.

56
Q

What environmental condition affects acidic and basic R groups?

A

pH level

57
Q

What happens to 1. acidic 2. basic amino acids at neutral and basic pHs. What about at acidic pH?

A

Basic/neutral pH
1. become negatively charged
2. become protonated/positively charged
Acidic pH
1. neutral
2. protonated

58
Q

What determines the secondary protein structure?

A

The backbone torsion angles phi and psi between the alpha carbon and its amine and carboxyl groups (the peptide bond does not rotate restricting the possible conformations). Different torsion angles create different secondary structures. Stereochemical clashing of R groups effects the torsion angles.

59
Q

How is an alpha helix formed?

A

Hydrogen bonds form between the slight positive charge on the amine groups hydrogen and the slight negative charge on the carboxyl groups slight positive charge (both on the peptide backbone chain) creating a single stranded helix structure. The hydrogen bonds able to form due to the specific torsion angles dictated by the R groups. The R groups stick outwards from the helix.

60
Q

What secondary structure is haemoglobin comprised of?

A

Alpha helices.

61
Q

What are the units of beta pleated sheets?

A

Single beta strands that hydrogen bond together to make the sheets.

62
Q

Are beta strands parallel or antiparallel?

A

They can be either
Parallel: every strand = N -> C
Antiparallel: one strand = N -> C stacked on a strand C -> N
If they are parallel an alpha helix is needed to loop from the end of one strand to another

63
Q

What properties often make amino acids good for forming b sheets

A

Large, bulky, awkward/branched or containing a large S atom side chains

64
Q

What can break secondary structures

A

Glycine because its small side chain of H means it cant protect the backbone stereochemically.
Amino acids with side chains that preferentially form H bonds will directly compete with backbone elements that form H bonds for the secondary structure.
Other amino acids can cause loops to form that either break up or link secondary structures
These amino acids will be found at the ends of secondary structures.

65
Q

What is a beta turn?

A

When slightly distant oxygens on a carbonyl group and hydrogens on an amide group hydrogen bond forcing a beta strand to bend/kink inwards.
Carbonyl and amide = carboxyl and amine groups following the formation of a peptide bond: R-CO-R , R-CO-N-R
there are different variations of beta turns

66
Q

What is tertiary structure of a protein?

A

The tertiary structure describes the 3D conformation of a single peptide chain in space> the units of tertiary structures are super secondary structures or motifs.

67
Q

Define quaternary structure?

A

The conformation assumed by a multimeric protein.

68
Q

What interactions shape the structure of proteins?

A

Hydrogen bonds (the involved atoms can be from the peptide backbone, R groups or water molecules)
Disulfide bonds
Dipole/dipole interactions and van der waals
Ionic bonds between acidic and basic R groups
Hydrophobic interactions: clusters of hydrophobic R groups away from water (think how oil droplets group up to avoid water).

69
Q

What are salt bridges and under what conditions do they form?

A

At neutral pH, an ionised acidic side chain will electrostatically interact with a protonated basic side chain creating an ionic bond.

70
Q

Where are hydrophobic amino acids typically found?

A

In an aqueous environment hydrophobic molecules will aggregate so hydrophobic amino acids are often found in the centre of a protein.

71
Q

Give the definition of these properties used to describe different multimeric proteins.
1. homo-
2. hetero-
3. dimer
4. trimer
5. tetramer

A
  1. identical chains
  2. different chains
  3. 2 chains
  4. 3 chains
  5. 4 chains
    ect…
72
Q

What is the purpose of fibrous proteins and their structure

A

They perform structural roles. They are elongated and very strong. They often have a specific repeated sequence which allows them to self assemble and organise themselves in a repetitive structure.

73
Q

Where is collagen found and what is it comprised of?

A

Mostly in connective tissues such as tendons. It consists of three polypeptide chains that form left-handed helices and all together form a triple helix. Humans have 16 different forms of collagen. It is highly repetitive sequence mostly consisting of hydroxyproline (makes a polyproline chain)

74
Q

Where are globular proteins found and what is their generic shape?

A

Fucking everywhere lad (much more common that fibrous proteins) their shape is like globs you know, globular. All membrane proteins are globular.

75
Q

What are protein-protein interfaces?

A

Highly specific sequences on the surface of a protein that only allows certain interactions or bonds to form to make sure a particular protein bonds in the right way. There also specific interfaces for the binding of an array of molecules depending on the function of the protein such as DNA/RNA, carbohydrates and metal ions just to name a few. These interactions can be permanent or transient (impermanent)

76
Q

What are the common general characteristics of protein-protein interaction sites?

A

Hydrophobic
Surface accessible
Protruding side chains
They have planar regions
Specific residue properties

77
Q

What factors affect the thermodynamics of protein folding?

A
  • Size, amino acid content, hydrophobic/phillic content
  • strength of intramolecular interactions e.g. no. of disulfide bridges
  • domain architecture
78
Q

What does Levinthal’s paradox teach us?

A

Folding cannot occur randomly as there are too many possible conformations that a given polypeptide chain can take and not enough time to try them all out. Therefore folding must follow specific folding pathways. Some proteins fold by themselves, driven by hydrophobic burial and/or formation of secondary structural elements but some proteins cannot.

79
Q

What are chaperone proteins?

A

During stress (of any kind) proteins unfold and need chaperone proteins or ‘heat shock protein’ to aid them in their reassembly into protein complexes. Chaperone proteins also ensure that misfolded proteins are disposed of and that newly translated proteins do not aggregate and fold correctly.

80
Q

What do chaperonin proteins do?

A

They are essentially a capsule in which the correct hydrophilic conditions for a protein to fold correctly are provided. They are structured as a hollow cylinder in which the unfolded protein enters then the capsule lid closes allowing the protein to fold before the lid opens again releasing it.

81
Q

What protein misfolds due to Alzheimer’s disease?

A

The amyloid beta protein, creating insoluble amyloid protein that aggregates and makes amyloid plaques in neural tissue. Amyloid plaques are universal and can fuck over a lot of different places.

82
Q

What happens in terms of chaperone proteins as we age and what does this cause?

A

Chaperone protein system becomes less and less efficient leading to more proteins aggregating and therefore disease.

83
Q

Why are amyloid plaques dangerous?

A

Amyloid proteins have a simple repetitive structure of beta sheets that create fibers. This makes their structure very strong and insoluble meaning they are very hard to be removed.

84
Q

What protein primary structure are the precursor to amyloid protein.

A

A variety of proteins are capable of being the precursor to amyloid fibers. The primary structure is relatively unimportant as amyloid proteins consists of beta sheets and therefore all that is required is the ability to form hydrogen bonds to create the structure.

85
Q

What are the self assembling steps of amyloid plaques?

A

Monomers begin to aggregate into oligomer. Oligomers begin to elongate with the further accumulation of proteins into proto-fibrils. The elongation continues to make amyloid fibrils which congregate into amyloid plaques.

86
Q

What type of disease is mad cow disease?

A

A prion disease.

87
Q

What is PrPc and its structure?

A

A cellular prion protein that is believed to play a role in circadian rhythm.
-50% alpha helix
-20% beta-sheet content
-single disulfide bond
-flexible polypeptide tail (very felxible in solution)

88
Q

What are prion diseases and their cause?

A

A form of infectious disease caused by misfolded proteins that makes brain tissue ‘spongy’

89
Q

How are prion diseases infectious?

A

The infectious agent is believed to be a beta sheet structure that continually has new peptides bound to it creating a toxic structures. These structures can fragment and go and infect more healthy proteins propagating the infection. This results in spongiform structures in vacuoles.