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FLC > Molecular Protein Structure > Flashcards

Molecular Protein Structure Flashcards

1
Q

How are motifs and domains formed?

A

Simple secondary structures combine to form structural motifs or larger functional domains

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2
Q

What is a Protein sequence motif?

A

A protein sequence motif is a pattern of amino acids found in related genes or proteins

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3
Q

Where can motifs and domains be identified within a proteins structure?

A

Motifs and Domains are independent orders of structure identified within overall tertiary structures
- found and conserved in functionally related proteins

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4
Q

Define what is meant by a motif?

A

Combination of 2 or more secondary structures to form a recognisable folded arrangement

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5
Q

What is the function of the greek key motif?

A

Associated with the formation of Β amyloid aggregates and fibrils in alzheimers

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6
Q

Describe what a domain is in molecular terms

A

Complex structure at tertiary or Quaternary level often involving interactions between distant parts of
proteins or motifs

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7
Q

Explain the structure of Parallel Β sheet motifs

A

Parallel strands of a Β sheet interlinked with an ɒ helix

=> forming an Β-ɒ-Β motif

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8
Q

How do α helices specifically bind to DNA?

A

Bind to major groove in DNA

  • amino acid sequence of a DNA Binding motif provides specificity
  • different DNA binding domains and motifs present the binding helix using different arrangements of the structural motif
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9
Q

Define domain

A

Functional protein folding units found across different genes and phyla

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10
Q

Describe the structure of beta barrels

A

Β sheets twisted around forming a closed circular structure

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11
Q

Define what a dimer is

A

An oligomer consisting of two monomers joined by (strong/weak, covalent/intermolecular) bonds

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12
Q

Describe the domains present in Phospholipase C

A

4 different recognisable domains present

- each is found individually in other proteins

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13
Q

What are DNA Binding motifs?

A

Independently folded proteins containing at least one structural motif that can recognise single/double stranded DNA

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14
Q

What is the function of beta barrels?

A

Acts as transporters for ions and small molecules

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15
Q

How do the domains present in haemoglobin show evolutionary characteristics from myoglobin?

A

Each chain if haemoglobin has a tertiary structure similar to the single chain of myoglobin

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16
Q

How do motifs bind to the major groove in DNA?

A

α helices or β sheets are inserted into the major grooves in a sequence specific manner

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17
Q

Where are motifs found?

A

Many different protein motifs exist in unrelated proteins that share functional properties

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18
Q

Name some examples of motifs in the body

A
  • Calmodulin
  • Greek Key Motif
  • Beta Barrel
  • Parallel Beta Sheets
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19
Q

Why do motifs bind to the DNA helix major groove?

A

The major groove contains sufficient information to distinguish one DNA sequence form any other

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20
Q

Describe the structural properties of a domain

A
  • typically larger
  • can be contiguous segments
  • functional units
  • modular in nature
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21
Q

Explain what the Helix turn Helix consists of

A

2 short helices perpendicular to one another, connected by a turn

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22
Q

What is the result of domain shuffling?

A

Causes modular units of function being conserved but shuffled between genes

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23
Q

What is the role of the EF hand motifs?

A

Allow the binding of Ca2+ for myosin light chain

24
Q

Describe the structure of the Helix Loop Helix motif

A

Exists as a homo- and heterodimers
Central part made up of overlapping helices - form structure enabling dimerisation
Terminal ends of lower opposing helices contain basic amino acids - interact with DNA major groove

25
Q

How can the leucine zippers regulatory function be increased?

A

Heterodimerisation expands the regulatory potential of leucine zippers

26
Q

Where is the 7 transmembrane arrangement seen in polypeptides in the body?

A

Found in

  • Rhodopsin
  • Thyroid Stimulating Hormone Receptor (TSHR)
  • Pharamalogical receptors
  • Polypeptide hormone receptors
27
Q

Describe the structure of the EF hand motifs

A

Helix loop helix motif

enables calmodulin and troponin binding

28
Q

Where are helix turn helix motifs commonly found?

A

In prokaryotic and eukaryotic DNA binding proteins

29
Q

Which part of the leucine zipper enables interactions with DNA major groove?

A

The lower helix dominated by basic amino acids forming a motif to interact with DNA major groove

30
Q

What is Domain shuffling?

A

Segments of genes coding for functional domains are shuffled between different genes during evolution

31
Q

Which motifs are present in calmodulin?

A

Contains 4 EF hand motifs each binding single calcium atoms

32
Q

Explain what a heterodimer is

A

An oligomer made of 2 different monomers

33
Q

What is the structure of the Zinc finger motif?

A

α helix and β sheet held together by non covalent interactions with Zinc

  • dimer with two motifs on separate polypeptide chains
  • each chain contains 2 Zn atoms
34
Q

Name an example of a helix turn helix motif containing protein

A

Cro repressor protein

35
Q

What is Calmodulin?

A

Calcium modulated protein

36
Q

What is the Greek Key Motifs structure?

A

Consists of 4 anti parallel beta strands

connected by hydrogen bonds

37
Q

How do Transcription Factors obtain their function?

A

Each TF contains a small no. of conserved motifs which combine to form functional domains allowing interactions with DNA

38
Q

How is the coil in a Leucine Zipper motif held together?

A

By hydrophobic interactions down the opposing sides

39
Q

Give an example of a common domain

A

The 7 transmembrane arrangement of α helices

40
Q

What are transcription factors?

A

Proteins that bind to DNA regulating transcription

41
Q

What is the function of the Zn atoms on the polypeptide chains in the zinc finger motif?

A

Provides stability to the recognition helix and loop structure

42
Q

Where are structural & functional domains commonly found?

A

Individual domains can be found in different proteins (not necessarily with the same group of domains as in one protein)
Commonly represented in membrane bound receptors

43
Q

What is a homodimer?

A

Oligomer formed from 2 identical monomers

44
Q

How does the Cro protein operate?

A

Binds to DNA major groove
Recognition helix interacts with nucleotides
Represses transcription

45
Q

Explain the common structure of functional and structural domains

A

Come in several forms; most commonly in bundles

  • bundles of α helices or β sheets
  • lone helices
46
Q

What is the role of the conserved motifs in transcription factors?

A

They form DNA binding domains that allow regulatory function of their respective proteins

47
Q

Which part of the zinc finger motif structure interacts with the DNA major groove?

A

α helix of each structure interacts with the major groove an recognises specific DNA sequences

48
Q

What do the basic amino acids in the Helix loop Helix motif give rise to ?

A

Gives rise to the b/HLH functional domain

49
Q

What is the function of the cro protein?

A

Recognises palindromic sequences

Represses Transcription

50
Q

What are the different types of DNA binding motifs?

A
  • Helix loop Helix
  • Helix turn Helix
  • Leucine Zipper
  • Zinc Finger
51
Q

Which proteins contain Zinc finger motifs?

A

Many hormone receptors e.g.

  • Glucocorticoid
  • Mineralocorticoid oestrogen
  • Progesterone
  • Vitamin D receptors
52
Q

Describe the structure of a Leucine Zipper motif

A

Formed from 2 contiguous α helices

  • dimetric protein formed from 2 polypeptides
  • the dimers ‘zip’ together in top ‘stalk’ - forming short coiled coil
53
Q

How do proteins incorporate all the folding into one structure?

A

Proteins fold into 3 basic units of structure which combine to provide complexity and diversity

54
Q

How much of the motifs are conserved?

A

Motifs are conserved across all phyla

55
Q

Give examples of protein structures containing helix loop helix motifs

A
  • MAX gene
  • MAD gene
  • MYC gene
  • MyoD regulatory factor

FLC (34 decks)

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