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Fundamentals Of Living Cells > Modular Protein Structure > Flashcards

Modular Protein Structure Flashcards

1
Q

What is some evidence for parallel evolution (relating to proteins?)

A

A comparison of unrelated proteins with a similar structure

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2
Q

What is a protein sequence motif?

A

A pattern of amino acids that are found in related genes or proteins

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3
Q

What is a protein structure motif?

A

The structure of protein found in similar genes or proteins that don’t have similar primary structures

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4
Q

Where are motifs and domains commonly found?

A

Across functionally related proteins but may not be sequentially related?

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5
Q

What is a motif

A

Minimum arrangement Of independently forming secondary structures combining recognisable folds (arrangements) across many different proteins

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6
Q

What is a domain?

A

A more complex structure at the tertiary or quaternary level, often involving interaction between distant parts of a protein or motif

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7
Q

Both domains and motifs are what in nature?

A

Modular

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8
Q

What do domains often relate to?

A

A specific exon in a gene

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9
Q

How many different structural motifs exist?

A

1400-1500

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10
Q

What is an ef hand?

A

Ca2+ binding motif resembles a helix turn helix but combines with a metal ion.

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11
Q

Give two examples of ca2+ binding motifs

A

Calmodulin and troponin-C

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12
Q

What is calmodulin?

A

Part of a mechanism for sensing cellular calcium leads

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13
Q

What does the Greek key motif consist of?

A

Antiparallel beta strands forming a beta sheet

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14
Q

Why is the Greek key motif important?

A

It is such a common motif that isnt generally associated with a specific function

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15
Q

What is the beta- alpha- beta motif

A

Parallel strands of a beta sheet interlinked with an alpha helix. Beta strands are connected to an alpha strand which sits on top of the betas

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16
Q

What’s a beta barrel?

A

Beta strands wrapped around to form a circular tunnel

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17
Q

What is a DNA binding motif?

A

Helices inserted into the major groove of DNA in a sequence specific manner. Arranged to recognise specific DNA sequences

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18
Q

Give some examples of helix loop helix

A

Max and mad and ca2+ binding

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19
Q

Give some examples of helix turn helix

A

Cro, tryptophan and lac repressors

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20
Q

Give some examples of a leucine zipper

A

GCN4

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21
Q

Give some examples of a zinc finger

A

Hormone receptors

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22
Q

Give the most common example of a form of membrane bound receptors

A

Bundles of alpha helices

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23
Q

What is the most common arrangement of alpha helices in membrane bound receptors?

A

7-transmembrane arrangement

24
Q

Where is the 7-transmembrane arrangement of alpha helices found?

A

Rhodopsin, TSHr pharmacological receptors and some polypeptide hormone receptors

25
Q

What are the membrane bound receptor domains called in the extracellular region?

A

Ligand binding domain

26
Q

Where are the membrane bound receptor domains in the transmembrane region?

A

Domain embedded in the lipid bilayer

27
Q

What does genome shuffling in the genome cause?

A

Modular units of function being conserved but shuttled between genes

28
Q

What are the four different genes founds in mammalian phospholipids C?

A

Troponin C
Bacterial phospholipase C
Synaptotagmin
Recoverin

29
Q

How are myoglobin and haemoglobin similar and why?

A

Both have a tertiary structure, which suggests evolution from a common ancestral O2 binding polypeptide

30
Q

What are transcription factors?

A

Proteins that bind to DNA and regulate transcription

31
Q

What does each transcription factor contain a small number of?

A

Conserved motifs that combine to form domains that interact with the DNA

32
Q

Are motifs different across phyla?

A

No, all conserved

33
Q

What do DNA binding domains do?

A

Allow the regulatory function of their respective proteins

34
Q

What is a recognition helix?

A

When an alpha helix fits inside the major groove of DNA

35
Q

What does the amino acid sequence of a DNA binding motif provide?

A

Specificity

36
Q

The helix-loop-helix motif only binds DNA in what form?

A

Dimeric

37
Q

What are the two names for the dimers of the helix - loop - helix motif?

A

Heterodimer and homodimer

38
Q

What is a homodimer?

A

Identical monomers

39
Q

What is a heterodimer?

A

Different monomers

40
Q

What is the central portion of the helix-loop-helix motif made from?

A

Overlapping helices that form a structure enabling dimerisation

41
Q

What does the terminal part of the Lower opposing helices contain in the helix-loop-helix motif?

A

Basic amino acids that interact with the major groove of DNA- giving rise to the b/HLH functional domain

42
Q

Give some examples of a helix-loop-helix motif

A

MAD, MAX, MYC, MYOD

43
Q

What is the leucine zipper motif formed from?

A

2 contiguous alpha helices

44
Q

What type of protein is the leucine zipper motif?

A

Dimeric

45
Q

What do the dimers in the top stalk zip together to form?

A

A short coiled coil

46
Q

How is the coil held together?

A

By hydrophobic interactions down opposing sides of the helix

47
Q

What type of amino acids dominate the lower part of the helix

A

Basic

48
Q

What does heterodimerisation do in the leucine zipper motif?

A

It expands with the regulatory potential of leucine zippers

49
Q

What does the helix-turn-helix motif consist of?

A

Two short helices oriented at right angles to train each other - connected by a turn

50
Q

Where is the helix-turn-helix found?

A

In both prokaryotic and eukaryotic DNA binding proteins

51
Q

Give some examples of where the helix-turn-helix motif is found

A

CRO repressor and homeobox proteins

52
Q

What is the CRO protein?

A

Homodimer

53
Q

What does the CRO repressor do?

A

Recognises palindromic sequence and by binding DNA represses transcription

54
Q

What is the zinc finger motif comprised of?

A

Alpha helix and beta sheet held together by non-covalent interactions with zinc

55
Q

What does the alpha helix of each motif do with DNA in the zinc finger motif?

A

Knots with the major groove of the DNA and recognises specific DNA sequence

56
Q

What hormones may have the zinc finger motifs in?

A

Glucorticoid
Mineral corticoid
Progesterone
Vitamin D

Fundamentals Of Living Cells (41 decks)

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