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Protein Structure & Function > Structure Determines Function > Flashcards

Structure Determines Function Flashcards

1
Q

Describe the central dogma of biology

A

DNA polymerase replicates DNA
RNA polymerase makes sense RNA from DNA
RNA made into mRNA after PTM
mRNA made into proteins in ribosome

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2
Q

Where are proteins synthesized?

A

Endoplasmic reticulum

Trafficked to Golgi

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3
Q

What are the two secretory pathways for proteins?

A

Constitutive secretory pathway
Regulated secretory pathway

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4
Q

What happens in the constitutive secretory pathway?

A

Aka default pathway = does not require signal for cargo to enter this pathway

Transport soluble proteins or plasma membrane proteins

Uses transport vesicles

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5
Q

What happens in the regulated secretory pathway?

A

Found mainly in specialized cells that release hormones or NTs

Uses secretory vesicles

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6
Q

What is the difference between transport vesicles and secretory vesicles?

A

Transport = fuse with plasma membrane and release their contents

Secretory = blocked from fusing with plasma membrane without proper signal

Extracellular ligand binds cellular receptors = causing intracellular signal to release block on secretory vesicle, then it fuses with plasma membrane to release cargo

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7
Q

What is the budding event?

A

Start of forming vesicle

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8
Q

Explain the curvature of a vesicle

A

Circular part = positive
Stem = negative

Straight parts = zero

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9
Q

What is the difference in charge of a vesicle?***

A

Cytoplasmic side is negatively charged compared to exoplasmic side

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10
Q

How is vesicle curvature made by lipid properties?

A

Positive curvature = convex membrane, lipid with large-head group section and small tails

Negative curvature = concave membrane lipids with small head-group section and large tails

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11
Q

What do membrane proteins do when they capture light?

A

Convert light energy into electric and chemcial potential across the membrane

Example = synthesizing ATP

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12
Q

What is the role of membrane proteins in signalling?

A

Send signals across membrane into and out of cell

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13
Q

What do membrane proteins control in terms of transport?

A

Control traffic of metabolites across membrane
Allow DNA to enter cells
Transport entire proteins across cell membrane

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14
Q

How do membrane proteins protect the cell?

A

Pump undesired molecules out of cell

Function as vacuum cleaner = remove unwanted “polluting hydrophobic molecules from the bilayer”

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15
Q

Name the two types of membrane proteins

A

Integral membrane proteins (IMPs)

Peripheral membrane proteins

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16
Q

What two architectures are integral membrane proteins limited to?

A

Alpha helical bundle = 90%
Beta-barral = 10%

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17
Q

How are peripheral membrane proteins bound to membrane?

A

Loosely bound or associated to IMPs

Can also be anchored to lipid bilayer = GPI-linked of by palmitoylation

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18
Q

What are the two domains of IMPs?

A

Extracellular domain
Transmembrane domain

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19
Q

Describe the core and loops in the globular-like domain of IMPs

A

Core = non-polar, densely packed, conserved and contains few functional polar residues

Loops = involved in ligand binding and signal transduction

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20
Q

Describe alpha-helical IMPs with single TM segment and its function

A

Called a bitopic transmembrane protein = function as recognition and/or adhesion molecules, receptors of growth factor-like messengers

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21
Q

What is the function of bitopic TM proteins’ cytoplasmic region?

A

Passes signal into the cell by binding soluble elements or cytosekeltal proteins

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22
Q

Give two example of a-helical IMPs with multiple TMS

A

G-protein coupled receptors = 7 different segments

K+ channel

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23
Q

Describe a-helical IMPs with multiple TMS and their function

A

Polytopic proteins = usually function as receptors or transporters

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24
Q

What is usually found at the end of integral membrane proteins?

A

Signalling peptides

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25
Q

What are the most common TMS amino acids and why?

A

TMS are overall NON-POLAR

Leucine
Isoleucine
Valine
Phenylalanine

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26
Q

Where are polar residues found in TMS?

A

Buried in core, masked by other polar groups and/or water molecules

27
Q

What is the difference between globular proteins and TMS in polarity?

A

TMS core is more polar than surface

Globular protein core is less polar than surface

28
Q

In TMS, which residues are found in alpha helices and which are found in beta-sheets?

A

Small residues in closely packed a-helices = Gly, Ala & Ser

b-branched residues = Leu, Val, Ille, Phe

29
Q

How is the length of TMS determined?

A

Matches width of HYDROPHOBIC part of membrane

30
Q

What is the hydropathy index for?

A

As long as we know the sequence, can then say which amino acids are most hydrophobic

Hydropathy index for any segment = average of hydrophobicity values for its residues

Used to predict where and how many hydrophobic TMS there are

31
Q

Where are Gly and Pro preferred locations in TM a-helices?

A

Near kinks

32
Q

What is special about Pro?

A

Helix breaker or hinge of motion

33
Q

What is the role of aromatic amino acids and where are they found in TMS?

A

Aromatic ‘belt’ anchors proteins to membrane

These amino acids have large, hydrophobic aromatic side chains that interact with the hydrophobic core of the membrane. The aromatic belt acts as an anchor, stabilizing the protein’s insertion into the membrane. This configuration helps the protein to maintain its position and ensures that the hydrophobic transmembrane segments are properly shielded from the aqueous environment, facilitating the protein’s functional role in the membrane.

34
Q

What do Arg and Lys do in TMS?

A

They are positively charged, so interact with negatively charged lipid head groups of cytoplasmic memrbane

35
Q

Why are some TMS distorted and how are they compensated?

A

Distorted because they exceed the thickness of bilayer

Compensated by their tertiary structure

36
Q

What happens to medium and long TM helices?

A

Medium = tilted at angle
Long = helix-distorting kink (Proline)

37
Q

Name the two functional roles of distortion?

A

Allow greater proximity between helices in the membrane

Create binding sites

38
Q

What two numbers characterize beta-sheet integral membrane proteins?***

A

Strand number = antiparallel beta sheets

Shear number = total shift in strand registry between first and last strand

This determines hydrophobic packing arrangement and diameter of the barrel

39
Q

Example of beta-sheet integral membrane protein

A

Bacterial porins

40
Q

3 properties of bacterial porins

A

Non-selective channel in outer membrane

Some are toxins

Some are attachment sites for phage and bacterial toxins

41
Q

How are TMS adapted for better packing?

A

Have ridges and grooves = created by different amino acids/MOTIFS

Then tilted at 20 degrees

42
Q

What do PTMs do and where do they occur?

A

PTMs mainly occur in Golgi

Increase functional diversity of proteins by covalent additional of functional groups etc

43
Q

What PTM changes physical-chemical properties?

A

Glycosylation = increases stability and water solubility

44
Q

What PTM regulates activity of protein?

A

Hormone-induced phosphorylation = turns activity of many enzymes on and off

45
Q

What PTM affects protein transport?

A

Acylation serves as membrane anchor

46
Q

What PTM regulates half-life of protein?

A

Ubiquitination tags proteins for proteolysis

47
Q

Describe the steps in insulin PTM

A
  1. Signal peptide removal
  2. Disulphide bond formation
  3. C-peptide cleavage
48
Q

Which amino acids do N-linked and O-linked glycosylation occur on?

A

N-linked glycans attached to Asparagine or Arginine side chains

O-linked glycans mainly attached to Ser or Thr side chains

49
Q

Where does N-linked glycosylation take place and what is its function?

A

In the ER = N-glycosylation directs INITIAL steps of protein folding and its quality control

Alls newly synthesized glycoprotein to interact with lectin-based chaperone system in ER

50
Q

Where does O-linked glycosylation take place, and what is its function?

A

Primarily takes place in Golgi

Accelerates proteins degradation and decreases protein stability

Regulating activities such as aggregation and phase separation

51
Q

How is glycosylation important in the immune response?

A

Effective immune response depends on successful activation and maturation of dendritic cells

Abnormally glycosylated protein antigens impair the function of dendritic cells = allowing cells to evade the host’s immune response

52
Q

Role of phosphorylation and enzymes involved

A

Kinase and phosphatase

Activate, inactivate or change binding affinities = phosphorylation-induced conformational change

53
Q

Role of ubiquitylation and enzymes involved

A

Ubiquitin ligase and deubiquitinases

Covalent bond between C-terminal of ubiquitin (proteint) and lysine residue

Marked for degradation

54
Q

What is the role of protein metalation?

A

Metal cation addition = bound directly or via prosthetic group

Many roles = stabilization, ligand binding, catalysis, electron transport

55
Q

How are metals or metal clusters inserted into polypeptides?

A

Either transferred from a pool of free metal ions
OR
Via delivery by metallocharperones

56
Q

At what stage are metals added to polypeptides, and what can removal of metal results in?

A

Metal can be inserted at unfolded state, intermediate state or native folded state

Removal from protein’s native state can cause unfolding/misfolding = leading to disease
Or can result in a foled APO conformation with vacant metal binding site

Apo state = metal free state

57
Q

Name 3 methods of detecting PTMs

A

Western Blotting
Mass spectrometry
Immunofluorescence

58
Q

How does western blotting detect PTMs?

A

Different proteins separated from cell according to MW in the gel

Transferred to membrane for blotting with 1 & 2 Ab for the selected PTMs

59
Q

Advantages and disadvantages of western blotting

A

Able to investigate endogenous alterations of PTMs
No specific tools required

Specific Ab against target protein required
No site specificity
False negatives possible = due to PTM modifications may block Ab binding site of target protein

60
Q

How does mass spectrometry detect PTMs?

A

Digest protein lysate of interest, by specific protease (trypsin)

Enrich the specific PTM and analyse

After collecting data = comupatational algorithms are employed to identify peptides and proteins

Used to detect PTMs substrates and map PTM sites

61
Q

Advantages and disadvantages of mass spectrometry

A

Can detect large numbers of modified proteins with high sensitivity and specificity

Time-consuming and highly PTM specific

62
Q

How does immunofluorescence detect PTMs?

A

Useful to investigate global and spatial changes in PTM profiles in tissues or cells

63
Q

Advantages and disadvantages of immunofluorescence

A

Used to examine localization of proteins throughout the cell

Can determine localization of specific forms of proteins in response to different cell conditions
Not available to identify a target specific PTM

Protein Structure & Function (11 decks)

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