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Biochemistry > Module 4: V6 - V10 > Flashcards

Module 4: V6 - V10 Flashcards

1
Q

What roles do membrane proteins play?

A
  1. permit selective entry and exit of molecules from cell e.g. via transporters
  2. provide recognition signals e.g. receptors for growth factors
  3. provide structural support to the cell
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2
Q

How do proteins interact with the membrane?

A

most membrane proteins are free to diffuse laterally in lipid matrix

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3
Q

What are two types of protein that interact with the membrane?

A

integral membrane protein and peripheral protein

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4
Q

What are integral membrane proteins?

A

proteins which are firmly attached / embedded in the membrane

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5
Q

What are peripheral membrane proteins?

A

proteins which associate with outside surfaces

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6
Q

How do peripheral membrane proteins associate with membranes?

A

by ionic interactions and H-bonding with polar head groups of lipids and integral membrane proteins

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7
Q

How do integral membrane proteins interact with membranes?

A

by hydrophobic interactions with acyl chains of membrane lipids

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8
Q

Which reagents can be used to disrupt ionic interactions and release peripheral membrane proteins?

A

high salt, change pH, chelating agent

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9
Q

Which reagents can be used to disrupt hydrophobic reactions and release integral membrane proteins? How does this process work?

A

detergents such as SDS

dissolves membranes and maintains extracted protein in solution by interacting with hydrophobic regions of proteins

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10
Q

How can we determine orientation and arrangement of membrane proteins?

A

treating these proteins with an enzyme that chops them up will determine which parts are exposed to the protease and which parts aren’t

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11
Q

What does trypsin do?

A

trypsin cleaves on the carbonyl side of lysine and arginine, but only has access to the “outside” part of the protein of an intact cell

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12
Q

What does analysis of remaining protein after trypsin digestion of cells identify?

A

identifies the domains of the protein buried in the bilayer and/or exposed on the inner surface

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13
Q

Based on sequence can we predict transmembrane protein domains?

A

yes, genome sequencing allows the sequences of all proteins to be predicted

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14
Q

What information do we know about proteins which we can use to predict transmembrane protein domains?

A

sequence will consist of hydrophobic amino acids
conformation will be an alpha helix
span (segment of protein) equal to width of membrane

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15
Q

How many hydrophobic residues are required to span a 3 nm membrane?

A

20 hydrophobic residues

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16
Q

How is hydrophobicity measured? How is this measure derived?

A

the hydropathy index which is derived from the free energy change required to move an organic solvent to water
therefore, (+) values for hydrophobic amino acid residues as this process is not favourable and (-) values for hydrophilic amino acid residues as this process is favourable

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17
Q

What is indicative of a transmembrane region on a hydropathy plot?

A

a region in which 20 or more amino acid residues are hydrophobic (positive)

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18
Q

Which molecules are permeable?

A

oxygen and carbon dioxide

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19
Q

What are transport proteins in membranes responsible for?

A

transferring small water soluble molecules across the lipid bilayer

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20
Q

Do transport proteins transfer more than one type of molecule?

A

no, they are specific

21
Q

What are the two classes of membrane transport proteins?

A

carriers (transporters) and channels

22
Q

What are the different types of carriers and what type of transport do they mediate?

A

channel-mediated carriers which allow for passive transport across the membrane
carrier-mediated carriers which allow for both passive and active transport depending on the concentration gradient of the molecule

23
Q

How do carriers prevent molecules from constantly passing through?

A

they are closed on one side and opened on the other and they undergo a conformational change during the transport process

24
Q

What type of protein is GLUT1 and what process does it facilitate?

A

GLUT1 is a transporter found in membranes of many cells and it facilitates passive transport (facilitated diffusion) of glucose down a concentration gradient

25
Q

How does GLUT1 manage glucose transport?

A

exists in two conformations (T1 and T2)
binding of glucose (from blood plasma) may induce a conformational change from T1 to T2
explains net transport of solute down its concentration gradient

26
Q

What are active transporters used for? How do they do this?

A

transport solutes against a concentration gradient

use ATP hydrolysis mediated by P-type ATPases to pump ions across membranes

27
Q

Why is an Na and K gradient in animal cells important?

A

to maintain cell volume and create transmembrane electrical potential

28
Q

What are the three roles of sugars in biology?

A

carbohydrates are an important source of energy/stored fuels, provide structure to cells and organisms and play a significant role in cell biology

29
Q

Why are sugars important in cell biology?

A

major component of the cell surface

important in influencing the function of proteins and important in specific recognition interactions

30
Q

How do sugars convey information?

A

carbohydrates have enormous structural diversity

31
Q

What are cell surface sugars important in?

A

cell-cell adhesion
bacteria adhesion
virus attachment to host cells
binding of toxins to cell surface

32
Q

What are monosaccharides?

A

are aldehydes or ketones that have two or more hydroxyl groups

33
Q

What does aldose mean?

A

contains an aldehyde group

34
Q

Do most naturally occurring sugars belong to the D- or L-series?

A

the D-series

35
Q

What is a Fischer projection?

A

a diagram which provides a clear and simple view of the stereochemistry at each carbon centre

36
Q

How many carbon atoms do monosaccharides have?

A

≥ 3 carbon atoms

37
Q

What are the most common monosaccharides in nature?

A

hexoses (6C)

38
Q

Which carbon is C1 in a monosaccharide?

A

the first carbon after the aldehyde group

39
Q

What are sugars that differ only in the configuration around one carbon atom?

A

these sugars are called epimers

40
Q

Are hexoses mostly open chains or cyclised?

A

open chains are mostly cyclised into rings (pyranose rings)

41
Q

How does glucose become cyclised?

A

the C1 aldehyde reacts with the C5 hydroxyl group to form an intramolecular hemiacetal

42
Q

What is the conformation of monosaccharides?

A

chair form (boat form is not stable)

43
Q

Membrane rafts can be up to 0.9 nm thicker than the surrounding membrane. What could you say about the phospholipid acyl chains of the lipids found in membrane rafts, compared to the rest of the membrane?

A

the phospholipid acyl chains of the lipids found in membrane rafts are longer compared to the rest of the membrane

44
Q

Do you think the membrane proteins found in membrane rafts will be the same or different to those in the rest of the membrane?

A

the membrane proteins will be different to those in the rest of the membrane

45
Q

What can you say about the number of residues you would expect in the transmembrane alpha-helices of membrane raft proteins? Could you put a number on this difference?

A

approximately 26 amino acid residues. 20 residues to span 3nm and then an extra 6 residues to span the extra 0.9nm

46
Q

What exactly is a carbohydrate?

A

any of a large group of organic compounds occurring in foods and living tissues and including sugars, starch, and cellulose
they contain hydrogen and oxygen in the same ratio as water (2:1) and typically can be broken down to release energy in the animal body

47
Q

How can monosaccharides be both straight chain and cyclic molecules?

A

monosaccharides are able to cyclise into rings as a result of the reaction between the C1 aldehyde and the C5 hydroxyl group
monosaccharides are also able to form open chains because they are not bound by glycosidic linkages

48
Q

Why are naturally occurring sugars called ‘D’ sugars?

A

this is because the “D” designates the configuration of the asymmetric carbon furthest from the aldehyde group

49
Q

Which aldohexoses are common in biology and how are they related?

A

mannose, glucose and galactose

they share the same overall structure, but they differ in the configuration around one carbon atom

Biochemistry (30 decks)

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