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AH biology - unit 1 (Proteomics) > Unit 1.2 - Proteomics > Flashcards

Unit 1.2 - Proteomics Flashcards

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1
Q

What is the proteome?

A

The entire set of proteins expressed by the genome

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2
Q

Why is the proteome bigger than genome?

A

Alternative RNA Splicing

Post Translational Modification

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3
Q

What are the two functional groups found in all amino acids?

A

Amine

Carboxylic Acid

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4
Q

What happens to an amino acid when it is in aqueous solution?

A

NH2 gains a hydrogen to become NH3+

COOH loses a hydrogen to become COO-

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5
Q

What are the four classes of amino acids?

A

Acidic
Basic
Polar
(Non-polar) Hydrophobic

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6
Q

What class of amino acids are negatively charged?

A

Acidic

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7
Q

Describe the characteristics of a basic R group

A

Positively Charged
Functional group example: -NH2
Example: Lysine

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8
Q

What class of R groups are found at the surface of a protein?

A

Polar

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9
Q

What constitutes a peptide bond?

A

C, O, N , H

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10
Q

What is the primary structure of a protein?

A

Order in which the amino acids are synthesised into the polypeptide

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11
Q

What stabilises secondary structure of the protein?

A

Hydrogen Bonds

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12
Q

Where does the hydrogen bonding occur between in secondary structure?

A

N-H has a weak positive charge and C=O has a weak negative charge

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13
Q

What are the three types of secondary structure?

A

Alpha Helix
Beta Sheets
Turns

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14
Q

Where are the R groups facing in an alpha helix?

A

Outwards

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15
Q

Where are the R groups sitting in a beta sheet?

A

Above and Below

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16
Q

What are the two types of beta sheets?

A

Antiparallel and parallel

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17
Q

If chains run in opposite directions(in respect to N-C polarity) what type of beta sheet is it?

A

Antiparallel

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18
Q

What causes tertiary structure?

A

Interactions between R groups of amino acids

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19
Q

State some possible interactions between R groups

A

Ionic Bonds
LDF/Van der Waals
Disulphide Bridges

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20
Q

What is special about the R groups that are connected with disulphide bridges?

A

R groups contain sulphur

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21
Q

How does temperature affect the proteins?

A

-Tertiary structure is destabilised, leading to denaturation
-Increased heat = more kinetic energy, polypeptide chain shakes more
-Weaker interactions such as H bonds are broken

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22
Q

How does pH affect the proteins?

A

Effects ionisation of the acidic and basic R groups
Changes the charge, so they no longer bond correctly
Polypeptide Unfolds

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23
Q

What is Quaternary structure?

A

When more than one polypeptide sub-unit join together to form a protein

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24
Q

Give an example of a protein with Quaternary structure

A

Collagen

Haemoglobin

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25
Q

What is co-operativity?

A

When ligand binding at one protein subunits alters the conformation of the other subunits

26
Q

State three important functions of R groups

A

-Determine the structure of a protein
-Allows the binding of ligands
-Determines the location of proteins in the cell

27
Q

How do cytoplasmic proteins become more soluble in aqueous solutions?

A

Greater proportion of hydrophyllic amino acids
Prosthetic groups are added to increase hydrophyllic - ness
Hydrophobic R groups cluster towards centre

28
Q

How could you tell if a protein is not soluble?

A

If there is no net charge on the surface of the protein at the isoelectric point

29
Q

What kind of molecules can pass through the membrane?

A

non polar (small) (hydrophobic)

30
Q

What acts as a barrier to charged ions and polar molecules passing through the membrane?

A

hydrophobic centre

31
Q

What are the two types of membrane proteins?

A

integral ,(transmembrane), periphal,

32
Q

What type of bonds do integral proteins form?

A

hydrophobic bonds

33
Q

Where do the integral membrane proteins interact?

A

tails of phospholipids

34
Q

Describe the bonding of peripheral proteins to the membrane

A

form weak bonds on surface of membrane

35
Q

What is a ligand?

A

A substance that can bind to a protein

36
Q

In what ways are the ligand binding sites complementary to the ligand?

A

Shape (conformation) and chemistry

37
Q

What is caused in the protein by a conformational change?

A

functional change

38
Q

What charges do histones carry?

A

positive

39
Q

What charge is the sugar phosphate backbone of DNA?

A

negative

40
Q

State important roles of DNA binding

A

Help to form linear chromosomes

Regulating the transcription of genes

41
Q

Describe induced fit

A

Small changes in bonding pulls the enzyme structure towards the substrate
Increases interaction between active site and substrate
Enzyme is trying to revert to original state
Places the substrate under tension
Lowers activation energy
Once the experiment is completed the active site has less affinity for products
Products are released
Enzymes return to original confirmation

42
Q

How can the rate of product formation in a metabolic pathway be regulated?

A

Raising or lowering the activity of an enzyme (allosetric enzyme)

43
Q

What do positive modulators do?

A

Increase affinity and enzyme activity

44
Q

How many polypeptide sub-units are there in haemoglobin?

A

4

45
Q

What does each subunit of haemoglobin contain?

A

Haem

46
Q

What is the function of Haem?

A

Allow for oxygen binding

47
Q

What conditions reduce affinity of oxygen?

A

Low pH

High Temperature

48
Q

Conditions to increase affinity

A

high pH, low temp

49
Q

What do inactive proteins need to become active?

A

Post Translational Modification

50
Q

What is the most of common of activation?

A

The addition of a phosphate to R groups

51
Q

What are Kinases?

A

Proteins that catalyse the process of phosphorylation

52
Q

A protein catalyses dephosphorylation. What type of protein is this?

A

Phosphatases

53
Q

What are ATPases?

A

Proteins that can cause their own conformational change by phosphorylating themselves.

54
Q

What two conditions would increase the product yield of an enzyme reaction?

A

Adding a positive modulator
Increasing enzyme concentration

55
Q

What happens if further translation of a cytosolic ribosome occurs?

A

(further translation) -> cytosolic proteins -> remain in cytosol , e.g (used in glycolysis)

56
Q

What happens if a signal sequence is added to a cytosolic ribosome (1) ?

A

Translation is stopped -> inserted into membrane of RER -> signal sequence removed -> embedded in membrane of RER

57
Q

What happens if signal sequence is added to cytosolic ribosome (2) ?

A

Translation is stopped -> inserted into lumen of RER -> s.s removed then transported via vesicles -> Golgi apparatus

Golgi apparatus (post-translational mod.) (all via vesicles)
(1) lysosomes - phagocytosis
(2) mitochondria + chloroplasts
(3) plasma membrane
(i) embedded in plasma membrane
(ii) secreted from cell (peptide hormones (insulin)/digestive enzyme), secreted as inactive precursors need proteolytic cleavage to activate

58
Q

What organelle is responsible for protein transport?

A

Rough ER

59
Q

What organelle is responsible for lipid synthesis?

A

Smooth ER

60
Q

What organelle is responsible for post-translational modification?

A

Golgi apparatus

61
Q

One example of post-translational modification in the golgi apparatus?

A

Addition of a carbohydrate to form a glycoprotein, (most secreted proteins are glycoproteins)

AH biology - unit 1 (Proteomics) (11 decks)

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