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A/ AH Biology: Unit 1 > Key Area 2: Proteins > Flashcards

Key Area 2: Proteins Flashcards

1
Q

What is the proteome?

A

Entire set of proteins expressed by the genome

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2
Q

What is the genome?

A

Entire hereditary information encoded in the dna

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3
Q

What accounts for the proteome being larger than the genome?

A

RNA splicing and post translational modifications

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4
Q

Why is the entire protein not expressed in all cells?

A

Differentiation

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5
Q

What molecule determines protein structure?

A

Amino acids

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6
Q

What are the four main amino acid groups?

A

Acidic
Basic
Polar
Non-polar

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7
Q

What are the main features of the acidic r group?

A

Hydrophilic
Negatively charged
Carboxyl groups that ionise to make them acidic

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8
Q

What are the main features of the basic r group?

A

Hydrophilic
Positively charged
Additional amino groups that ionise to NH3+

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9
Q

What are the main features of the polar r group?

A

Hydrophilic

OH, SH or O

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10
Q

What are the main features of the non-polar r group?

A

Hydrophobic

Hydrocarbons

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11
Q

What bond occurs between amino acids and how does it form?

A

A Peptide bond forms between amino group of one acid and the carboxyl group of the next and they are formed through loss of water (dehydration)

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12
Q

What is the primary structure of a protein?

A

Polypeptide

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13
Q

What results in the secondary structure of proteins?

A

Hydrogen bonding

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14
Q

What are the secondary structures of proteins?

A
  • alpha helix-helix formation
  • beta sheet-can be parallel or anti parallel
  • turns-direction of chain is reversed
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15
Q

What type of bonding holds the tertiary structure of a protein together?

A
  • ionic bonding
  • hydrogen bonding
  • Van Der Waals forces
  • disulphides bridges
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16
Q

Explain how hydrophobic interactions affect a molecule.

A

Hydrophobic interactions occur in non-polar molecules and tend to get placed in the centre of the molecule causing globular proteins

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17
Q

What is a prosthetic group?

A

A non-protein part added to a protein

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18
Q

Give three examples of prosthetic groups.

A
  • haeme-haemoglobin protein
  • lipid-lipid protein
  • nucleic acid-nucleoprotein protein
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19
Q

What is quaternary structure of a protein?

A

When two or more tertiary subunits join together

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20
Q

What are two factors that influence R group interactions?

A
  • temperature- increased temperature means increased kinetic energy so more stress on bonds
  • pH- changes in pH changes the concentration of ions in solution which changes the relative charge on the protein and places stress on the bonds
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21
Q

What does hydrophobic mean?

A

To repel water

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22
Q

What does hydrophilic mean?

A

Mixes with water

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23
Q

What is the current accepted model of the plasma membrane structure?

A

The fluid mosaic model

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24
Q

Where are hydrophilic r group predominantly found?

A

The surface of a protein in the cytoplasm

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25
Where are the hydrophobic r groups predominantly found?
In the centre of a protein in the cytoplasm
26
How are globular proteins formed?
A result of the hydrophobic and hydrophilic r group interactions in the cytoplasm
27
What are the two main components of the fluid mosaic membrane model?
Phospholipids and proteins
28
How do hydrophobic and hydrophilic interactions hold together the membrane?
Hydrophobic interactions in the membrane between lipid tails holds the double membrane together and hydrophilic heads of phospholipids allow the outer layers of the membrane to be surrounded by aqueous solutions
29
What is an integral membrane protein?
They span the membrane and have a stretch of non-polar amino acids in the hydrophobic region
30
What are three examples of integral membrane proteins?
* channels * transporters * many receptors
31
What are peripheral proteins?
Not embedded in the lipid layer but have loose associations with the surface of the membrane and few hydrophobic r group interactions with the phospholipids
32
What are peripheral proteins responsible for?
Cell-cell interactions
33
What is a ligand?
A substance that binds to a protein
34
What is the regions of proteins that are involved in ligand binding?
The amino acid R groups that are not involved in the confirmation of the protein
35
How does the dna backbone bind to proteins?
The dna backbone has a negative charge and the protein has a positive charge so they are attracted to each other
36
What protein does dna bind to?
Histones
37
What forms when dna binds to histones?
Nucleosomes
38
What linear structure forms as a result of tight packaging of dna in eukaryotes?
Chromosomes
39
What other proteins can bind to double stranded dna?
Transcription factors
40
What is a transcription factor?
Initiate or halt transcription by recruiting RNA polymerase
41
What happens when a ligand binds to a protein?
Conformational change
42
What does conformational change cause?
A change in affinity therefore a change in the function/behaviour of the protein
43
What is the function of phosphatase?
Removal of phosphate by hydrolysis
44
What is the function of ATPase?
Hydrolysis of ATP
45
What is the function of kinase?
Transfer of phosphate group to another molecule
46
What is the function of synthase?
Joining two molecules by dehydration
47
What is the function of nuclease?
Breakdown of nucleic acid by hydrolysis
48
What is the function of polymerase?
Addition of molecules in series in a chain
49
What is the function of protease?
Breaking down proteins by hydrolysis
50
What happens in induced fit?
The enzyme active site forms a complimentary shape to the substrate after binding to the ligand
51
What does the chemical environment from the enzyme/substrate binding do?
Lowers the activation energy needed for the reaction
52
What happens to the confirmation of the enzyme after catalysis?
It reverts to its original confirmation
53
What is an allosteric enzyme?
An enzyme that can have its activity altered by a ligand called a modulator
54
What is a modulator?
A ligand that binds to an area of the protein that is not the active site
55
What is a positive modulator?
Changes the conformation to promote the binding of enzyme and substrate so increase enzyme activity
56
What is a negative modulator?
Prevents the enzyme and substrate binding so decrease enzyme activity
57
What level of protein structure shows cooperativity?
Quaternary
58
What is cooperativity?
Changes in any protein binding site changes affinity of all other groups
59
What is an example of a protein that shows cooperativity?
De-oxyhaemoglobin
60
What are two factors that influence the binding of de-oxyhaemoglobin?
* temperature | * pH
61
What level of temperature reduces affinity of ligand?
High temperature
62
What level of pH reduces affinity of ligand?
Low pH
63
What is phosphorylation?
The addition or transfer of phosphate to another molecule
64
What is dephosphorylation?
The removal of a phosphate from a molecule
65
What occurs when a phosphate is added or removed from a molecule?
Conformational change
66
What are two types of protein that can be regulated using post-translational modifications?
* enzymes | * channels
67
What type of protein used ATP for their phosphorylation?
ATPase
68
What are the steps in a muscle contraction?
- muscle receives an impulse from a nerve cell generated by calcium - impulse causes myosin binding sites on actin to be exposed - myosin Hess from a flexed shape and bind to the actin - ADP and Pi are released from the myosin, causing it to return to its relaxed shape and moving the actin filament to the centre of the sacromere - ATP binds to the myosin head which causes it to release the actin - the myosin head acts as ATPase as it breaks down the ATP to ADP and Pi causing the head of the myosin to flex again

A/ AH Biology: Unit 1 (6 decks)

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