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Advance Biology - Unit 1 > Topic 1 & 2 - Proteomics and protein structure, binding and conformational change > Flashcards

Topic 1 & 2 - Proteomics and protein structure, binding and conformational change Flashcards

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1
Q

What is a genome ?

A

Entire hereditary information encoded in the DNA. It’s made of genes and other DNA sequences that don’t code for proteins
Eg: introns and Exons

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2
Q

What is a proteome

A

Entire set of proteins expressed by a genome.

It’s larger than the genome due to RNA Splicing and post- transitional modifications

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3
Q

What is a transcriptome

A

Full range of messenger RNA, or mRNA oR messenger mRNA and molecules expressed by an organism

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4
Q

What is micro- array analysis

A

Technique used to study transcriptome.

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5
Q

Step 1 of micro - array analysis

A

Makes copies of all the genes in the genome

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6
Q

Step 2

A

Separates all strands into single strands

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7
Q

Step 3

A

Places copies at each separate gene onto a specific point on a neatly ordered slide suspends on a droplet

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8
Q

Step 4

A

Take the cell type being studied and apply to microarray

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9
Q

Step 5

A

Scan microarray for attached cDNA

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10
Q

Step 6

A

Use logged locations to determine which genes at active in the studied cells

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11
Q

_____________ __________ can drive the function and often altering the structure back

A

Conformational change

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12
Q

_________ causes a conformational change in the protein, which may result in an altered function, may be reversible

A

Binding

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13
Q

Proteins are polymers of _________

A

Amino acids

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14
Q

Amino acids link _________ to form ________ ________

A

Peptide

Polypeptides

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15
Q

What is the primary sequence

A

It’s the order in which the amino acids are synthesised into the polypeptide

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16
Q

Secondary structure

A

Result from hydrogen bonding along the back bone of the protein strand

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17
Q

3 types of secondary structure formed

A

Alpha helices
Parallel or anti parallel beta
Turns

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18
Q

4 types of R Groups

A

Negatively charged/ acidic
Positively charged/ basic
Non-polar/ hydrophobic amino acids

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19
Q

Acidic amino acids have a _______ on the R Group

A

COOH

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20
Q

Are they positively or negatively charged

A

Negatively

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21
Q

Hydrophobic or hydrophilic

A

Hydrophilic

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22
Q

They ____ a proton to another atom

A

Donate

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23
Q

Two types of amino acid in this group

A

Aspartame and glutamate

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24
Q

Basic amino acids have ____ on the R group

A

NH2

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25
Q

They _____ a proton

A

Accept

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26
Q

Positively or negatively charged

A

Positively

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27
Q

Hydrophilic or hydrophobic

A

Hydrophilic

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28
Q

Name 3 basic amino acids

A

Lysine, arginine and histidine

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29
Q

3 things o the R side chain on polar amino acids

A

Oxygen nitrogen or sulfur

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30
Q

Hydrophilic or hydrophobic

A

Hydrophilic

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31
Q

They form ____ hydrogen bonds

A

Weak

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32
Q

Six polar acids name 2

A

Define and cysteine

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33
Q

Do they or do they not have OH,COOH,NH2 or SH

A

Don’t have

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34
Q

Negatively or positively charged

A

Neither

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35
Q

Hydrophilic or hydrophobic

A

Hydrophobic

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36
Q

They have ___________ and a lot of carbon atoms

A

Benzene rings

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37
Q

2 types

A

Glycine and phenylalanine

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38
Q

When polypeptide folds they become ________

A

Tertiary structure

39
Q

Effects include _

A 
Interactions of R groups in hydrophobic Regions
Ionic bonds
Hydrogen bonds 
Van der waals interactions 
Disulphides bridges
40
Q

______________ groups give proteins added functions

A

Prosthetic

41
Q

An example of a prosthetic group

A

Haem in haemagloblin

42
Q

Quaternary structure is ____________

A

Several connected polypeptide subunits

43
Q

2 things that influence interactions of R groups

A

Temperature and pH

44
Q

Name for protein that has lost its shape

A

Denatured

45
Q

Increasing temperature effect

A

Melt weak bonds and then stronger bonds

46
Q

pH effect

A

Shift acidic base characters of the R group on particulate amino acids

47
Q

This results in ___________

A

Change in ionic interactions of amino acids

48
Q

Hydrophilic are __________

A

Water loving

49
Q

These R groups predominate on ________

A

Surface of a soluble protein in the cytoplasm

50
Q

Hydrophobic are ___________

A

Water hating

51
Q

There R groups ________

A

Cluster in the centre to form a globular structure

52
Q

Fluid mosaic model

A 
Phospholipid bilayer
Hydrophilic
hydrophobic
 hydrophilic 
Contains proteins [ intergral/transmembrane channels/ peripheral/ transmembrane]
53
Q

What is a ligand

A

Substance that bonds to a protein

54
Q

Ligand effects the _____ of a protein

A

Activity

55
Q

Eg enzymes, the specific shape give the _______ _____ for the substance to bind

A

Active site

56
Q

In cell signalling why is ligand binding essential

A

Activate receptors or channels

57
Q

Is a histone positively or negatively charged

A

Positive

58
Q

What’s the next step

A

Bonds to sugar phosphate back bone

59
Q

Is that positively or negatively charged

A

Negatively

60
Q

What is a nucleosome

A

DNA weapped around a histone

61
Q

Other protein binding sites either stimulate or inhibit _______

A

Transcription

62
Q

Ligand binding changes ______

A

The confirmation of a protein

63
Q

What does this cause

A

The functional change in a protein

64
Q

Eg enzymes what two things relate to induced fit

A

Specified between active site and substrate

65
Q

What happens when the substrate binds

A

Temporary change in the active site occurs

66
Q

This then _______ binding and integration with the substrate

A

Increases

67
Q

What produces lower activation energy

A

Chemical environment

68
Q

Once _________ takes place, the original enzyme is resumed and products are ________ from active site

A

Catalysis

Released

69
Q

What is an allosteric enzyme

A

Enzyme that can have its activity alerted by a ligand

70
Q

What’s this type of ligand called

A

Modulator

71
Q

These modulators bind to _________ binding sites

A

Secondary

72
Q

The _____________ changes and alter the _______ of the active site

A

Confirmation

Affinity

73
Q

What is the role of negative modulators

A

Reduce enzyme affinity for the substrate

74
Q

Deoxyhaemoglobin has a ____ ________ for oxygen

A

Low affinity

75
Q

When one molecule of oxygen binds to one of four haem groups it _______ the affinity of the remaining three haem goups

A

Increases

76
Q

Oxyhemoglobin ______ it’s ability to ______ oxygen

A

Increase

Lose

77
Q

This creates what ?

A

Oxygen dissociation curve

78
Q

Low ph =

A

Low affinity

79
Q

High temp =

A

Low affinity

80
Q

Exersice increases body ___ and produces ___________ the body

A

Temp

Co2 acidifying

81
Q

What is a phosphate

A

Highly charged group

82
Q

If added or removed what does it create

A

A reversible conformational change in proteins

83
Q

What does this charge do

A

Alter the r group interactions within a protein

84
Q

Types of protein involved in phosphate movement

A

Kinease
phosphatase
ATPase

85
Q

What is kinase

A

Group of enzymes that move things (kinetic)
Adds phosphate
Phosphorylates other proteins though ATP

86
Q

What is phosphatase

A

Enzyme that dephosphoryaltes groups

87
Q

What’s is ATPase

A

Enzymes use phosphate for ATP

Eg: glucose symport and muscle contractions

88
Q

___________ hydrophilic signaling molecules are involved in the ________ of extracelluar _______ proteins

A

Extracellular
Activation
Receptor

89
Q

What do they interact with ?

A

Intercellular proteinsthrough a series of kinases and phosphatases

90
Q

The cascade of ________ and __________ activates ___________ events

A

Phosphorylation and dephosphoralation

Intracellular

91
Q

What’s controlled this way

A

Insulin and blood sugar level

92
Q

What happens when muscle contracts

A

Actin and myosin slide past each other

93
Q

Step 1

A

Myosin heads act as cross bridges as they bind to actin at specific binding sites allowing muscle to contract

94
Q

Step 2

A

When actin binds to myosin , the head detaches from actin singing forward and reminds. The rebounding releases the ADP and a phosphate and drags the myosin along the actin filament

Advance Biology - Unit 1 (3 decks)

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