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

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

Flashcards in Topic 1 & 2 - Proteomics and protein structure, binding and conformational change Deck (94):
1

What is a genome ?

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

2

What is a proteome



Entire set of proteins expressed by a genome.
It’s larger than the genome due to RNA Splicing and post- transitional modifications

3

What is a transcriptome

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

4

What is micro- array analysis

Technique used to study transcriptome.

5

Step 1 of micro - array analysis

Makes copies of all the genes in the genome

6

Step 2

Separates all strands into single strands

7

Step 3

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

8

Step 4

Take the cell type being studied and apply to microarray

9

Step 5

Scan microarray for attached cDNA

10

Step 6

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

11

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

Conformational change

12

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

Binding

13

Proteins are polymers of _________

Amino acids

14

Amino acids link _________ to form ________ ________

Peptide

Polypeptides

15

What is the primary sequence

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

16

Secondary structure

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

17

3 types of secondary structure formed

Alpha helices
Parallel or anti parallel beta
Turns

18

4 types of R Groups

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

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Acidic amino acids have a _______ on the R Group

COOH

20

Are they positively or negatively charged

Negatively

21

Hydrophobic or hydrophilic

Hydrophilic

22

They ____ a proton to another atom

Donate

23

Two types of amino acid in this group

Aspartame and glutamate

24

Basic amino acids have ____ on the R group

NH2

25

They _____ a proton

Accept

26

Positively or negatively charged

Positively

27

Hydrophilic or hydrophobic

Hydrophilic

28

Name 3 basic amino acids

Lysine, arginine and histidine

29

3 things o the R side chain on polar amino acids

Oxygen nitrogen or sulfur

30

Hydrophilic or hydrophobic

Hydrophilic

31

They form ____ hydrogen bonds

Weak

32

Six polar acids name 2

Define and cysteine

33

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

Don’t have

34

Negatively or positively charged

Neither

35

Hydrophilic or hydrophobic

Hydrophobic

36

They have ___________ and a lot of carbon atoms

Benzene rings

37

2 types

Glycine and phenylalanine

38

When polypeptide folds they become ________

Tertiary structure

39

Effects include _

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

40

______________ groups give proteins added functions

Prosthetic

41

An example of a prosthetic group

Haem in haemagloblin

42

Quaternary structure is ____________

Several connected polypeptide subunits

43

2 things that influence interactions of R groups

Temperature and pH

44

Name for protein that has lost its shape

Denatured

45

Increasing temperature effect

Melt weak bonds and then stronger bonds

46

pH effect

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

47

This results in ___________

Change in ionic interactions of amino acids

48

Hydrophilic are __________

Water loving

49

These R groups predominate on ________

Surface of a soluble protein in the cytoplasm

50

Hydrophobic are ___________

Water hating

51

There R groups ________

Cluster in the centre to form a globular structure

52

Fluid mosaic model

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

53

What is a ligand

Substance that bonds to a protein

54

Ligand effects the _____ of a protein

Activity

55

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

Active site

56

In cell signalling why is ligand binding essential

Activate receptors or channels

57

Is a histone positively or negatively charged

Positive

58

What’s the next step

Bonds to sugar phosphate back bone

59

Is that positively or negatively charged

Negatively

60

What is a nucleosome

DNA weapped around a histone

61

Other protein binding sites either stimulate or inhibit _______

Transcription

62

Ligand binding changes ______

The confirmation of a protein

63

What does this cause

The functional change in a protein

64

Eg enzymes what two things relate to induced fit

Specified between active site and substrate

65

What happens when the substrate binds

Temporary change in the active site occurs

66

This then _______ binding and integration with the substrate

Increases

67

What produces lower activation energy

Chemical environment

68

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

Catalysis
Released

69

What is an allosteric enzyme

Enzyme that can have its activity alerted by a ligand

70

What’s this type of ligand called

Modulator

71

These modulators bind to _________ binding sites

Secondary

72

The _____________ changes and alter the _______ of the active site

Confirmation
Affinity

73

What is the role of negative modulators

Reduce enzyme affinity for the substrate

74

Deoxyhaemoglobin has a ____ ________ for oxygen

Low affinity

75

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

Increases

76

Oxyhemoglobin ______ it’s ability to ______ oxygen

Increase
Lose

77

This creates what ?

Oxygen dissociation curve

78

Low ph =

Low affinity

79

High temp =

Low affinity

80

Exersice increases body ___ and produces ___________ the body

Temp
Co2 acidifying

81

What is a phosphate

Highly charged group

82

If added or removed what does it create

A reversible conformational change in proteins

83

What does this charge do

Alter the r group interactions within a protein

84

Types of protein involved in phosphate movement

Kinease
phosphatase
ATPase

85

What is kinase

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

86

What is phosphatase

Enzyme that dephosphoryaltes groups

87

What’s is ATPase

Enzymes use phosphate for ATP
Eg: glucose symport and muscle contractions

88

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

Extracellular
Activation
Receptor

89

What do they interact with ?

Intercellular proteinsthrough a series of kinases and phosphatases

90

The cascade of ________ and __________ activates ___________ events

Phosphorylation and dephosphoralation
Intracellular

91

What’s controlled this way

Insulin and blood sugar level

92

What happens when muscle contracts

Actin and myosin slide past each other

93

Step 1

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

94

Step 2

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