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

Question 1

What is a genome ?

Answer 1

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

Question 2

What is a proteome

Answer 2

Entire set of proteins expressed by a genome.

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

Question 3

What is a transcriptome

Answer 3

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

Question 4

What is micro- array analysis

Answer 4

Technique used to study transcriptome.

Question 5

Step 1 of micro - array analysis

Answer 5

Makes copies of all the genes in the genome

Question 6

Step 2

Answer 6

Separates all strands into single strands

Question 7

Step 3

Answer 7

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

Question 8

Step 4

Answer 8

Take the cell type being studied and apply to microarray

Question 9

Step 5

Answer 9

Scan microarray for attached cDNA

Question 10

Step 6

Answer 10

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

Question 11

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

Answer 11

Conformational change

Question 12

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

Answer 12

Binding

Question 13

Proteins are polymers of _________

Answer 13

Amino acids

Question 14

Amino acids link _________ to form ________ ________

Answer 14

Peptide

Polypeptides

Question 15

What is the primary sequence

Answer 15

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

Question 16

Secondary structure

Answer 16

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

Question 17

3 types of secondary structure formed

Answer 17

Alpha helices
Parallel or anti parallel beta
Turns

Question 18

4 types of R Groups

Answer 18

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

Question 19

Acidic amino acids have a _______ on the R Group

Answer 19

COOH

Question 20

Are they positively or negatively charged

Answer 20

Negatively

Question 21

Hydrophobic or hydrophilic

Answer 21

Hydrophilic

Question 22

They ____ a proton to another atom

Answer 22

Donate

Question 23

Two types of amino acid in this group

Answer 23

Aspartame and glutamate

Question 24

Basic amino acids have ____ on the R group

Answer 24

NH2

Question 25

They _____ a proton

Answer 25

Accept

Question 26

Positively or negatively charged

Answer 26

Positively

Question 27

Hydrophilic or hydrophobic

Answer 27

Hydrophilic

Question 28

Name 3 basic amino acids

Answer 28

Lysine, arginine and histidine

Question 29

3 things o the R side chain on polar amino acids

Answer 29

Oxygen nitrogen or sulfur

Question 30

Hydrophilic or hydrophobic

Answer 30

Hydrophilic

Question 31

They form ____ hydrogen bonds

Answer 31

Weak

Question 32

Six polar acids name 2

Answer 32

Define and cysteine

Question 33

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

Answer 33

Don’t have

Question 34

Negatively or positively charged

Answer 34

Neither

Question 35

Hydrophilic or hydrophobic

Answer 35

Hydrophobic

Question 36

They have ___________ and a lot of carbon atoms

Answer 36

Benzene rings

Question 37

2 types

Answer 37

Glycine and phenylalanine

Question 38

When polypeptide folds they become ________

Answer 38

Tertiary structure

Question 39

Effects include _

Answer 39

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

Question 40

______________ groups give proteins added functions

Answer 40

Prosthetic

Question 41

An example of a prosthetic group

Answer 41

Haem in haemagloblin

Question 42

Quaternary structure is ____________

Answer 42

Several connected polypeptide subunits

Question 43

2 things that influence interactions of R groups

Answer 43

Temperature and pH

Question 44

Name for protein that has lost its shape

Answer 44

Denatured

Question 45

Increasing temperature effect

Answer 45

Melt weak bonds and then stronger bonds

Question 46

pH effect

Answer 46

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

Question 47

This results in ___________

Answer 47

Change in ionic interactions of amino acids

Question 48

Hydrophilic are __________

Answer 48

Water loving

Question 49

These R groups predominate on ________

Answer 49

Surface of a soluble protein in the cytoplasm

Question 50

Hydrophobic are ___________

Answer 50

Water hating

Question 51

There R groups ________

Answer 51

Cluster in the centre to form a globular structure

Question 52

Fluid mosaic model

Answer 52

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

Question 53

What is a ligand

Answer 53

Substance that bonds to a protein

Question 54

Ligand effects the _____ of a protein

Answer 54

Activity

Question 55

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

Answer 55

Active site

Question 56

In cell signalling why is ligand binding essential

Answer 56

Activate receptors or channels

Question 57

Is a histone positively or negatively charged

Answer 57

Positive

Question 58

What’s the next step

Answer 58

Bonds to sugar phosphate back bone

Question 59

Is that positively or negatively charged

Answer 59

Negatively

Question 60

What is a nucleosome

Answer 60

DNA weapped around a histone

Question 61

Other protein binding sites either stimulate or inhibit _______

Answer 61

Transcription

Question 62

Ligand binding changes ______

Answer 62

The confirmation of a protein

Question 63

What does this cause

Answer 63

The functional change in a protein

Question 64

Eg enzymes what two things relate to induced fit

Answer 64

Specified between active site and substrate

Question 65

What happens when the substrate binds

Answer 65

Temporary change in the active site occurs

Question 66

This then _______ binding and integration with the substrate

Answer 66

Increases

Question 67

What produces lower activation energy

Answer 67

Chemical environment

Question 68

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

Answer 68

Catalysis | Released

Question 69

What is an allosteric enzyme

Answer 69

Enzyme that can have its activity alerted by a ligand

Question 70

What’s this type of ligand called

Answer 70

Modulator

Question 71

These modulators bind to _________ binding sites

Answer 71

Secondary

Question 72

The _____________ changes and alter the _______ of the active site

Answer 72

Confirmation | Affinity

Question 73

What is the role of negative modulators

Answer 73

Reduce enzyme affinity for the substrate

Question 74

Deoxyhaemoglobin has a ____ ________ for oxygen

Answer 74

Low affinity

Question 75

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

Answer 75

Increases

Question 76

Oxyhemoglobin ______ it’s ability to ______ oxygen

Answer 76

Increase | Lose

Question 77

This creates what ?

Answer 77

Oxygen dissociation curve

Question 78

Low ph =

Answer 78

Low affinity

Question 79

High temp =

Answer 79

Low affinity

Question 80

Exersice increases body ___ and produces ___________ the body

Answer 80

Temp | Co2 acidifying

Question 81

What is a phosphate

Answer 81

Highly charged group

Question 82

If added or removed what does it create

Answer 82

A reversible conformational change in proteins

Question 83

What does this charge do

Answer 83

Alter the r group interactions within a protein

Question 84

Types of protein involved in phosphate movement

Answer 84

Kinease phosphatase ATPase

Question 85

What is kinase

Answer 85

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

Question 86

What is phosphatase

Answer 86

Enzyme that dephosphoryaltes groups

Question 87

What’s is ATPase

Answer 87

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

Question 88

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

Answer 88

Extracellular Activation Receptor

Question 89

What do they interact with ?

Answer 89

Intercellular proteinsthrough a series of kinases and phosphatases

Question 90

The cascade of ________ and __________ activates ___________ events

Answer 90

Phosphorylation and dephosphoralation | Intracellular

Question 91

What’s controlled this way

Answer 91

Insulin and blood sugar level

Question 92

What happens when muscle contracts

Answer 92

Actin and myosin slide past each other

Question 93

Step 1

Answer 93

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

Question 94

Step 2

Answer 94

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