1.2 proteins

Question 1

what is the proteome?

Answer 1

the entire set of proteins expressed by a genome

Question 2

why is the proteome larger than the genome?

Answer 2

due to alternative splicing and post-transational modification (more than one protein being produced by a single gene)

Question 3

what is the name for genes that do not code for a protein?

Answer 3

non-coding RNA genes

Question 4

which genes are included in non-coding RNA genes?

Answer 4

those that are needed to transcribe tRNA, rRNA, and other RNA molecules that directly control the expression of other genes

Question 5

the set of proteins expressed by a given cell
type can vary over time and under different
conditions. what are some factors that affect this?

Answer 5

metabolic activity
cellular stress
response to signalling molecules
diseased vs healthy cells

Question 6

eukaryotes have a relatively small surface area : volume ratio. what does this mean?

Answer 6

the plasma membranes of these cells are too small to carry out the vital functions required

Question 7

what is present in eukaryotic cells to account for the small plasma membrane?

Answer 7

a system of internal membranes to increase the total surface area

Question 8

what are the endoplasmic reticula? (ER)

Answer 8

a network of membrane tubules that are continuous with the nuclear membrane

Question 9

what are the golgi apparatus?

Answer 9

a series of flattened membrane discs

Question 10

what are lysosomes?

Answer 10

membrane-bound organelles that contain a variety of hydrolases that digest
proteins, lipids, nucleic acids and
carbohydrates

Question 11

what is the role of vesicles?

Answer 11

transport materials between membrane compartments

Question 12

where are lipids made before being inserted into the membrane?

Answer 12

in the SER

Question 13

in which type of ribosome are all proteins made?

Answer 13

in the cytosolic ribosomes

Question 14

what happens once cytosolic proteins are synthesised?

Answer 14

they remain in the cytosol (liquid part of the cytoplasm)

Question 15

what is the purpose of the signal sequence carried by transmembrane proteins?

Answer 15

to halt translation and direct the ribosome synthesising the protein to dock
with the ER, forming RER

Question 16

what is a signal sequence?

Answer 16

a short stretch of amino
acids at one end of the polypeptide that
determines the eventual location of a protein
in a cell

Question 17

what happens after docking?

Answer 17

translation continues and the protein is inserted into membrane of the ER

Question 18

what happens once proteins have been synthesised at the ER?

Answer 18

they are transported to the Golgi apparatus by vesicles that bud off of the ER

Question 19

how do molecules move through the Golgi?

Answer 19

in vesicles that come from one disc and fuse to another

Question 20

what happens at the Golgi apparatus?

Answer 20

post-translational modification

Question 21

what is classed as major protein modification?

Answer 21

the addition of sugars in steps to form carbohydrates (catalysed by enzymes)

Question 22

what happens once post-translational modification is completed?

Answer 22

vesicles take the modified proteins to the plasma membrane and lysosomes, which bind to the membrane and allow the proteins to be released

Question 23

how to vesicles move from one structure to another?

Answer 23

along microtubules, fusing to other membranes within the cell

Question 24

what are examples of secreted proteins?

Answer 24

peptide hormones and digestive enzymes

Question 25

what are the steps of the secretory pathway?

Answer 25

1) translation in RER, proteins enter lumen 2) proteins move through Golgi and packaged into vesicles 3) vesicles fuse to pm and proteins are released

Question 26

many proteins are synthesised as inactive precursors. what is required to produce active proteins from them?

Answer 26

proteolytic cleavage

Question 27

what is proteolytic cleavage?

Answer 27

another type of post-translational modification

Question 28

what is an example of secreted proteins that require proteolytic cleavage?

Answer 28

digestive enzymes

Question 29

what are factors that are different between R groups?

Answer 29

size, shape, charge, H bonding capacity, chemical reactivity

Question 30

are peptide bonds strong?

Answer 30

oui oui

Question 31

how are amino acids classified?

Answer 31

according to their R group

Question 32

what are the 4 amino acid classifications?

Answer 32

basic acidic polar hydrophobic

Question 33

what are the characteristics of acidic R groups?

Answer 33

donates a H+ ion negatively charged

Question 34

what are the characteristics of basic R groups?

Answer 34

accepts H+ ions positively charged

Question 35

what are the characteristics of polar R groups?

Answer 35

include oxygen and nitrogen in the side chain

Question 36

what are the characteristics of hydrophobic R groups?

Answer 36

do not include oxygen and nitrogen in the side chain

Question 37

what is the primary protein structure?

Answer 37

the order in which the amino acids and synthesised into a peptide

Question 38

what is the secondary protein structure?

Answer 38

where hydrogen bonding in the backbone of the protein forms alpha helices, beta pleated sheets and turns

Question 39

what is tertiary protein structure?

Answer 39

refers to the overall folding of the peptide and its final shape, stabilised by many different interactions between the R groups

Question 40

describe hydrogen bonds

Answer 40

weak, between hydrogen and electronegative atom (NOF)

Question 41

describe ionic bonds

Answer 41

strong, between positive and negative ions

Question 42

describe LDFs

Answer 42

very weak

Question 43

describe hydrophobic interactions

Answer 43

strong, reversion to avoid water

Question 44

describe disulfide bridge

Answer 44

strong, between two R groups containing sulfur

Question 45

what is the purpose of prosthetic groups?

Answer 45

to give the protein added function

Question 46

in which type of protein structure are prosthetic groups found?

Answer 46

in the tertiary structure

Question 47

what is an example of a prosthetic group?

Answer 47

haem group on haemoglobin is essential for oxygen binding

Question 48

describe quaternary structure

Answer 48

exists in proteins with several connected polypeptide subunits. it is a description of the spatial arrangement of the subunits

Question 49

how do increasing temperatures affect proteins?

Answer 49

it disrupts the interactions that hold the protein in shape, causing the protein to unfold, eventually becoming denatured.

Question 50

how does pH affect proteins?

Answer 50

it affects the charges of acidic and basic R groups as pH strays from its optimum, the normal ionic interactions between charged groups are lost, which changes the conformation of the protein until it becomes denatured

Question 51

what is a ligand?

Answer 51

a substance that can bind to a protein

Question 52

what happens when a ligand binds to a protein binding site?

Answer 52

conformational change

Question 53

what happens in allosteric enzymes?

Answer 53

modulators bind at secondary binding sites which are separate from the active site

Question 54

what occurs during cooperativity?

Answer 54

binding of one subunit changes the affinity of the remaining subunits

Question 55

what is an example of cooperativity?

Answer 55

the binding and release of oxygen to haemoglobin - binding of one increases affinity for the others

Question 56

what happens when temperature in haemoglobin increases or pH decreases?

Answer 56

the affinity is lowered and oxygen binding is reduced

Question 57

what happens in actively respiring tissue?

Answer 57

affinity for oxygen decreases, releasing it into the tissue

Question 58

what does the binding of an activator to an active/allosteric site do?

Answer 58

increases the affinity of the other active site for binding

Question 59

what happens when a modulator binds to an allosteric site?

Answer 59

they change the conformation and alter the affinity of the active site for the substrance

Question 60

how can the addition or removal of phosphates affect proteins?

Answer 60

can cause reversible conformational changes in proteins, affecting protein activity

Question 61

what is phosphorylation of proteins a form of?

Answer 61

post-translational modification

Question 62

what is kinase?

Answer 62

an enzyme that catalyses phosphorylation

Question 63

what is phosphatase?

Answer 63

an enzyme that catalyses dephosphorylation

Question 64

are proteins activated or inhibited by phosphorylation?

Answer 64

either

Question 65

how does adding a phosphate group alter a protein?

Answer 65

it adds negative charges interrupts original ionic interactions and creates new ones