protein structures

Question 1

how do you write amino acid sequence

Answer 1

written from amino or N terminus to carboxy or C terminus

Question 2

what are 5 properties of peptide bonds

Answer 2

• very stable
• cleaved by proteolytic enzymes proteases or peptidases
• partial double bond
• flexibility around C atoms not involved in bond, allows multiple conformations
• usually one preferred native conformation, determined mainly by the type of side chains and their sequence in the polypeptide

Question 3

what are the 2 types of ways to represent protein structure

Answer 3

backbone - a line following the peptide bonds
cartoon - a representation showing the fundamental secondary structures (helix/sheet)

Question 4

how is the folded state of proteins stabilised

Answer 4

by interactions between amino acids which can be very far apart in the primary sequence

Question 5

what are the 5 types of forces that hold proteins together

Answer 5

van der waals forces
hydrogen bonds
hydrophobic forces
ionic bonds
disulphide bonds

Question 6

what are van der waals forces

Answer 6

weak attractive interactions between atoms due to fluctuating electrical charges

Question 7

when are van der waals important

Answer 7

when 2 macromolecular surfaces fit closely in shape
can also be repulsive at very short distance

Question 8

what are hydrogen bonds

Answer 8

interaction between dipoles
involving hydrogen and an oxygen/nitrogen
partial negative charges on negative atoms bound to H which has a partial positive charge
the partial charges allow weak attractive interactions between some amino acid side chains, main chain O and N and water

Question 9

what are hydrophobic forces

Answer 9

uncharged and non polar side chains are repelled by water because they are poorly soluble
the side chains then form tightly packed cores in the interior of proteins, excluding water molecules
this attraction is the hydrophobic force

Question 10

what are ionic bonds

Answer 10

bonds between fully or partially charged groups
they are weakened in aq systems by shielding by water molecules and other ions in solution

Question 11

what are disulphide bonds

Answer 11

covalent bonding between side chains of cysteine residues
occurs in extracellular domains of proteins because conditions can be harsher so need extra stability

Question 12

what is the primary structure of a protein

Answer 12

a linear sequence of amino acids linked by peptide bonds

Question 13

what does the primary structure of a protein determine

Answer 13

it’s 3D conformation - the way in which the chain will fold to form its native structure

Question 14

what are the 2 types of protein secondary structure

Answer 14

alpha helix
beta pleated sheet

Question 15

what is the alpha helix protein structure

Answer 15

H bonds between each carbonyl group
H attached to the N which is 4 aa along the chain
side chains look outwards
proline breaks the helix (ring + no H)

Question 16

what is the beta pleated sheet protein structure

Answer 16

H bonds between linear regions of polypeptide chains
chains from 2 proteins or same protein
parallel or antiparallel chains, pleated or not
if the chain is folding back, structure is usually a 4 aa turn, called hairpin loop or B-turn

Question 17

what does the tertiary structure of protein mean

Answer 17

the overall 3D conformation of the protein
can be changed with pH and temperature

Question 18

what forces are involved in protein tertiary structure

Answer 18

electrostatic
hydrophobicity
H bonds
covalent bonds

Question 19

what are the types of conformational domains of tertiary structure (3)

Answer 19

barrel
bundle
saddle

Question 20

what does the quarternary structure of a protein mean

Answer 20

3D structure of a protein composed of multiple sub units
same non covalent interactions as tertiary structures

Question 21

how do we determine protein structure

Answer 21

X ray diffraction of protein crystals

Question 22

what are enzymes

Answer 22

biological catalysts that bind the reactants (substrates) and convert them to products
then they release the products and return to their original form

Question 23

what are benefits of enzymes (2)

Answer 23

speed up reactions
provide a way to regulate the rate of reactions

Question 24

what occurs in mitochondria (3)

Answer 24

TCA cycle
fatty acid oxidation
decarboxylation of pyrvate

Question 25

what occurs in cytosol (3)

Answer 25

glycolysis
HMP pathway
fatty acid synthesis

Question 26

what occurs in nucleus

Answer 26

DNA & RNA synthesis

Question 27

what occurs in lysosome

Answer 27

degradation of complex molecules

Question 28

how do enzymes act as disease markers

Answer 28

an enzyme marker is a blood test to measure enzymes, and proteins in your blood that can indicate tissue damage or disease.
eg elevated cardiac enzymes after a heart attack are a sign of serious heart damage

Question 29

what are 2 uses of enzymes

Answer 29

disease markers
drug targets

Question 30

how do enzymes act as drug targets

Answer 30

they act as a target for drugs for the desired therapeutic effect, which are thereby called biological targets.

Question 31

what is the porphyrin ring

Answer 31

the framework for the heme molecule, the pigment in haemoglobin and red blood cells.

Question 32

what is the structure of the porphyrin ring

Answer 32

contains an iron atom which is the site of oxygen binding

Question 33

what makes up a haemoglobin molecule

Answer 33

a chain x2
B chain x2
heme group

Question 34

what factors affect haemoglobin saturation

Answer 34

body temperature
arterial carbon dioxide
H+ level

Question 35

how is haemoglobin saturation affected

Answer 35

• structure gets modified
• affinity for oxygen is altered

Question 36

what happens when haemoglobin saturation increases

Answer 36

• its affinity for oxygen decreases
• oxygen unloading from the blood is enhanced

Question 37

what happens when haemoglobin saturation decreases

Answer 37

• its affinity for oxygen increases
• oxygen unloading from the blood is reduced

Question 38

what is sickle cell anaemia

Answer 38

a genetic disorder characterized by the formation of hard, sticky, sickle shaped red blood cells rather than normal bioconcave shaped red blood cells

Question 39

what causes sickle cell anaemia

Answer 39

a mutation in haemoglobin

Question 40

what are immunoglobulins

Answer 40

antibodies
they bind to antigens which are typically toxins or proteins on the surface of microbial agents
these targets are consequently labelled for destruction by cells of the immune system or by lysis through the complement system

Question 41

what is the structure of an immunoglobulin

Answer 41

4 polypeptide chains
two heavy (H) and two light (L) chains
Complementarity-determining regions (CDRs) are immunoglobulin hypervariable domains that determine specific antibody binding

Question 42

where are the antigen binding domains on immunoglobulins

Answer 42

at the tip of supporting structural frameworks