1.6. Proteins

Question 1

Proteins are responsible for…

Answer 1

…every task of cellular life.

Question 2

monomers of protein

Answer 2

amino acids (a-a)

Question 3

proteome

Answer 3

all proteins produced by a cell, tissue, or an organism (differ among tissues, basis for cell differentiation)

Question 4

genome

Answer 4

all DNA of a cell - genome of all cells of the same multicellular organism is the same (originating from the same first cell - zygote)

Question 5

structure of a-a (+draw)

Answer 5

common group and radical/side/functional group (20 different types- 20 diff. a-a)
…

Question 6

common group
radical/side/functional group

Answer 6

. same for all a-a, central C atom, amine group, and carboxyl group
- varies between different a-a (gives them their character)

Question 7

zwitterion model of a-a

Answer 7

more accurate, a-a has both plus and minus charge (overall neutral) because it gains an H in the amine group and loses an H in carboxyl group when in water (ionized in an aq. solution)

Question 8

amino acids are grouped according to their chemical properties (R group):

Answer 8

1. non-polar
2. positive charge
3. polar
4. negative charge

Question 9

there are more than __ a-a but only __ of them…

Answer 9

20, 20, make proteins of all life

Question 10

how do a-a speak about common ancestry of all life

Answer 10

all 20 were made before origin of life and the 1st organism used all of them - life still uses the same set of a-a as back then

Question 11

a-aˇ1+a-aˇ2 =

Answer 11

dipeptide

Question 12

bond connecting two a-a

Answer 12

peptide bond

Question 13

oligopeptide
peptide
polypeptide

Answer 13

• 2-20
• 20-40
• 40> (10 000)

Question 14

approximate number of different proteins that can be made out of a-a is:

Answer 14

20^1000 (generalized: 20^n - n is the number of a-a in a chain)
- but our body makes a lot less (few thousand)

Question 15

What determines protein function?

Answer 15

structure of proteins (3D shape) which is determined by the sequence of a-a in a protein (chain) which is determined by genes (sequence of nucleotides)

Question 16

Sequence of a-a is determined by __ and it is…

Answer 16

the gene, crucial for protein function.

Question 17

explain what causes the specific shape of each polypeptide chain

Answer 17

the sum of all interactions between a-a; some a-a form attraction forces between them, some repel each other so they will stey further apart… (e.g. - charged R group and + charged R group of a-a)

Question 18

draw the formation of a dipeptide (a-aˇ1=glycine, a-aˇ2=alanine)

Answer 18

…

Question 19

Some proteins consist of 1 (___) and some of more polypeptide chains (___, ___, ___, ___).

Answer 19

lysozyme (enzyme important for immune system), hemoglobin (Hb)(4), insulin (2), collagen (2), antibody (4)

Question 20

In water, ___ a-a are outside, sheltering the ___ a-a, and in oil ___ a-a are outside, sheltering ___ a-a.

Answer 20

hydrophilic, hydrophobic, hydrophobic, hydrophilic

Question 21

name for protein shape (used in biochemistry)

Answer 21

protein conformation

Question 22

primary protein structure

Answer 22

only speaks about the amino acid sequence and number of a-a in a polypeptide chain (encoded by a specific gene)

Question 23

secondary protein structure

Answer 23

Formation of patterns within a chain.
H-bonds cause folding of a-a into repeating patterns.
Random coils, alpha helix structures or beta-pleated sheets depending on H-bonds connecting the non-adjacent a-a along a single polypeptide chain.
H-bonds form between (former) carboxyl and amine groups of a-a.

Question 24

random coil

Answer 24

• no specific relationship between a-a
• determined by temperature, pressure and pH of the environment
• no particular patern

Question 25

alpha helix

Answer 25

• a-a form helical structures
• stabilized by H-bonds (H and O try to come as close to each other as possible - attraction force) - H-bonds NEVER bond charged a-a only polar

Question 26

beta-pleated sheets

Answer 26

• represented by a straight arrow in models
• stabilized by H-bonds (attraction force)

Question 27

tertiary protein structure

Answer 27

Due to interactions between R-groups of non-adjacent a-a, the chain undergoes additional folding.
Final shape is achieved by:
- ionic bonds (+R and - R)
- hydrophobic interactions (hydrophobic a-a in the chain’ interior to avoid contact with H2O)
- H-bonds (polar R groups)
- disulfide bridges (covalent bonds, cysteine a-a: CH2-S)

Question 28

What are prosthetic groups?

Answer 28

non-protein groups attached to proteins (conjugated proteins)

Question 29

How are the proteins that have attached prosthetic groups called? Give an example.

Answer 29

conjugated proteins, hemoglobin (Fe)
- the 4 polypeptide chains are not functional without Fe atoms at their core (protected) - O2 will bind to Fe (in red blood cells)

Question 30

draw a benzene ring

Answer 30

…

Question 31

quaternary protein shape

Answer 31

the way polypeptide chains fit together when there are more than 1 of them in a protein

Question 32

Why is protein denaturation (or ___) irreversible?

Answer 32

coagulation; because:
1) increase in temperature - when all atoms absorb the extra E, they will start vibrating, tertiary bonds will be broken and structures will fall apart - meaning that the function of the protein will be lost as well
2) pH too low - H+ concentration too big
- extra H+ ions will intervene with H-bonds and break them - many structures will be broken - loss of all levels of the protein structure - cannot be reformed - works the same when pH is too high (too many OH- ions)

Question 33

protein denaturation

Answer 33

Some factors (pH, temp.) can alter the conformation of the protein molecule and disrupt its biological function (complete loss of function) by breaking the intermolecular bonds within the chain. E.g. cooking an egg white - cannot go back to transparent from white.