Week 7_levels of protein structure

Question 1

describe the amino acid structure

Answer 1

central carbon

amino terminal end

carboxyl terminal end

R group

Question 2

what is an R group?

Answer 2

variable part of amino acids

give amino acids their individual electrochemical characteristics

Question 3

how many levels of protein structure are there?

Answer 3

4

Question 4

what is primary structure?

Answer 4

sequence of amino acids in a protein

Question 5

are R groups part of the peptide backbone?

Answer 5

no

Question 6

what is secondary structure in a protein?

Answer 6

folding of the protein that is caused by interactions w/in the peptide backone

Question 7

where do hydrogen bonds form in secondary structure?

Answer 7

form b/n amino hydrogen and carboxyl oxygen atoms

Question 8

what type of secondary structures are there in proteins?

Answer 8

alpha-helix

beta-pleated sheets (consist of 2 or more hydrogen bonded B-strands)

Question 9

what is a super secondary structure?

Answer 9

forms when alpha-helices and beta-pleated sheets combine in various ways to form motifs

Question 10

what are examples of super secondary structures?

Answer 10

B-barrel

B-a-B-unit

Question 11

what type of bonding holds secondary structures together within the peptide backbone?

Answer 11

H-bonding

Question 12

what is the tertiary structure?

Answer 12

the entire 3D structure of the entire folded protein

Question 13

tertiary structure is stabilized by interactions between…

Answer 13

R groups of the amino acids

Question 14

what are the types of R group interactions?

Answer 14

electrostatic interactions
- H bonding
- ionic bonding

disulfide bridges

Van der Waals interactions

hydrophobic interactions

Question 15

what are electrostatic interactions?

Answer 15

form b/n R groups to help stabilize tertiary structure

hydrogen bonds b/n R groups

ionic bonds b/n R groups

Question 16

what are disulfide bridges?

Answer 16

form b/n R groups to help stabilize tertiary structure

cysteines have a sulfhydryl (SH) group

the SH groups of 2 cysteine residues can form covalent bonds called disulfide (S-S) bridges

Question 17

what are Van Der Waals interactions

Answer 17

help stabilize tertiary structure

a weak attractive force b/n non polar molecules due to charge fluctuations in the electron clouds of atoms

Question 18

what are hydrophobic interactions?

Answer 18

hydrophobic (water-fearing) R groups will fold to the interior of the protein to avoid contact with aqueous environment

Question 19

what are protein domains?

Answer 19

functional subunits of a protein

Question 20

how are protein domains formed?

Answer 20

from a combination of secondary and tertiary interactions

Question 21

one protein can form multiple ___

Answer 21

domains

Question 22

any protein that directly binds to DNA (ex. transcription factors) needs a ___

Answer 22

DNA binding domain

Question 23

activating transcription of gene requires a ___ to recruit ___

Answer 23

transcriptional activation domain (TAD)

RNA polymerase

Question 24

what is the highest level of structure for a single protein?

Answer 24

tertiary structure

Question 25

what is quaternary structure?

Answer 25

the interaction of multiple proteins into multi-protein complexes

Question 26

what is an example of quaternary structure?

Answer 26

hemoglobin protein in RBC's

Question 27

what does a hemoglobin consist of?

Answer 27

2 alpha and 2 beta proteins (4 proteins = tetramer)

Question 28

what does hemoglobin do?

Answer 28

carries oxygen from lungs to cells of body

Question 29

proper folding is critical to ___

Answer 29

protein function

Question 30

what are chaperone proteins?

Answer 30

enzymes that help proteins fold and/or refold provide an optimal folding environment for other proteins

Question 31

chaperones are critical to the proper ___ and ___ of most proteins

Answer 31

folding refolding

Question 32

___ are unable to function properly and are the cause of certain diseases

Answer 32

misfolded proteins

Question 33

what is cystic fibrosis?

Answer 33

disease in which abnormally thick mucus blocks airways, causing difficulty breathing

Question 34

what does the CFTR protein do?

Answer 34

regulates the thickness of mucus

Question 35

what does a mutation in the CFTR gene do?

Answer 35

blocks the interaction b/n the CFTR protein and its chaperone protein CFTR protein cannot fold properly and is unable to function

Question 36

describe relationship between Alzheimer's disease and protein folding

Answer 36

misfolded Tau proteins and beta-amyloid proteins form protein clumps (tangles and plaques) that collect inside and outside of neurons in the brain and destroy them

Question 37

protein misfolding is believed to be the primary cause of:

Answer 37

- PD - HD - CJD - many other degenerative and neurodegenerative disorders

Question 38

therapeutic strategies to reverse ___ or introduce ___ versions of the proteins are an active area of research

Answer 38

reverse misfolding introduce properly folded versions