Levels of protein structure -- Lecture 16

Question 1

amino acid structure:

parts of amino acid:

Answer 1

central carbon

amino terminal end

carboxyl terminal end

R group

Question 2

amino acid structure:

what makes an amino acid special?

Answer 2

R group

Question 3

amino acid structure:

R group (what is it)

Answer 3

variable part of amino acids

give amino acid their individual electrochemical characteristics

Question 4

4 levels of protein structure (what are they?)

Answer 4

primary

secondary (and super secondary)

tertiary

quaternary

Question 5

4 levels of protein structure:

primary structure (what is it)

Answer 5

sequence of amino acids in a protein

Question 6

4 levels of protein structure:

primary structure:

what bonds hold the amino acids together?

what are the 2 ends of the peptide backbone?

Answer 6

peptide bonds

amino end (N-terminus) and carboxyl end (C-terminus)

Question 7

4 levels of protein structure:

primary structure:

are the R groups part of the peptide backbone?

Answer 7

no

Question 8

secondary structure:

what causes the protein folding?

Answer 8

folding caused by interactions w/in the peptide bond

Question 9

secondary structure:

what bonds are present in the secondary structure? How are they formed?

Answer 9

hydrogen bonds form b/n amino hydrogen and carboxyl oxygen atoms

Question 10

secondary structures:

what are they?

Answer 10

alpha-helix

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

Question 11

super secondary structure (how is it formed)

Answer 11

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

Question 12

super secondary structure:

alpha-helices and beta-pleated sheets combine in various ways to form ___

types of ___:

Answer 12

motifs

beta-barrel

beta-alpha-beta unit

Question 13

protein structure:

all ___ are formed by H-bonding w/in the peptide backbone

Answer 13

secondary structures

Question 14

protein structure:

all secondary structures are formed by ___ w/in the peptide backbone

Answer 14

H-bonding

Question 15

protein structure:

all secondary structures are formed by H-bonding w/in the ___

Answer 15

peptide backbone

Question 16

protein structure:

how do we refer to the entire 3D structure of a folded protein?

Answer 16

tertiary structure

Question 17

tertiary structure (what is it)

Answer 17

3D shape of the entire protein

Question 18

tertiary structure is stabilized by interactions b/n the ___ of the amino acids

Answer 18

R groups

Question 19

stabilizing tertiary structure:

electrostatic interactions:

Answer 19

H-bonds b/n R groups

ionic bonds b/n R groups

Question 20

stabilizing tertiary structure:

disulfide bridges:

Answer 20

cysteine have a sulfhydryl (SH) group

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

Question 21

stabilizing tertiary structure:

van der Waals interaction:

Answer 21

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

Question 22

stabilizing tertiary structure:

hydrophobic interactions:

Answer 22

hydrophobic (water fearing) R groups will fold to the interior of the protein to avoid contacting w/ aqueous environment

Question 23

protein domains:

domains are formed from a combination of ___ and ___ interactions

Answer 23

secondary and tertiary

Question 24

protein domains:

domains are the ___ of a protein

Answer 24

functional subunits

Question 25

protein domains:

1 protein can contain ___ domains

Answer 25

multiple

Question 26

examples of protein domains:

DNA binding domains (DBD):

Answer 26

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

Question 27

examples of protein domains:

activating transcription of a gene requires a ___ to attract/interact w/ RNA Polymerase

Answer 27

transcriptional activation domain (TAD)

Question 28

examples of protein domains:

activating transcription of a gene requires a transcriptional activation domain (TAD) to ___

Answer 28

attract/interact w/ RNA Polymerase

Question 29

examples of protein domains:

the function of a protein is defined by what ___ it has

Answer 29

domain

Question 30

the highest level of a structure for a single protein is ___ structure

Answer 30

tertiary

Question 31

quaternary structure (what is it)

Answer 31

the interaction of multiple proteins into multi-protein complexes

Question 32

quaternary structure:

example and what it consists of

Answer 32

hemoglobin protein in RBC’s

consists of 2 alpha and 2 beta proteins

4 proteins = tetramer

Question 33

quaternary structure:

hemoglobin function

Answer 33

carries oxygen from the lungs tot eh cells of the body

Question 34

___ is critical to protein function

Answer 34

proper folding

Question 35

proper folding is critical to protein function:

chaperone proteins (what they do)

Answer 35

enzymes that help proteins fold and/or refold

they provide an optimal folding environment for other proteins

critical to the proper folding and refolding of most proteins

Question 36

proper folding is critical to protein function:

misfiled proteins are unable to function properly and are the cause of ___

Answer 36

certain diseases

Question 37

cystic fibrosis (CF):

what is it

Answer 37

disease in which abnormally thick mucus blocks airways causing difficulty breathing

Question 38

cystic fibrosis (CF):

the CFTR protein regulates the ___

Answer 38

thickness of mucus

Question 39

cystic fibrosis (CF):

a mutation in the CFTR gene blocks the interaction b/n the ___ and its ___

CFTR ___ fold properly and is ___ to function

Answer 39

CFTR protein and its chaperone protein

cannot fold properly –> unable to function