Application/concepts for proteins

Question 1

What is protein shape determined by?

Answer 1

amino acid sequence

Question 2

What are individual amino acids held together by?

Answer 2

long, lineat chains bc amino acids can only be linked together in one way called covalent peptide bonds, also called polypeptides or polypeptide chains

Question 3

What does the polypeptide backbone include?

Answer 3

the core atoms and everything bonded to them, except for the side chains (R groups)

Question 4

Why doesn;t the polypeptide backbone include the side chains/r groups?

Answer 4

because the side chains/r groups are unique to each amino acid

Question 5

How many amino acid side chains are there and are they polar/nonpolar and acidic/basic?

Answer 5

there are 20, and there are some that are nonpolar, some polar, and some acidic, and some basic

Question 6

What do different combinations of R groups result in?

Answer 6

different 3D conformations of proteins

Question 7

What levels of organization do all proteins have?

Answer 7

1. primary structure
2. secondary structure
3. tertiary structure

Question 8

What provides energy for the tertiary structure?

Answer 8

deltaG

Question 9

What level of organization do some proteins have?

Answer 9

quaternary structure

Question 10

What is the main type of bond in the primary structure?

Answer 10

covalent

Question 11

What is the main type of bond in the secondary structure?

Answer 11

hydrogen

Question 12

What is the main type of bond in the tertiary structure?

Answer 12

hydrogen, ionic, hydrophobic interactions
-all noncovalent

Question 13

What is/are the main type of bonds in the quaternary structure?

Answer 13

hydrogen, ionic, hydrophobic interactions
-all non-covalent

Question 14

What do R group interactions allow for?

Answer 14

allow tertiary and quaternary structures to form

Question 15

What assumption can be made if you see disulfide bridges?

Answer 15

the structure can be classified as quaternary

Question 16

What are disulfide bonds?

Answer 16

covalent bonds that occur between -SH groups in cysteine residues

Question 17

What are disulfide bonds involved in, but not responsible for?

Answer 17

involved in reinforcing the 3D structure of proteins after the protein is folded due to non-covalent interactions
-NOT responsible for the actual bending and folding of the protein shape

Question 18

Where are disulfide bonds typically found?

Answer 18

not in sytosol, but often in proteins and protein complexes in the membrane,
-responsible for external conditions such as keratin in hair and nails

Question 19

Do all proteins contain functional domains?

Answer 19

No

Question 20

What is each domain associated with?

Answer 20

a specific function, such as Dna binding or protein binding

Question 21

What is a protein family?

Answer 21

proteins with similar sequenxes and 3D structure are grouped into protein families

Question 22

What do abnormal proteins, often prions, do?

Answer 22

prevent neuron signal from being sent to other neurons

Question 23

What are covalent modifications?

Answer 23

use covalent bond to attach a small functional group to the protein in order to control the activity, function and localization

Question 24

What is an example of a covalent modification?

Answer 24

phosphorylation, which involves transfer of a phosphate group from ATP to a hydroxyl group of an amino acid
-phosphates are added by kinases (protein type)
-phosphates are removed by posphatasas

Question 25

What do cavalent modifications affect?

Answer 25

interactions with other proteins and localization in the xell

Question 26

What is an important chacteristic of phosphate groups?

Answer 26

they have a strong negative charge

Question 27

What is and occurs during Acetylation?

Answer 27

it is a type of protein modification that neutralizes histone charge, loosens negatively charged DNA, and ultimately turns offf transcription

Question 28

What are the 4 ateps to protein purification?

Answer 28

aside from a LOT of pure protein, 1. break cells and tissues 2. separate proteins 3. separate protein of interedt 4. analyze protein

Question 29

What are 4 ways to breaking cells and tissues

Answer 29

1. ultrasonic sound waves 2. chemical breakdown of membranes 3. high pressure filtation 4. mortar and pestle

Question 30

What should be the end product of breaking cells and tissues for protein purification?

Answer 30

end product should be the contents of the cell, with organelles intact

Question 31

What is an example of how to separate the proteins in protein purification?

Answer 31

centrifugation, which results in the spearation of larger, more dense components from smaller, less dense components

Question 32

How can we separate the protein of interest in protein purification?

Answer 32

1. Gel Electrophoresis 2. Chromatography 3. Ion Exchange Chromatography 4. Affinity Chromatography

Question 33

What does gel electrophoresis result in?

Answer 33

western blot where the direction and speed at which the proteins move depends on their size and charge

Question 34

What are the 2 different types of Ion Exchange Chromatography and what is it often used in?

Answer 34

-often used in purification and quality control 1. cation exchange uses negatively charged resins or beads 2. anion exchange uses positively charged beads

Question 35

What is the function of antibodies?

Answer 35

function to recognize and respond to foreign molecules -bind tightly to targets called antigens

Question 36

Is the binding of Antibodies to antigens specific?

Answer 36

there is a different antibody for antigen, so they bind with very high specificity

Question 37

How does affinity chromatography work?

Answer 37

matrix beads are coated in either antibody specific to the desired protein - the desired protein then binds to the bead, while the rest of the impurities flow through the column -later, wash off the desired protein by changing pH or using high salt concentration to disrupt the interactions

Question 38

What is helpful in analyzing proteins?

Answer 38

antibodies because the high specificty they have for their antigen can be used to visualize distribution of or presence of specific molecules in a celll

Question 39

What is the biggest predictor of structure and function?

Answer 39

protein sequence

Question 40

What method can be used to determine protein sequence?

Answer 40

mass spectrometry

Question 41

How can amino acid sequence help in determining the protein sequence?

Answer 41

can be used to determine the possible folding, presence of functional domains, and comparison to other known proteins

Question 42

What are the only 3 ways to truly know the folding pattern of a protein structure?

Answer 42

1. cryo EM 2. X-ray crystallography 3. NMR (nuclear magnetic resonance) spectroscopy