Ch 1.7 Proteins

Question 1

What are examples that proteins do?

Answer 1

• transcription/translation, regulation, transport, structure, catalyst, signaling etc.

Question 2

What are the 4 levels of proteins?

Answer 2

1. Primary
2. Secondary
3. Tertiary
4. Quaternary

Question 3

What are the parts of an amino acid?

Answer 3

• alpha carbon
• R group
• amino group
• carboxyl group

Question 4

What’s two amino acids together?

Answer 4

Amino acyl residue

Question 5

What are 3 types of side chains in amino acids?

Answer 5

• Hydrophobic
• Hydrophilic polar
• hydrophilic charged

Question 6

What is primary structure?

Answer 6

• liner sequence amino acids encoded by gene that was transcribed to mRNA
• the sequence will determine the folding and the function

Question 7

Why are proteins flexible

Answer 7

• many bonds can rotate

Question 8

Directionality proteins?

Answer 8

• N - C

- numbered 1 at N

Question 9

What determines the structure in proteins?

Answer 9

The R group

Question 10

What is the secondary structure?

Answer 10

• alpha helix ( forms h- bonds along the backbone)

- beta pleaded sheet ( H- bonds between areas peptide backbone)

Question 11

What is tertiary structure?

Answer 11

• determines by non covalent interactions of R- group
• a and B folds up
• stabilized by side chain interactions (non- covalent and disulfide) and interactions side chain backbone

Question 12

Quaternary structure?

Answer 12

2+ tertiary structure combined

Question 13

Alpha vs Beta secondary structure ( 6 points)

Answer 13

Alpha: right hand coil, h bonds formed in chain, bonds between NH and CO, R-group orientated outside, can be single chain, 1 type

Beta: paper fan like structure, formed by linking 2+ beta by h bonds, bonds between neighboring NH CO, R both in and outside, can’t exist as single B strand, parallel, anti-parallel or mixed

Question 14

Integral protein?

Answer 14

Through bilayer

Question 15

Peripheral proteins?

And why can they be removed with salts?

Answer 15

On each side bilayer

Cuz salt disrupts covalent bonds

Question 16

Where are the hydrophobic and hydrophilic R groups located in a protein?

Exceptions?

Answer 16

Hydrophobic inside ( not all inside hydrophobic)

Hydrophilic outside

Some exceptions like when phobic used ID- ID with other subunit in cellar

Interior hydrophilic can be used active site

Question 17

What is the enzyme active site?

Answer 17

Where the reactants go

Then proteins folds up to bring active site amino acids together

Question 18

What does a catalyst do?

Answer 18

Speed up the reaction without changing the thermodynamics

Question 19

Transition state in enzyme reaction?

Answer 19

Intermediate state between area tans and products

Question 20

What do enzymes do?

Answer 20

• Make tradition state more stable

- less activation energy

Question 21

What are the catalyst steps?

Answer 21

1. Initiation: enzyme binds substrate forming enzyme substance complex
2. Transition state stabilization: makes it go to transition state
3. Termination : reaction finishes and enzyme goes back normal

Question 22

Confirmation change in enzyme réactions?

Answer 22

When a substrate binds to an enzyme the shape of the enzyme changes

Helps enzyme bind transition state better = more stable transition state

Question 23

How are enzymes regulated?

Answer 23

Many allosterically: a molecules different from substrate binds somewhere other active site protein: trigger conformation change

Question 24

What is denaturation and how do you do it?

Answer 24

• unfolding protien
• high temp, pH, sovelnts

Some can refile but some can’t

Question 25

How can denaturation be used for scientist?

Answer 25

Mesure the stability of the protien