chapter 4: proteins

Question 1

amino acids are linked via

Answer 1

peptide bonds

Question 2

4 consistent protein groups? learn to draw

Answer 2

amine/amino terminus (NH3+)

carboxyl group (COO-)

alpha carbon (central)

H+ off of alpha carbon

aka BACKBONE

Question 3

___ gives structural and behavioral uniqueness

Answer 3

R

Question 4

synthesis of amino acids

Answer 4

hydrolysis/condensation reaction

NH3+ loses 2 H and carboxyl on another loses its O to form a water which comes off. The C then binds to the N.

Question 5

synthesis of amino acids starts at

Answer 5

amino terminus (a is first letter of alphabet)

Question 6

how is R positioned in a chain of amino acids

Answer 6

it alternates due to spacial reasons.

Question 7

types of noncovalent bonds that help proteins fold:

Answer 7

H bonds

electrostatic attractions (charged groups)

vaan der waals

hydrophobic interactions (not a bond but it does contribute)

understand all of these

Question 8

protein conformation

Answer 8

folded shape of protein

Question 9

denatured proteins can or cannot recover

Answer 9

can, under certain circumstances with the removal of the stressor to maintain lowest energy

Question 10

denaturation breaks ___ bonds

Answer 10

noncovalent

Question 11

prion diseases

Answer 11

misfolding proteins
understand basic process

Question 12

chaperone proteins

Answer 12

guide folding

some act as isolation chambers that fold a peptide

Question 13

levels of protein organization

Answer 13

primary: linear amino acid sequence

secondary: repeating folding patterns (alpha helices, beta pleated sheets)

tertiary: fully folded form

quaternary: protein-protein interaction

Question 14

alpha helices are a ____
The ___ group of every peptide bond is ___ bonded to what to form an alpha helix? How many amino acids away? ___ Groups are NOT involved in formation.

Answer 14

common helix folding pattern

amino group, hydrogen bonded, carboxyl
4 AAs away

R/Variable groups

Question 15

explain how an alpha helix can cross lipid bilayer.

Answer 15

Hydrophobic R-groups that stick out and have hydrophobic interactions with the lipid bilayer

Question 16

Intertwined alpha-helices form a ___

R groups are/aren’t involved?

Helices wrap in order to minimize?

Explain what would happen in a lipid bilayer building off of previous question

Answer 16

coiled-coil

ARE!

hydrophobic R-group exposure to aqueous environment.

Opposite would happen. Hydrophobic R-groups would be on outside since environment is not aqueous.

Question 17

How are beta sheets formed?

How are side chains projected in beta sheets?

Are side chains involved in beta sheet formation?

Two variations? Explain?

Can stack to form ____

Answer 17

Hydrogen bonds in different segments

alternatively above and below the strands

Not involved

Parallel: AA sequences point in same direction

Antiparallel: AA strands point in alternating directions

Amyloid Structure

Question 18

In the tertiary structure, proteins are composed of ____ domains.

separated by

can have how many?

Answer 18

functional

function

1 or more

Question 19

Many proteins are not active at ____ structure and assemble to form complex structures.

Dimer:

an actin filament is composed of

collagen molecules form

Answer 19

tertiary

two proteins bound together at the quaternary level

many identical actin molecules

triple helices

Question 20

Disulfide bonds? Exist in

Answer 20

help stabilize favored protein conformation

tertiary and quaternary structures

Question 21

scaffold proteins

Answer 21

concentrate interacting proteins in a cell to facilitate reaching of quaternary structure

Question 22

Feedback inhibition?

Draw it out!

Answer 22

regulates flow through biosynthetic pathways

A –> B –> C
|—-
X |
| |
Y |
| |
Z—-
B is first metabolite that makes Z. Z inhibits enzyme for its synthesis and controls its own cell concentration.

Question 23

Phosphorylation is a very common way to __ via ___

reversible?

alters ___ and therefore ___ of protein

what enzyme does this?

what enzyme does the reverse?

Answer 23

regulate protein activity, covalent addition of a phosphate anion to 1 or more amino acids.

yes.

conformation, function

protein kinase

protein phosphatase

Question 24

phosphorylation can activate or deactivate a protein?

Answer 24

either. Protein specific.

Question 25

Explain molecular switches.

Answer 25

Proteins can bind to activated carrier molecules (such as ATP) and the ACM can hydrolyze and act as a molecular switch. Example w/ GTP Binding Protein (GBP) GBP is active when bound with GTP Via hydrolysis, the GTP loses its P_i and the GBP is bound to a GDP and is inactive. The GDP SLOWLY dissociates and the GBP is still inactive. The GBP can bind to a new GTP and become active again

Question 26

covalent mods on AAs these require

Answer 26

methylation: addition of methyl acetylation: addition of acetate ubiquitination: addition of ubiquitin an enzyme since covalent

Question 27

most protein modifications require an ____ all protein regulation is ___

Answer 27

enzyme reversible