BIOLOGY 151 Chapter Notes - Chapter 6: Groes, Amine, Peptide

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PROTEIN FOLDING AND TRAFFICKING

PROTEIN STRUCTURE

● Consists of an alpha (central) carbon atom linked to an amino group, carboxyl group, a

hydrogen atom, and a variable component aka a side chain

WHAT ARE PROTEINS MADE OF?

● PRIMARY STRUCTURE: linear sequence of amino acids within a protein

● Largest group of amino acids have nonpolar side chains; these side chains can bond with

one another to hold a length of protein in a certain shape

● Charged amino acid side chains can form ionic bonds, and polar amino acids are capable

of forming hydrogen bonds

● Cysteines are the only amino acids able to form covalent bonds

● The primary structure of a protein drives the folding and intramolecular bonding of the

linear amino acid chain which determines their 3D shape

● ALPHA HELICES AND BETA SHEETS: these stable folding patterns make up the

SECONDARY STRUCTURE of a protein

● POLYPEPTIDE: constitutes the TERTIARY STRUCTURE of a protein

● QUATERNARY STRUCTURE: macromolecules with multiple polypeptide chains or

subunits

● The final shape is the most energetically favorable one

● Chemical forces between a protein and its immediate environment contribute to protein

shape and stability

● Atoms within these proteins remain capable of making small movements

● X-RAY CRYSTALLOGRAPHY: common way to study protein structures; solid crystals

of purified protein are placed in an X-ray beam and the pattern of deflected X rays is used

to predict the positions of the thousands of atoms within the protein crystal

HOW DO PROTEINS ARRIVE AT THEIR FINALS SHAPES?

● CHAPERONE PROTEINS: cells rely on this to prevent these inappropriate associations

with unintended folding partners

○ They surround a protein during the folding process, sequestering the protein until

folding is complete

○ Abundant in cells

○ Use energy from ATP to bind and release polypeptides as they go through the

folding process

○ Assist in the refolding of proteins in cells

○ Molecules of a second chaperone, GroES then form a lid over the chamber

WHAT ARE PROTEIN FAMILIES?

● Proteins bind to other molecules in order to complete their tasks and the function of a

protein depends on the way its exposed surfaces interact with those molecules

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Document Summary

Consists of an alpha (central) carbon atom linked to an amino group, carboxyl group, a hydrogen atom, and a variable component aka a side chain. Primary structure: linear sequence of amino acids within a protein. Largest group of amino acids have nonpolar side chains; these side chains can bond with one another to hold a length of protein in a certain shape. Charged amino acid side chains can form ionic bonds, and polar amino acids are capable of forming hydrogen bonds. Cysteines are the only amino acids able to form covalent bonds. The primary structure of a protein drives the folding and intramolecular bonding of the linear amino acid chain which determines their 3d shape. Alpha helices and beta sheets: these stable folding patterns make up the. Polypeptide: constitutes the tertiary structure of a protein. Quaternary structure: macromolecules with multiple polypeptide chains or subunits. The final shape is the most energetically favorable one.

Related Questions

The sequence of amino acids is considered to be the ________ structure of a protein.

Select one:

a. secondary

b. tertiary

c. quaternary

d. primary

The pattern the backbone folds, for example alpha-helix or beta pleated sheet, is the ________ structure of a protein.

Select one:

a. quaternary

b. secondary

c. tertiary

d. primary

Which type of forces stabilizes the primary structure of a protein?

Select one:

a. Salt bridges

b. Hydrogen bonding between the carbonyl group and amino group

c. Dipole-dipole

d. Peptide bonds

The interaction of the side chains on the amino acids, for example hydrophobic attractions, is the ________ structure of a protein.

Select one:

a. quaternary

b. secondary

c. tertiary

d. primary

violetyellowjacket662

Protein Structure

a.Different function of proteins and examples:

b. Protein building blocks:

1. atomic composition of building block:

2. "parts" or "functional groups" of the building block:

c. Importance of side chain (R group):

d. Hydrophobic amino acids characteristics:

e. Hydrophilic amino acids characteristics:

f. Charged amino acids characteristics

Copy and complete the table below regarding the characteristics and which groups in the polypeptide interact together at each structural level of the protein.

	characteristics	groups interacting
Primary structure
Secondary structure
Tertiary structure
Quartenary structure

Value: 2

Choose the correct statement(s). You may choose more than one answer.

[mark all correct answers]
a. Proteins are the building blocks of amino acids.

b. Enzymes are a type of protein.

c. Quartenary structure consists of two or more polypeptide chains interacting.

d. Amino acids are made of carbon, hydrogen, nitrogen and phosphorus.

e. The primary structure of a protein is formed due to the interaction of side groups.

Value: 3

Put the following statements regarding the structural levels of a protein formation in the correct order.

Below is a sequence of events. Place them in the order they should occur, number 1 being the first item. Select the step number from the drop down next to each item.

Items to order:

1. Individual amino acids are bonded together via peptide bonds.

2. Two or more polypeptide chains interact via bonds.

3. Hydrogen bonds form between neighboring amino acids within a polypeptide chain allowing the chain to coil or form pleated sheets.

4. Side groups (R) of the individual amino acids interact with each other allowing the protein to assume its three dimensional shape.

Value:4

Put the following statements regarding the structural levels of a protein formation in the correct order

Individual amino acids are bonded together via peptide bonds.	1 2 3 4
Two or more polypeptide chains interact via bonds.	1 2 3 4
Hydrogen bonds form between neighboring amino acids within a polypeptide chain allowing the chain to coil or form pleated sheets.	1 2 3 4
Side groups (R) of the individual amino acids interact with each other allowing the protein to assume its three dimensional shape.	1 2 3 4

Value: 5

Hydrophobic amino acids will be found _______________.

a. In the interior (inner core) of a protein, away from the watery environment.

b. in the interior of a plasma membrane.

c. Both A and B

d. Neither

Value: 6

A protein's function is defined by ____________.

a. enzymatic reactions

b. it's shape.

c. chain of nucleotides.

d. the presence of carbon and hydrogen.

Value: 7

Which of the following is NOT considered a protein function?

a. transport of substances across membrane

b. enzymatic reactions

c. provides structural support

d. carries genetic information

1. Amino acid changes in the primary structure of the protein arenot capable of causing changes in the
overall shape of a protein.
a.) True
b.) False

2. An alpha helix:
a.) is destabilized by the amino acid alanine
b.) can only form by hydrogen bonding between different polypeptidechains
c.) can only form when cysteines form disulfide bridges within thisstructure
d.) all of the above
e.) none of the above

3. What will likely happen if two aspartates at pH 5 are next toeach other in a polypeptide chain?
a.) The side chains of these amino acids will be uncharged andthere will be no effect.
b.) The side chains of these amino acids will be charged and theywill attract each other.
c.) The side chains of these amino acids will be charged and theywill repel each other.
d.) Not enough information is given to determine the effect.

4. Consider the amino acid phenylalanine. Which of the followingbest describes where you predict this
amino acid would be found?
a.) This amino acid is hydrophobic and would be on the surface of aprotein that is in the middle
of a membrane.
b.) This amino acid is hydrophilic and would be on the surface of aprotein that is in the middle
of a membrane.
c.) This amino acid is hydrophobic and would be in the interior ofa protein that is in the middle
of a membrane.
d.) This amino acid is hydrophilic and would be in the interior ofa protein that is in the middle of
a membrane.
e.) Not enough information is given to determine.

5. The difference between fetal and adult hemoglobin with regard tooxygen binding occurs because fetal
hemoglobin has an amino acid substitution in one of its chains thatresults in a histidine being replaced by a
serine.
a.) True
b.) False

BIOLOGY 151 Chapter Notes - Chapter 6: Groes, Amine, Peptide

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