Unit 1: Protein Structure

Question 1

What are the roles of protein in cellular activities?

Answer 1

• some proteins aggregate to form relatively stiff filaments that help define the cell’s shape and hold organelles in position
• some span the cell membrane and form channels or pores through which ions and small molecules can move
• others are enzymes that catalyze the thousands of chemical reactions needed to maintain life
• some are signalling proteins that enable cells to coordinate their internal activities or to communicate with other cells

Question 2

What is the amino group of an amino acid?

Answer 2

• NH2

- NH3+in physiological pH

Question 3

What is the carboxyl group of an amino acid?

Answer 3

• COOH

- COO- in physiological pH

Question 4

What is the significance of the R group in an amino acid? (2)

Answer 4

• R group is chemically diverse and are grouped according to their properties (particularly whether they are hydrophobic or hydrophilic, or have special characteristics that might affect the protein structure)
• properties strongly influence how polypeptides fold and affect the 3-dimensional shape of the protein

Question 5

Characteristics of hydrophobic amino acids (3)

Answer 5

• hydrophobic amino acids do not readily interact with water or form hydrogen bonds, most hydrophobic R groups are composed of hydrocarbon chains or uncharged carbon rings
• water cells tend to form hydrogen bonds with each other instead of R groups making them aggregate with each other, aggregation is stabilized by weak ID-ID interactions
• most hydrophobic amino acids tend to be buried in the interior of folded proteins, where they do not interact with water

Question 6

Characteristics of polar R groups (2)

Answer 6

• have permanent charge separation, where one end of the R group is slightly more negatively charged than the other
• tend to form hydrogen bonds with each other or with water molecules

Question 7

Characteristics of basic and acidic R groups (3)

Answer 7

• R groups are typically charged and are strongly polar, they usually appear on the outside surface of the folded molecule
• At the pH of the cell, R groups if basic amino acids gain a proton and becomes positively charged, and the acidic amino acid lose a proton and become negatively charged
• charged groups can form ionic bonds with each other and with other charged molecules in the environment

Question 8

Characteristics of glycine R group (3)

Answer 8

• glycine molecule is asymmetric
• glycine is nonpolar and small enough to tuck into spaces where other r groups would not fit
• small size allows freer rotation around the C–N bond as it doesn’t affect the rotation of neighbouring amino acids: increases flexibility of polypeptide backbone which can be important for folding

Question 9

Characteristics of proline R group

Answer 9

• linkage back to amino group creates a kink or bend in the polypeptide chain which restricts the rotation of the C–N bond: imposes constraints on protein folding in its vicinity

Question 10

Characteristics of cysteine R group (2)

Answer 10

• when 2 cysteine side chains in the same or different polypeptides come into proximity, they can react to form and S–S disulfide bond, which covalently joins the side chains
• bonds are stronger than ionic interactions of other pairs of amino acids: forms cross-bridges that can connect different parts of the same protein or even different proteins, contributes to the overall structure of single proteins or combinations of proteins

Question 11

peptide bond

Answer 11

• covalent bond that links the carbon atom in the carboxyl group of one amino acid to the nitrogen atom in the amino group if another amino acid
• a water molecule is released and the R groups of each amino acid point in different directions

Question 12

Which bond is unable to rotate freely between 2 amino acids?

Answer 12

• the electrons of the peptide bond are more attracted to the C = O group than the NH group because of greater electronegativity of the oxygen atom
• peptide bond has come characteristics of a double bond as a result and is shorter than a single bond: it is not free to rotate like a single bond

Question 13

amino acid residues

Answer 13

• any of the amino acids that is incorporated into a protein

Question 14

amino end

Answer 14

• end of a polypeptide chain that has a free amino group

Question 15

carboxyl end

Answer 15

• end of polypeptide that has a free carboxyl group

Question 16

primary structure

Answer 16

• the sequence of amino acids in a protein

Question 17

secondary structure

Answer 17

• structure formed between stretches of amino acids in a protein

Question 18

tertiary structure

Answer 18

• overall the 3-dimensional shape of a protein, formed by interactions between secondary structures
• its structure determines function

Question 19

quaternary structure

Answer 19

• structure that results from the interactions of several polypeptide chains

Question 20

How does a proteins 3-dimensional shape determine roles of proteins? (4)

Answer 20

• some proteins contain positive or negative holes that can trap small molecules
• surfaces that can bind with anther protein or a sequence of nucleotides in DNA or RNA
• some form rigid rods for structural support
• some keep hydrophobic side chains away from water molecules by inserting them into the cell membrane

Question 21

How are secondary structures formed?

Answer 21

• hydrogen bonds can form between the carbonyl group in one peptide bond and the amide group in another, allowing localized regions of the polypeptide to fold

Question 22

alpha helix (3)

Answer 22

• one of the two principle types of secondary structures found in proteins, stabilized by hydrogen bonding that form along each amino acid’s carbonyl group and the amide group four amino acids apart
• backbone is twisted tightly in a right-handed coil
• R groups project outwards from the alpha helix, they largely determine where the alpha helix is positioned in the folded protein and how it might interact with other molecules

Question 23

beta sheet (3)

Answer 23

• one of the two principle types of secondary structures found in proteins, stabilized by hydrogen bonding along a polypeptide backbone
• polypeptide folds back and forth on itself, forming a pleated sheet this is stabilized by hydrogen bonds between carbonyl groups in one chain and amide groups in the other chain across the way
• R groups project alternately above and below the plane of the B sheet

Question 24

How are tertiary structures formed? (3)

Answer 24

• defined largely by interactions between the amino acid R groups (formation of secondary structures rely on interactions in the polypeptide backbone and are relatively independent of R groups)
• determined by spatial distribution of hydrophilic and hydrophobic R groups along the molecule as well as different types of chemical bonds and interactions (ionic, hydrogen, ID-ID) that form between R groups
• structures usually include loops and turns in the backbone that allow R group to sit near each other in space and for bonds to form

Question 25

denature (4)

Answer 25

• unfolding of proteins by chemical treatment (high pH or certain solvents) or high temperature
• separation of paired, complementary strands of nucleic acid
• under these conditions, proteins lose their functional activity
• function and structure can be recovered in some cases after environment is removed
• only breaks apart the NON-COVALENT interactions

Question 26

What would happen if a random amino acid replaced another in a functioning protein

Answer 26

• if the amino acid prevents folding, the protein will often become inactive and will not function properly

Question 27

What are examples of quaternary structures(2)

Answer 27

• hemoglobin: made up of 4 different subunits

- protein produced by HIV consists of 2 identical polypeptide subunits

Question 28

Summarize functions of proteins (7)

Answer 28

• regulation
• transport
• signalling
• force generation
• catalysis
• structure
• transcription and translation

Question 29

Describe the process of protein folding within cells (5)

Answer 29

• the process is spontaneous
• it is energetically favourable
• free energy charge < 0 (negative)
• folded proteins are more stable
• this happens due to the hydrophobic effect

Question 30

In proteins, what are 4 things you need to know?

Answer 30

1. the level of non-covalent interactions and bond strength
2. the characteristics of R-groups of the amino acid
3. recognize of the molecular group is polar, nonpolar, hydrophilic, hydrophobic, or charged
4. understand types of non-covalent interactions the amino acid R-groups make

Question 31

enzyme

Answer 31

protein that performs a biochemical reaction

Question 32

Why is a protein being too stable (stronger interactions) an issue?

Answer 32

• proteins and enzymes often need to be flexible and change shape as a part of their function
• required breaking some non-covalent interactions and making new ones

Question 33

Where are hydrophobic amino acids usually found

Answer 33

• usually found in the interior of a protein due to the hydrophobic effect, although NOT all interior amino acids are hydrophobic
• decrease in non-polar group decreases, but this is lest significant than the increase in entropy of the water

Question 34

How do interactions within a protein affect denaturation?

Answer 34

• stronger interactions = more stable protein and is harder to denature