2.4 & 2.5 (Topic 2)

Question 1

Describe polypeptide chain formation in terms of the formation of peptide bonds and condensation reactions.

Answer 1

Primary structure
- Order of amino acids
- Peptide bonds
Secondary structure
- Structure of amino acid
- Alpha helix
- Beta sheet
- Based on base group of amino acid
- Hydrogen bonds
Tertiary Structure
- Alpha helix and beta sheets fold into a structure based on R group
- Polar interactions, ionic interactions, hydrogen bond
Quaternary Structure
- 2+ polypeptide chains associate to form a single protein
- Proteins link together to carry out a single function

Question 2

Determine the number of peptide bonds given the number of amino acids in a polypeptide.

Answer 2

• just take the number of amino acids and minus 1

- ex. a protein with 22 amino acids will have 21 peptide bonds

Question 3

Define dipeptide and polypeptide.

Answer 3

dipeptide: molecule consisting of two amino acids joined by a single peptide bond
polypeptide: molecule consisting of two or more amino acids joined by peptide bonds

Question 4

State the number of amino acids used by living organisms to make polypeptides.

Answer 4

20

Question 5

Given an image of an amino acid, classify the amino acid chemical properties based on R group properties.

Answer 5

can be nonpolar, polar (contains highly electronegative atoms), or ionic (positive or negative charge)

Question 6

Calculate the possible number of amino acid sequences given n number of amino acids.

Answer 6

20^n where n is the number of amino acids

Question 7

Outline the relationship between genes and polypeptides.

Answer 7

gene sequences are transcribed into mRNA, which are translated to link amino acids together

Question 8

Contrast the structure of globular proteins with the structure of fibrous proteins.

Answer 8

globular proteins have a compact and rounded structure

fibrous proteins are composed of long and narrow strands

Question 9

Contrast the generalized function of globular proteins with generalized function of fibrous proteins.

Answer 9

globular proteins have functional roles

fibrous proteins have structural roles

Question 10

Describe the function of enzyme proteins.

Answer 10

• help speed up metabolism/chemical reactions in our bodies

- catalyst

Question 11

Describe the function of hormone proteins.

Answer 11

hormones are chemical messengers. They create a response in living things. Not all hormones are proteins, some are.

Question 12

Describe the function of immunoglobulin proteins.

Answer 12

used in immune response

Question 13

Describe the function of pigment proteins.

Answer 13

Used in your eyes to detect light and color

Question 14

Describe the function of structural proteins

Answer 14

structural proteins maintain cell shape, skin to a skeleton, and they compose structural elements in connective tissues like cartilage and bone invertebrates

Question 15

define proteome

Answer 15

entire complement of proteins that is or can be expressed by a cell, tissue, or organism.

Question 16

Contrast proteome with genome.

Answer 16

The genome is the sum total of genetic information encoded in the organism, while the proteome is the outcome of the interaction between environment and the genome

Question 17

define denaturation

Answer 17

• structural change in a protein that results in the loss (usually permanent) of its biological properties
• Because the way a protein folds determines its function, any change or abrogation of the tertiary structure will alter its activity
• can usually be caused by two key conditions – temperature and pH

Question 18

Outline the effect of heat and pH on protein structure.

Answer 18

heat

• High levels of thermal energy may disrupt the hydrogen bonds that hold the protein together
• As these bonds are broken, the protein will begin to unfold and lose its capacity to function as intended
• Temperatures at which proteins denature may vary, but most human proteins function optimally at body temperature (~37ºC)

pH

• Amino acids are zwitterions, neutral molecules possessing both negatively (COO–) and positively (NH3+) charged regions
• Changing the pH will alter the charge of the protein, which in turn will alter protein solubility and overall shape
• All proteins have an optimal pH which is dependent on the environment in which it functions (e.g. stomach proteins require an acidic environment to operate, whereas blood proteins function best at a neutral pH)

Question 19

State the relationship between enzyme substrate and enzyme active site.

Answer 19

A substrate enters the active site of the enzyme. This forms the enzyme-substrate complex. The reaction then occurs, converting the substrate into products and forming an enzyme-products complex. The products then leave the active site of the enzyme.

Question 20

Explain the relationship between enzyme structure and enzyme specificity, including the role of the active site.​

Answer 20

• The relationship between enzyme structure and enzyme specificity is that the specificity of an enzyme results from its shape, which is a consequence of its amino acid sequence.
• The shape of an enzyme’s active site corresponds to the shape of the substrate it interacts with, like a lock and key

Question 21

Outline the three stages of enzyme activity

Answer 21

1. separate enzyme and substrate
2. enzyme - substrate complex
3. enzyme and product

Question 22

Explain the role of random collisions in the binding of the substrate with the enzyme active site.

Answer 22

Collisions between substrate molecules and the active site occur because of random movements of both substrate and enzyme. Successful collisions are ones in which the substrate and active site are correctly aligned to allow binding to take place.

Question 23

Describe the induced fit model of enzyme action.​

Answer 23

• According to the induced fit model, the enzyme’s active site is not a completely rigid fit for the substrate
• instead, the active site will undergo a conformational change when exposed to a substrate to improve binding

Question 24

Explain how temperature affects the rate of enzyme activity.

Answer 24

As with many chemical reactions, the rate of an enzyme-catalysed reaction increases as the temperature increases. However, at high temperatures the rate decreases again because the enzyme becomes denatured and can no longer function.

Question 25

Explain how pH affects the rate of enzyme activity.

Answer 25

• Changing the pH will alter the charge of the enzyme, which in turn will alter protein solubility and overall shape
• Changing the shape or charge of the active site will diminish its ability to bind the substrate, abrogating enzyme function
• Enzymes have an optimal pH (may differ between enzymes) and moving outside this range diminishes enzyme activity

Question 26

Identify the optimum temperature or pH for enzyme activity on a graph.

Answer 26

peak of graph

Question 27

Explain how substrate concentration affects the rate of enzyme activity.

Answer 27

Initially, an increase in substrate concentration leads to an increase in the rate of an enzyme-catalyzed reaction. As the enzyme molecules become saturated with substrate, this increase in reaction rate levels off. The enzymes can only work so fast.

Question 28

State the effect of denaturation on enzyme structure and function.

Answer 28

The enzyme, including its active site, will change shape and the substrate no longer fit. The rate of reaction will be affected, or the reaction will stop.