Biology 1001A Lecture Notes - Lecture 3: Disulfide, Actin, Protein Folding

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12 Mar 2014

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Proteins are the major structural and functional molecules of the cell. Independent studies outcomes: basic structure of an amino acid and what are the different classes of amino acids. Amino acids share a similar structure with a central carbon atom attached to an amino group (-nh2), a carboxyl group (-cooh), and a hydrogen atom. The remaining bond of the central carbon is to 1 of 20 different side groups represented by the r (the side chain). Differences in the side groups give the amino acids their individual properties. Positively charged (basic ) polar amino acids: chemistry of the peptide bond and how it is formed. A peptide bond is formed by a dehydration synthesis reaction between nh2 group of one amino acid and the cooh group of a second. An amino acid chain always has an nh2 groups at one end, called the n-terminal end, and a. Cooh group at the other end, called the c-terminal end.

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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. Compounds that are made of carbon, hydrogen, oxygen, nitrogenand/or sulfur are:

a. ionic compounds

b. molecular compounds

2. A peptide bond is a...

a. covalent bond

b. intermolecular force

3. In chemistry, what is an R group?

a. a real group

b. a free radical

c. Argon

d. a functional group

4. A hydrogen bond is a type of

a. dispersion force

b. dipole-dipole force

c. covalent bond

d. ion-dipole force

5. In general chemistry, what do weak acids do?

a. accept a proton

b. donate a proton

6. In general chemistry, what do weak bases do?

a. accept a proton

b. donate a proton

7. What happens to a weak acid when it donates a proton?

a. it becomes positively charged

b. it becomes negatively charged

c. it become neutral

8. what happens to a weak base when it accepts a proton?

a. it becomes positvely charged

b. it becomes negatively charged

c. it becomes neutral

9. R groups that cluster in the center of proteins or are foundadjacent to the hydrocarbon chains of membrane phospholipids tendto have R groups with alkyl groups, such as (âCH₃) or(âCH₂âCH₃). Using your General Chemistryknowledge, what bond, force or interaction would form between thesegroups?

a. chemical bond

b. hydrogen bond

c. van der waals interaction

d. covalent bond

10. A amino acid has an R group containing an amide group(âCONH₂), and another amino acid has an R groupcontaining a hydroxyl group (âOH). Using your General Chemistryknowledge, what bond or force would form between these groups?

a. chemical bond

b. hydrogen bond

c. van der waals interaction

d. covalent bond

tansea-lion662

1. What is an organic molecule?

2.Name three hydrocarbons and be able to draw their structural formulas.

3. What is an isomer? List and describe the three types (structural, geometric, and enantiomers).

4. Be able to recognize and describe the properties of these functional groups: aldehyde, ketone, hydroxyl, sulfhydryl, carboxyl, amino, and phosphate groups.

5. What is a monosaccharide? Give two examples of these molecules and their functions.

6. Describe these chemical reactions: dehydration synthesis (condensation reaction) and hydrolysis (rehydration).

7. What is a disaccharide? List two and give their functions.

8. What is a polysaccharide? List two storage forms and two structural forms. How are they formed and what is their specific function?

9. How do the pancreatic hormones insulin and glucagon regulate blood sugar levels?

10. What is molting and why is it necessary in certain animals?

11. What four molecules are bonded together to form a triglyceride or fat? Why are fats nonpolar? What are some functions of fats as well as other lipids such as oils and waxes?

12. How do saturated and unsaturated fats differ? Discuss bonding patterns and possible sources of these fats. Which type is healthier for you? Why?

13. Why do animals store most of their excess glucose as fats or oils rather than as glycogen or protein? Give two reasons.

14. What are phospholipids? Identify parts of the phospholipid bilayer that are hydrophobic or hydrophilic? What important cell structure do these molecules help create?

15. Describe the structure of a steroid. How is cholesterol used in beneficial ways in your body?

16. What are LDLs and HDLs? Which is considered good or bad cholesterol? What condition could result from high blood pressure?

17. What are four ways to either reduce high blood cholesterol or maintain a safe level?

18. What is the composition of an amino acid? Why would they be considered nonpolar, polar, acidic, or basic?

19. Define dipeptides and polypeptides.

20. Describe the primary structure of a protein. What type of bonding creates it?

21. What is the secondary structure of a protein? Name two types of secondary structure and indicate what type of bonding holds them together. List three fibrous proteins.

22. What is the tertiary structure of a protein? What types of bonds or chemical interactions allow a protein to maintain this structure? List three globular proteins.

23. What is the quaternary structure of a protein? Describe a hemoglobin molecule.

24. What are the subunits of nucleic acids and what is their composition? How are these subunits bonded together? What is DNS's basic shape?

25. List three differences between DNA and RNA.

Biology 1001A Lecture Notes - Lecture 3: Disulfide, Actin, Protein Folding

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