BIOC12H3 Lecture Notes - Lecture 2: Hydrophile, Aromatic Amino Acids, Isoleucine

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4 Dec 2012

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Bioc12fall2012 lecture week 2: amino acids and peptide bonds (chapter 4) The acidic amino acids: at ph =7, they have a net negative charge so they are found in the form of aspartate and glutamate (-coo-) important for proteins that bind metal ions. Naming amino acids the alpha carbon is always next to the carboxyl group in systematic names though, the carboxyl group c is always number 1 and the adjacent c are numbered sequentially. The amino acids can be grouped by their side chains (r-group) can be grouped as aliphatic, aromatic, sulphur containing amino acids, and small amino acids. The aliphatic amino acids: (blue indicates the hydrophobic side chain) 5: 2 cysteins for a disulfur bond which can be broken by a reducing agent. Overlap of classification: c (h-h) refers to the reduced form of cysteine. C (s-s) indicates that there are 2 cys molecules linked together.

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For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. Proteins are ______________ built from amino acids, which each have an amino group and a _____________ group attached to the central _______________. There are twenty possible _______________ that differ in structure and are generally referred to as âR.â In solutions of neutral pH, amino acids are _______________, carrying both a positive and negative charge. When a protein is made, amino acids are linked together through _______________, which are formed by condensation reactions between the carboxyl end of the last amino acid and the ___________________ end of the next amino acid to be added to the growing chain.

a: amino	b: ionized	c: polypeptides
d: alpha-carbon	e: length	f: protein
g: carbon	h: noncovalent	i: R group
j: carboxyl	k: peptide bonds	l: side chains

m: hydroxide

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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

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BIOC12H3 Lecture Notes - Lecture 2: Hydrophile, Aromatic Amino Acids, Isoleucine

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