BIOL 1000 Lecture Notes - Lecture 4: Amino Acid, Disulfide, Thiol

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pucemole333

9 Nov 2018

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The side chains of these amino acids are hydrophobic and are unable to form electrostatic bonds or interact with water. Amino acids including this categories are, alanine, valine, leucine, isoleucine, tryptophan, phenylalanine, and methionine. The side chains of the nonpolar amino acids generally lack oxygen and nitrogen. The size and shape allows them to tightly pack into a particular space within the core of a protein, associating with one another, as a result of the van der waals forces and hydrophobic interactions. Other amino acids such as glycine, proline and cysteine, have unique properties that are different from the other amino acids. For instance, the side chains of glycine consists of only a hydrogen atom which makes an important amino acid, solely for this reason. Glycine is also very flexible than other amino acids and allows part of the backbone to move or form a hinge.

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Amino Acid	M.W. g/mol	pK_a for side chain
Alanine	89.1
Arginine	174.2	12.48
Asparagine	132.1
Aspartate	133.1	3.90
Cysteine	121.1	8.37
Glycine	75.0
Glutamate	147.1	4.07
Glutamine	146.1
Histidine	155.1	6.04
Isoleucine	131.2
Leucine	131.2
Lysine	146.2	10.54
Methionine	149.2
Proline	115.1
Phenylalanine	165.2
Serine	105.1
Threonine	119.1
Tryptophan	204.2
Tyrosine	181.2	10.46
Valine	117.1

Take a look at your pK_a table for the amino acids. It turns out that when these side chains are in a protein, they can have very different pK_a values. Explain the following observations:

a. In the enzyme medium chain acyl-CoA dehydrogenase (b-oxidation of fatty acids), E376 has a measured pK_a ~ 8.0. It is found in a very hydrophobic environment. What could account for it elevated pK_a?

b. For the enzyme aconitase (Krebbâs Cycle), a catalytic serine is known to have a pK_a ~ 8. What kind of factors could account for this decrease in pK_a?

lilacbee20

Type molecular weight Number in lysozyme

Alanine 89 12

Arginine 174 11

Asparagine 132 13

Aspartic acid 133 8

Cysteine 121 8

Glutamic acid 147 2

Glutamine 146 3

Glycine 75 12

Histidine 155 1

Isoleucine 131 6

Leucine 131 8

Lysine 146 6

Methionine 149 2

Phenylalanine 165 3

Proline 115 2

Serine 105 10

Threonine 119 7

Tryptophan 204 6

Tyrosine 181 3

Valine 117 6

1. The sequence of amino acids of the enzyme lysozyme is known. Below is a list of amino acids

and the number of each in the lysozyme molecule

Questions:

a. What is the average molecular weight of the 20 amino acids?

b. What is the molecular weight of lysozyme?

c. What is the average molecular weight of the amino acids in lysozome?

d. How many S-S bonds are possible in lysozyme?

(hint: look at the structures of each amino acid, and figure out which of these have sulphurs

that are FREE to form bonds).

e. Is the net charge on lysozyme positive or negative?

jadechinchilla39

Question 9

Codominance is a form of inheritance in which two different allelesfor a gene are both expressed, and neither allele is dominant overthe other. One example of codominance is fur color in cattle; thealleles for red fur and white fur are codominant. If a homozygousred cow and a homozygous white bull mate, what would you expect tofind in their offspring?.912.l.16.2>

They will all have white fur.

Their fur will be a mixture of red and white hairs.

Their fur will be a lighter shade of red.

They will all have red fur.

Question 10

If a tRNA molecule has an anticodon which reads AUG, what will itmatch up with and what amino acid is it carrying?
.912.l.16.5>

	U		C		A		G
	UUU	Phenylalanine	UCU	Serine	UAU	Tyrosine	UGU	Cysteine	U
U	UUC	Phenylalanine	UCC	Serine	UAC	Tyrosine	UGC	Cysteine	C
	UUA	Leucine	UCA	Serine	UAA	Stop	UGA	Stop	A
	UUG	Leucine	UCG	Serine	UAG	Stop	UGG	Tryptophan	G
	CUU	Leucine	CCU	Proline	CAU	Hisitidine	CGU	Arginine	U
C	CUC	Leucine	CCC	Proline	CAC	Hisitidine	CGC	Arginine	C
	CUA	Leucine	CCA	Proline	CAA	Glutamine	CGA	Arginine	A
	CUG	Leucine	CCG	Proline	CAG	Glutamine	CGG	Arginine	G
	AUU	Isoleucine	ACU	Threonine	AAU	Asparagine	AGU	Serine	U
A	AUC	Isoleucine	ACC	Threonine	AAC	Asparagine	AGC	Serine	C
	AUA	Isoleucine	ACA	Threonine	AAA	Lysine	AGA	Arginine	A
	AUG	Methionine/Start	ACG	Threonine	AAG	Lysine	AGG	Arginine	G
	GUU	Valine	GCU	Alanine	GAU	Aspartate	GGU	Glycine	U
G	GUC	Valine	GCC	Alanine	GAC	Aspartate	GGC	Glycine	C
	GUA	Valine	GCA	Alanine	GAA	Glutamate	GGA	Glycine	A
	GUG	Valine	GCG	Alanine	GAG	Glutamate	GGG	Glycine	G

It is carrying arginine and will match with a CGU codon on themRNA.

It is carrying methionine and will match with a TAC codon on theDNA.

It is carrying methionine and will match with a UAC codon on themRNA.

It is carrying tyrosine and will match with a UAC codon on themRNA.

Question 11

While the DNA in a human skin cell was being replicated, a singlebase was miscopied. What will be the most likely result of this forthe cell in which it happened?.912.l.16.3>

All the proteins the cell creates from the miscopied strand willdo different jobs than the old ones.

If the new sequence codes for the same amino acid as theoriginal cell, it will function normally.

Both new DNA strands will end up together in a new cell, and theinaccurate one will be discarded.

Any miscopied DNA will be replaced with an accurate DNA copyonce the cell divides.

Question 12

A ferret's haploid number of chromosomes is 20. How would thenumber of chromosomes in the ferret's body cells compare to thenumber of chromosomes in its gametes?.912.l.16.17>

Its body cells would have 20 chromosomes, and its gametes wouldhave 40 chromosomes.

Its body cells and gametes would both have 40 chromosomes.

Its body cells and gametes would both have 20 chromosomes.

Its body cells would have 40 chromosomes, and its gametes wouldhave 20 chromosomes.

Question 13

A body cell is in the longest stage of its life cycle. The cellgrows, synthesizing proteins and increasing in size. Eventually,the cell will grow too large to carry out normal activities. Whichof the following is the best conclusion you can make about the lifecycle of this cell?.912.l.16.14>

The cell is close to the end of its life cycle, and a chemicalsignal will initiate cell death.

The cell is ready to undergo mitosis, and a chemical signal willsend the cell to prophase.

The cell is in the G1 phase of interphase, and a chemical signalwill send the cell to the S phase.

The cell is in the S phase of interphase, and a chemical signalwill move the cell to the G2 phase.

Question 14

While mRNA strands are being created a sequence is sometimesmiscopied. What is the best possible outcome for the cell shouldthis take place?.912.l.16.5>

The miscopied sequence codes for the same amino acids as theoriginal sequence.

The new sequence creates a protein that serves a differentfunction from the original.

The ribosomes will correct the mistake before the tRNA matchesan amino acid to it.

The mRNA will only be used to create non-critical proteins forthe cell.

Question 15

Over the last several decades, the scientific community hasgathered a large amount of information regarding genetics andgenetic variation. What are two main sources that lead toincreased genetic variation?.912.l.15.15>

Selective breeding

Gamete mutations

Recombination

Genetic drift

salmonlouse680

BIOL 1000 Lecture Notes - Lecture 4: Amino Acid, Disulfide, Thiol

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