1. Amines, Amides, Amino Acids, Proteins
General, Organic, and Biological Chemistry

2. Classification of Amines
Amines are classified as primary, secondary, or tertiary.
In a primary (1°) amine, one carbon group is bonded to the nitrogen atom.
A secondary (2°) amine has two carbon groups.
A tertiary (3°) amine has three carbon groups.
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3. Guide to IUPAC Naming of Amines
General, Organic, and Biological Chemistry

4. 3° amines do not H-bond with themselves
Amines have boiling points between alcohols and alkanes. Not as soluble as alcohols
The polar N—H bond
provides hydrogen bonding in 1° and 2° amines (with itself and with water)
3° amines do not H-bond with themselves
is not as polar as the —OH in alcohols. WHY?
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5. Amines React as Bases
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6. Amides
In amides, an amino group(–NH-) replaces the –OH group of carboxylic acids. The peptide bond in proteins are amides. Amides can be base or acid hydrolyzed back into carboxylic acid and amine.
O O
|| || I
R—C—OH + -NH- (1o or 2o amine) R—C—N- + H2O
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7. General, Organic, and Biological Chemistry
Functions of Proteins
Proteins perform many different functions in the body.
General, Organic, and Biological Chemistry

8. General, Organic, and Biological Chemistry
Amino Acids
Amino acids
are the building blocks of proteins
contain a carboxylic acid group and an amino group on the alpha () carbon
are ionized in solution
each contain a different side group (R)
General, Organic, and Biological Chemistry

9. Examples of Amino Acids
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10. Types of Amino Acids Amino acids are classified as
nonpolar with hydrocarbon side chains (hydrophobic)
polar (neutral) with polar or ionic side chains (hydrophilic)
polar (acidic) with acidic side chains (hydrophilic)
polar (basic) with –NH2 side chains (hydrophilic)
Nonpolar Polar (neutral)
Acidic
Basic
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11. Non-Polar
Polar Neutral
DO NOT MEMORIZE THE STRUCTURE OF EACH AMINO ACID
Polar Acidic
Polar Basic

12. Essential Amino Acids Essential amino acids
are the ten amino acids not synthesized by the body
must be obtained from the diet
are in meat and diary products
are missing (one or more) in grains and vegetables
General, Organic, and Biological Chemistry
PVTTMHILL (private TM HILL)

13. Learning Check
Identify each of the following as a polar (P) or nonpolar (NP) amino acid. +
A. H3N—CH2—COO− (Glycine)
CH3 │
CH—OH
+ │
B. H3N—CH—COO − (Threonine)
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14. Fischer Projections of Amino Acids
are chiral except glycine, which has two H atoms
attached to the alpha carbon atom
have Fischer projections that are stereoisomers
that are L isomers are used in proteins
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15. Zwitterions and Isoelectric Points
A zwitterion
has an equal number of —NH3+ and COO– groups
forms when the H from —COOH in an amino acid transfers to the —NH2
The isoelectric points (pI) are the pH at which zwitterions have an overall zero charge
nonpolar and polar (neutral) amino acids have pI values from 5.1 to 6.3
O O
║ ║
NH2—CH2—C—OH H3N—CH2—C—O–
Glycine Zwitterion of glycine
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16. General, Organic, and Biological Chemistry
pI, pH, and Charge
General, Organic, and Biological Chemistry

17. Ionized Forms of Polar (Acidic) and Polar (Basic) Amino Acids
Have extra COO and NH3+ in their polar R groups
Acidic amino acids have an extra carboxylic acid group (COOH)
At pH 7 the COOH donates its proton to become conjugate base COO .
net negative charge at pH 7
Zwitterions at pH values from 2.8 to 3.2. (Net neutral charge)
Basic amino acids have extra -NH2
At pH 7, -NH2 accepts proton to become conjugate acid, NH3+
Net positive charge at pH 7
Zwitterions pH values from 7.6 to (Net neutral charge)
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18. Learning Check 1) CH3 2) CH3 + | | H3N—CH—COOH H2N—CH—COO–
| |
H3N—CH—COOH H2N—CH—COO–
Which structure represents:
A. alanine at a pH above its pI?
B. alanine at a pH below its pI?
General, Organic, and Biological Chemistry Copyright © 2010 Pearson Education, Inc.

19. General, Organic, and Biological Chemistry
The Peptide Bond
an amide bond
forms between the carboxyl group of one amino acid and the amino group of the next amino acid
contains an N (amino, free H3N+) terminal written on the left
contains a C (carboxyl, free COO –) terminal written on the right
Seen in dipeptides (2 amino acids), tripeptide (3 amino acids) etc.
Seen in polypeptides (usually less than 30 amino acids)
Seen in proteins (usually greater than 30 amino acids)
General, Organic, and Biological Chemistry

20. General, Organic, and Biological Chemistry
Naming Polypeptides
A dipeptide is named with
a yl ending for the N-terminal (free H3N+) amino acid
the full amino acid name of the free carboxyl group (COO–) at the C-terminal end
General, Organic, and Biological Chemistry

21. Learning Check
Draw the condensed structural formula, and give the name and abbreviation for the dipeptide Ser-Thr.
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22. Primary Structure of Proteins
The primary structure of a protein is
the particular sequence of amino acids
the backbone of a peptide chain or protein +
Ala─Leu─Cys─Met
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23. Secondary Structures 1) Alpha Helix
The secondary structures of proteins indicate the
three-dimensional spatial arrangements of the
polypeptide chains.
An alpha helix (α-helix) has
a coiled shape held in place by hydrogen bonds between the amide groups and the carbonyl groups of the amino acids along the chain
hydrogen bonds between the H of an —NH group and the O of C═O of the fourth amino acid down the chain
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24. Secondary Structure: Alpha Helix (continued)
General, Organic, and Biological Chemistry

25. Secondary Structures 2) Beta-Pleated Sheet
A beta-pleated sheet (β-pleated sheet) is a secondary structure
consists of polypeptide chains (β-strands) arranged side by side
hydrogen bonds between chains
R groups above and below the sheet
typical of fibrous proteins such as silk
Beta strands can be connected by peptide turns
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26. Learning Check Indicate the type of protein structure as:
1) primary ) alpha helix
3) beta-pleated sheet
A. polypeptide chains held side by side by H bonds
B. sequence of amino acids in a polypeptide chain
C. corkscrew shape with H bonds between amino
acids
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27. Tertiary Structure The tertiary structure of a protein
gives a specific three-dimensional shape to the polypeptide chain. The interactions of the R groups give a protein its specific three-dimensional tertiary structure.
involves interactions and cross-links between different parts of the peptide chain.
is stabilized by:
hydrophobic interactions
hydrophilic interactions
salt bridges
hydrogen bonds
disulfide bonds
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28. Learning Check Select the type of tertiary interaction as:
1) disulfide 2) ionic
3) H bonds 4) hydrophobic
A. leucine and valine
B. two cysteines
C. aspartic acid and lysine
D. serine and threonine
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29. Quaternary Structure The quaternary structure Hemoglobin
is the combination of two or more tertiary units (or subunits)
Ex. Each alpha and beta chain of hemoglobin is a subunit with its own tertiary structure
is stabilized by the same interactions found in tertiary structures
Hemoglobin
General, Organic, and Biological Chemistry

30. Protein folding simulation based on energy minimization calculations
Vijay Pande, Stanford University
General, Organic, and Biological Chemistry

31. Learning Check Identify the level of protein structure as:
1) primary 2) secondary
3) tertiary 4) quaternary
A. beta-pleated sheet
B. order of amino acids in a protein
C. a protein with two or more peptide chains
D. the shape of a globular protein
E. disulfide bonds between R groups
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32. Protein Hydrolysis Hydrolysis of peptide (amide) bond
Products are smaller peptides and amino acids
occurs in the digestion of proteins
occurs in cells when amino acids are needed to synthesize new proteins and repair tissues
HEAT and water
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33. Denaturation Does NOT break primary structure (peptide bonds)
the disruption of bonds in the secondary, tertiary, and quaternary protein structures
heat and organic compounds that break apart H bonds and disrupt hydrophobic interactions
acids and bases that break H bonds between polar R groups and disrupt ionic bonds
heavy metal ions that react with S—S bonds to form solids
agitation, such as whipping, that stretches peptide chains until bonds break
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34. Nucleic Acids
molecules that store information for cellular growth and reproduction
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
large molecules consisting of long chains of monomers called nucleotides
comprised of monomers called nucleotides that consist of a
base with nitrogen
pentose sugar
phosphoryl group
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35. General, Organic, and Biological Chemistry
Bases
The bases in DNA and
RNA are
Where genetic information is stored
Consists of:
pyrimidines C, T, and U
purines A and G
General, Organic, and Biological Chemistry

36. Primary Structure of Nucleic Acids
nucleotides are joined by phosphodiester bonds
the 3′ —OH group of the sugar in one nucleotide forms an ester bond to the phosphate group on the 5′ carbon of the sugar of the next nucleotide
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37. Primary Structure of Nucleic Acids
A nucleic acid polymer
has a free 5′-phosphate group at one end and a free 3′ —OH group at the other end
is read from the free 5′ end, using the letters of the bases
segment shown here is read as:
5′—A—C—G—T—3′
The sequence of bases provides the genetic code – information to synthesize proteins
General, Organic, and Biological Chemistry

38. DNA Secondary Structure: Double Helix
The DNA structure is a
double helix that
consists of two strands of nucleotides that form a double helix structure like a spiral stair case
has hydrogen bonds between the bases A–T and G–C
has bases along one strand that complement the bases along the other
DNA strands are anti-parallel A C T G 5’ 3’ 3’ 5’
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39. DNA Secondary Structure - Double Helix Relies on Complementary Base Pairs:
General, Organic, and Biological Chemistry Copyright © 2010 Pearson Education, Inc.

40. Learning Check 5′—A—G—T—C—C —A—A—T—C—3′
Write the complementary base sequence for the matching strand in the following DNA section:
5′—A—G—T—C—C —A—A—T—C—3′
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41. DNA Replication unwinding the DNA
Replication catalyzed by DNA polymerase
pairing the bases in each strand with new bases to form new complementary strands
Forming new phosphodiester bonds to form phosphate-sugar backbone
two new DNA strands that exactly duplicate the original DNA
Semi-conservative: one old + one new strand +
Simple replication video
General, Organic, and Biological Chemistry

42. RNA RNA transmits information from DNA to make proteins
has several types:
Messenger RNA (mRNA) carries genetic information from DNA to the ribosomes.
Transfer RNA (tRNA) brings amino acids to the ribosome to make the protein.
Ribosomal RNA (rRNA) makes up 2/3 of ribosomes where protein synthesis takes place. Catalyzes translation into the protein.
General, Organic, and Biological Chemistry Copyright © 2010 Pearson Education, Inc.

43. Gene Expression (Protein Synthesis)
Protein synthesis involves
transcription, in which
mRNA is formed from a gene on a DNA strand
translation, in which
tRNA molecules bring amino acids to mRNA to
build a protein
General, Organic, and Biological Chemistry

44. Transcription: Synthesis of mRNA Catalyzed by RNA Polymerase
a section of DNA in gene unwinds
Only one strand of DNA is copied, starting at the start site
RNA polymerase synthesize the corresponding mRNA using complementary base pairing; reactions similar to replication except uracil (U) replaces thymine(T).
mRNA itself is synthesized in 5’-3’ direction.
transcription animation
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45. Learning Check What is the sequence of bases in mRNA produced
from a section of the template strand of DNA that has
the sequence of bases: 3′–C–T–A–A–G–G–5′?
1) 5′–G–A–T–T–C–C–3′
2) 5′–G–A–U–U–C–C–3′
3) 5′–C–T–A–A–G–G–3′
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46. The Genetic Code: mRNA Codons
Do NOT memorize
General, Organic, and Biological Chemistry

47. Mutations A mutation alters the nucleotide sequence in DNA
results from mutagens such as radiation and chemicals
In the structural gene (or transcribed region) produces one or more incorrect codons in the corresponding mRNA
produces a protein that incorporates one or more incorrect amino acids
Can also happen in regulatory regions (eg. Promoters, enhancers) affect levels of transcription and, finally, levels of proteins expressed.
causes genetic diseases that produce defective proteins and enzymes (or insufficient levels of proteins)
In structural regions of the genome (eg. Telomeres and centromeres) alter cell cycle, increasing aging and cancer
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48. Codons and Amino Acids
Suppose we want to determine the amino acids coded
for in the following section of a mRNA:
5′—CCU —AGC—GGA—CUU—3′
According to the genetic code, the amino acids for these
codons are:
CCU = Proline AGC = Serine
GGA = Glycine CUU = Leucine
The mRNA section codes for the amino acid sequence:
Pro—Ser—Gly—Leu
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49. Learning Check 5′—GCC—GUA—GAC—3′
Write the amino acids coded for by a section of mRNA with the following base sequence:
5′—GCC—GUA—GAC—3′
Some possible codons to use are the following:
GGC = Glycine GAC = Aspartic acid
CUC = Leucine GUA = Valine
GCC = Alanine CGC = Arginine
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50. Solution
Write the amino acids coded for by a section of mRNA with the following base sequence:
5′—GCC—GUA—GAC—3′
Ala——Val——Asp
General, Organic, and Biological Chemistry Copyright © 2010 Pearson Education, Inc.

51. Translation Requires Transfer RNA (tRNA) Activation
The activation of tRNA
occurs when a synthetase attaches an amino acid to a specific tRNA
prepares each tRNA to use a triplet called an anticodon to complement a codon on mRNA
Amino acid 3’
Example: This tRNA only puts on serines! 5’
Anticodon on tRNA
Codon on mRNA
General, Organic, and Biological Chemistry

52. Translation occurs on the ribosome Ribosomes - many proteins + ribosomal RNA (rRNA)
codon
anticodon
Ribosome
Large subunit
Ribosome
small subunit

53. Summary of Translation
An mRNA attaches to a ribosome and first tRNA binds START codon.
tRNAs with their amino acids base pair with codons on mRNA
Peptide bonds form between an amino acid and the peptide chain.
The ribosome shifts to each codon the STOP codon.
The polypeptide chain detaches to function as an active protein.
Step-by-step animation of translation
translation
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54. Protein Synthesis Translation
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55. Overview of Gene Expression
NUCLEUS
Catalyzed by RNA polymerase
-links nucleotides together to make mRNA
Messenger RNA (mRNA)
Catalyzed by and within the ribosome
CYTOPLASM
General, Organic, and Biological Chemistry