macromolecules 2 proteins are polymers of amino acidsdstratto/bcor011/06_macromolecules2.pdf ·...
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Macromolecules 2 • Proteins
– Amino Acids • Different R groups
– 4 Levels of protein structure • What stabilizes
protein shape?
• Nucleic Acids – Nucleotides – DNA and RNA 16 Sept. 2020
Can Keep adding to the end
R5 Oil OH Duracell
SH
Nonpolar Polar Charged
Proteins are polymers of Amino Acids
• Amino Acids differ only by their �R� group • 20 kinds of amino acids
– Same chasis, different cargo
Side chain (R group)
Amino group
Carboxyl group
Proteins are polymers of Amino Acids
Structure identical, except for the R group
Nonpolar Side Chains
Glycine (Gly or G)
Alanine (Ala or A)
Valine (Val or V)
Leucine (Leu or L)
Isoleucine (Ile or I)
Methionine (Met or M)
Phenylalanine (Phe or F)
Tryptophan (Trp or W)
Proline (Pro or P)
Polar Side Chains
Serine (Ser or S)
Threonine (Thr or T)
Cysteine (Cys or C)
Tyrosine (Tyr or Y)
Asparagine (Asn or N)
Glutamine (Gln or Q)
Charged Side Chains
Basic (positively charged)
Acidic (negatively charged)
Aspartic acid (Asp or D)
Glutamic acid (Glu or E)
Lysine (Lys or K)
Arginine (Arg or R)
Histidine (His or H)
2
The amino and acid groups couple the monomers together
• Can make polymers that are 100s or 1000s of amino acids long
Can Keep adding to the end
R1 R2 R3 R4 R5
4 Levels of Structure
Secondary Structure: Local folding α helix and β sheet
Primary Structure: Amino acid sequence
Tertiary Structure: 3-D shape of one polypeptide Quaternary Structure:
Assembly of several polypeptides to form one functional protein
Primary structure: amino acid sequence
Individual Polypeptides (proteins) differ by • Length • Abundance of different A.A.s • Order of A.A.s
Met - Ala - Cys - Glu - Ser - Thr - Val - Val - Leu - Cys - Arg
NP NP P - P P NP NP NP P +
Secondary Structure
Hydrogen bond
Hydrogen bond
Β sheet
α helix
Secondary structure is stabilized by hydrogen bonding of peptide bonds
H R O \ | || H - N - C - C - / | H H
H | N - C - C - | | ||
H R O
H R O | | || N - C - C - | H
H | N - C - C - O- | | ||
H R O
-
+ -
+ -
+ -
+
Secondary Structure
-
+ -
+ -
+ -
+
-
+ -
+ -
+ -
+
Hydrogen bonds
R groups are NOT involved in secondary structure
3
R groups are on the outside
�Fuzzy can� & �Shag carpet�
--R
--R R
R
-R
R--
R-- R-
R--
R--
R |
R |
R |
R |
R |
R |
R | R
| R |
R R
R |
Means that the R groups can interact with other molecules
Often, A.A.s are ordered so one side has mostly polar R groups and the other has mostly non-polar R groups. Why?
R groups are on the outside
--R
--R R
R
-R
R--
R-- R-
R--
R--
R |
R |
R |
R |
R |
R |
R | R
| R |
R R
R |
Membrane
Water inside cell
Tertiary Structure (3-D shape of the entire peptide)
• Formed by interactions among R groups •
Mostly α helices
Mostly β sheets
Mixture
Hydrophobic interactions help determine the folding
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3D structure stabilized by interactions among R groups
Hydrogen bonding
Disulfide Bridges
Ionic bonding Hydrophobic interactions
4
Quaternary Structure • Sometimes a single functional PROTEIN
is made of several POLYPEPTIDES that work together as a unit
Hemoglobin Postassium Channel
How do you curl hair?
Nucleic Acids
ATP
Nucleotides have three components
• Sugar • Base • Phosphate
Use dehydration reactions to connect these molecules
Carbons in the sugar are numbered with primes
3� 2�
The nucleotide ATP is a common energy carrier
Also GTP, CTP, etc.
These are high-energy phosphate bonds
5
Nucleotides
The bases each have a polar edge for hydrogen bonding
Thymine
Cytosine
Adenine
Guanine
Polynucleotide (DNA, RNA) chains are assembled by yet another type of dehydration reaction
• Link the -OH on the 3� carbon of one nucleotide
• to the phosphate on the 5� carbon of the next.
5� end
3� end
RNA DNA
DNA copying is the basis of heredity
The sequences of bases is the hereditary information
Flow of information
DNA --> RNA --> Protein
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