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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)

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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

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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

https://chem.libretexts.org/

3D structure stabilized by interactions among R groups

Hydrogen bonding

Disulfide Bridges

Ionic bonding Hydrophobic interactions

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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

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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