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Agenda 12/14
• Protein Warm Up
• Protein/Nucleic Acids Notes
• Protein Folding Model
• Homework: Protein Video and Notes, Finish
biomolecules WS, quick protein quiz
tomorrow!
• Turn in: Video Notes
1
Warm Up
• In your notes, name five different specific
functions or classes of proteins
2
The Structure and Function of Macromolecules
Part II: Proteins & Nucleic Acids
The FOUR Classes of Large Biomolecules
• All living things are made up of four classes of
large biological molecules:
•
•
•
•
Carbohydrates
Lipids
Protein
Nucleic Acids
• Macromolecules are large molecules composed
of thousands of covalently bonded atoms
• Molecular structure and function are inseparable
4
Proteins Come In Many Varieties!
• Proteins include a diversity of structures,
resulting in a wide range of functions
• Proteins account for more than 50% of the dry
mass of most cells
• Protein functions include structural support,
storage, transport, cellular communications,
movement, and defense against foreign
substances
5
Amino Acids: Yet Another Monomer
• Amino acids are
organic molecules with
carboxyl and amino
groups
• Amino acids differ in
their properties due to
differing side chains,
called R groups
Side chain (R group)
 carbon
Amino
group
Carboxyl
group
6
Polypeptides
• Polypeptides are unbranched polymers built
from the same set of 20 amino acids
• A protein is a biologically functional molecule
that consists of one or more polypeptides
7
Hydrophobic: Therefore retreat from water!
Nonpolar side chains; hydrophobic
Side chain
Glycine
(Gly or G)
Methionine
(Met or M)
Alanine
(Ala or A)
Valine
(Val or V)
Phenylalanine
(Phe or F)
Leucine
(Leu or L)
Tryptophan
(Trp or W)
Isoleucine
(Ile or I)
Proline
(Pro or P)
Hydrophilic: Therefore Are Attracted to Water
9
Hydrophilic: But Electrically Charged!
10
Peptide Bonds
• Amino acids are linked by peptide bonds
• A polypeptide is a polymer of amino acids
• Polypeptides range in length from a few to more
than a thousand monomers (Yikes!)
• Each polypeptide has a unique linear sequence
of amino acids, with a carboxyl end (C-terminus)
and an amino end (N-terminus)
11
Peptide Bonds
12
Peptide Bonds
13
Protein Structure & Function
• At first, all we have is a string of AA’s bound with
peptide bonds.
• Once the string of AA’s interacts with itself and its
environment (often aqueous), then we have a
functional protein that consists of one or more
polypeptides precisely twisted, folded, and coiled into
a unique shape
• The sequence of amino acids determines a protein’s
three-dimensional structure
• A protein’s structure determines its function
14
Protein Structure: 4 Levels
• Primary structure consists of its unique
sequence of amino acids
• Secondary structure, found in most proteins,
consists of coils and folds in the polypeptide
chain
• Tertiary structure is determined by interactions
among various side chains (R groups)
• Quaternary structure results when a protein
consists of multiple polypeptide chains
15
Primary Structure
• Primary structure,
the sequence of
amino acids in a
protein, is like the
order of letters in a
long word
• Primary structure is
determined by
inherited genetic
information
• (Like the letters of the
alphabet)
Secondary Structure
• The coils and folds of
secondary structure
result from hydrogen
bonds between repeating
constituents of the
polypeptide backbone
• Typical secondary
structures are a coil called
an  helix and a folded
structure called a 
pleated sheet
• (Like letters forming
words)
17
Secondary Structure
Tertiary Structure
• Tertiary structure is determined by interactions
between R groups, rather than interactions
between backbone constituents
• These interactions between R groups include
actual ionic bonds and strong covalent bonds
called disulfide bridges which may reinforce the
protein’s structure.
• (Like words forming sentences)
19
Tertiary Structure
20
Quaternary Structure
• Quaternary structure results when two or
more polypeptide chains form one
macromolecule
• Collagen is a fibrous protein consisting of
three polypeptides coiled like a rope
• (Like sentences forming a full-functioning
story)
21
Quaternary Structure
• Hemoglobin is a globular protein consisting of
four polypeptides: two alpha and two beta
chains
22
Four Levels of Protein Structure Revisited
23
Sickle-Cell Disease:
A change in Primary Structure
• A slight change in primary
structure can affect a
protein’s structure and
ability to function
• Sickle-cell disease, an
inherited blood disorder,
results from a single amino
acid substitution in the
protein hemoglobin
“Normal” Red Blood Cells
24
Sickle-Cell Disease:
A change in Primary Structure
• A slight change in primary structure can affect a
protein’s structure and ability to function
• Sickle-cell disease, an inherited blood disorder,
results from a single amino acid substitution in
the protein hemoglobin
25
Sickle-Cell Disease:
A change in Primary Structure
26
What Determines Protein Structure?
• In addition to primary structure, physical and
chemical conditions can affect structure
• Alterations in pH, salt concentration,
temperature, or other environmental factors can
cause a protein to unravel
• This loss of a protein’s native structure is called
denaturation
• A denatured protein is biologically inactive
27
Denature: Break Bonds or Disrupt IMFs
28
Nucleic Acids
• Nucleic acids store, transmit, and help
express hereditary information
• The amino acid sequence of a polypeptide is
programmed by a unit of inheritance called a
gene
• Genes are made of DNA, a nucleic acid
made of monomers called nucleotides
29
Two Types of Nucleic Acids
• There are two types of nucleic
acids
– Deoxyribonucleic acid
(DNA)
– Ribonucleic acid (RNA)
• DNA provides directions for its
own replication
• DNA directs synthesis of
messenger RNA (mRNA) and,
through mRNA, controls protein
synthesis
• Protein synthesis occurs on
ribosomes
30
The Components of Nucleic Acids
• Each nucleic acid is made of monomers called
nucleotides
• Each nucleotide consists of a nitrogenous base,
a pentose sugar, and one or more phosphate
groups
31
Figure 5.26ab
Sugar-phosphate backbone
5 end
5C
3C
Nucleoside
Nitrogenous
base
5C
1C
5C
3C
3 end
(a) Polynucleotide, or nucleic acid
Phosphate
group
(b) Nucleotide
3C
Sugar
(pentose)
The Devil is in the Details
• There are two families of nitrogenous bases
– Pyrimidines (cytosine, thymine, and uracil)
have a single six-membered ring
– Purines (adenine and guanine) have a sixmembered ring fused to a five-membered ring
• In DNA, the sugar is deoxyribose; in RNA, the
sugar is ribose
33
Link to Evolution
• The linear sequences of nucleotides in DNA
molecules are passed from parents to offspring
• Two closely related species are more similar in
DNA than are more distantly related species
• Molecular biology can be used to assess
evolutionary kinship
34
Could Prove Useful
35
Protein Models
• Each level of protein structure modeled with
bonds labeled
• A sketch of each level of protein structure and
on overall picture of quaternary structure with
all bonds labeled
– Bonds you need to include: peptide bonds,
hydrogen, ionic, covalent, hydrophobic
interactions, disulfide
36
Exit Ticket
• Make a table of all four classes of
biomolecules. Include:
– The basic structure of each
– Monomers and Polymers
– Biological Function
37