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AP Bio- Matter 2: Macromolecules

2 of 7 of my Matter Domain (two discussions) Image Credits: Biology (Campbell) 9th edition, copyright Pearson 2011, & The Internet. Provided under the terms of a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 license. By David Knuffke
by David Knuffke on 27 June 2014

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Transcript of AP Bio- Matter 2: Macromolecules

Macromolecules
Proteins
Carbohydrates
Lipids
Nucleic Acids
Hexose sugars are the most "famous"
monosaccharides
Three kinds:
Glucose
,
Galactose
, &
Fructose
They are typically shown as carbon rings.




Combine 2 by dehydration synthesis, and you get a "
disaccharide
" (What are their molecular formulas?)
Glucose + Glucose =
Maltose
("Malt sugar")
Glucose + Fructose =
Sucrose
("Table sugar")
Glucose + Galactose =
Lactose
("Milk sugar")
Polysaccharides are great for short term storing of energy.
In plants,
amylose
("starch") is the major energy storage polysaccharide.





Animals use
glycogen
for energy storage
Chitin
= a modified polysaccharide.
Used in fungi cell walls, arthropod
exoskeletons
, and dissolving stitches!





Peptidoglycan
= another modified polysaccharide. Used in bacterial cell walls
So, What's a Macromolecule?
Big! (hence "
macro
")
Made of few, common atoms
Accomplish all life functions
Put together in a special way
Can be incredibly complex
Building Macromolecules
Dehydration Synthesis
Builds more complex molecules from smaller ones by removing 2 H & 1 O, and replacing it with a bond.

Water is produced!

Builds complexity ("
anabolic
")
Requires energy ("
endergonic
") & enzymes (more later)
Hydrolysis
Reverse of dehydration synthesis
-lysis
= "breaking"

Water is needed!

Reduces complexity ("
catabolic
")
Releases energy ("
exergonic
")
Enzymes still required!
We will now take a tour
Things to focus on:
1. Structure & Function 2. Atoms Needed
3. Monomer 4. Polymer
4 Main Kinds
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids
It's easy to get confused!
Don't hesitate to ask questions!!!
General info:
"
Sugars
" & "
Starches
"
Made of C, H, and O (1:2:1 ratio in monomers)
Used for short term energy storage & structure
Monomers = "
monosaccharides
"
Different Sugar monomers can have different #'s of Carbon
Herbivores
need to digest cellulose.
Animals lack the enzymes necessary to break beta linkages
Several strategies are employed.
The Problem of Herbivory
Monosaccharides & Disaccharides
These are the major carbohydrates used for energy
Polysaccharides
Massive polymers of sugars are called "
polysaccharides
"
Glucose polymers have two main functions in organisms
Energy Storage
Structural Support
Cellulose
is the major component of plant-like cell walls.






The difference between starch and cellulose is in the linkages between glucose units.
Starch =
alpha linked
. Cellulose =
beta linked
Other Carbohydrates
General info:
Fats
,
Oils
,
Waxes
Made of C, H, and O
Used for long term energy storage & insulation
No polymers.
3 major groups:
triglycerides
,
phospholipids
, &
steroids
Triglycerides
Triglycerides are made of one glycerol & 3 fatty acids.
Connected by dehydration synthesis x 3 (
ester

linkages
)
Refers to the bonding of carbon in the fatty acids.
Saturated
= no double bonds between carbons.
Unsaturated
= at least one double bond.
Influences shape which influences properties.
Oils vs. fats
Which ones stay liquid at lower temperatures? Why?
Which ones are healthier for you? Why?
Saturated vs. Unsaturated
Phospholipids
Modified triglycerides. Replace on fatty acid with a phosphate
Makes the molecule have a polar and a non-polar region ("
amphipathic
")
The major component of cell membranes (arranged as a "
bi-layer
")
Steroids
1 class of
hormones
, &
cholesterol
.
Notable structure = fused rings
Presence of different functional groups leads to different functions
General info:
The most complex biological molecules.
Made of C, H, O, N & a little S
Used to accomplish all life functions
All proteins are polymers of
amino acid
monomers
Amino acids are joined by "
peptide bonds
"
The information storage molecules for biological systems.
Made of C, H, O, N & P
2 kinds of nucleic acids:
DNA
&
RNA
All nucleic acids are polymers of
nucleotides
.
Nucleotides consist of a
phosphate
, a
pentose sugar
, and a
nitrogenous base
. 4 different bases in DNA & RNA
General info:
Amino Acids
There are 21 known amino acids used in biological systems.
All amino acids contain an
amino
&
carboxyl
group, bonded to a central "
alpha
" carbon.
Every amino acid differs in the structure of a variable group (symbolized as
R
) bonded to the alpha carbon.
The structure of the R-group varies widely.
Chains of amino acids have a directionality, with an amino end ("
N-terminus
") & a carboxyl end ("
C-terminus
")
Because of the diversity of amino acids, proteins have very complex 3-D structures.
Generally, we can consider 4 levels of protein structure:
Protein Structure
Primary Structure
Secondary Structure
Tertiary Structure
Quartenary Structure
What it is:
The sequence of amino acids in one polypeptide chain
What it is:
Regular, repeating 3D structures found in all polypeptide chains.
What it is:
The specific 3D shape of a particular polypeptide chain (aka the "
conformation
")
What it is:
The specific 3D shape of any protein that is made of more than one polypeptide chain (many are).
The only "optional" level of structure.
How it happens:
Peptide bonds between amino acids.

How does the cell "know" the order of amino acids?
How it happens:
Hydrogen bonding between atoms in the CN backbone of the polypeptide (no R-groups involved)
Why do all proteins have similar secondary structures?
How it happens:
Interactions between R-group atoms with other R-groups and the local environments of the cell
What kinds of interactions can occur to determine tertiary structure?
How it happens:
The overall structure when multiple chains form a functional protein.

Why do some proteins consist of more than 1 polypeptide chain?
There is a direct relationship between a protein's conformation and its function.
If the conformation is altered, the function of the protein will also be altered.

Denaturation
: Change in the structure of a protein.
Denatured proteins do not work well (if at all).

What sorts of conditions can denature proteins? Why?
Denaturation
What do proteins do?

Generally speaking: Proteins are responsible for
all life activities of the cell
(and by extension, the organism, population, etc.)

Your text gives a pretty good overview:
Protein Function
Visualizing Proteins
Because of their complexity, studying protein structure & function ("
proteomics
") can be overwhelming.

(FREE!) Computer modeling software is frequently used to help visualize important structural aspects.
Sickle cell anemia
: One example of the relationship between protein structure and organismal physiology (not the only one, by any means!)
An Illustrative Example
This is
Hemoglobin!
It carries oxygen in your red blood cells
IT IS
CRAZY
IMPORTANT!
Some unlucky folks have a mutation that results in valine (hydrophobic) replacing glutamic acid (hydrophilic) in the beta chains of hemoglobin
OOPS!
This change in the structure of hemoglobin affects the function.
Sickle-cell hemoglobin gets clumpy, and the red blood cells change shape.
They don't carry as much oxygen, and get stuck in blood vessels.
Sickle-cell anemic people die at a young age from the disease.
While similar in structure, there are a few key differences which lead to major differences in function.
Pentose:
DNA =
deoxyribose
RNA =
ribose
Bases:
DNA =
Adenine, Thymine, Guanine, Cytosine
RNA =
Adenine, Uracil, Guanine, Cytosine
Strands
DNA = 2 strands
RNA = 1 strand
DNA vs. RNA
DNA: Deoxyribonucleic Acid
DNA serves 2 functions in all life on Earth:
1. Stores information about the primary structure of proteins, and the sequences of RNA molecules.
2. Is
heritable
.
DNA Structure:
2 chains of covalently bonded nucleotides, from sugar to phosphate... ("
phosphodiester bonds
")
Chains are bonded to each other by
hydrogen bonds
between N Bases.
A bonds to T, G bonds to C.
Purine
(A,G) always opposite
Pyrimidine
(T,C)
The most important biological discovery of the 20th century (and arguably, the 2nd most important ever).
Watson & Crick
- published the paper
Wilkins & Franklin
- did the X-Ray diffraction work
Some controversy about ethics of Watson & Crick.
Nobel Prize (1962)- Watson, Crick, & Wilkins (Franklin was dead)
Discovery of DNA Structure
RNA serves many functions for life:
1. Transmits and translates DNA information into protein.
2. Many enzymatic and regulatory functions.
3. 1 kind of DNA, ~15 types of known RNA at current (3 main types)

Turns out it is MUCH more interesting than DNA is.
RNA: Ribonucleic Acid
RNA Structure:
less stable than DNA.
1 strand, but base-paring can still occur (A bonds to U)
Biological systems are process matter, energy, & INFORMATION.
The information stored in DNA moves to RNA before some of that information finally directs the construction of proteins.
This is known as the "
Central Dogma
" of molecular biology.
It will be the underpinning of the most important biological advances during your lifetime (it already is!)
Information in Biology
...or how to make a hairless cat (and every other living thing)
Warm Bald Cat Belly!
Big Questions
Make sure you can
Topoisomerase (a protein)
DNA:
Computers are often required!
Except for lipids, macromolecules exist in two forms
Monomer
- the simplest unit
Polymer
- a large molecule made of repeating monomers
The movement between monomers and polymers is facilitated by adding/removing water.
We'll only see these one more time:
Really important for DNA & RNA:
Really important for energy & structure:
Termites!
The most famous wood-eater of the animal kingdom has a
symbiotic
relationship with a protist.
In exchange for a place to live (the termite gut), the protist does the cellulose digestion
Ruminants!
Caecophores!
Ruminants
like cows have a vastly expanded upper GI tract. The action of bacteria, and continual regurgitation and chewing of "cud" leads to the digestion of cellulose
Caecophores
like bunnies have an expanded lower GI tract. Food can not be regurgitated, but there is still a way to put partially digested cellulose back in to the animal...
...they eat (some of) their poop!
JAWS as SAWS!
Cholesterol!
ff
"Alpha helix"
"Beta Pleated Sheet"
Primary structure of Transthyretin:
Tertiary structure of 1 Transthyretin unit:
Quaternary structure of Transthyretin (four identical subunits):
Denaturation
Renaturation
(a)

&
(b)
:

two different views of the lysozyme protein

By only focusing on the interacting elements of the flu virus and an antibody, scientists can better understand these interactions
Plenty of proteins can be seen with the naked eye!
James Watson & Francis Crick
Maurice Wilkins
Rosalind Franklin
Photo 51: X marks the helix!
X-Ray Diffraction!
How are the molecules of biological systems constructed?

Why are particular groups of molecules needed in biological systems?

How do the interactions of biological molecules lead to the emergence of life functions?
Identify the structures of the monomers and polymers of the four major classes of macromolecules.

Diagram the synthesis and hydrolysis of carbohydrates and polypeptides.

Explain the biological functions of all of the molecules discussed in this presentation.

Explain the emergence of all four levels of protein structure.

Describe the role of general role of nucleic acids in living systems.
Major R-group interactions
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