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Copy of AP Bio- Chemistry 2: Macromolecules

2 of 2 of my chemistry unit (two days of class) 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

Jackie Snow

on 22 February 2013

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Transcript of Copy of AP Bio- Chemistry 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 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 facillitated by adding/removing water. 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, phospolipids, & 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? 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" 1 class of hormones, & cholesterol.
Notable structure = fused rings
Presence of different functional groups leads to different functions Steroids 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 book 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
IMPORTANT! Some unlucky folks have a mutation that results 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.
DNA = deoxyribose RNA = Ribose
DNA = Adenine, Thymine, Guanine, Cytosine
RNA = Adenine, Uracil, Guanine, Cytosine
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 Gyrase (a protein) DNA: Computers are often required! 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... 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.
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