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Carbohydrates

Monosaccharides & Disaccharides

Polysaccharides

These are the major carbohydrates used for energy

Massive polymers of sugars are called "polysaccharides"

Glucose polymers have two main functions in organisms

Structural Support

Energy Storage

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")

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

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

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

Really important for DNA & RNA:

Really important for energy & structure:

We'll only see these one more time:

The Problem of Herbivory

Other Carbohydrates

Herbivores need to digest cellulose.

Animals lack the enzymes necessary to break beta linkages

Several strategies are employed.

Caecophores!

Termites!

JAWS as SAWS!

Chitin = a modified polysaccharide.

Used in fungi cell walls, arthropod exoskeletons, and dissolving stitches!

Peptidoglycan = another modified polysaccharide. Used in bacterial cell walls

Ruminants!

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

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!

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

Lipids

Proteins

So, What's a Macromolecule?

Topoisomerase (a protein)

General info:

4 Main Kinds

  • Big! (hence "macro")
  • Made of few, common atoms
  • Accomplish all life functions
  • Put together in a special way
  • Can be incredibly complex

Amino Acids

Protein Structure

General info:

Because of the diversity of amino acids, proteins have very complex 3-D structures.

Generally, we can consider 4 levels of protein structure:

  • 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.

Primary Structure

Secondary Structure

Primary structure of Transthyretin:

  • Fats, Oils, Waxes
  • Made of C, H, and O
  • Used for long term energy storage & insulation
  • No polymers.
  • 3 major groups: triglycerides, phospholipids, & steroids

What it is:

Regular, repeating 3D structures found in all polypeptide chains.

  • 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"

What it is:

The sequence of amino acids in one polypeptide chain

"Alpha helix"

How it happens:

Hydrogen bonding between atoms in the CN backbone of the polypeptide (no R-groups involved)

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic acids

"Beta Pleated Sheet"

How it happens:

Peptide bonds between amino acids.

How does the cell "know" the order of amino acids?

Computers are often required!

Why do all proteins have similar secondary structures?

Chains of amino acids have a directionality, with an amino end ("N-terminus") & a carboxyl end ("C-terminus")

DNA:

Major R-group interactions

Tertiary Structure

Quartenary Structure

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.

What it is:

The specific 3D shape of a particular polypeptide chain (aka the "conformation")

Quaternary structure of Transthyretin (four identical subunits):

Tertiary structure of 1 Transthyretin unit:

How it happens:

Interactions between R-group atoms with other R-groups and the local environments of the cell

How it happens:

The overall structure when multiple chains form a functional protein.

Why do some proteins consist of more than 1 polypeptide chain?

What kinds of interactions can occur to determine tertiary structure?

Protein Function

An Illustrative Example

Triglycerides

Cholesterol!

Steroids

Sickle cell anemia: One example of the relationship between protein structure and organismal physiology (not the only one, by any means!)

  • Triglycerides are made of one glycerol & 3 fatty acids.
  • Connected by dehydration synthesis x 3 (ester linkages)

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:

  • 1 class of hormones, & cholesterol.
  • Notable structure = fused rings
  • Presence of different functional groups leads to different functions

...or how to make a hairless cat (and every other living thing)

This is Hemoglobin!

It carries oxygen in your red blood cells

Warm Bald Cat Belly!

Macromolecules

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.

IT IS

CRAZY

IMPORTANT!

Saturated vs. Unsaturated

Dehydration Synthesis

Building Macromolecules

Some unlucky folks have a mutation that results in valine (hydrophobic) replacing glutamic acid (hydrophilic) in the beta chains of hemoglobin

  • 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?

OOPS!

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)

ff

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.

Denaturation

Phospholipids

Hydrolysis

Visualizing Proteins

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?

  • 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")

Reverse of dehydration synthesis

-lysis = "breaking"

Water is needed!

Reduces complexity ("catabolic")

Releases energy ("exergonic")

Enzymes still required!

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.

Denaturation

We will now take a tour

Plenty of proteins can be seen with the naked eye!

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

Things to focus on:

1. Structure & Function 2. Atoms Needed

3. Monomer 4. Polymer

It's easy to get confused!

Don't hesitate to ask questions!!!

Nucleic Acids

DNA vs. RNA

General info:

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
  • 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

DNA: Deoxyribonucleic Acid

Discovery of DNA Structure

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.

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)

Photo 51: X marks the helix!

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)

Maurice Wilkins

Rosalind Franklin

James Watson & Francis Crick

X-Ray Diffraction!

RNA: Ribonucleic Acid

Information in Biology

Big Questions

Make sure you can

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.

  • 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!)

RNA Structure:

  • less stable than DNA.
  • 1 strand, but base-paring can still occur (A bonds to U)

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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