Download Introduction to Biochemistry

Introductions
Jessica Torres
About MIT
• MIT is the Massachusetts Institute of Technology located in Cambridge,
Massachusetts
• The mission of MIT is to advance knowledge and educate students in
science and technology to serve the world in the 21st century
About Me
• Hometown: Houston, Texas
• Major: Chemical Biological Engineering
• Concentration: Education
• Graduation: 2016
• I am currently a Junior
More About Me
• XXX = Fun pictures
The Basics
• I love class participation!
• Ask questions
• Answer my questions
• Tell me if I speak too quickly
• Anything!
Feedback
• I love feedback
• At the end of every class, write down thoughts about the class
• Things you liked or disliked
• Suggestions you have
• Things you did not understand or want more information about
• Questions were too hard or too easy
Question: Which U.S. State is the best?
1. California
2. New York
3. Texas
Teach Me Italian!
1. Form a line at the chalkboard
2. Introduce yourself to me
3. Put a word on the board in Italian and write the English translation next to
it
Ex. Per favore - Please
Introduction to
Biochemistry
Why Biochemistry?
• Biochemistry: study of chemical processes for living organisms
• It explains things happening inside you right now!
• How we get energy
• How we grow
• How we move
• Research in modern science almost always involves biochemistry
Building Blocks - Elements
• Elements are necessary for life
• Only 6 elements make up make up
99% mass of human body
• Carbon (C), Hydrogen (H), Oxygen (O),
Nitrogen (N), Phosphorus (P), and
Calcium (Ca)
Macromolecules
• Macromolecule: large molecule made by putting together smaller repeating
units
• polymers = monomer + monomer + monomer + … + monomer
• There are 4 main macromolecules in biochemistry
Carbohydrates
Lipids
Nucleic Acids
Proteins
Lipids
Lipids
• Main functions: energy storage, signaling, and structure
• Types: fats, oils, waxes, steroids
Lipids
• Properties: hydrophobic or amphipathic
• Hydrophobic: nonpolar; water-hating
• Hydrophilic: polar; water-loving
• Amphipathic: has both hydrophobic and hydrophilic parts
Fatty Acids
• Fatty acids are parts of lipids
• Fatty acid = hydrocarbon chain ending with a carboxylic acid group
• Ex.
Question: Which end of the fatty acid is
hydrophilic?
1
2
Correct Answer: 2
• Hydrophilic: polar; water-loving
Saturated v. Unsaturated
• Saturated fatty acid
characteristics:
• Solid at room temperature
• Contains no double bonds in
hydrocarbon chain
• Unsaturated fatty acid
characteristics:
• Liquid at room temperature
• Contains double bonds in
hydrocarbon chain
• Linear structure
• Typically Kinked structure
• Examples: animal fats
• Examples: plant oils (olive oil, corn
oil)
Fatty Acid Saturation
• Saturated: no double bonds in hydrocarbon chain
• Unsaturated: 1 or more double bonds in hydrocarbon chain
Cis v. Trans Unsaturated
Kinked
Linear
• Most naturally occurring fatty acids are
found as the cis isomer
• Trans fats are uncommon in nature,
but can be man-made
• Dangerous to our health
• Raises bad cholesterol levels (LDLs) and
lowers good cholesterol levels (HDLs)
• Shown to increase risk of coronary
heart disease
Question: Is the fatty acid shape 1)
linear, 2) kinked, or 3) circular?
Correct Answer: 2) kinked
• Unsaturated fatty acid: 1 or more double bonds in hydrocarbon chain
• This is an example of a monounsaturated fatty acid, because it has only 1
double bond in the hydrocarbon chain
Correct Answer: 2) kinked
→
• This fatty acid is considered an omega-3 (ω-3) fatty acid
• ω-3 fatty acid: first double bond is on the 3rd carbon (C)
• ω -3s in a diet has health benefits
• Found in many fish (salmon, mackerel) and fruits and vegetables
Triacylglycerols
• Triacylglycerols are a types of lipids
• Triacylglycerols = glycerol + 3 fatty acids
Triacylglycerols
• Function: energy storage
• Storage fat in animal tissues
• How do we get energy from triacylglycerols?
• Answer: breaking hydrocarbon bonds to form lower energy products
• β-oxidation converts components of triacylglycerols into a form that can be converted
to energy like carbohydrates
Sterol Lipids
• Sterol lipids can act as signaling molecules
• Hormone: signaling molecule produced by glands that regulate physiology and behavior
• Used to communicate between organs and tissues
• Ex. Estrogen and testosterone
Sterol Lipids
• Sterol lipids also play a role in cell structure
• Cholesterol is the principle sterol synthesized by animals
Cholesterol
• Cholesterol is an essential structural component of animal cells
• Helps maintain membrane structural integrity and fluidity
• Because of cholesterol, animal cells do not need a cell wall, thus it can:
• Change shape
• Move around
Cholesterol
• Dietary sources: cheese, egg yolk, meats
• Certain cholesterol is not good for your body
• Bad: LDL
• Diseases: atheroma
Good: HDL
Phospholipids
• Phospholipid = phosphate +
glycerol + 2 fatty acids
• Phospholipids are lipids that make
up cell membranes
• They form a lipid bilayer
Discovering the Lipid Bilayer
• How do we know the cell membrane is a lipid bilayer?
• Scientific discovery!
• Here is how
• 1925: Gorter and Grendel red blood cell experiment
Review
• Macromolecules: large molecule made by putting together smaller repeating
units
• Main function of lipids:
1. Energy storage
2. Signaling
3. Structure
Review
• Fatty acids are amphipathic
• Triacylglycerol: glycerol + 3 fatty acids
• Energy storage
• Sterol lipids are important for signaling and structure
• Hormones and cholesterol
• Phospholipids are important for structure
Proteins
Protein
• Functions:
• Catalyzing metabolic reactions
• Replicating DNA
• Molecule transport
• Structure
• Skin, nails, muscles
Protein
• Protein: macromolecules made up of amino acids
• Polymer: polypeptide
• Monomer: amino acid
• Our polypeptide is our puzzle and our amino acid is our puzzle piece
• Proteins differ mainly in their amino acid sequence
Standard Amino Acids
• Sequence of amino acids in a protein is specified by a gene
• Gene says which puzzle pieces to put together
• Our genetic code specifies 20 amino acids
• We have 20 different types of puzzle pieces to choose from
• We can put any combination of amino acids together
• Our puzzle can be as big or as small as we want
Peptide Bonds
• Peptide bond: covalent chemical bond formed between 2 amino acid
molecules
• Carboxyl group of 1st amino acid bonds with amine group of 2nd amino acid
• Condensation reaction – water is released
Primary (1º) Structure
• Primary structure: amino acid sequence
• A chain of puzzle pieces put together
• Ex. Serine-Threonine-Valine-Leucine-Valine
Secondary (2º) Structure
• Secondary structure: repeating structures stabilized by hydrogen bonds
α helix
β sheet
Question: What is the main secondary structure
in the protein myoglobin?
1. α helices
2. β sheets
Answer: 1. α helices
• Myoglobin was the first protein to
have its structure solved by X-ray
crystallography
Tertiary (3º) Structure
• Tertiary structure: 3-dimensional structure of a protein
• Protein folding
• Controls basic function of a protein
Question: Which amino acid is most
likely to interact with leucine?
Quaternary (4º) Structure
• Quaternary structure: multiple protein subunits
Question: How many quaternary subunits does
the following protein have?
• Video is here
1.
2.
3.
4.
5.
1
2
5
10
20
Answer: 10 subunits
Enzymes
• Enzyme: catalyzes chemical reactions
• Responsible for thousands of biological processes that sustain life
• Enzymes are HIGHLY specific
E + S ↔ ES → E + P
Question: Which
interaction is not
favorable?
Answer: Interaction 4
Design Challenge
• Work in groups of 2 or 3
• Think of a function of the body and design an enzyme that can accomplish
this function
• Think about primary, tertiary, and quaternary structures
• Remember: structure determines function!
Example Project
• Function: transporting Na+ outside the cell and K+ inside the cell
Quaternary structure:
2 subunits
Hydrophobic/Nonpolar Amino Acids
Hydrophilic/Polar Amino Acids
Protein Functions
•
•
•
•
Catalyzing metabolic reactions
Replicating DNA
Responding to stimuli
Transporting molecules from one location to another
Present!
1.
2.
3.
4.
Introduce your group
Say which function you chose
Draw your protein
Explain its structure
1. Primary, secondary, tertiary, and quaternary
Studying Protein
• We study proteins for many reasons
• Medicines
• Diseases
• Methods to studying proteins:
• Protein purification
• Cellular localization
• Proteomics
• Bioinformatics
Protein Purification
• Protein purification: isolation of proteins from cells or organisms
• Why? Here.
Steps:
1. Isolate all proteins from mixture
2. Separate protein of interest from other proteins
Protein Purification
1.
2.
3.
4.
5.
Cell lysis
Ultracentrifugation
Precipitation
Chromatography
Gel electrophoresis, spectroscopy, or enzyme assays
Review
• Protein: macromolecules made up of
amino acids
• Peptide bond: covalent chemical bond
formed between 2 amino acid molecules
Review
•
•
•
•
Primary structure: amino acid sequence
Secondary structure: repeating structures stabilized by hydrogen bonds
Tertiary structure: 3-dimensional structure of a protein
Quaternary structure: multiple protein subunits
Review
• Enzyme: catalyzes chemical reactions
• Protein purification: isolation of proteins from cells or organisms
Carbohydrates
Carbohydrates
• Carbohydrates: macromolecules
consisting of C, H, and O atoms
• Monomer – monosaccharide
• Polymer – polysaccharide
• Glucose – the main monosaccharide
Monosaccharides
Glucose (C6H12O6)
Fructose (C6H12O6)
Galactose (C6H12O6)
Function
• Energy release
• Starch and glycogen
• Structure
• Cellulose in plants
Energy Release
• Glycolysis + TCA/Citric Acid/Krebs Cycle +Electron Transport Chain
• Generate energy in the form of ATP
ATP
Glycolysis
TCA Cycle
Electron Transport Chain
Nucleic Acids
Nucleic Acids
• Nucleic acids: macromolecules essential for all forms of life
• Monomer – nucleotide
• Polymer – nucleic acid
• Examples: DNA and RNA
DNA
• Deoxyribonucleic acid (DNA): encodes genetic instructions for development
and functioning of all living organisms
• DNA is only recently understood
• 1953: Discovery of the double helix – Watson and Crick
• 1984-2003: Human Genome Project
• World’s largest collaborative biological project
• Really cool video here
Fun Stuff
Want to See Cool Chemical Reactions?
Here is a few.
Here is another.
How about this one?
I think this is pretty neat.
But wait, watch this!