Lesson 1: Proteins Proteins Made of amino acids linked by peptide bonds There are 20 types of amino...
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Transcript of Lesson 1: Proteins Proteins Made of amino acids linked by peptide bonds There are 20 types of amino...
Lesson 1:Proteins
ProteinsMade of amino acids linked by peptide bondsThere are 20 types of amino acids that we use (though many more exist)
Be able to draw a generalized amino acid!
The Amino Acids
Condensation and Hydrolysis
Condensation: joins amino acids into a dipeptide or polypeptide, produces water
Hydrolysis: breaks a polypeptide into amino acids, uses water
Peptide bondsAlthough “peptide bond” refers specifically to the bond C-N bond formed between two amino acids, it refers to a larger structure:
The dark grey bond is the peptide bond, but the entire pink area is needed .
Be able to draw two amino acids forming a peptide bond!
Primary structure Number (can be ~50–1000) and order of amino acids in a chain (polypeptide) held together by peptide bonds
Each polypeptide is coded for by a gene (in the DNA).
Enormous range of possibilities! (20n, n=# of amino acids)
Type / location of amino acids used relate to the protein’s function
Secondary structureHeld together by hydrogen bondsRegular and repeating, formed by N-C-C backboneTwo main forms
-helix (myosin, hair) -pleated sheet (silk)
Tertiary structure Final 3-dimensional folded shape of polypeptide R-groups mostly determine bonding; may include:
ionic bondsHydrogen bondscovalent (disulfide) bondshydrophobic interactions
Quaternary structure(Only in some proteins) 2+ polypeptide chains held together by all types of bonds, primarily through R-groupsConjugated proteins also include elements and structures called prosthetic groups that are not amino acids (part of quaternary structure)
Protein StructureReview
Primary - order of amino acidsSecondary - H-bonds in backboneTertiary - 3D shape from R-groupsSOMETIMES Quaternary - 2+ polypeptides and prosthetic groups
What levels can you find?
Explore the biotopics jsmol library. You should compare and contrast: glucagon, myogloblin, and hemoglobin.
Functions of proteinsStructure and support - microtubules influence cell shape, collagen in skin, spider silk in websTransport - hemoglobin carries oxygen, microtubules serve as highways in cells Movement - actin and myosin make muscle fibersCommunication - hormones, ex. insulinDefense – immunoglobin antibodies, lysozyme in tearsResponse – response, eg. rhodopsin in eyesEnzymatic reactions - speed up reactions, eg. Digestion of food, building cell parts, Rubisco in photosynthesisEnergy storage - ~4 Cal/gram (not considered a primary function)
Final Protein shapes: Fibrous
Fibrous - long, thin, insoluble in water
Collagen: STRUCTURE in skin, tendonsActin and myosin: muscle fibers allow MOVEMENT
Final protein shapes: Globular
Globular - rounded, bulky, mostly soluble in water
Hemoglobin: TRANSPORT oxygen in red blood cellsImmunoglobin: antibody DEFENSE against foreign substances
Significance of amino acid variety
The different R-groups allow a variety of shapes
The active sites of enzymes have the correct polarity and/or charge to attract the substratesNon-polar amino acids can be anchored in non-polar membranesA membrane channel protein can have non-polar R-groups on the outside and polar R-groups on the inside, creating a hydrophilic passageway through the membrane
Final Protein Shape Depends on Environment
A protein that has lost its function (usually permanent) is “denatured”Excessive heat (not cold) or unsuitable pH (acidic or alkaline) can disrupt bonding and denature the protein
Look at the production of “century eggs” (ไข่�เยี่��ยี่วม้า) – using pH to denature!
Genes and ProteinsDNA is for information storage only, while proteins have a huge variety of functions.Each individual of a species has a slightly different set of DNA (genome).Each gene in the DNA codes for a protein
Almost all species have the same code for translating from DNA to protein sequence!
Each individual has a unique proteome, influenced primarily by DNA but also by environment (stimuli like stress can turn genes on or off).
Discuss the connections between stem cell differentiation and proteomes.
Map of C. elegans (nematode worm) proteins
and their interactions
Lesson 2:Enzymes
Enzymes Made of protein
Globular Catalyze ONE (or very few) specific
reactions Speed up rate of reaction Lower the activation energy of a reaction Very specific to substrate molecule(s)
Activation Energy (Ea)
Collision TheoryIn liquids (like cytoplasm) molecules are moving around, knocking into each other (colliding)When some molecules strike at the right orientation, with enough energy they will react (split apart, combine, shift bonds, etc)
The rate of reaction without an enzyme can be noticeable, or it can be so rare that it’s basically never.
Enzyme structure The active site is where
the substrate binds (other molecules bounce off)
The enzyme is like a lock, and the substrate(s) are like the key(s) that fits it
Enzymes and Collision Theory
Enzymes capture substrate(s) that collide with the active site and hold them at an angle that places stress on existing bonds and aligns substrates (if more than one)This increases the rate of reaction, often by millions of times.
Which factors affect enzyme activity?
[ ] means concentration
Temperature = increased energy increased collisions increased rate, BUT increased too much will break bonds, denature the structure
pH = [H+] affects bonding, attracting or repulsing R-groups, can denature the protein
[Substrate] = at low levels more substrate increases rate of reaction because more collision, at high levels no effect because enzymes already saturated
Rate of reaction is also affected by [Enzyme] = a higher concentration will lead to more collisions, therefore more reactions
Factors Affecting Enzyme Function
Temperature
pH
[Substrate]
[Enzyme]
Be able to draw these graphs and discuss what is happening at each part!
Enzymes are evolved to work in their environments
Eg. All enzymes can be denatured by a pH that is unsuitable, but which pH is optimal (best) depends on the enzyme
Using animations to collect data
We will use this animation for modeling enzyme activity.
Inhibition of EnzymesCompetitive Substrate and inhibitor
both bind to active site Inhibitor and substrate
are often chemically related
Inhibitor physically blocks substrate
Non-competitive Substrate binds to
active site, inhibitor binds to allosteric site
Inhibitor and substrate not chemically similar
Inhibitor changes the shape of the enzyme and active site
Inhibition of Enzymes, cont.
Competitive Non-competitiveIn which case would the [substrate]
affect the rate of reaction?
Answer: Competitive; more substrate molecules will more successfully for the active site against the inhibitor
Competitive inhibition
• Ethanol is the alcohol found in drinks• Ethanol is converted to acetaldehyde• Aldehyde dehydrogenase immediately converts acetaldehyde to acetate so it never builds up•Further enzymes modify acetate for energy release or energy storage
• Disulfiram binds to the active site of aldehyde dehydrogenase, so acetaldehyde builds up causing nausea and discomfort• Used as a pill to treat alcoholism
Non-competitive inhibition Lead replaces zinc at an
allosteric site in aminolevulinic acid dehydratase (ALAD), an enzyme that helps produce hemoglobin
Changes shape of active site so ALAD does not function, leading to anemia
Lead inhibits many enzymes leading to many other symptoms including headache, insomnia, insanity, death
Why do both types of inhibition have an increased rate of reaction at low levels of [substrate]? Why does non-competitive inhibition show no effect from [substrate] at higher levels?
Compare the three conditions.
Metabolic pathways Many reactions are actually a
series of steps, each catalyzed by a different enzyme, in a chain or cycle
End-product inhibition -- Negative feedback
Helps maintain balance (homeostasis) by preventing overproduction
The final product serves as an allosteric inhibitor for an enzyme early in the pathway
End-product inhibition in threonine isoleucine
pathwayIsoleucine is an allosteric inhibitor of threonine deaminase, the first enzyme in the metabolic pathway that converts threonine to isoleucine.
Discuss the role(s) of:•Threonine•Threonine deaminase•Isoleucine
What happens when levels of isoleucine are low? High?
Use of lactase enzyme in lactose-free milk production Specific yeast is cultured to
harvest its lactase Lactase breaks lactose
disaccharide into glucose and galactose
People who lack this enzyme are lactose-intolerant
May have diarrhea, gas, and intestinal pain when eating dairy products
Lactase can be added to produce lactose-free dairy foods
Lactose Free Milk
MethodsAdd lactase directly to
milkImmobilize lactase on
a screen and slowly pour milk over (no lactase in final product)Non-enzyme method
Ultrafiltration
AdvantagesSweeter taste Digestible by
lactose-intolerant people
Fewer allergiesIf made into ice
cream, less grittyIf made into yogurt,
process is faster
Uses of immobilized enzymes
Removal of wastes from contaminated water
Pectinase and cellulase to release juice
Antibiotic production
Much more!
Using Databases to look for Anti-Malarial Drug
TargetsDeveloping medicines is extremely expensive and time consumingDatabases and pool knowledge and lab resultsAllows selection of most useful enzymes to target, or drugs that are known to be tolerated in humansEfficient and more rapid development
Read this abstract. What did the authors do?Explore the research database site TDRtargets.org. What makes a gene a good target?Links allow further exploration, including amino acid sequencing (see BRENDA)
Optional Challenge Activity!
Are you a gamer?Want a real challenge?Want to make a difference?Try Foldit!
Learn how amino acids interactLike a crazy-hard puzzle
Read an article here: Gamers took 3 weeks to solve a protein researchers had worked on for 10 years!
Can be used by HS students – see how far you can go!!
Lesson 3:Nucleic Acids
Nucleic Acid StructureNucleotide:Sugar (ribose /
deoxyribose)
PhosphateNitrogen Base
Nucleic acids are chains of covalently-bonded nucleotides
Nucleotides are the monomers (building blocks) of nucleic acids
Each nucleotide has thee parts.
Nucleic Acid FunctionsNucleic acids polymers include:
DNA: stores genetic informationRNA: relays relevant information from DNA to the rest of the cell; directs the production of proteins
One nucleotide (monomer):ATP: the energy currency used in cells
The Nitrogenous Bases Purines – two rings, the same in DNA and RNA
AdenineGuanine
Pyrimidines – one ringCytosineThymine (in DNA)Uracil (in RNA)
Nucleotides form Nucleic
AcidsEnergy is released from nucleoside triphosphates; two phosphates break away.
The phosphate of one nucleotide links to the 3rd carbon in the sugar of another
Creates a covalently bonded phosphate – sugar backbone
The DNA Double HelixNitrogen bases form specific (complementary) pairs
Adenine pairs with Thymine (A – T)Guanine pairs with Cytosine (G – C)
Notice that a purine always pairs with a pyrimidineEach complementary base pair forms hydrogen bonds
A-T form 2 hydrogen bondsG-C form 3 hydrogen bonds
DNA Double helix•Antiparallel
strands: in order for the nitrogen bases to form hydrogen bonds, the two DNA strands must be facing opposite directions
•Constant width: Because a small pyrimidine always bonds with a larger purine, the two strands are always the same distance apart
DNA double helix•The sugar-phosphate
backbones are on the outside of the helix
•The nitrogen bases form the flat inner rungs (steps on the ladder) of DNA
•If you know the order of Nitrogen bases on one strand of DNA, you can determine the other:
•Practice: ACTTGCCA
•Answer: TGAACGGT
DNA packaging in Eukaryotes
•In eukaryotes and archaea (NOT eubacteria) DNA is organized into nucleosomes:– 8 histone proteins, 2 loops of DNA, one histone
“tie”
DNA to
Chromosomes• DNA must be
uncoiled for the information to be “read” (transcribed)• DNA must be supercoiled when not in use or it will tangle and tear •Histone proteins organize the DNA by winding it up
RNA types•mRNA (messenger)
– Carries a copy information from individual genes to ribosomes (as needed)
•rRNA (ribosomal)– Acts as a catalyst (enzyme,
except not protein) joining amino acids into a polypeptide.
•tRNA (transfer)– Translates from nucleotide code
to assemble correct amino acid sequence
RNA v. DNA
Nucleic acid polym
er
# of strand
s
Nitrogenous bases
Pentose sugar Function
DNA 2, double helix
Thymine, Adenine, Guanine,Cytosine
Deoxyribose Genetics, information storage
RNA 1, not a helix
Uracil, Adenine, Guanine,Cytosine
Ribose Information transfer (DNA to protein), protein synthesis
Hershey-Chase Experiment, 1952
• For a long time, protein was considered most likely to be the genetic material– Complex enough to
store large amounts of information
• In the 1940s, evidence started to accumulate that DNA might be the genetic material– Led to many
researchers racing to determine the structure!
Hershey-Chase showed that that bacteriophage viral proteins do not infect bacteria cells, but viral DNA does!
Hershey Chase – experimental procedure
The Structure of DNA:The Great Race!
Three teams:
Caltech Cambridge King’s College
Linus Pauling James Watson & Francis Crick
Rosalind Franklin / Maurice Wilkins
Franklin (and Wilkins): X-ray crystallography
Photo 51: Go through this interactive.
Know at least that:•The “X” suggests a helix•The 4 white “diamonds” suggest a repeating helix•The “missing band” in the X suggests a double helix
Watson and Crick models• Like an early type of
“foldit” using cardboard cutouts of the different pieces
• Made to accurately represent bond length and atomic location
• Relies on modeler’s understanding of how elements would interact
• Published paper 1953