Download Modified from Carley Karsten Lecture 8

Modified from Carley Karsten
Lecture 8-10 Study Guide
I have organized some terms and topic that I think are important. This does not mean that
other topics mentioned during lecture or in the book will not be tested. This guide is meant
to clarify and emphasize certain points, NOT to list everything you need to know. I will focus
on tying things together across lectures, and giving real-life examples of the biological
principles that we are learning. Details that I include that I think will be helpful, but that you
don’t need to know, I will write in green. Questions to think about I will write in blue.
Lecture 8: Carbohydrates and lipids
Chemistry review:
1. Valence electrons = electrons in the outer ring of an atom that participate in bonding.
These are the atoms that are SHARED in covalent bonds, and EXCHANGED in ionic
bonds.
a. atoms generally “want” to have eight electrons in their outer ring: bonds form so
that as many atoms as possible can fill their outer rings.
b. for the purposes of this class, remember that these common atoms have the
listed number of valence electrons:
Hydrogen – H – 1 *Hydrogen is unique because it only needs 2 valence electrons
(rather than 8, like other atoms) in order to be stable.
Carbon – C – 4
Nitrogen – N – 5
Oxygen – O – 6
c. Consider water: H—O – H
Each H has one valence electron to share, and needs one more electron to feel
stable (remember, hydrogen only wants 2). The O has six valence electrons to
share, and needs two more to feel stable (it wants 8). When we put them all
together, each H shares its single valence electron with O, giving O 8 total
electrons, and O shares one extra valence electron back with each H, giving each
H 2 total electrons.
Draw a diagram like this one, pushing electrons around, to show how an ionic bond
forms between Na (one valence electron) and Cl (7 valence electrons). Where do the
charges on the atoms come from?
2. Drawing carbon-based molecules: in organic chemistry every point is a carbon and CH bonds are not shown. Look at the following examples:
Name
All atoms shown
Structurally Accurate
Short Hand
Modified from Carley Karsten
Propane
C3H8
Isopropanol
C3H80
I will be using this drawing style throughout this guide and my discussion. Please let me
know if you have questions.
Functional groups
1. Hydroxyl
2. Carbonyl
3. Carboxyl
4. Amino
5. Sulfhydryl
6. Phosphate
7. Methyl
-OH
-C=O
-COOH
-NH2
-SH
-PO4
-CH3
polar
polar
polar / acidic
polar / basic
polar
ionic
nonpolar
important for hydrogen bonding
can give up an H to make –COOcan accept an H to make –NH3+
covalent bonds can form between –SH groups
makes molecules unstable. source of energy.
binds to nucleotides to change gene expression
Carbon-based macromolecules = carbohydrates + proteins + lipids + nucleic acids
1. all are polymers in the sense that they are strings of smaller units connected by
covalent bonds, BUT lipids are technically NOT polymers because their subunits are
not all the same.
a. polymerization = addition of monomers = lengthening of polymer =
dehydration / condensation reaction  Why is this called “dehydration”?
(think about the role that water plays in the reaction)
b. depolymerization = removal of monomers = shrinking polymer = hydrolysis
2.
Carbohydrates
a.
polar molecules
b. monomers = monosaccharides. Glycosidic bonds form between subunits.
c.
often contain hydroxyl, carbonyl, and methyl groups
d. used for energy storage and cell structure
3.
Lipids
a.
hydrophobic molecules
b. ester linkage = bond between subunits
c.
rich in nonpolar functional groups made of lots of C—H bonds
d. three types of lipids
i. fats = glycerol + 3 fatty acids. What is the difference between saturated
Modified from Carley Karsten
and unsaturated fats? Why are saturated fats generally worse for health
than unsaturated fats?
ii. phospholipids = glycerol + 2 fatty acids + phosphate group + choline.
Don’t worry about choline. What’s important here is that phospholipids
are amphipathic- they have both hydrophobic and hydrophilic domains.
This is very important for the plasma membrane, as you may remember.
iii. steroids = based on carbon rings, therefore nonpolar. example: cholesterol.
Lecture 9: Proteins
Proteins do all the exciting things in cells: transmit signals, catalyze reactions, transport
molecules and organelles, and more! Enzymes and receptors are both specialized types of
proteins.
Protein structure
1. Proteins are polymers. monomers = amino acids; polypeptide = string of amino acids.
protein = polypeptide with 3D structure (folding, coiling, etc.)
a. amino acids = amino group + α carbon + side chain + carboxyl group. The
backbone of any polypeptide will follow this same pattern:
The amino acid “backbone” is shown in blue. This is the repeating pattern (NC-C) that you should look for to identify a polypeptide. Note that the center
carbon is the “α carbon”, or the carbon with a side chain (“R group”).
Question: when a dehydration reaction takes place, which Hs and O leave as
water?
b. the side chain (or R group) is what determines how an amino acid behaves. If
you are asked to identify whether an amino acid is polar, nonpolar, or ionized,
look at the side chain ONLY. The amino group and the carboxyl group in the
amino acid backbone are part of EVERY amino acid, and thus don’t affect any
single amino acid’s function. The side chain is what matters!!
c. amino acids are connected by peptide bonds (which are covalent bonds) that
are formed by dehydration reactions
*Note: polypeptides, cytoskeletal filament polymers, polysaccharides, and
nucleic acids ALL use dehydration reactions to form. They also all have
polarized ends – for example, microtubules have plus and minus ends,
polypeptides have amino and carboxy ends, and nucleic acids have 5’ and 3’
ends.
d. polarized ends:
i. amino end = “N terminus” because it’s based on –NH2 group
ii. carboxy end = “C terminus” because it’s based on –COOH group
2. four levels of protein structure
Modified from Carley Karsten
a. primary: amino acid sequence. determined by covalent (peptide) bonds
between amino acids.
b. secondary: coils and folds. determined by hydrogen bonds between amino
and carboxy groups in the backbone.
c. tertiary: complex folding. determined by all kinds of bonding between any of
the different R groups. strongest possible R group interactions are between
two amino acids containing sulfur (disulfide bridge).
d. quaternary: two or more polypeptides interacting.
3. environmental effects on protein structure
a. pH / salt concentration / temperature: usually only affects higher levels of
structure, but if you get REALLY extreme then you can mess up even primary
structure. Why would this be? (think about the kinds of bonds involved in
primary structure vs. secondary or tertiary structure)
b. chaperone proteins help proteins to fold correctly, and to STAY folded
correctly
c. proteins that aren’t folded properly are degraded by proteasomes (remember:
enzymes are usually named with “-ase” at the end… “proteasome” =
“protease” = “protein” – “ase” = something that chops up proteins)
Lecture 10: Nucleic acids and ATP
Nucleic acid structure = string of nucleotides
1. nucleotide = nitrogenous ring + sugar + phosphate group(s)
a. nitrogenous ring = rings made of carbon and nitrogen. Either pyrimidine (one
ring) or purine (two rings).
i. pyrimidines = C, T, U (T exists only in DNA, and U exists only in RNA)
ii. purines = A, G
b. sugar = 5-carbon ring. DNA uses deoxyribose, RNA uses ribose. Deoxyribose =
ribose without a hydroxyl group (“de-oxy” means “without oxy”).
c. phosphate group = -PO4. Important for linking together the sugars of
adjacent nucleotides to make a polynucleotide.
2. DNA is double stranded: THIS IS IMPORTANT!
a. the double helix structure is formed from hydrogen bonds between base
pairs. We will talk more about this in a couple weeks when we get into
transcription, etc.
b. considering the sugar/phosphate backbone of DNA, there are two distinct
ends:
i. phosphate end – 5’
ii. hydroxyl end – 3’
these ends arrange “antiparallel” to each other. That is, the 5’ end of one
strand of the DNA double helix will be next to the 3’ end of the other strand.
Again, we will talk more about this in a couple weeks. For now, just
remember the term “antiparallel”
Energy
1. EXERGONIC reactions: HIGH  low energy state. May also think about this as going
from an unstable to a stable state (e.g. a molecule losing a phosphate group). Since
the system is losing energy, these reactions can occur spontaneously.
Modified from Carley Karsten
2. ENDERGONIC reactions: low  HIGH energy state. Alternatively, going from a stable
to an unstable state (e.g. adding a phosphate group to a molecule). These reactions
require an input of energy to occur. Thus, they can’t occur spontaneously.
3. ATP is the most common source of cellular energy because it can donate phosphate
groups.
a. ATP = ribose + adenine + 3 phosphate groups.
b. The three phosphate groups are what make ATP so energetic: all those
negative charges crammed together “want” to get away from each other.
When they do, ATP goes from a high energy state (3 phosphates, unstable) to
a low energy state (2 phosphates, stable), thereby releasing energy (exergonic
reaction).
Question: look at the structure of ATP. Which other macromolecule does it most
resemble? (carbohydrates, lipids, proteins or nucleic acids)
4. ATP is constantly regenerated
a. cellular respiration (more details in the next lecture) uses fuels such as
glucose to CREATE more ATP
b. ATP hydrolysis occurs all the time and everywhere in order to power cellular
activities such as transportation, signal transduction, and building
macromolecules
5. Enzymes
a. allow reactions to occur using LESS ENERGY by changing the shape or location
of reagents
b. allow reactions to happen FASTER because there is less energy needed
c. allow reactions to be SPECIFIC because the shape of the active site is specific
d. enzymes are usually named with “-ase” at the end, and whatever comes
before the “-ase” usually gives some hint as to what the enzyme acts on (e.g.
peptidase breaks down peptides; lipase breaks down lipids; cellulase breaks
down cellulose; lactase breaks down lactose… people lacking the enzyme
lactase are unable to digest lactose, a sugar found in milk, and become
lactose intolerant)