Topic 4

1. What kinds of differently-shaped polymers can carbohydrates make?

Cellulose, starch, and glycogen
2. Why can most organisms hydrolyze starch, but not cellulose?
Because the polymers pack together to make a tough cell wall, while the in starch the polymers
branch out allowing for easier access for the enzymes.
3. Know the basic structure of nucleotide monomers (and how the sugars differ slightly in DNA and
RNA), and the 2 main types of bases (purines & pyrimidines)
RNA is more reactive because of the O (it is more electronegative) short term storage
DNA is missing an O in the 2
nd
position- allows for long tern storage

RNA is able to form 3 dimensional structures by pair bonding with itself or pair bonding with
DNA
Pair bonding is very specific- always a pyrimidine with a purine
4. In the NYTimes article "Chemist Shows How RNA..."
1. What problem have chemists encountered for many years in supporting the hypothesis
that the foundation of life began with self-replicating RNA molecules?
RNA did not spontaneously appear
2. What did Dr Southerland (the chemist of the title and of the new research) do
differently?
Half base, half sugar, then shone an ultra violet on them
3. How have other chemists responded to his conclusions? Has the response been
unanimous?
They disagreed stating that cyanoacetylene is to easily destroyed also they chemical
reaction would need to take place in 60 degree Celsius and ultra violet light.
5. Why does a purine always base pair with a pyrimidine? (What would happen if two purines, or
two pyrimidines were to pair-bond?
If a purine-purine bonded together there would not be enough space between the molecules
If a pyrimidine with a pyrimidine were together there would be too much space
6. What are the 2 types of polymers that nucleotides make? What kind of bonding is involved?
What is the name of the covalent bond?
The two polymers are purine and a pyrimidine- they come together in weak bonds.
Nucleotides form phosphodiester bonds.

1. How do lipids differ from the other 3 classes of macromolecules?
Lipids are non-polar and do not form polymers
2. What does "saturated" mean, in the context of fatty acids? What is the effect on the shape of
the fatty acid if it is not saturated? Which are liquid or solid, and why?
Saturated because the carbons can each bond to 2 hydrogens: they are saturated with
hydrogens Higher H:C
Unsaturated with short kinked tails are liquid at room temperature
Saturated lipids with long straight tails are solid at room temperature
Saturated fats can make straight linear shapes and thus can pack tightly together as solids at
ambient room temperature

3. Which kinds of fats can be problems in human diets: saturated, unsaturated,
polyunsaturated, or partially hydrogenated?
Poly unsaturated and unsaturated fats are best for human consumption
Saturated and hydrogenated fats are bad for human consumption
4. What is special about phospholipids and how are they able to form barriers in cells?
Phospholipids are amphipathic they have a hydrophilic head and two hydrophobic fatty acid tail.
The tails are driven to the middle spontaneously because they do not like water.
The bilayer is an effective barrier to the simple diffusion of polar molecules in and out of the cell.
5. What are the three classes of macromolecules that make up membranes?
Lipids, proteins and carbohydrates
6. Explain the "fluid mosaic model."
The membrane is fluid in the sense that all of the molecules that make it up are constantly
moving and shifting. It is mosaic that it is made up of many part, lipids, proteins, and
carbohydrates
7. How do cells regulate the fluidity of membranes? What membrane elements would be
beneficial to an organism living in a very cold environment? In a very hot one?
More unsaturated fats means more diffusion
More cholesterol means less diffusion
Long fatty acids means less diffusion
Short tails means more diffusion
Cholesterol- only in animals- help regulate the stiffness in the membrane, more cholesterol
means more stiffness.
8. How does membrane function to keep important transmembrane proteins close to one another
(and why would they need to do that?)
They use lipid rafts to hold them together because in order to complete primary and secondary
transport more efficient, binding sites need to be clumped together so that another call has not
just one attachment site but several that are close together (cell communication)
9. What is it about phospholipids that enables them to form the barriers necessary to regulate cell
contents?
Their hydrophobic hydrocarbon tails make it difficult for polar molecules to pass through the
plasma membrane. This aids in regulating reactions in the cell
10. Proteins that are embedded in and cross the plasma membrane must have regions that are
hydrophilic and others that are hydrophobic. Where must each region be located, and why?
The proteins that are emended in the plasma membrane must be non-polar or they would not
be able to interact with the middle of the plasma membrane. The ends that interact with the
cellular and extra cellular fluid must be polar or they would fold in to not react with water
11. What functions do carbohydrates play in membranes?
The carbohydrates are attached to the outer surface of the proteins (glycoproteins) or lipids
(glycol lipids) as carbohydrate ID tags that allow for cell recognition
12. What role does cholesterol play?
Cholesterol is only found in animal cells. Cholesterol aid in stiffening the membrane and
reducing fluidity
13. Why can't amino acids, sugars, and ions simply diffuse across the plasma membrane with their
concentration gradients?
They are polar and thus blocked by the non-polar hydrocarbon chains of the phospholipids they
are also large and have a hard time getting through the tight clustering of the lipids.
14. How can cells regulate their permeability by regulating the lipid tails in their membranes? How
does this work?
By increasing the amount of cholesterol and saturated fats in the fatty acid tails that make up
the membrane or making longer fatty acid tails, all result in stiffer membranes. Low cholesterol
more unsaturated fatty acid tails and short fatty acid tails make for more fluid membranes
15. List/describe at least eight specialized functions that proteins play in membranes (including the
3 different kinds of junctions).
Homeotyphic binding- identical cells are able to freely bind with each other
Tight junctions- form a quilted seal - barring the movement of dissolved materials through the space
between the epithelial cells
Gap junctions- they allow for adjacent epithelial cells to communicate through the plasma
membrane
Channel and carrier proteins- Allow for specific substances through the lipid bilayer
Heterotypic binding- different cells have specialized shapes at hook up sites in order to connect to
one another
Desmosomes- they link adjacent epithelial cells tightly but permit materials to move around them in
the intercellular space
Energy transformation- proteins embedded in the membranes are used in energy transformation
such as proteins used in photosynthesis were ATP is produced
Information processing- proteins receive signals from outside cell that results in a cell reaction.

16. Diffusion proceeds until molecules reach equilbrium. What does this mean? Do the molecules
stop moving? What drives diffusion?
Diffusion is the process of random movement towards a state of equilibrium. Equilibrium is
when there is a uniform distribution of solutes. Solutes will continue to move but the
concentration of solutes will be distributed equally in the solution. Diffusion is driven by entopy,
but its rate can be effected by a concentration gradient. When a concentration gradient exists,
there is a net movement from regions of high concentration to regions of low concentration; it a
spontaneous process because it results in an increase in entropy (disorder)
17. Understand the terms "hypotonic, isotonic, hypertonic", and be able to explain the results of
placing a cell in each of these types of solutions.
i. hypertonic: there is a concentration of solutes outside the cell which leads to the cell shrinking
as water diffuses outside the cell (the solutes outside the cell can't diffuse through the membrane
into the cell, but the water can easily diffuse to the outside)
ii. hypotonic: there are less solutes outside the cell than inside which leads to water diffusing
into the cell and often causing them to burst
iii. isotonic: there is an equivalent solute concentration inside and outside the cell which allows a
cell to retain its normal shape
18. What are the main differences between passive and active transport? (And be familiar with the
different kinds of each.)
Passive/facilitated transport is the process of spontaneous passive transport driven by a
concentration gradient.
i. channel proteins: each channel protein has a structure that permits only a particular type
of ion or small molecule to pass through
ii. carrier proteins: facilitate diffusion by binding to the molecules they allow across; they
change shape during the transport process
19. How do cells take in or get rid of molecules too big to pass through protein channels?
i. endocytosis: wraps a part of the plasma membrane around the molecule and often breaks it
down within that vesicle
ii. exocytosis: a vesicle full of proteins that will be secreted fuses with the plasma membrane and
is released into the extracellular space and picked up by the circulatory system
20. Beyond the role of regulating the contents of cells, what are three additional functions of
membranes?
i. organizing chemical reactions
ii. energy transformation
iii. information processing
21. In what way are membranes "dynamic"?
Elements of the membrane are continually forming, moving, fusing, and breaking down.
Topic 6

1. All cells come from pre-existing cells (= Cell Theory), and therefore have in common many
processes, molecules, and structures.
All organisms consist of cells, and all cells are derived from pre-existing cells, and therefore have
in common many processes, molecules, and structures.
i. nucleic acids that store and transmit information
ii. proteins that perform most of the cell's funcitons
iii. carbohydrates that provide chemical energy, carbon, support and identity
iv. a plasma membrane, which serves as a selectively permeable membrane barrier
2. What is a cell, and what is thought to be the adaptive advantage of this?
Cells consist of organelles enclosed in a plasma membrane in order to regulate the internal
environment to encourage favorable reactions.
3. Why are cells limited in size by their surface area-to-volume ratio?
The surface area becomes proportionally smaller and smaller compared to the volume so that
the effectiveness of a plasma membrane is limited. Diffusion takes too long within a large
volume.
4. What is the function of the plasma membrane, and what is it about phospholipids that allow this?
The plasma membrane functions:
i. regulate the cell's contents
ii. energy transformation
iii. organizing chemical reactions
iv. information processing
The phospholipid bilayer consists of a hydrophobic interior and hydrophilic heads.
5. What are the functions of the cell wall (for those cells that have them)?
Only prokaryotes have a cell wall which is a tough fibrous layer that surrounds the plasma
membrane and protects the organism and gives it its shape.
6. How do prokaryotes differ from eukaryotes in size and structure?
Prokaryotes:
-the DNA is in the nucleoid and not membrane bound; plasmids common
-limited organelles
-limited cytoskeleton
-small and single celled
-flagella

Eukaryotes:
-DNA in the nucleus
-many organelles (mitochondria, golgi, ER, centrioles)
-extensive cytoskeleton
-multicellular and larger
7. Are some prokaryotes able to perform photosynthesis and respiration, even though they have
no chloroplasts or mitochondria? Explain.
Yes; some prokes have photosynthetic membranes.
8. What are the main differences between prokaryotes and eukaryotes?
Prokes are single-celled and small with very few organelles while eukaryotes are multicellular
and have organelles (compartmentalization).
9. What is the function of the 1) nucleus, 2) endoplasmic reticulum, 3) Golgi apparatus, 4)
lysosomes, 5) mitochondria, 6) chloroplasts 7) peroxisomes, 8) vacuoles, 9) cytoskeleton (there
are several), and 10) the extracellular structures presented in class?
-rough ER: newly manufactured proteins undergo folding and other types of processing
-smooth ER: synthesize and destroy lipids; detoxification; calcium iron reservoir
-golgi apparatus: protein sorting and vesicle transportation
-lysosomes: recycling centers that hydrolyze macromolecules
-mitochondria: site of ATP production
-chloroplasts: where sunlight is converted to chemical energy during photosynthesis
-peroxisomes: reduction-oxidation (redox) reaction centers of fatty acids, enthanol, etc
-vacuoles: (found only in plant and fungi cells) are storage depots and give the plant's cells
shape (also filled with pigments or noxious compounds)
-cytoskeleton (there are several): give cell's shape, shift its contents, move the cell itself
-the extracellular structures presented in class: providing support, segregating tissues from one
another, and regulating intercellular communication. The extracellular matrix regulates a cell's
dynamic behavior
10. What cellular structures would be involved in the production and export of a protein that needs
to be excreted by the cell?
1.RER
2. cis Golgi cisternae
3. medial Golgi cisternae
4. trans Golgi cisternae
5. plasma membrane
11. How do the nuclear pores regulate what goes in and out of the nucleus?
Nuclear pores only allows specific molecules to pass in and out.
12. What are the functions of the cytoskeleton? (see section 7.4 in the text). What functions do the
molecular motors dynein and kinesin perform?
Functions of the cytoskeleton include producing cell shape, support cell (ex: microvilli of gut
epithelial cells), shift cell's contents, move the cell (ex. cilia).
Dynein and kinesin both are protein motors that move the cell.
13. What are the functions of the extracellular matrix?
Functions include providing support, segregating tissues from one another, and regulating
intercellular communication. The extracellular matrix regulates a cell's dynamic behavior.
14. What is the evidence that supports the endosymbiotic theory of the evolution of mitochondria
and chloroplasts?
Organelles have their own DNA which is circular like prokes. They are also proke-sized and
divide separately from the cell.
15. Do eukaryotes have any advantages over prokaryotes? How about the reverse? Which is the
predominant life-form on Earth?
Eukaryotes are larger, but prokaryotes can live in more extreme and variety of environments.
Prokes are the dominant life-form on earth.
16. Regarding the Natalie Angiers NYTimes cell article:
o In trying to create artificial cells, what are scientists continually impressed with?
o What are "extremophiles"?
o How are some extremophiles able to live in extremely high radiation (what happens to
them, and how do they respond?)
o What did scientist discover when they began looking for new genetic material in the
world's seas? Did they find new life forms? Can they culture these potential new life
forms in the lab?
o What kinds of lipids must microorganisms that live in very high temperatures have in
their membranes? How about those that live in very low temperatures?
i. They are impressed by real living cells with their flexibility and versatility.
ii. An organism that thrives in physically or geochemically extreme conditions that are
detrimental to most life on Earth.
iii. The chromosome gets blown apart but then it stitches itself back together and starts
replicating again.
iv. They found 6 million new genes.
v. No, just DNA. They were unable to identify the microbe organism.
vi. They were unable to cultivate it in the lab because it doesn't liked to be confided to plates.
vii. They have stiffening lipids in their membranes = cholesterol.
viii. They have very fluid membranes.
17. Regarding the Carl Zimmer NYT article on the "Body's Microbial Garden"
o What kinds of beneficial things do bacteria do for us?
o Are bacteria the only members of the beneficial microbiome?
i. They maintain the health of our bodies.
ii. Our bodies also host viruses.
Topic 7

1. Metabolism is ... , and it consists of two main categories of reactions:
Metabolism consist of all chemical reactions involved in maintain the living state of an organism
and consist of
i. catbolic reactions
ii. anabolic reaction
2. What is the main idea of the first law of thermodynamics, and how does this relate to the
biological reactions we'll be studying?
Energy is neither created nor destroyed. The amount of energy after the transformation equals
the amount of energy before the transformation.
3. What is the main idea of the second law of thermodynamics, and how does this relate to the
biological reactions we'll be studying?
Not all energy after the conversion can be used and is never 100% efficient. Illustrates that the
nature of the Universe tends towards disorder (entropy).
4. What is an exergonic reaction, and why is its G less than 0?
An exergonic reaction is spontaneous and are catabolic (releases energy). G less than 0 because
the products are NOT absorbing any energy.
5. What is an endergonic reaction, and why is its G greater than 0?
An endergonic reaction is non-spontaneous and is anabolic (requires an input of energy) which
leads to its G being more than 0.
6. Life requires a constant input of energy in order to fight disorder. Where does the energy
required to drive endergonic reactions usually come from? Where is the energy in this molecule?
This energy comes from covalent bonds, most often from phosphates that release ATP.
7. What is meant by the term "coupling" in the context of using ATP to fuel endergonic reactions?
ATP must first be synthesized into ADP in order to be used later in an endergonic reaction. An
endergonic reaction takes places to hydrolize ADP + Pi = ATP. When energy is needed later ATP
undergoes an exergonic reaction and breaks a Pi from the ATP. This energy is then transferred
and utilized in a cellular endergonic reaction.
8. What is activation energy, and why do even exergonic reactions have them?
Activation energy is the energy needed to get molecules into their unstable transition states,
where they are more likely to undergo the reaction/change. Even exergonic reactions have
activation energy because their bonds begin stable and need to be made unstable in order to
later release a large amount of energy (the released energy in an exergonic reaction is
ALWAYS larger than the activation energy).
9. Enzymes do not effect the equilibrium point or the G of a reaction. What DO enzymes do, and
how?
Enzymes work to speed up reactions by lowering the activation energy of the reaction by 1)
brining molecules together so they are more likely to react and/or 2) making molecules unstable
by stressing their bonds or by changing the molecules' chemical properties.
10. How do the specific 3-dimensional shape and chemical properties of enzyme active sites
determine enzymes ability to function?
The enzyme's 3D shape fits their specific substrate only in a very precise way so that each
enzyme catalyzes only one reaction and fits only one (or one set of) substrate(s).
11. Why do enzymes change shape when they bind substrate?
This is called induced fit, and enzymes do this so that the substrate can precisely fit into the
active site. This also explains why enzymes are so large because there must be a precise 3-D and
chemical property fit between the enzyme and substrate, and the only way to maintain that
specificity through a shape change in the active site during binding is to have a large, stable
superstructure around the active site that can bring the active site back into its proper
configuration after the bind-and-release.
12. Look at Fig. 6.14 above. Why does the reaction rate plateau (level off)? Why does the addition of
more substrate not increase the reaction rate, past a certain point?
Reaction rates plateau because as the enzyme concentration remains constant the substrate
concentration rises until it has saturated all the enzymes. The only way to increase the rate even
more is by adding more enzymes.
13. What do coenzymes and cofactors do?
Coenzymes are organic molecules that reversibly interact with enzymes. Cofactors are inorganic
ions that reversibly interact with enzymes.
14. Why do cells need to regulate enzyme activity?
In order to active or inactivate an enzyme according to a cell's needs.
15. Since most metabolic processes consist of cascades (long pathways) of reactions, there are
many points at which to control the production of the end product. What are these points?
The enzymes (arrows)
16. There are 2 main categories of enzyme inhibition: reversible and irreversible. How do they differ,
and why?
Inhibitors can regulate enzyme activity. Irreversible inhibitors chemically (covalent bonded)
alter the active site of their target. Reversible inhibitors come in two forms and bind non-
covalently.
17. Within the category of reversible inhibition, there are two subcategories of enzyme regulation:
competitive and noncompetitive. How do they differ?
i. competive (reversible) inhibitors - competes with substrate for access to the enzyme's active
site
ii. noncompetitive (reversible) inhibitors - has its own differently shaped substrate; it binds to
the enzyme to close it form the substrate so that they won't make product
18. Allosteric enzymes are regulated by one type of noncompetitive inhibition. How does regulation
of these enzymes work, and why do they respond differently to increases in substrate
concentration? (Look at Fig. 6.20)
Allosteric enzymes are enzymes that 1) have multiple active sites (substrate-binding sites) and
multiple regulatory sites (inhibitor binding sites); and 2) cycle between active (active sites open,
inhibitor sites closed) and inactive (active sites closed, inhibitor sites open).

Due to cooperative binding, once substrate binds to an active site or inhibitor binds to a
regulatory site, it increase the affinity of another active site/regulatory site so that the reaction
rate increases exponentially in the middle of the reaction before plateauing.
19. Specifically, can increasing substrate concentration overcome 1) competitive inhibition or 2)
noncompetitive inhibition (including allosteric) and why/why not?
No, because once all the enzymes are saturated with substrate, there are no further enzymes to
be used, so the reaction rate cannot increase (it plateaus). In order to increase the reaction rate
you would have to add more enzymes for the substrates to bind to.
20. The synthesis of the amino acid isoleucine from threonine (Fig. 6.21) involves a metabolic
pathway that is regulated by negative feedback. What is negative feedback and how does it
work?
Negative/feeback inhibition is a convenient way for pathways to shut themselves down when
their activity is no longer needed. As the concentration of the product molecule becomes
abundant, it "feeds back" to stop the reaction sequence. By inhibiting a step early in the pathway,
the amount of the initial substrate is not depleted unnecessarily, allowing it to be stored or used
for other reactions.
21. How and why is enzyme function affected by pH and temperature?
Each enzyme works best at a certain pH (optimum), its activity decreasing at values above and
below that point. This is because of the importance of tertiary structure (i.e. shape) in enzyme
function and forces

As temperature increase the reaction rate increases until it hits the maximum rate.