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Study list for HON1070 (Fall 2012)

1.  Basic chemistry

a.  Chemical properties of the major biologically-relevant elements: CHNOPS

Electronegativity scale: H (2.1), C (2.5) S (2.7?) N (3.0) O (3.5) F(4.0)

i.  Valence – the number of valence bonds a given atom has formed.

The amount of possible bonds an atom can make or has made. H  – has a

valence of one. O- two.  – this needs to be checked

ii.  Electronegativity – how strongly an atom pulls an electron towards it.

b.  Types of chemical bonds and their properties, with examples

i.  Covalent – electrons are shared.

1.  Polar – electrons spend most of their time closer to one atom.

2.  Non-polar – electrons are shared equally between atoms.

ii.  Non-covalent

1.  Ionic – between metal and non-metal. Electrons are transferred

from one atom to the other, and the two charged atoms stick

together through electrostatic forces.

2.  Hydrogen bonds – A bond between a Hydrogen atom that has a

partially positive charge and another highly electronegative atom

(that has a partially negative charge. Water forms hydrogen bonds

with other water molecules. )

3.  Hydrophobic bonds (Van derWaals; Entropy minimization)

Hydrophobic bonds are bonds are between non polar molecules;

low water-soluble molecules. Low soluble molecules are

generally non polar molecules with long carbon tails that do no t

interact with water.

c.  Van derWaals - In physical chemistry, the van der Waals force (or van der Waals

interaction), named after Dutch scientist Johannes Diderik van der Waals, is the

sum of the attractive or repulsive forces between molecules (or between parts of

the same molecule) other than those due to covalent bonds, the hydrogen

bonds, or the electrostatic interaction of  ions with one another or with neutral

molecules

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2.  Isotopes – definition, use as tools – isotopes are atoms with an additional or a lost

neutron(s).

3.  Organic Chemistry

a.  Molecular shapes – Molecular shapes determine the way biological molecules

interact with each other. For example An enzyme will only catalyze a specificreaction and no other reaction. A protein that responds to a signal molecule can

only be activated by that specific molecule (or something very similar to that

shape).

b.  Functional groups and their properties – (Some page in the text book). Pg 64 

4.  Biochemistry

a.  Macromolecules – monomers and basic structure (be able to recognize)

i.  Polysaccharides – complex sugars, made up of two or more glucose

molecules. (pg 71)

1.  Sugars – types and basic structure; ring structure in aqueous

solution. Two different glucose molecules: alpha and beta

glucose.

2.  Glycosidic bonds – There are alpha glucoses and beta glucoses

that can form different structures depending on how the glucose

molecules are bounded to one another. It is a covalent bond

formed between two monosaccharides by a dehydration reaction.

3.  Types of polysaccharides (cellulose, amylose) a polysaccharide is a

substance of many monosaccharides linked together by glycosidic

linkages. Cellulose (pg 72) is made up of glucose, but in glucose of

two different forms (alpha and beta). Cellulose is a major

component of the cell walls of plants – it is indigestible to

humans. (Bacteria in cows’ stomachs contain the enzyme that can

break down the bonds of cellulose.) Amylose is a form of starch (a

polysaccharide) that is made up of only alpha form glucose

molecules. It is used as energy and can be found in plants.

Animals have glucose polysaccharides too, but the one found in

animals is called glycogen.

ii.  Lipids (pg 74) 

1.  Triglycerides and fatty acids – glycerol is an alcohol. A fatty acid

has a long carbon skeleton , usually 16-18 carbon atoms in length.

The carbon at one end of the skeleton is part of a carboxyl group,

the functional group that gives these molecules the name fatty

acid. The rest of the skeleton is a hydrocarbon chain. In making a

fat, three fatty acid molecules are each joined by an ester linkage,

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a bond between a hydroxyl group and a carboxyl group. The

resulting fat, a triacylglycerol, consists of three fatty acids linked

to one glycerol molecule.

2.  Steroids – (pg 77) are lipids characterized by a carbon skeleton

consisting of four fused rings. Different steroids, such ascholesterol and the vertebrate sex hormones, are distinguished by

the particular chemical groups attached to the rings.

3.  Phospholipids – (pg76) A polar (hydrophilic head) made of a

phosphate group between a glycerol and a choline molecule. The

molecule is a fatty acid with two hydrocarbon tails, with the

phosphate group with the attached choline attached to the

glycerol end of the fatty acid. The hydrocarbon tail is non-polar

(hydrophobic).

iii.  Nucleic acids – Made of a phosphate, a sugar and a nitrogenous base.

There are 5 different nucleic acids. (pg 87)

1.  Monomer structures (memorize) – the 5 monomers are: adenine

and guanine which are purines (2 rings) and thymine, cytosine and

uracil which are pyrimidines (1 ring).

2.  Differences and similarities between DNA and RNA – DNA uses

Adenine and Thymine pairs and Guanine and Cytosine pairs, while

RNA uses Uracil instead of Thymine.

iv.  Proteins

1.  Amino acids – structures and properties (memorize) Are the

building blocks of polypeptides which form proteins.

2.  Levels of 3-dimensional structure

a.  Primary – linear sequence of amino acids.

b.  Secondary – a-helix & b-pleated sheet – made up of the

molecular interactions between amino acids. Formed

through hydrogen bonds.

c.  Tertiary – contribution of amino acid functional groups – 

The overall structure of the polypeptide; it is formed

through interactions of alpha helix and beta pleated

sheets.

d.  Quaternary – the interaction of multiple polypeptides to

form a protein.

3.  Denaturation and renaturation – When an enzyme is moved to an

area of PH that it doesn’t normally function in, or a temperature

that it doesn’t normally function in, the enzyme can unfold and be

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inactive. – It has been denatured. By placing the enzyme back in

its original environment, or by removing that which is causing it to

be denatured, it is possible for the enzyme to resume native

shape. There are permanent denaturing substances (molecules)

that bind to enzymes causing them to permanently change shape.Those enzymes cannot be renatured.

a.  Anfinsen experiment – the experiment on protein folding.

Renaturing RNase and then testing to see if activity

returned to the enzyme. The more time we allowed for

the enzyme to return to activity, the greater its activity

was. After a certain amount of time, the enzyme would

have been able to hydrolyze so much product that theproduct would inhibit its activity, causing a lower

percentage than previous samples (see XL graph in bio lab

folder).

b.  Sickle cell anemia: molecular mechanism. Sickle cell is the

replacement of one amino acid in a hemoglobin molecuse

polypeptide sequence by another, a valine replacing a

glutamic acid. (pg84) With this substitution, ahydrophobic region of the cell is to the outside instead of

the inside. “Normal red blood cells are disk-shaped, but in

sickle-cell disease, the abnormal hemoglobin molecules

tend to crystallize, deforming some of the cells into a sickle

shape.

c.  Degradation – Proteasome, ubiquitin, ubiquitin ligases

Proteasomes are protein complexes inside all eukaryotes and

archaea, and in some bacteria. In eukaryotes, they are located

in the nucleus and the cytoplasm.[1] The main function of the

proteasome is to degrade unneeded or damaged proteins by

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proteolysis, a chemical reaction that breaks peptide bonds. 

Enzymes that carry out such reactions are called proteases. 

Proteasomes are part of a major mechanism by which cells 

regulate the concentration of particular proteins and degrade

misfolded proteins. The degradation process yields peptides ofabout seven to eight amino acids long, which can then be

further degraded into amino acids and used in synthesizing 

new proteins.[2] Proteins are tagged for degradation with a

small protein called ubiquitin. The tagging reaction is

catalyzed by enzymes called ubiquitin ligases. Once a protein

is tagged with a single ubiquitin molecule, this is a signal to

other ligases to attach additional ubiquitin molecules. The

result is a polyubiquitin chain that is bound by the

proteasome, allowing it to degrade the tagged protein.[2]

Ubiquitin - Ubiquitin is a small regulatory protein that has

been found in almost all tissues (ubiquitously ) of  eukaryotic 

organisms. It directs proteins to compartments in the cell,

including the proteasome which destroys and recycles

proteins. Ubiquitin can be attached to proteins and

label them for destruction. 

Ubiquitin ligases - A ubiquitin ligase (also called an E3 ubiquitin ligase) is a protein that in

combination with an E2 ubiquitin-conjugating enzyme causes the attachment of  ubiquitin to a

lysine on a target protein via an isopeptide bond; the E3 ubiquitin ligase targets specific protein

substrates for degradation by the proteasome. In general, the ubiquitin ligase is involved in

polyubiquitination: A second ubiquitin is attached to the first, a third is attached to the second,

and so forth. Polyubiquitination marks proteins for degradation by the proteasome.

However, there are some ubiquitination events that are

limited to mono-ubiquitination, in which only a single

ubiquitin is added by the ubiquitin ligase to a substrate

molecule. Mono-ubiquitinated proteins are not targeted to

the proteasome for degradation, but may instead be altered in

their cellular location or function, for example, via binding

other proteins that have domains capable of binding ubiquitin

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d.  Prions and their associated diseases

5.  A prion - is an infectious agent composed of  protein in a misfolded form.[2] This is the

central idea of the Prion Hypothesis, which remains debated.[3] This would be in

contrast to all other known infectious agents (virus/bacteria/fungus/parasite) which

must contain nucleic acids (either DNA, RNA, or both). The word prion, coined in 1982

by Stanley B. Prusiner, is derived from the words protein and infection.[4] Prions are

responsible for the transmissible spongiform encephalopathies in a variety of  mammals, 

including bovine spongiform encephalopathy (BSE, also known as "mad cow disease") in

cattle and Creutzfeldt –Jakob disease (CJD) in humans. All known prion diseases affect

the structure of the brain or other neural tissue and all are currently untreatable and

universally fatal.[5] Prions cause other prteins to miss-fold.

a.  Enzymes

i.  Basis of catalysis - Catalysis is the change in rate of a chemical reaction 

due to the participation of a substance called a catalyst. Unlike other

reagents that participate in the chemical reaction, a catalyst is not

consumed by the reaction itself

Enzymes are the things which catalyze reactions. They are shaped to help specific

reactions occur, and no other. Enzymes are proteins made up of one or more

polypeptides. (A strand of RNA can also function as an enzyme). Enzymes havespecific shapes that allow specific molecules to enter the binding-site. At the

binding-site, the bonds of the substrates are stressed, lowering the activation energy

required for the reaction between the two reactants to occur. Enzymes may not be

reuired to cause a reaction occur, but they can greatly cause a reaction to speed up.

For example, one can make a reaction that on its own would not show any

appreciable change, even over many years, but with an enzyme present, the

reaction may take place in minutes.

ii.  Equilibrium and reversibility of chemical reactions

Equilibrium is when the reactants and the products of a reaction are proportionally balanced

(The actual amount of substances does not have to be equal). In equilibrium, there is no net

change of product of reactant.

iii.  Thermodynamics – The study of the energy transformations that occur in

a collection of matter. (pg144-145)

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1.  Go, DS : definition and importance – 

G – Free-energy change. (pg146) Free energy is the portion of a system’s energy that can

perform work when the temperature and pressure are uniform throughout the system, as in a

living cell. The change in free energy, G = H -TS. This equation uses only properties of the

system (the reaction) itself: H symbolizes the change in the system’s enthalpy (in biological

systems, equivalent to total energy); S is the change in the system’s entropy; and T is the

absolute temperature in Kelvin (K) units (K=C + 273)

2.  Exergonic vs. Endergonic reactions

Exergonic Reactions – An exergonic reaction proceeds with a net release of free energy.

Because the chemical mixture loses free energy (G decreases),  is negative for an exergonic

reaction. Using G as a standard for spontaneity, exergonic reactions are those that occur

spontaneously. (Remember, the word spontaneous implies that it is energetically favorable,

not that it will occur rapidly).

Endergonic Reaction – is one that absorbs free energy from its surroundings. Because this kind

of reaction essentially stores free energy in molecules (G increases), G is positive. Such

reactions are nonspontaneous, and the magnitude of G is the quantity of energy required to

drive the reaction. If a chemical process is Exergonic (downhill), releasing energy in one

direction, then the reverse process must be Endergonic (uphill), using energy. A reversible

process cannot be downhill in both directions. If G = -686 kcal/mol for respiration, which

converts glucose and oxygen to carbon dioxide and water, then the reverse process – the

conversion of carbon dioxide and water to glucose and oxygen – must be strongly Endergonic,

with G = +686 kcal/mol. Such a reaction would never happen by itself.

iv.  Active site – (pg 154) Only a restricted region of the enzyme molecule

actually binds to the substrate. This region, called the active site, is

typically a pocket or groove on the surface of the enzyme where catalysis

v.  Catalytic cycle – in chemistry is a term for a multistep reaction

mechanism that involves a catalyst. The catalytic cycle is the main

method for describing the role of catalysts in biochemistry,

organometallic chemistry, materials science, etc. Often such cycles showthe conversion of a precatalyst to the catalyst. Since catalysts are

regenerated, catalytic cycles are usually written as a sequence of

chemical reactions in the form of a loop. In such loops, the initial step

entails binding of one or more reactants by the catalys, and the final step

is the release of the product and regeneration of the catalyst.

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vi.  Regulation by inhibitors – structural basis

1.  Competitive – something that is similar in shape to the reactanct,

therefore able to bind at the binding site, preventing the desired

substrate from entering the active site, and thereby slowing down

the rate of the reaction.

2.  Non-competitive – allosterically (bind to a site other than the

active site) bind to the enzyme, changing its shape and keeping it

from performing its function. These molecules can bind reversibly

or permanently.

6.  Energy metabolism -

a.  ATP (memorize structure) (pg 149)

b.  Glycolysis (know: hexokinase, pyruvate, NAD+/NADH, substrate-level

phosphorylation, ATP requirement and yield, input-output, location in cell) – 

“sugar splitting”. Glucose, a sic-carbon sugar, is split into two three-carbon

sugars. These smaller sugars are the oxidized and their remaining atoms

rearranged to form fwo molecules of pyruvate.

Hexokinase - An enzyme that transfers a phosphate group from ATP to glucose,

making it more chemically reactive. The charge on the phosphate also traps the

sugar in the cell.

Pyruvate – The beginning of their formation begins when glucose molecule is cut

into two 3 carbon sugars. These smaller sugars are then oxidized and their

remaining atoms rearranged to form two molecules of pyruvate.

c.  TCA cycle (know roles of: oxaloacetic acid, citric acid, Acetyl CoA, input-output,

cellular location) – Kreb’s cycle – (in mitochondrial matrix)

d.  Pyruvate has to go into mitochondria. When Pyurvate is becoming acetal CoA

you get one NADH in intermediate step per pyruvate. (one glucose molecule

produces two pyruvate). Each acetyl coA goes into the cirtic acid cycle. In thecitric acid cycle you get 3NADH one FADH and two CO2. You also get a CO2 in

the process that makes Acetyl CoA –so 3CO2 are produced all together. (pg 170)

e.  Oxidative phosphorylation

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i.  Cell location - is a metabolic pathway that uses energy released

by the oxidation of nutrients to produce adenosine

triphosphate (ATP). Although the many forms of life on earth

use a range of different nutrients, almost all aerobic organisms 

carry out oxidative phosphorylation to produce ATP, themolecule that supplies energy to metabolism. This pathway is

probably so pervasive because it is a highly efficient way of

releasing energy, compared to alternative fermentation 

processes such as anaerobic glycolysis. 

The electron transport chain in the mitochondrion is the site of oxidative

phosphorylations in eukaryotes.

ii.  Electron transport and cytochromes – An electron transport chain

couples electron transfer between an electron donor (such as NADH) andan electron acceptor (such as O2) with the transfer of H+ ions (protons)

across a membrane. The resulting electrochemical proton gradient is

used to generate chemical energy in the form of adenosine triphosphate

(ATP). Electron transport chains are the cellular mechanisms used for

extracting energy from sunlight in photosynthesis and also from redox

reactions, such as the oxidation of sugars (respiration).

Cytochromes – are, in general, membrane-bound hemoproteins that

contain heme groups and carry out electron transport. They are found

either as monomeric proteins (e.g., cytochrome c) or as subunits of bigger

enzymatic complexes that catalyze redox reactions.

iii.  Electrogenic pump & proton gradient – The sodium-potassium pump is

an example of en electrogenic pump, because it pumps unequal

quantities of Na+ and K+ across the membrane; 3Na+ out of and 2K+ into

the cell per pump cycle. In other words, it generates electricity by

producing a net movement of positive charge out of the cell.

Proton gradient – An electrochemical gradient is a gradient of

electrochemical potential, usually for an ion that can move across a

membrane. The gradient consists of two parts, the electrical potential and

a difference in the chemical concentration across a membrane. The

difference of electrochemical potentials can be interpreted as a type of

potential energy available for work in a cell. The energy is stored in the

form of chemical potential, which accounts for an ion’s concentration

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gradient  across a cell membrane, and electrostatic energy, which accounts

for an ion’s tendency to move under the influence of the transmembrane

potential.

iv.  Input and output – essentially – glucose is put in, CO2 and H2) are put

out.

v.  ATP synthase & how it works

f.  Fermentation – why and how? Why: cells do it in the absence of energy. Cells

only perform the glycolysis part of cellular respiration.

7.  Cell structure and Function

a.  Cytoskeleton, especially structure and function of microtubules –Microtubules

shape the cell, guide organelle movement, and separate chromosomes in

dividing cells. Cilia and flagella are motile appendages containing microtubules.

Primary cilia also play sensory and signaling roles. Microfilaments are thin rods

functioning in muscle contraction, amoeboid movement, cytoplasmic streaming,

and microvillus support. Intermediate filaments support cell shape and fix

organelles in place.

b.  Organelles

i.  Nucleus, nucleolus – Is surrounded by nuclear envelope (double

membrane) perforated by nuclear pores; nuclear envelope is continuous

with endoplasmic reticulum. The nucleus houses chromosomes, which

are made of chromatin (DNA and proteins); contains nucleoli, where

ribosomal subunits are made; pores regulate entry and exit of materials.

Nucleolus – a small dense spherical structure in the nucleus of a cellduring interphase.

ii.  Endoplasmic reticulum (rough, smooth) – An extensive network of

membrane-bounded tubules and sacs; membrane separates lumen from

cytosol; continuous with nuclear envelope. Smooth ER: synthesis of

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lipids, metabolism of carbohydrates, Ca2+ storage, detoxification of drugs

and poisons (The liver is made of cells that have a lot of smooth ER).

Rough ER: aids in synthesis of secretory and other proteins from bounds

ribosomes; adds carbohydrate to protein to make glycoproteins;

produces new membrane.

iii.  Golgi – Stacks of flattened membranous sacs; has polarity (cis and trans

faces). Modification of proteins, carbohydrates on proteins, and

phospholipids; synthesis of many polysaccharides; sorting of golgi

products, which are then released in vesicles.

iv.  Peroxisomes – Specialized metabolic compartment bounded by a singlemembrane. Contains enzymes that transfer hydrogen atoms from

substrates to oxygen, producing hydrogen peroxide (H2O2) as a by-

product; H2O2 is converted to water by another enzyme.

v.  Chloroplasts – Typically two membranes around fkuid stroma, which

contains thylakoids stacked into grana (in cells of photosynthetic

eukaryotes, including plants). Performs photoynthesis.

vi.  Mitochondria – Bounded by double membrane; inner membrane has

infoldings (cristae). Site in an animal cell where cellular respiration takes

place. Mitochondria can be found in plant cells too…

1.  Structure – Both are double membranes.

2.  Evolutionary origin (evidence) – It is believed that Mitochondria

were once bacteria that lived on their own, and that they merged

with other cells to form eukaryotic cells that exist today. This is

the endosymbiotic theory; the evidence for this is riquetzzia.

(LOOK UP)

Cellular Respiration – (Sara’s notes)

3 Stages – 

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1. Glycolysis

2. Kreb’s cycle

3. Oxidative phosphorylations.

A.  Glycolysis – There are ten steps. Substrate level phosphorylation

is used to form ATP. Gain: 2 pyruvates, 2 ATP, 2NADH, 2H2O.

B.  Kreb’s Cycle – Before the kreb’s cycle occurs, pyruvate is oxidized

o acetyl CoA; this occurs when the pyruvate enters the

mitochondria.

The acetyl CoA joins with the oxaloacetate to begin the process.

Substrate level phophorylation is again used here to create ATP.

(used Sara’s notes for the rest of this because I decided it was useless

to continue to type her notes.)

vii.  Cilia and flagella – A specialized arrangement of microtubules makes up

cilia and flagella. Flagella usually undulate (the way they move) – think

sperm. Cilia have a back and forth motion. Cells would usually have one

flagellum, or many cilia.

c.  Differences and similarities between Prokaryotes and Eukaryotes – Prokaryotes

are single celled organisms. No membrane bound organelles or DNA. In some

bacteria (I don’t know if all) DNA is circular (ex. E. Coli). Prokaryotes are smaller

than eukaryotes.

Eukaryotes – Large. Have membrane bound organelles/nucleus.

d.  Biological Membranes – Lipid bilayer made of phospholipids. Cholesterol is a

steroid that stabilizes the lipid bilayer. Temperature affects the fluidity of the

membrane. Colder – less fluid, warmer more fluid. Too fluid or too slow are

both bad.

Fluid mosaic structure and properties - The plasma membrane is described to be fluid  

because of its hydrophobic integral components such as lipids and membrane proteinsthat move laterally or sideways throughout the membrane. That means the membraneis not solid, but more like a 'fluid'. (pg125) – In the fluid mosaic moel, the membraneis a fluid structure with a “mosaic” of various proteins embedded in or attached

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to a double layer (bilayer) of phospholipids.

The membrane is depicted as mosaic  because like a mosaic that is made up of manydifferent parts the plasma membrane is composed of different kinds of  macromolecules, such as integral proteins, peripheral proteins, glycoproteins, phospholipids, glycolipids,and in some cases cholesterol, lipoproteins. 

i.   According to the model, the plasma membrane is a lipid bilayer

(interspersed with proteins). It is so because of its phospholipid

component that can fold in itself creating a double layer - or bilayer

- when placed in a polar surrounding, like water. This structural

feature of the membrane is essential to its functions, such as

cellular  transport and cell recognition. 

1.  Phospholipid distribution – inner and outer leaflets

2.  “f lippase” - are a family of transmembrane lipid

transporter enzymes located in the membrane responsible for aiding the movement of phospholipid 

molecules between the two leaflets that compose a

cell's membrane (transverse diffusion). Their existence

was predicted in 1972 by Mark Bretscher, who also

named them, to explain how an asymmetric

phospholipid bilayer could be formed.[1] Although

phospholipids diffuse rapidly in the plane of the

membrane, their polar head groups cannot pass easily

through the hydrophobic center of the bilayer, limitingtheir diffusion in this dimension. Phospholipid molecules

that are synthesized in the cell are incorporated into the

cytoplasmic face of the membrane, where flippases can

transfer them to the exoplasmic face. Energy-dependent

flippases require energy input in the form of ATP to

carry out their function, often known as a flip-flop.

However, there are energy-independent flippases that

do not require the hydrolysis of ATP and are

unidirectional in their action. These energy-independentflippases are responsible for transferring newly

sythesised lipids from the outer to the inner leaflet of

membranes. 

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ii.  Transmembrane proteins - is a protein that goes from one side of

a membrane through to the other side of the membrane. Many

TPs function as gateways or "loading docks" to deny or permit

the transport of specific substances across the biological

membrane, to get into the cell, or out of the cell as in the caseof waste byproducts. As a response to the shape of certain

molecules these "freight handling" TPs may have special ways

of folding up or bending that will move a substance through

the biological membrane. 

There are two types of transmembrane proteins:

8.  Alpha-helical. These proteins are present in the inner membranes ofbacterial cells or the plasma membrane of eukaryotes, and sometimes in

the outer membranes.[3] This is the major category of transmembraneproteins. In humans, 27% of all proteins have been estimated to be alpha-helical membrane proteins.[4] 

Beta-barrels. These proteins are so far found only in outer

membranes of Gram-negative bacteria, cell wall of Gram-

positive bacteria, and outer membranes of mitochondria and

chloroplasts. All beta-barrel transmembrane proteins have

simplest up-and-down topology, which may reflect their

common evolutionary origin and similar folding mechanism. 

1.  Amphipathic helices - High amphiphilicity is ahallmark of interfacial helices in membrane

proteins and membrane-active peptides, such as

toxins and antimicrobial peptides. Although

there is general agreement that amphiphilicity is

important for membrane-interface binding, an

unanswered question is its importance relative

to simple hydrophobicity-driven partitioning.

 We have examined this fundamental question

using measurements of the interfacial

partitioning of a family of seventeen-residue

amidated-acetylated peptides into both neutral

and anionic lipid vesicles. Composed only of Ala,

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Leu, and Gln residues, the amino acid sequences

of the peptides were varied to change peptide

amphiphilicity without changing total

hydrophobicity. We found that peptide helicity

in water and interface increased linearly with

hydrophobic moment, as did the favorable

peptide partitioning free energy. This

observation provides simple tools for designing

amphipathic helical peptides. Finally, our results

show that helical amphiphilicity is far more

important for interfacial binding than simple

hydrophobicity. 

2.  Lateral movement & lipid rafts – lateral movement – 

phospholipids can move from side to side within the membrane.

Proteins can be free-moving throughout the membrane of can be

anchored in place.

3.  Functions

a.  Transport – non-polar molecules have an easy time

diffusing across the plasma membrane, where as polarmolecules diffuse slowly across the membrane.

Membranes display selective permeability – allowing some

(non-polar) substances an easier time moving across the

membrane than others (polar).

i.  Active transport – symport, antiport, Na-K ATPase – 

Symport – an integral membrane protein that is involved in movement of two or more different

molecules or ions across a phospholipid membrane such as the plasma membrane in the same

direction, and is, therefore, a type of co transporter. Typically, the ion(s) will move down the

electrochemical gradient, allowing the other molecule(s) to move against the concentration

gradient. The movement of the ion(s) across the membrane is facilitated diffusion, there may

be several molecules transported of each type.

Antiport – An antiporter is an integral membrane protein involved in secondary active transport

of two or more different molecules or ions across a phospholipid membrane such as the plasma

membrane in opposite directions. In secondary active transport, one species of solute moves

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along its electrochemical gradient, allowing a different species to move against its own

electrochemical gradient. This movement is in contrast to primary active transport, in which all

solutes are moved against their concentration gradients, fueled by ATP. Transport may involve

one or more of each type of solute. For example, the Na+/Ca2+ exchanger, used by many cells

to remove cytoplasmic calcium, exchanges one calcium ion for three sodium ions.

ii.  Facilitated diffusion – is a process of passive

transport (as opposed to active transport), with

this passive transport aided by integral membrane

proteins. Facilitated diffusion is the spontaneous

passage of molecules or ions across a biological

membrane passing through specific

transmembrane integral proteins.

aquaporin – aquaporins are special channels in thecell membrane that facilitate the movement of water

across the cell’s membrane. Are proteins embedded

in the cell membrane that regulate the flow of water.

Aquaporins are integral membrane proteins from a

larger family of major intrinsic proteins that form

pores in the membrane of biological cells.

Integral protein – permanently attached to the

plasma membrane.

Major intrinsic proteins are a large family of

transmembrane protein channels that are grouped

together on the basis of sequence similarities.

b.  Signaling (receptors) – Receptors on the cell’s surface (like

a receptor tyrosine kinase) will be activated when the

proper ligand interacts with the binding site.

c.  Cellular adhesion – oligosaccharides act as recognition tagson the surface of cells. They act as “glue” to adhere cells

together; this helps provide uniformity. This helps in

tissue identity, and protein sorting and targeting within

cells; kind of like a “postal code”.

9. What Is Atherosclerosis?

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10. Atherosclerosis is hardening and narrowing of medium-size and

larger blood vessels, such as the aorta and those found in the

heart (coronary arteries), brain, and legs. Atherosclerosis is by

far the most common type of hardening of the arteries. It is

caused by the slow buildup of plaque on the inside walls ofarteries. Plaque is made up of fat, cholesterol, calcium, and

other substances found in your blood. As it grows, the buildup of

plaque narrows the inside of the artery and, in time, may restrict

blood flow. 

11. Cell signaling

a.  Basis of Ligand-receptor interaction and specificity

b.  Types of receptors and examples:

i.  G-protein-linked (G protein mechanism)

ii.  Tyrosine kinases

iii.  Ligand-gated ion channels

iv.  Steroid receptors

v.  2nd

 messengers

1.  cAMP and adenyl cyclase – both act as secondary messengers.

2.  IP3 and Ca2+

 - both can cause cellular responses when released in

a cell.

Second messengers are small non-protein

molecules that act as intermediaries in signal

transmission. Two important second

messengers are cyclic AMP and calcium ions.

Phospholipase C cleaves IP3 from a membrane

protein, and IP3 then binds to a calcium

channel on the ER. Adenylyl cyclase makescAMP which then phosphorylates other proteins

in the chain.

c.  Signal transduction - occurs when an extracellular signaling[1] molecule

activates a cell surface receptor. In turn, this receptor alters

intracellular molecules creating a response 

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i.  Phosphorylation cascades - is a sequence of events where one

enzyme phosphorylates another, causing a chain reaction

leading to the phosphorylation of thousands of proteins.

Receptor proteins (located in the plasma membrane or inside

the cell) bind signaling molecules. The reception of the signal

causes a shape change in the receptor molecule, to which

other molecules inside the cell respond. The message is then

relayed through signal transduction, which may involve a

phosphorylation cascade or second messengers such as

cAMP, Ca2+, or IP3. Possible responses to the signal may

include synthesis of a particular protein or regulation of a

particular enzyme. 

ii.  Nuclear targets – the final proteins that are meant to be activated, found

in nucleus.

d.  Protein kinases (esp. tyrosine & serine/threonine) – Phosphorylate specific

proteins in the beginning of transduction pathway. This begins when a ligand

binds to a receptor protein. This causes a confirmational change that causes the

GDP attached to the inactive form of a G-protein to be change for a GTP, causing

the protein to enter its active form. This then begins a phosphorylations

cascade, causing proteins in the chain to be phosphorylated in order to transfer

the message from the signal molecule at the cell’s surface to whatever the

intended target may be. (chpt 11)

e.  Quorum-sensing in bacteria - is a system of stimulus and response

correlated to population density. Many species of bacteria use

quorum sensing to coordinate gene expression according to the

density of their local population

f.  Signaling disruption and cancer -

12. Mitosis – the process by which a cell replicates.

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a.  Why and how? Names of recognized phases – the cell gets too big and sow in

order to survive divides.

b.  Chromosomes, chromatids, centromere, centriole, spindle, kinesin motors – 

chromosomes – condensed DNA that has genes on it. Chromatids  – sister

chromatids are held together at the centromere during replication. They aresplit during the teleophase. Centriole - Centrioles are involved in the

organization of the mitotic spindle and in the completion of

cytokinesis.[9] Centrioles were previously thought to be required for

the formation of a mitotic spindle in animal cells. However, more

recent experiments have demonstrated that cells whose centrioles

have been removed via laser ablation can still progress through the

G1 stage of interphase before centrioles can be synthesized later in

a de novo fashion.[10] Additionally, mutant flies lacking centrioles

develop normally, although the adult flies lack flagella and cilia.[11] 

Spindle – pushes the two nucleus apart in order to allow the cell to divide.

Kinesin motor - A kinesin is a protein belonging to a class of motor

proteins found in eukaryotic cells. Kinesins move along microtubule 

filaments, and are powered by the hydrolysis of ATP (thus kinesins are

ATPases). The active movement of kinesins supports several cellular

functions including mitosis, meiosis and transport of cellular cargo, such

as in axonal transport. Most kinesins walk towards the plus end of a

microtubule, which, in most cells, entails transporting cargo from thecentre of the cell towards the periphery. This form of transport is known

as anterograde transport. 

13. Cell cycle

a.  Recognized phases (M, G1, S, G2; G0). What happens in each.

M phase is mitosis – cell division. G1 – is the first part of interphase, cell growth

occurs during this phase. S – DNA is replicated during this phase (S for “synthesis” – DNA synthesis). G2 – second part of interphase, more growing. G0 – cells that

aren’t dividing/that don’t divide at all are in this phase (nerve cells and muscle cells).

b.  Check points (where and why? Tumor suppressors as cell cycle inhibitors) – 

There are three major check points: found at G1, G2 and M phases. The G1

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seems to be the most important. If a cell receives the “go-ahead” at G1, it will

usually complete G1, S, G2 and M phases.

c.  MPF, cyclins and cyclin-dependent protein kinases

d.  Role of oncogenic mutations

14. Geneticsa.  Meiosis – why and how? Meiosis allows for the reproduction of a new organism,

not just a cell. It’s like meiosis only twice. A cell duplicates its chromsomes, but

differently then when just dividing. Homologus chromosomes line up and lock

together. For ex: chromosome 1 from Dad lines up with 1 from Mom (after each

chromosome has been duplicated [sister chromatids stay together]) and the two

are locked together. This is called a tetrad (4 – 2 from Dad and 2 from Mom

locked together) the pairs will be divided twice. In one cell from the first

division, you can have a pair of Dad’s from 1, but a pair of Mom’s from 2. (Pieces

of Mom’s and Dad’s can switch through recombination. Each tetrad is attached

to a spindle and pulled to the center; the homologus pairs are then pulled apart.

(homologus pairs have been separated) – the cell divides and now you have two

daughter cells each with 23 DOUBLE STRANDED chromosomes. These two

daughter cells will divide (this is called meiosis 2 – the first division is meiosis

one) the same thing happens – chromosomes are lined up in spindle, and sister

chromatids are separated. In the end we have four cells each with 23

chromosomes INSTEAD of 23 PAIRS.

i.  Synapsis and crossing-over; recombinant genotypes

ii.  Diploid vs haploid, zygote, gamete

iii. 

b.  Mendelian inheritance

i.  Gene (“trait”), allele, phenotype vs genotype

ii.  Dominant vs Recessive: genetic definition, molecular definition

iii.  Parental, F1, F2 generations

iv.  Homozygous vs heterozygous

v.  Test cross

vi.  Punnet square

vii.  Mendel’s laws of segregation, independent assortment 

viii.  Incomplete dominance, multi-allelic vs multi-gene inheritance

ix.  Sex-linked inheritance

x.  Karyotype; chromosomal non-disjunction and its consequences

c.  Molecular Genetics

i.  Basic experiments establishing DNA as the genetic material

1.  Griffeth; Avery, McLeod & McCarty

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2.  Hershey & Chase

ii.  Double helix and base pairs (memorize structures and positions of the

hydrogen bonds)

1.  Chargaff’s rules 

2.  Watson & Crick model – antiparallel strandsiii.  DNA replication

1.  Meselsen & Stahl experiment

2.  Leading vs lagging strand

3.  The replisome: roles of proteins/enzymes

a.  Primers and primase

b.  Helicase, DNA polymerases, ligase, topoisomerase, single-

stranded DNA-binding proteins

c.  Telomeres and telomerase

iv.  Response to DNA damage

1.  Repair (e.g. thymine dimer excision) -

2.  Mutation and its relationship to repair

3.  Cell cycle arrest

15. Accessing genetic information

a.  Transcription

i.  RNA polymerases (3 in Eukaryotes, 1 in prokaryotes)

ii.  Regulatory sequences associated with genes: promoters vs terminators

iii.  Initiation complex

b.  Post transcriptional RNA processing

i.  5’capping, polyadenylation 

ii.  Splicing and the spliceazome: introns, exons, lariats and SnRNPs

iii.  mRNA vs primary transcript

c.  Translation

i.  The genetic code (memorize the three “stop” codons and the codons for

methionine and one other amino acid of your own choice)

ii.  tRNA & aminoacyl-tRNA-aynthases

iii.  Ribosome and the role of “structural RNA” 

16. Regulation of Gene activity

a.  In prokaryotes: the operon (operators, repressors & co-repressors/inducers,

activators)

i.  Lac operon: induction

ii.  Trp operon: repression

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iii.  Catabolite repression – concept of additional regulatory proteins to

integrate different signals

b.  In eukaryotes: basal promoter vs enhancer sequences

i.  Sequence-specific DNA binding proteins

ii.  The “transcriptasome” c.  Multiplex analysis of gene expression: the microarray and individualized

medicine.

Some Basic Concepts

Importance of 3-dimensional structure of macromolecules

Molecular machines

Carrier molecules in metabolism

Electrons as carriers of energyMetabolic pathways

Cell organization - compartmentalization

Good reading, but not on final exam this year

17. Microbial models for molecular genetics

a.  Bacteria – useful as simple cells

b.  Viruses – analogy to flash drive (cell has the OS, virus has a case, information,

and a way to attach to the computer circuitry)i.  Structure of capsid

1.  Simple – icosahedral, helical (examples)

2.  Composite – T-even bacteriophage (stepwise assembly via a

genetic program)

3.  Enveloped – lipid blayer membrane derived from host cell + viral

glycoproteins

ii.  Nucleic acid DNA or RNA, circular or linear, single or double-stranded,

one chromosome or multiple chromosomes

iii.  Host cell specificity provided by physical attachment to receptors on cellsurface

iv.  Mode of replication – lytic vs. lysogenic

v.  HIV life cycle as it reflect all of the above; reverse transcriptase

18. Recombinant DNA

a.  Restriction endonucleases, vector, clone, host

b.  DNA sequencing

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c.  PCR

Semi-autonomous organelles and evolutionary symbiosis

Apoptosis and programmed cell death