Typed study guide
Lecture 1: Small Molecules
Hydrogen, carbon, nitrogen, oxygen, sulfur and phosphorous are what living matter are made up of.
Sodium and Potassium are important as ions.
The number of protons defines the identity of the element (the atomic number = number of protons)
Atomic mass/weight is the number of protons and neutrons added together (daltons)
-Isotopes have the same number of protons, but a different number of neutrons
- can be radioactive, which is useful for bio and medicine (ex. carbon-14)
- share electrons, strong, predictable length and angle
-covalent bonds are made of 2 electrons
- theses 2 electrons are shared, one electron comes from each atom
- atoms can form bonds until their outermost shell is filled
But: electrons are not always shared equally!
Why does carbon form 4 covalent bonds?
Because it has 4 electrons in its outer shell and it wants to have 8 valence electrons so it will form 4
covalent bonds to fill the shell.
Electronegativity: Increasing positive electrical charge in nucleus means increasing electronegativity
H < C < N < O < F
Apolar molecule has polar covalent bonds (dipoles)
Due to the electronegativity of water, it has dipoles. The dipoles are attracted to each other.
The oxygen has higher electronegativity so the electron spends more time closer to the oxygen,
therefore the oxygen is a negative dipole and attracts a hydrogen from another water because the
hydrogen is a positive dipole.
Lecture 2: Small molecules 2; Bonds, Acids
Ionic bonds- electrons are not shared, one is grabbed
- are formed by the electrical attraction between ions with opposite charges
ex. NaCl → Na+ Cl-
Ions are formed when an atom loses or gains electrons
Cation (+),Anion (-)
Polar molecules tend to be hydrophilic
- dissolves in water due to hydrogen bonding
Nonpolar molecules are hydrophobic
- tend to aggregate with other nonpolar molecules (hydrophobic interactions)
- water forces nonpolar molecules together because doing so minimizes their disruptive effects
on the hydrogen bonded water network
Van der Waals Interaction (transient dipoles)
- nonpolar molecules are also attracted to each other via relatively weak attractions
Chemical reaction = covalent bond
Moles are the amount of substance in grams whose weight is equal to its molecular weight
(moles = same # atoms in all elements)
1 molar solution is one mole of a compound dissolved in water to yield 1 liter.
Acids release/donate H+ ions
Strong acids (ex. HCl) are when the dissociation is complete
The carboxyl group (-COOH) is common in biological compounds. It functions as a weak acid
because it dissociates partially and reversibly.
-COOH → -COO- + H+
Bases accept H+ ions (releases OH-)
Strong bases (ex. NaOH) will ionize completely in solution. OH- released with absorb H+ to form
The amino group (-NH2) is important, it functions as a weak base by partially and reversibly accepting
H+ -NH2 + H+ → (-NH3)+
pH is the measure of hydrogen ion concentration.
It is defined as the negative logarithm of the hydrogen ion concentration in moles per liter.
ApH 7 means the concentration of hydrogen ions is 1 x 10-7 per liter of water
Lecture 3: Buffer and Large Molecules I: Sugars
Buffer make the overall solution resistant to pH change, because they react with both added bases and
To make a buffer: add equal amounts of a weak acid and a weak base (using conjugate bases and acids)
ex. CH3COOH → CH3COO- + H+
Even if you add HCl or NaOH to a buffer solution, the pH won't change until a very high concentration
of either has been added.
Buffers illustrate the Law of MassAction :Addition of reactants accelerates the reaction. Likewise,
removal of products accelerates the reaction (towards the right side).
The titration curve of a weak acid or base gives you the protonation (addition of a proton to a molecule)
state of a given pH.
Carboxyl Carboxyl acid R-C=O-OH
Amino Amines R-N-H-H
Hydroxyl Alcohols R-OH
Aldehyde Aldehydes R-C=O-H
Keto Ketones R-C=O-R
Phosphate Organic phosphates R-O-P=O-O(-)-O(-)
Sulfhydryl Thiols R-SH
BOLDEDARE CARBONYL GROUPS What are we made up of?
Ions and small molecules
2) Nucleic acids
(bolded words are macromolecules that can form polymers)
Macromolecules are made in the same way in all living things and in the same proportions.
An advantage of this biochemical unity is that organisms acquire needed biochemicals by eating other
Condensation → making polymers
H- Monomer-OH + H-Monomers-OH → H2O + H-Monomer-Monomer-OH
Hydrolysis- breaking up polymers takes one water molecule
Isomers: molecules that have the same chemical formula but different arrangements of the atom (a
Structural isomer- group attached to different C atoms
Optical isomer- group is attached in different ways to the same carbon atom
Sugars- carbohydrates (sugars) act as energy storage and building blocks for other molecules (nucleic
multiples of CH2O for monosaccharides
Glucose (forms 16-32 isomers), C6H12O6:
In solution glucose exists as a straight chain or ring, ring form is predominant, alpha and beta ring
forms exist in equilibrium.
Alpha- glucose C1 bond with H on top and OH on bottom
Beta- glucose C1 bond with OH on top and H on bottom
Hexoses (6-carbon sugars)- with optical isomers glucose, mannose and galactose and structural isomer
Pentose(5-carbon sugars) → part of DNA
Monosaccharide + Monosaccharide = disaccharide (condensation reaction)
Glycosidic linkage is a covalent bond between two monosaccharides to form a disaccharide
2 glucose molecules can form 11 different disaccharides
Starch + cellulose = disaccharides Glucose → mostly ring form in solution, but can change back and forth between forms
Glycosidic bond → alpha conformation of glucose is fixed
Maltose = 2 glucose
Starch / unbranched, amylose in plants
squiggly end = reducing end (b/c -CHO can be oxidized to -COOH)
amylopectin – moderately branched starch
glycogen- highly branched starch
Beta 1-4 linkage = cellobiose
beta glucose + beta glucose = cellobiose
Cellulose (always unbranched) – chain of glucose molecules
- Symmetrical, therefore stronger covalent bonds
- hydrogen bonding
Chitin modified glucose
Lecture 4: Nucleic acids and lipids
Nucleic acids – DNA, RNA
nucleotides (monomers of nucleic acids)
Nucleic acids consists of:
1) Pentose sugar – two types a) ribose b) deoxyribose (lacks one oxygen)
2) Phosphate – a)AMP b)ADP c)ATP
3) Bases → have NH2 group
Pyrimidine → uracil (RNA), cytosine, thymine
Purine → adenine, guanine
Thymine pairs with adenine (pairs with 2 hydrogen bonds)
Cytosine pairs with guanine (pairs with 3 hydrogen bonds)
Erwin Chargaff discovered base pairing rulse
Rosalind Franklin collected the X-Ray diffraction pattern of DNA
Watson and Crick discovered the double helical structure of DNA
Polymerization of DNAoccurs in 5' → 3' direction
-Phosphodiester linkage - Abond between a two sugar groups and a phosphate group; such
bonds form the sugar-phosphate-sugar backbone of DNAand RNA.A diester bond (between
phosphoric acid and two sugar molecules) linking two nucleotides together to form the
nucleotide polymers DNAand RNA.
-Successive nucleotides add to the 3' end of the polymer
- Other strand organized in antiparallel orientation RNAprobably came first evolutionarily because it can function as a protein and is like DNA
-insoluble in water
- insolubility results from many nonpolar covalent bonds of hydrogen and carbon in lipids
- Lipids aggregate away from water, which is polar
- energy storage (fats/oils)
- cell membranes (phospholipids)
- capture light energy (carotinoids)
- hormones and vitamins (steroids)
- Thermal insulation
- Electrical insulation of nerves (myelin sheath)
- Water repellent
Fat = 3 covalent bonds between glyeroid and fatty acid → ester linkage
Fats are triglycerides
Saturated fatty acids (solid)– only single carbon-carbon
Unsaturated (fluid)– single and double covalent bonds
Phosopholipids → 2 hydrophobic fatty acids and 1 hydrophilic head attached to glycerol
→ will automatically form bilayer
Lecture 5: Large Molecules 3- Proteins
Proteins are polymers of amino acids (polypeptides)
Proteins range in size from a few amino acids to thousands of them (titin = 38000 amino acids)
Folding is crucial to the function of a protein and is influenced largely by the sequence of amino acids.
All amino acids have the structure:
H -consists of hydrogen, carbon, amino group and carboxyl group
| - is a charged molecule
+H3N-Calpha-COO- - can have 2 optical isomers
| - to form peptide → condensation reaction releases H2O
R - peptide linkage connects amino acids
-Proteins start at the amino end (N terminus) and end at the carboxyl group (C terminus). So
polymerization starts N terminus → C terminus
-Peptide backbone : Calpha – C – N – Calpha – C – N
- The precise sequence of amino acids is called its primary structure
20 kinds of amino acids; 100 amino acids in one protein
20^100 = 10^130 possible combinations which explains why there is such diversity on earth.
-Aprotein's secondary structure consists of regular, repeated patterns in different regions in the poly peptide chain.
- This shape is determined primarily by hydrogen bonds between amino acids
- The two common secondary structures are the alpha helix and the beta pleated sheet.
A-helix: -forms a straight rod
-The H bonds (N- H -----O=C) are formed by the backbone and are parallel to the axis of the
- The side groups (R groups) of the amino acids project outward (away) from the helix
- Because all the H-bonds run parallel to the helix axis, alpha helices can insert in plasma
membranes, if the helix contains only hydrophobic amino acids side chains
-Coiled Coils arise when two a-helices have hydrophobic amino acids at every 4 position (one
complete turn 3.6 amino acids)
- Fibrous structural proteins consist mainly of a- helices arranged as coiled coils, such as the
keratins in hair and feathers
B-pleated sheet: -makes flat plates
- R groups project up and down from the sheet
- The strands of the b-sheet can run in antiparallel or in parallel direction. They can even come
from different polypeptides.
- B-sheets can occasionally be inserted into the plasma membrane but its very rare.
Proline (an amino acid) fits neither in an a-helix nor in a b-sheet, because it makes a kink in the
peptide, and because the N carries no H for hydrogen bonding. Also N cannot rotate because it is
attached to CH2.
Tertiary structure is the three- dimensional shape of the completely folded polypeptide.
-Structure is determined by:
a) location of disulfide bridges (covalent bond between 2 amino acids that are far away from
each other, provides stability, releases 2H)
b) location of secondary structures
c) Ionic interactions between positive and negative charges deep in the protein, away from
water. (folding is about energy minimization), hydrophobic interactions are important.
d) Hydrophobic aggregation of R groups stabilized by van der Waals forces.
Quaternary structure is the structure of multiple polypeptides forming a protein complex.
Protein bonds to a specific stretch of DNAby hydrogen bonding to bases. Bases are the only thing that
makes a piece of DNAunique. Protein can bond with sugar or phosphate but base is the only way
protein knows which specific stretch to bind with.
The loss of a protein's normal three dimensional structure and function is called denaturation
Proteins refold (renature) in the test tube. This shows that: a)proteins automatically fold into a
conformation of lowest energy b) all folding information is contained within the primary sequence
Why do denatured proteins in a cell typically not refold?
Other partially unfolded proteins prevent folding.
Changes in temperature or pH can cause denaturation (ex. cooking, fever, lemon in milk)
Usually, a denatured protein cannot be refolded; it is degraded by the proteasome. Protein turnover (breakdown and resynthesis) occurs constantly in cells.
Chaperones are specialized proteins that help keep other proteins (temporarily exposed hydrophobic
regions) from interacting inappropriately with one another. They do so by sequestering some newly
synthesized proteins to give them time to fold.
Lecture 6: Membranes
2 layers → phopholipid bilayer
Automatically rearrange away from water.
Cholesterol has a rigid structure which makes the membrane more solid (counteracts the effect of
unsaturated fatty acids). It allows the cell to fine tune rigidity.
It is energetically favorable for bilayers to seal, that is, to form an enclosed space. Self assembles into
cell like shape, so no phospholipids are exposed at all.
Two dimensional fluid- it can all move freely, only connected by hydrophobic force.
4 types of movement:
a) Lateral diffusion
d) Flip-flop: very rare because hydrophilic head has to cross hydrophobic interior. Fluidity
important for cell shape changes and lateral diffusion of membrane proteins
Fluidity is important for cell shape changes and lateral diffusion of membrane proteins.
Phospholipids and glycolipids are asymmetrically distributed; sugar modifications are added in Golgi,
therefore on outer surface. Some proteins bind to specific cytosolic phospholipids.
The fluid mosaic model: a mosaic of proteins embedded in a two-dimensional fluid.
How do proteins insert into the membrane? - By exposing hydrophobic amino acids in transmembrane
Proteins cannot move vertically out of the lipid bilayer, some have hydrophobic amino acids so it can
be placed in bilayer, by exposing hydrophobic amino acids in transmembrane areas.
Transmembrane proteins – have hydrophobic regions of amino acids that cross the phospholipids
bilayer. They have a specific orientation, showing different faces on the 2 sides of the membrane.
Function: signal transduction, transport of molecules, energy generation, cell adhesion
Peripheral membrane proteins- lack hydrophobic regions and are not embedded in the bilayer. They
are not covalently attached to lipids or bind noncovalently to other transmembrane proteins.
1. Diffusion- the passive mixing of substances resulting in transport along a concentration
gradient. Reason:“Random walk” or Brownian motion of individual molecules due to thermal
motions and collisions. The rate of diffusion is determined by:
c) size of molecule
d) steepness of concentration gradient 2. Biological membranes are selectively permeable. Which substances can/cannot pass?
Gases and water can pass freely through membrane, while large polar molecules and ions
cannot cross the membrane.
3. Osmosis is the diffusion of water across a selectively permeable membrane. Water moves
from regions of low solute concentration to regions of high solute concentration
4. Facilitated Diffusion – passive transport
- Large polar and charged substances do not diffuse across lipid bilayers.
So they enter through facilitated diffusion
- Facilitated diffusion depends on two types of membrane proteins:
Channel proteins – ion channels can be open or closed. Ions channels
are specific for one type of ion.
Carrier proteins – a carrier protein binds the transported substance.
Transition between these states is random and reversible. When all
binding sites are occupied, the carrier is saturated; therefore the rate of
diffusion levels off.
5. Active Transport requires the expenditure of energy (directly or indirectly), substances are
moved across the membrane against the concentration gradient.
Primary active transport- Sodium potassium pump in animal cells: pumps out 3Na+, pumps
in 2 K+, uses the energy of 1ATP. It controls osmolarity, generates membrane potential, sets up
a concentration gradient that allows other transport processes to occur.
Secondary active transport systems use established gradients to move substances. This form
of transport usesATP indirectly. TheATP molecules are consumed to established the ion
gradient. The gradient is then used to move a substance, as described for the symport and
Symport and Antiport- often use the concentration gradient of an ion to drive the transport of a
substance. Symport- sodium ion moves in the same direction as glucose. Antiport- Sodium
ion moves in opposite direction as glucose
Hypertonic- (salt water) higher solute concentration compared to cell. Causes cell to shrivel and water
Hypotonic- (normal situation) lower solute concentration compared to cell. Causes cell to swell and
water to enter.
Isotonic- Equal solute concentrations
Lecture 7: Cells I: The endomembrane system
Why are cells small?
Because most chemical reactions in cells require diffusion:
Diffusing molecules don't travel long distances because of their “random walk”, which works better
over small distances
Distance traveled is propotional to square root of time:
Big molecule travels 10 micrometers in 1 sec (distance = 10 x sqrt(1))
In 1 min = 10 x sqrt(60) Surface area is also an important factor.
Cell size is limited by the need for a high surface area to volume ratio. Only a high surface area
compared to the volume allows diffusion to take place fast enough.
Increasing size (volume) of a cell decreases the surface area to volume ratio dramatically, because
volume increases with the power of three, but surface area only with the power of two.
Prokaryotes are small with no nucleus and hardly any membrane compartments → biggest metabolic
Eubacterial ribosomes are smaller than eukaryotic ones, DNAis usually a single circular chromosome
located in a region called the nucleoid.
They can gain energy using light or oxidizing H2, sulfur, iron, nitrogen or organic compounds.
Eukaryotes have organelles and membrane enclosed nucleus (can be a lot bigger because of
Plant cells have some specialized organelles, vacuole for water storage and keeps cell rigid, cell wall
made of cellulose, chloroplasts for photosynthesis, plasmodesmata for cell to cell communication.
Golgi can transport things out of the cell.
The Nucleus contains most the cell's DNA, also has the nucleolus where ribosomes are assembled from
-DNAis replicated → DNAis transcribed into mRNA or rRNAby RNApolymerases → rRNAis not
translated; it directly folds into a 3D structure
-Ribosomes are made of 4 rRNAs and 80 proteins in the nucleolus
- Two lipid bilayers form the nuclear envelope which is perforated with nuclear pores. MRNAand
ribosomes pass through these pores. Ribosomes translate mRNA into proteins in the cytoplasm
In eukaryotes, function ribosomes are found free in the cytoplasm, in mitochondria, bound to the
endoplasmic reticulum and in chloroplasts.
The Endoplasmic Reticulum
- ER is a network of interconnecting membranes distributed throughout the cytoplasm
- Internal compartment is the lumen (a separate part of the cell, with a distinct protein and ion
composition, communicates only with the outside of the cell)
- ER's folding generates a surface area much greater than that of the plasma membrane.
- ER membrane can be continuous with outer nuclear envelope membrane
- made up of tiny spaces where chemical reactions can happen quickly
- Enzymes in ER detoxify many substances
Smooth ER → makes lipids, ribosome free
Rough ER → has ribosomes attached, they come from the cytosolic pool of ribosomes, and are
directed to the ER after they have translated the first few amino acids containing a signal sequence that
directs the ribosomes to the ER. Oligosaccharides (3-12 subunit sugars) are attached to proteins
- consists of flattened membranous sacs and small membrane enclosed vesicles.
- decides where a protein ends up
1) receive proteins from the ER and further modify them (especially oligosaccharides). Add
oligosaccharides to membrane lipids
2) Concentrate, package, and sort proteins before they are sent to their destinations (apical or basal side of plasma membrane, lysosome)
Lysosomes are vesicles contianing digestive enzymes that come in part from the Golgi. Lysosomes are
sites for breakdown of food and foreign material brought into the cell by phagocytosis. Lysosomes are
also the sites where digestion of spent cellular components occurs. Lysosomes can eat their host cell
(autophagy), either regulated (like the leaves in fall) or due to nutrient deprivation.
Lecture 8: Cells 2: Endosymbiotic organelles, the cytoskeleton and cell junctions
Mitochondria and Chloroplasts = bacteria that lie inside the cell
Mitochondria have an outer plasma membrane and a highly folded inner membrane.
- Folds of the inner membrane contain large protein molecules used in cellular respiration (ATP
- The region enclosed by the inner membrane contains many enzymes e.g. for citric acid cycle.
Inner membrane → respiration
Interior of Mitochondria → citric acid cycle/ DNA,RNAand ribosomes exist (this sets mitochondria
apart, they have their own genome and ribosomes)
Chloroplasts –> member of the Plastid family of organelles. Chloroplasts carry out photosynthesis,
other plastids store starch or pigments.
→ two membranes, and have an internal membrane system.
→ The internal stacks of membranes contain chlorophyll andATP synthase. They are derived from the
inner membrane, in prokaryotes the photosynthetic system also sits in the cell membrane
→ Interior for carbon fixation yielding sugars amino acids, all fatty acids
→ In folds, photosynthesis
→ own DNA, RNAand ribosomes
Mitochondria and chloroplasts are descendants of bacteria
Evidence: 1. Double membrane (likely taken up by endocytosis)
2. Own genome
3. Own ribosomes, more similar to Eubacteria
4. Genes more similar to bacterial genes
5. No vesicle exchange between the outer membrane and the endomembrane system
- maintains cell shape and polarity
- provides the mechanisms for cell movement
- acts as tracks for “motor proteins” that help move materials within the cells.
- made of actin
- add structures to the plasma membrane to shape cells
- together with motor myosin mediate cell shape changes, cell migration, muscle contraction
- actin exists in cells as monomers and filaments, and there are many proteins that regulate
polymerization and depolymerization
-Actin are polar, have + and - ends
Actin-myosin contraction- coiled coil tail domains of myosin II may interact to form antiparallel bipolar complexes.
The may contain as many myosin molecules as in thick filaments of skeletal muscle, or as few as 2
Myosin heads can move along actin filaments in only one direction.
Antiparallel actin filaments can “contract”
-found in multicellular organisms
- form ropelike assemblages in cells
- functions: a) stabilize nucleus (lamins) b) give mechanical strength to cells (coiled-coils of keratins)
- No polarity
- Hollow cylinders made from tubulin protein subunits.
- organize cell: provide intracellular skeleton, determine cell polarity, function as tracks, on which
motor proteins can move vesicles and organelles. They also move chromosomes – have centriole from
which they originate
- Form and disassemble as the needs of the cell change.
- there are many proteins that regulate growth or shrinkage of Mts (also with actin)
- Vesicles and organelles can be moved in both directions by dynein and kinesin → 1ATP = 1step
-Cilia are made of microtubules, common locomotory appendage, short and present in great numbers.
Made up: 9 doublet microtubules, around 2 in the middle
Two doublets are connected by linker proteins and dynein, therefore movement of dynein
results in bending
- cells can interact with environment
- In cell recognition, one cell specifically binds to another cell of certain type. This can lead to
phagocytosis, DNAexchange, sperm-egg fusion ect.
- In cell adhesion, cells stably bind to each other or the extracellular matrix
How did it evolve?
- single cell organisms ate another to get nutrients, phagocytosis
1. Tight Junction
Separates apical (faces lumen) and basolateral (facing extracellular matrix) membrane domains
and their membrane proteins.
Prevents substances from moving through the intercellular space
Prevents passage of material through epithelium
2. Adherens Junction
1 form in development/ most ancient in cell-cell junctions
made of transmembrane cadherins, several cadherins from two different cells bind together
Generally forms a circumferential belt close to the apical-basolateral boundary
Adherens junctions connect to actin filaments
3. Desmosomes Provide mechanical strength (skin); are connected to intermediate filaments
4. Gap junctions
connections that facilitate communication between cells – low molecular weight molecules can
freely diffuse from one cell to the next (e.g. Ca2+ ion to synchronize heart muscle contraction)
Gap junctions are made of proteins called connexins, which snap together to generate a pare
Allows diffusion to happen freely between cells
5. Focal adhesions
most important cell matrix junction
form distinct spots on the basal side of cells
connect skin to the underlying basal lamina, muscle to tendons ect.
Made of transmembrane integrins. Several integrins from one cell bind to extracellular matrix
Connect actin filaments
Lecture 9: Energy and Catalysis
Metabolism can be divided into two types of activites:
Anabolic reactions link simple molecules together to make complex ones. These are energy
storing reactions. They require energy
Catabolic reactions break down complex molecules into simpler ones. They release energy.
Cells must constantly acquire energy from their environment!
Potential energy due to position → kinetic energy → heat energy
2 H2 + O2 → 2H2O + heat
chemical bond energy → molecular motion → heat energy
What drives energy conversions?
First Law of Thermodynamics : during any conversion of energy, the total initial energy equals the
total final energy. Energy is neither created nor destroyed.
Energy wants to become evenly distributed or dispersed.
Second Law of Thermodynamics :
Energy spontaneously disperses from being localized to becoming spread out if its not hindered from
doing so (entropy increases).
Energy conversions, e.g. chemical reactions only occur if energy disperses in the universe.
Dispersing energy is driving force for energy conversions.
Energy transformations always result in a state of higher probability (a more disordered state).
To judge biochemical reactions, we need an equation that gives us the amount of energy released to
drive a reaction (change in entropy or free energy).
How can a cell release free energy (drive a chemical reaction?)
By dispersing energy/ increasing entropy. How?
1) with a chemical reaction creating disorder in the cell (digesting a polymer)
2) with a chemical reaction releasing heat which generates disorder/disperses energy in the surrounding (environment)
Both reactions require the constant uptake of energy-rich molecules.
Total Free energy G = H – TS
(H = enthalpy/ heat; S = entropy/ disorder; T= absolute temperature)
We don't want to know the total free energy of a molecule, but the change associated with a specific
chemical reaction. This change can be measured in calories or joules.
Free energy change: deltaG = deltaH – TdeltaS
deltaG = Gend – Gstart
If deltaG is negative, energy is released/dispersed (disorder is created)
If deltaG is positive, energy is required
Only four types of reactions:
1) heat is released and disorder is increased: always spontaneous (exergonic) – Most catabolic
reactions. DeltaG is the actual amount of energy dispersed during a chemical reaction.
2) heat is released, but disorder decreases: only spontaneous below a certain