00 Atoms in Motion
Saturday, January 14, 2023
11:14 AM
Richard Feynman (1918-88)
- Manhattan project
- Fun to Imagine (Video)
○ Jiggling atoms
▪ Hot is a lot of jiggling, cold is less jiggling
▪ Perfect elasticity, never lose energy
□ Hitting something with a hammer transfers
the energy by causing the atoms to jiggle
and get hot because of movement
- Atoms in Motion (Lecture)
○
○ Laws of Physics
▪ Govern every complex thing, giving a
foundation
▪ We do not know all the laws yet
○ Science
▪ The test of all knowledge is experiment.
○ Over-all picture of the world
▪ Matter is made of atoms.
▪ The atomic hypothesis.
□ That all things are made up of tiny atoms
attracting or repelling each other.
○ Sense of scale
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▪
▪ Real particles are continually jiggling and
rotating
○ Molecular dynamics
○ Angstroms
▪ Atoms are 1 or 2 angstroms in radius. Apple the
size of the earth has atoms the size of an apple.
▪
○ Force = Pressure x Area
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○
○
○ Pressure proportional to density
○ Slow compress increase temp, slow expansion
decrease temp (vibration)
○
▪ Ice has a crystalline structure
▪ Absolute 0 is the minimum amount of
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▪ Absolute 0 is the minimum amount of
vibrations (not zero)
▪
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▪
▪ Salt (solid crystal of salt atoms) dissolving in
water
□ The crystal is made of ions
Ions are atoms with more or less
electrons
◊ Chlorine with an extra electron,
sodium missing an electron
□ Held together by electrical attraction
□ Until added to water, when some jiggle lose
pulled by polar water
□ In the picture we cannot tell is salt
dissolving in water or crystallizing out of
water
It is a dynamic process with both
happening
Depends on if it is more or less than
equilibrium
◊ By which we mean a situation in
which the rate at which atoms are
leaving matches the rate at which
they're returning
□ Molecules of a substance can be
approximations and some substances are not
made strictly up by cohesive uniform
molecules
▪ As temperature increases more is dissolved and
more returns. It is difficult to predict which will
happen more, but more substances dissolve
more as temp increases
○ Chemical reaction
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▪
▪ Atoms can change partners and form new
molecules
▪ Chemical reaction
□ Process when the atoms rearrange
▪ CO - carbon monoxide molecule
▪ Motion energy = kinetic energy
□ Burning
Can generate light
▪ CO can attach another O = CO2, carbon dioxide
▪
▪ Every substance is some type of arrangement of
atoms
▪
▪ CO2 is straight and symmetrical, O-C-O
▪ Chemical formula is a 2d picture of a molecule
▪
▪ Organic chemistry. Measures where stuff is
because we can't just see it
▪
□ Using words to convey the 3 dimensional
form of a molecule
○ Push ball game
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▪
▪ How do we know that there are atoms?
□ First, we hypothesize that there are atoms
Experiments are run and the results
consistently prove align with the
hypothesis
▪ Brownian motion
□ Something is moving around small objects
in water and jiggling things around, that
something is atoms. The perpetual jiggling
of the particles from the collisions of atoms
is Brownian motion
▪
▪ Further evidence in structure of crystals
▪ X-ray analysis of spatial "shapes", confirm
several "layers" of atoms
○ Everything is made of atoms
▪
▪ The key hypothesis
▪ In biology, for example
□ Everything that animals do, atoms do
□ There is nothing that living things do that
cannot be understood from the point of view
that they are made of atoms acting according
to the laws of physics
▪ We are a complex pile of nonrepeating atoms.
The complex arrangement allowing for
"impossible" things compared to simple
repeating piles like water
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01 Biochemistry and the Unity of Life
Sunday, January 15, 2023
2:08 PM
-
- The biochemical workings of life regardless of size or
complexity are remarkably similar
- 1.1 Living Systems Require a Limited Variety of Atoms
and Molecules
○ 90 natural elements, 98% of any organism are only
oxygen, hydrogen, and carbon
▪ Ubiquity of H2O (humans about 60% H2O)
▪ Carbon due to its geometry, can make
connections
▪
▪ Carbon bonds in tetrahedron form
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○
▪ CNO
PS
(H in upper left) (biological processes)
□ Complementary binding patterns
Forming biological molecules
▪ Also plentiful and light
○
▪ Not much carbon in seawater or earth crust
▪ Concentrated by the carbon cycle
□ Plants take it out of the air, animals eat
plants
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□
plants
Animals exhale carbon back to plants
▪ No biological role for titanium
▪ Without any other element on the this list from
seawater and earth crust origins, humans would
die immediately
○
▪ Hydrogen while not as prevalent in whole earth,
is light and floats to the surface concentrated
there
- 1.2 There Are Four Major Classes of Biomolecules
○
▪ Atoms combine to make molecules
▪ Describe the key classes of biomolecules and
differentiate them?
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differentiate them?
○
▪ Proteins play many roles, such as signal
molecules, receptors for signal molecules and
enzymes, and biological catalysts
▪ Usually very large and very complex
□ Do most of the interesting stuff in cells
▪ They can be enzymes that break stuff apart, and
catalysts that encourage biological processes
○ Protein folding
▪
▪ The three-dimensional structure of a protein is
dictated by the sequence of amino acids that
constitute the protein.
▪ Protein made up of subunit amino acids
□ Strung to together linearly, then folded 3d
▪ Modelling coding schemes
□ Red represents Oxygen
□ Blue is Nitrogen
□ White is Carbon OR Hydrogen
○
▪ Nucleotides are the building blocks of nucleic
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▪ Nucleotides are the building blocks of nucleic
acids
▪ Two types of nucleic acids
□ DNA (deoxyribonucleic acid)
Polymer of deoxyribose, phosphate, and
four bases: A, G, C, T
◊ In the double helix,
A pairs with T,
G pairs with C,
usually found in double helix
□ RNA (ribonucleic acid)
Single-stranded polymer of ribose,
phosphate, and bases: A, G, C, U
▪ Nucleic acids are informational molecules of
the cell
□ They control the genetic expression and
contain all of the information for how to
build things in the cell
○ The structure of a nucleotide
▪
▪ A nucleotide consists of a base (blue), a fivecarbon sugar (black), and at least one
Biochemistry Page 12
carbon sugar (black), and at least one
phosphoryl group (PO3, red)
▪ The most famous nucleotide is adenosine
triphosphate (ATP)
□ The universal currency for energy in cells
□ An important signaling molecule
Easily recognizable and useful for
passing things around
▪ ATP is one of the components of RNA.
□ It's close relative deoxy-ATP is in DNA
□ It's found everywhere
○ The double helix
▪
▪ Two individual chains of DNA interact to form
a double helix.
□ The sugar-phosphate backbone of one of the
two chains is shown in red, the other is show
in blue. The bases are shown in green,
purple, orange, and yellow.
▪ David Goodsell
□ Specializes in visualizing molecules
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□ Specializes in visualizing molecules
○
▪
▪ A key property of lipids is that they have
hydrophilic and hydrophobic properties.
▪ Lipids form barriers, called membranes
□ That allow compartmentalization
▪ Lipids have two really important features
□ They are storage form of energy
□ They make membranes which are barriers
between different parts of the cell, allowing
compartmentalization
▪ Composition
□ Hydrophobic tail (green) is a hydrocarbon
(carbon and hydrogen) that doesn't interact
w water
□ Hydrophilic head (red), interacts with
water, has oxygen on it and other charged
elements. Water loving
▪ (shorthand drawing on right, much faster,
easier)
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▪
▪ Membrane formation by lipids is important
□ Due to forming a "lipid bilayer"
Green hydrophobic tails associate with
each other, while the red hydrophilic
heads associate with surrounding water
□ Other molecules can then not easily cross
○
▪
▪ Carbohydrates are an important fuel source.
Glucose is a common carbohydrate.
□ Glucose is stored as glycogen in animals.
▪ Necessary for energy. All sugars are
carbohydrates.
▪ Other functions
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▪ Other functions
□ Very soluble in water and they are
recognizable by other molecules, so function
as signaling molecules
Especially important for cell-cell
recognition
▪ Structure of glycogen
□
□ Glycogen is a branched polymer compose of
glucose molecules. The protein identified
by the letter G at the center of the glycogen
molecule is required for glycogen synthesis.
□ Carbohydrates (like proteins and nucleic
acids) can be strung together in really long
chains
- Quick quiz (name four classes, and function of each)
○ Protein
▪ Enzymes, catalysts, signaling
○ Nucleic acids
▪ Information and instructions
○ Lipids
▪ Energy storage and cellular membranes
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▪ Energy storage and cellular membranes
○ Carbohydrates
▪ Fuel and cell-cell recognition
- 1.3 The Central Dogma Describes the Basic
Principles of Biological Information Transfer
○ The Central Dogma states that information flows
from DNA to RNA to protein. Moreover, DNA is
replicated
▪
▪ The central dogma of biology.
□ DNA is the source of the information about
how to make proteins and it's able to
replicate;
□ And then becomes "transcribed" into RNA,
which means RNA are from a template of
DNA
□ Then those RNA molecules get "translated"
into proteins
Which means that they turn into amino
acid sequences, or are used as a guide to
assemble amino acid sequences
◊ Then the proteins are what do most of
the work
▪ DNA is heritable information: the genome
□ The first step in the central dogma
□ Contains all the genes telling your body how
to make proteins
□ Controls how and when these proteins are
made
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□
made
▪ DNA is replicated by a group of enzymes
collectively called DNA polymerase
○ DNA Replication
▪
▪ When the two strands of a DNA molecule are
separated, each strand can serve as a template
for the synthesis of a new partner strand. DNA
polymerase catalyzes replication
□ DNA polymerase splits the double helix and
then makes two new strands complementary
to original. Each original strand is a
template.
○ RNA is the second step of central dogma
▪ RNA polymerase (complex protein) catalyzes
transcription:
□ The process of copying DNA information
into RNA
▪ Selective transcription of the genome defines
the function of a cell or tissue
□ The genes that get transcribed are all the
things that define what a cell does and what
part of a tissue it can be
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part of a tissue it can be
▪ All the cells in your body have a complete set
of DNA, but none transcribe all the genes
□ Each cell only transcribes a subset of the
genes
○ Transcription of RNA
▪
▪ Transcription, catalyzed by RNA polymerase,
makes a RNA copy of one of the strands of
DNA
▪ The RNA polymerase complex crawls along the
DNA, splitting apart the two strands and then
synthesizing new RNA that's complementary to
the DNA
○ The third step of central dogma is Protein
▪ Translation converts the nucleic acid sequence
information in mRNA into protein sequence
information
▪ Translation occurs on ribosomes
▪ Protein is made out of RNA
□ The creation of protein from RNA is called
translation
□ The largest job of a cell, most energy goes
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□ The largest job of a cell, most energy goes
towards
□ Ribosomes actually make the proteins
Largest complexes in the cell (can see w
electron microscope)
○ Translation takes place on ribosomes
▪
▪ A ribosome decodes the information in mRNA
and translates it into the amino acid sequence of
a protein
▪ Ribosome crawls down mRNA, creating new
polypeptide chain.
- 1.4 Membranes Define the Cell and Carry Out Cellular
Functions
▪ A membrane is a lipid bilayer
▪ Eukaryotes contain membrane-enclosed
compartments inside the cell
□ Prokaryotes lack intracellular membranes
(only one exterior membrane)
▪ The most important structure in the cell is the
membrane
□ Separating it from the outside world.
Protects from bad, keeps in the good
▪ Major intracellular membrane is the nucleus
The bilayer structure of a membrane
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○ The bilayer structure of a membrane
▪
□ (A) Membranes are composed of two layers
or sheets
□ (B) The hydrophobic parts interact with each
other, hydrophilic parts interact with
environment surrounding
▪ Electron micrograph
□ Uses electrons to basically take a picture of
the cell and it can interact with other
electrons. Reality.
○ Prokaryotic and eukaryotic cells
▪
▪ Eukaryotic cells display more internal
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▪ Eukaryotic cells display more internal
structures.
□ Interior structures defined by membranes,
notably the nucleus.
▪ Prokaryote has the nucleoid (mass of DNA) on
the inside of out membrane.
▪ Differences
□ Prokaryotes often have a cell wall
Bunch of sugars that protect the cell
They can also have a double membrane,
outer membrane w second inner
membrane for protection
They infect us and cause disease
Allowing us to kill them and not us
○ Plasma membrane
▪ Plasma membrane separates the inside of the
cell from the outside.
▪ The plasma membrane is impermeable to most
biomolecules
▪ Selective permeability occurs because of the
presence of proteins associated with the
membrane.
▪ Plasma membrane defines what the cell is.
▪ Protein holes selectively allow glucose through
the plasma membrane
○ Membrane proteins
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▪
▪ Proteins, embedded (yellow) in membranes and
attached (blue) to them, permit the exchange of
material and information with the environment.
▪ Transmembrane protein
□ Extends through the membrane and has
domains inside and outside the cell for
recognition by other cellular elements,
communication
▪ Integral membrane protein
□ Function as channels between inside or
outside
▪ 2 more membrane proteins
□ One way is the blue which interacts with the
membrane proteins themselves
□ The other is the blue protein that interacts
directly with the lipid elements
○ Cytoplasm
▪ The cytoplasm is the part of the cell surrounded
by the plasma membrane but not enclosed by
any intracellular membranes.
▪ The cytoplasm is organized by a series of
structural filaments called the cytoskeleton.
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structural filaments called the cytoskeleton.
▪ The blood of the cell ("cyto" for cell, "plasm"
for blood)
▪ Important cellular activities site
□ Protein synthesis
○ The cytoskeleton
▪
▪ Actin filaments, intermediate filaments, and
microtubules are components of the
cytoskeleton, which provides cell shape and
contributes to cell movement.
▪ Microtubules the most important, long w hole
through middle
▪ Then the Actin filaments are shorter and
branched
▪ Intermediate filaments is a class of filaments
that do other cellular stuff
○ The nucleus
▪ Biochemical functions are sequestered in
cellular compartments
▪ The nucleus is the information center of the
cell.
□ Most important cellular compartment
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□ Most important cellular compartment
□ Contains DNA
▪
▪ Nucleolus
□ Where a lot of the ribosomes are assembled,
factory inside the nucleus
▪ The nucleus has two different lipid bilayers
▪ The nuclear membrane has holes called nuclear
pores, proteins selectively channeling
○ Mitochondrion
▪
▪ Mitochondria, organelles, are the primary site
of ATP generation in eukaryotic cells
▪ The mitochondrial matrix is show in light blue
(B)
▪ "Mighty mitochondria"
▪ Two membranes
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▪ Two membranes
□ The inner membrane folds and are where
ATP actually gets synthesized, giving more
surface area
○ Endoplasmic reticulum
▪ Some organelles process and sort proteins, and
exchange material with the environment
▪ The endoplasmic reticulum (ER) is a series of
membranous sacs in the cytoplasm
▪ There are two types of ER
□ Rough ER has ribosomes associated with it
and plays a special role in protein processing
□ Smooth ER lacks ribosomes and plays a
variety of biochemical roles
▪ Organelles are things inside cells that have their
own identity
▪ The ER is a large network of membranous
compartments throughout the cell
▪ Smooth ER is responsible for a lot of the
sorting and delivery of proteins
▪
▪ Cytoplasm inside the smooth ER is called the
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▪ Cytoplasm inside the smooth ER is called the
lumen
○ Golgi complex
▪ The Golgi complex is a series of stacked
membranes that play a role in protein sorting.
Carbohydrates are also attached to proteins in
the Golgi complex.
▪ Proteins are shuttled from the rER to the Golgi
complex by transport vesicles
▪ Very similar to ER.
▪ The ER communicates with the Golgi complex
by sending vesicles out which contain proteins
inside and outside
□ These vesicles bump into the Golgi complex
fusing to it and dumping the proteins into
the lumen where the Golgi complex
processes the proteins.
Carbohydrates get attached to the
proteins and many times end up exported
out of the cell.
▪
▪ Series of stacked compartments, bottom left
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▪ Series of stacked compartments, bottom left
bulge is fused vesicle from ER.
○ Exocytosis
▪
▪ Secretory vesicles secrete biomolecules in the
process of exocytosis
□ "exo" out and "cyto" cell, out of the cell
▪ Proteins begin in ER, transport vesicle to fuse w
Golgi complex, then secretory vesicle from
Golgi complex to the external cell membrane
fusing, then dumping contents outside in
surround media
○ Endocytosis
▪
▪ Endocytosis is a means of bringing crucial
biomolecules into the cell
▪ An endosome is the structure that forms when
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▪ An endosome is the structure that forms when
the plasma membrane invaginates and buds off
▪ Can contain just about anything, usually very
specific though
○ Phagocytosis
▪
▪ Large amounts of material can be taken into the
cell by the process of phagocytosis
▪ When very hungry will eat anything.
▪ "Phago" means eat, engulf
▪ Then slowly digests the extracellular material
○ Lysosomes
▪
▪ Lysosomes contain a variety of digestive
enzymes.
▪ Lysosomes fuse with endosomes to digest
material brought into the cell.
▪ {A micrograph of a lysosome in the process of
digesting a mitochondrion (M) and other
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digesting a mitochondrion (M) and other
cellular material}
▪ Controlled corrosive application, to not harm
cell
▪ "Lyse" means split apart
▪ Once finally digested can be distributed through
cell
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02 Water, Weak Bonds, and Order out of Chaos
Sunday, January 15, 2023
6:25 PM
- Weak interactions are reversible easily. Feeling
something, hearing something, touching something.
Can start and stop.
- 2.1 Thermal Motions Power Biological Interactions
▪ Weak bonds permit dynamic interactions that
form the basis of biochemistry and life itself.
□ Strong bonds are important to keep things
structured.
□ Weak bonds let things change (change is
necessary for life)
▪ Brownian motion is the movement of molecules
powered by random fluctuations of
environmental energy.
□ Movement of the molecules
Thermal motion is the motion of the
atoms
▪ Brownian motion of water initiates many
biochemical interactions
▪ Talking about actual energy of a specific atom
is challenging, but generalizations can be made
about systems
○ The Boltzmann Distribution
▪
▪ Shows the distributions of the energies that all
of the atoms or molecules in a system have.
□ Kinetic energy = speed
□ Height of the curve is the fraction of the
molecules that have that particular kinetic
energy
□ Majority have low kinetic energy, very few
have none
□ The shaded areas have enough energy, but
sometimes other properties must be fulfilled
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□
sometimes other properties must be fulfilled
also like location, so maybe the dark blue
line is molecules with enough energy and in
the right location
□ The red area is at a higher temperature so
the molecules are moving faster in general,
so a larger portion of molecules have
enough energy to react
- 2.2 Biochemical Interactions Take Place In an
Aqueous Solution
○ Water is a polar molecule
▪
▪ Water is a polar molecule, with the oxygen
atom carrying a partial negative charge and the
hydrogen atoms carrying partial positive charge
▪ It is everywhere in biological systems and they
require it
□ A lubricant for all things to move
▪ The water molecule is also bent, overall
negative on oxygen and positive on hydrogen
side
▪ A negative pole and positive pole
□ Overall molecule is neutral
○ Hydrogen bonds and cohesiveness
▪ The polarity of water allows the formation of
the hydrogen bonds between water molecules
and accounts for the cohesiveness of water.
□ The polarity of water also accounts for its
ability to dissolve many important
biochemicals.
▪ The inability of water to dissolve nonpolar
molecules results in an important organizing
principle called the hydrophobic effect.
▪ Most biomolecules are also polar
□ They also contain nitrogens, hydrogens, and
oxygens, which also have partial charges
Water interacts with these partial charges
and cracks these molecules apart, called
dissolving
◊ Only works with other polar
molecules
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molecules
- 2.3 Weak Interactions Are Important Biochemical
Properties
○
▪ The force of an electrostatic interaction between
two charges is given by Coulomb's law:
□
□ F is the force, q1 and q2 are the charges on
the ions, D is the dielectric constant, r is the
distance between two ions, and k is a
proportionality constant
▪ The study of the forces between positive and
negative charges is called electrostatics.
□ The polar molecules, the partial charges are
pretty stable, so electrostatics is a good way
to describe the interactions between them
▪ So basically if you increase the charge of either
one, you're going to increase the force
□ If you increase the distance between them,
you're going to decrease the force
Different charges will pull together,
same charges will push apart
○ Sodium chloride dissolves in water
▪
○
▪ Hydrogen bonds are not unique to water
molecules and can occur whenever H is
covalently bonded to an electronegative atom.
Biochemistry Page 33
▪
▪ Water disrupts hydrogen bonds between two
molecules by competing for the hydrogen
bonding capability
▪ Hydrogen only has one electron and one proton,
this makes it extraordinarily unique and
important.
□ It can float around in solution as a naked
proton
□ Form particularly strong interactions with
negative atoms such as oxygen and nitrogen
○ Hydrogen bonds that include nitrogen and oxygen
atoms
▪
▪ The four most common ways that hydrogen
bonds can form
□ They're usually between nitrogen and
oxygen
□ The two most common electronegative
substances are nitrogen and oxygen.
○ Disruption of hydrogen bonds
▪
▪ Competition from water molecules disrupts
hydrogen bonds in other molecules
○
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hydrogen bonds in other molecules
○
▪
▪ Nonpolar and uncharged molecules can interact
electrostatically with van der Waals interactions
▪ The basis of the van der Waals interaction is
that transient asymmetry in one molecule will
induce complementary asymmetry in a nearby
molecule
□ Due to the electrons sometimes
concentrating more on one side or another
creating a temporary dipole, so that one side
is temporarily partially charged, other side
partially negative
□ This interaction is weaker because the
movement is shifting constantly. But is still
a force to be accounted for
○ The energy of a van der Waals interaction as two
atoms approach each other
▪
▪ The energy is most favorable as the van der
Waals contact distance. The energy rises
rapidly owing to electron-electron repulsion as
Biochemistry Page 35
rapidly owing to electron-electron repulsion as
the atoms move closer together than this
distance
▪
▪ (chart the professor likes better)
▪ The van der Waals contact distance is the zero
point
▪ There are two opposing forces at play
□ Attractive forces, like van der Waals
interactions
□ Repulsive forces, the short range Coulomb
interactions
The two electrons of particles don't like
to overlap and occupy the same space, so
they push away when that's going to
happen
▪ The van der Waals radius
□ Where if you push them closer they will get
pushed away and if you try to pull them
apart they will be pushed together
▪ The van der Waals contact distance basically
means they're touching to the human eye, as
close as they can get
○ The power of van der Waals interactions
Biochemistry Page 36
▪
▪ Geckos hold on using weak van der Waal
forces, across flat surfaces
▪
▪ The gecko's feet are covered with foot hairs
called "setae." There are 1 million on each toe.
And each setae has 1000 spatular tips. They fill
all the gaps on the surfaces so close that van der
Waals interactions will actually take effect and
stick the gecko to the wall.
▪ At the microscopic level "flat" are surfaces are
quite rough. Two perfectly flat objects would
attach to each other because of the van der
Waals forces
○ Weak Bonds Permit Repeated Interactions
▪ Hydrogen bonds contribute to the stability of
the DNA double helix.
□ However, these bonds are weak enough to
be broken by the enzymes of DNA
metabolism, thereby allowing access to the
genetic information.
Biochemistry Page 37
▪
▪ Weak bonds allow things to come apart and
then back together a number of times. Ex. DNA
double helix hydrogen bonds
□ The bases are connected w hydrogen bonds
□ All the hydrogen bonded bases together of
the helix make a very stable structure, like a
zipper. Strong enough to close and hold
together, but not so strong they won't be
split and reconnected.
□ The three hydrogen bonds between
Guanine(G) - Cytosine(C) is 50% stronger
than the two hydrogen bond between
Adenine(A) - Thymine(T)
□ The free H off adenine and free H off
cytosine are also capable of hydrogen
bonding, and play a part in enzyme
recognition
- 2.4 Hydrophobic Molecules Cluster Together
▪
▪ Hydrophobic molecules such as benzene tend to
cluster together in aqueous solutions
□ This clustering of hydrophobic molecules in
water is called the hydrophobic effect.
The hydrophobic effect is powered by
the increase in the entropy of water that
results when hydrophobic molecules
come together.
□ The hydrophobic effect is a powerful
organizing force in biological systems
In protein folding for example, or the
formation of membranes
▪ Hydrophobic molecules do not have charges
that are permanently distributed, like the polar
molecules do, so they tend to cluster together.
The van der Waals interactions hold them
Biochemistry Page 38
The van der Waals interactions hold them
together and the lack of polarity doesn't allow
water to break that interaction apart
□ Water is polar, so it can still interact with it
with the hydrophobic van der Waals
interactions, but the polar nature means it
doesn't have much effect.
▪ The hydrophobic effect is one of the reasons
polar molecules can't cross membranes, they
don't interact with the membrane as strongly as
the membrane interacts with itself (each other
molecule in the membrane)
○ The hydrophobic effect
▪
▪ The aggregation of nonpolar groups in water
leads to an increase in entropy owing to the
release of water molecules into bulk water
▪ The water molecules surrounding nonpolar
molecules want to be free to bond with other
water molecules (water molecules want to bond
with water molecules)
□ So when two nonpolar molecules are near
each other, they are attracted which will take
away space that some of the water
molecules surrounding occupied attached,
no free to be with other water molecules
○ Membrane Formation is Power by the
Hydrophobic Effect
▪
▪ Phospholipids have hydrophilic and
hydrophobic properties. When exposed to
water, phospholipids form membranes.
□ This allows each end to be doing what it
loves
Biochemistry Page 39
□
loves
Without the hydrophilic heads, the tails
would just blob together in an oil droplet
○ Protein Folding is Powered (in large part) by the
Hydrophobic Effect
▪
▪ When proteins are synthesized, amino acid
string is ejected from the ribosome, it then starts
to fold up on itself.
□ Because in the cytosol you have a lot of
water. The hydrophobic elements of the
protein start finding other hydrophobic
elements, clumping together with the
hydrophilic side on the outside with the
water.
- Functional Groups Have Specific Chemical Properties
▪ Although there are many different
biomolecules, only a limited number of
functional groups are found in these molecules.
□ Functional groups are arrays of atoms that
have distinctive chemical properties.
□ The common configurations of atoms.
Can be a part of a larger molecule.
□ Always have the same chemical properties.
○ Some functional groups in biochemistry
Biochemistry Page 40
▪
▪ Hydrophobic functional group
□ Contains only carbon and hydrogen
No nitrogen or oxygen, therefore
nonpolar and hydrophobic
□ Two main types
Hydrocarbon chains CH3
Aromatic groups, rings of carbon
◊ often stabilized with double bonds
□ CH3 is called a methyl group
▪ Hydroxyl group -OH
□ An oxygen with a hydrogen attached, we
call them alcohols.
Ethanol is 2 carbons with a hydroxyl
group.
◊ Oxygen is one of the most reactive
elements, so the hydroxyl group is
very reactive.
▪ Aldehyde group COH
□ A carbon with a double bonded oxygen and
a hydrogen.
The oxygen makes it easier for the
carbon to attach to things, useful in
connecting
▪ Keto group CO
□ Ketones don't have a hydrogen, making the
one carbon particularly reactive
Biochemistry Page 41
□
one carbon particularly reactive
So if you have a carbon chain with a
ketone in the middle and there's some
sort of reaction occurring, you can bet it
will take place at that carbon.
▪
▪ Carboxyl group
□ COOH, carboxylic acid
□ Carboxyl groups on all amino acids, which
make up the acid part (in any biological
acid)
▪ Amino group
□ -NH2 amines
□ Nitrogen with a couple of hydrogens on it
Seen in adenine, in ATP
▪ Phosphate group
□ Extremely important, ATP example again
□ -OPO3 organic phosphate
□ Seen a lot in glycolysis, processing glucose.
And signaling. Important part of DNA
backbone
▪ Sulfhydrl group
□ Thiols, -SH
□ Kind of like an alcohol, but sulfur instead of
oxygen
Biochemistry Page 42
oxygen
Biochemistry Page 43
