Biochemistry Water, PH and Buffers Part 1 tutorial
Summary
TLDRIn this biochemistry segment, Professor Paul Bingham delves into the fundamental role of water as the universal solvent in biochemical reactions. He explains the molecular structure of water, its polarity, and the formation of hydrogen bonds, which are crucial for understanding the properties of water and its interactions with other molecules. The segment also touches on the hydrophobic effect, a key principle in the structure of biological macromolecules, such as DNA and proteins, highlighting the significance of water's behavior in shaping biological systems.
Takeaways
- 𧏠Water is the solvent in which most biochemistry occurs, playing a crucial role in the structure and function of biological molecules.
- đ The structure of a water molecule includes two hydrogen atoms and one oxygen atom, with the oxygen being more electronegative, attracting electrons towards itself.
- đ Water molecules can form hydrogen bonds due to the polarity created by the electronegative oxygen and the partial positive charges on hydrogen.
- âïž Ice floats on water because the orderly lattice structure of ice makes it less dense than liquid water, which is about 9% denser due to the dynamic formation and breaking of hydrogen bonds.
- đĄ The properties of water as a solvent are influenced by the constant movement of water molecules, even at room temperature, which is more vigorous than commonly perceived.
- đ§ The hydrophobic effect, where nonpolar molecules avoid interaction with water, is fundamental to the structure of macromolecules in biochemistry, such as DNA, proteins, and lipid membranes.
- đ« Hydrophobic molecules, like benzene, do not interact well with water due to their nonpolar nature and comparable electronegativity between carbon and hydrogen.
- đŹ The study of water's properties as a solvent helps in understanding biochemical molecules, as water itself can be considered a biochemical molecule.
- đ Life evolved in water, and the biochemical reactions of cells are designed to occur in an aqueous environment, similar to seawater's salt concentration.
- đ The van der Waals radii of water molecules define the spatial relationships and interactions between them, which are always present and relevant in biochemical contexts.
- đŹ Colligative properties of water will be discussed later in the segment, hinting at further exploration of water's unique characteristics in biochemistry.
Q & A
What is the primary focus of the segment presented by Professor Paul Bingham?
-The primary focus of the segment is to understand the structure of water, its role as a solvent in biochemistry, and its colligative properties.
Why is water considered the solvent of all biochemistry?
-Water is considered the solvent of all biochemistry because most biochemical reactions occur in an aqueous environment, and it is the medium in which life has evolved.
What is the significance of the van der Waals radii in the context of water molecules?
-The van der Waals radii are significant as they represent the spatial dimensions of the electron shell around the atoms in a water molecule, influencing how close two water molecules can approach each other before electrostatic repulsion occurs.
How does the electronegativity of oxygen in a water molecule affect its structure and interactions?
-The high electronegativity of oxygen causes it to attract electrons towards itself, creating a polar molecule with partial positive charges on hydrogen and partial negative charges on oxygen, which allows water molecules to form hydrogen bonds.
What is a hydrogen bond and why is it important in the context of water and biological molecules?
-A hydrogen bond is a type of dipole-dipole interaction where a hydrogen atom bonded to a highly electronegative atom (like oxygen) is attracted to another electronegative atom. It is important because it influences the structure and properties of water and is a key interaction in the structure of many biological molecules.
Why does ice float on water?
-Ice floats on water because the water molecules in ice form a highly ordered lattice structure that contains more space between the molecules compared to liquid water, making ice less dense.
What is the hydrophobic effect and why is it significant in biochemistry?
-The hydrophobic effect is the tendency of nonpolar molecules to avoid interaction with water and to aggregate together. It is significant in biochemistry because it influences the structure of macromolecules and biological systems, such as DNA, proteins, and lipid membranes.
How does the structure of a benzene molecule relate to the hydrophobic effect?
-The benzene molecule has a rigid planar structure with delocalized electrons around the ring, and the carbon and hydrogen atoms have comparable electronegativity, making the molecule nonpolar and thus subject to the hydrophobic effect.
What is the relationship between the structure of water and its ability to dissolve substances?
-The polar nature of water and its ability to form hydrogen bonds allow it to interact with a wide variety of substances, either by surrounding ions or by forming hydrogen bonds with polar molecules, enabling it to dissolve many different types of solutes.
What are colligative properties and how do they relate to the understanding of water as a solvent?
-Colligative properties are properties of solutions that depend on the ratio of the number of solute particles to the number of solvent molecules, not on the nature of the chemical species involved. They help in understanding how different solutes affect the physical properties of water, such as boiling and freezing points.
How does the movement of water molecules at the molecular level contribute to the properties of liquid water?
-The continuous movement and rapid formation and breaking of hydrogen bonds among water molecules contribute to the fluidity and cohesive properties of liquid water, which are essential for its role as a solvent in biochemical processes.
Outlines
đ Introduction to Water's Role in Biochemistry
Professor Paul Bingham introduces the fundamental role of water in biochemistry, emphasizing its status as the primary solvent in which most biochemical reactions occur. He outlines the segment's focus on understanding water's structure, its ability to dissolve substances (solvation), and its colligative properties. The professor highlights water's unique properties, such as its polarity due to oxygen's electronegativity, which allows it to form hydrogen bonds, a feature crucial for understanding biochemical molecules. The summary also touches on the rarity of reactions occurring outside an aqueous environment and the significance of water's properties for the study of biochemistry.
đ§ Hydrogen Bonds and the Hydrophobic Effect
This paragraph delves into the concept of hydrogen bonding, a phenomenon where slightly positive charges are attracted to slightly negative charges, facilitated by the hydrogen atom's efficiency in forming such bonds. The professor explains how water molecules can form up to three hydrogen bonds simultaneously, contributing to water's unique properties as a solvent. The summary discusses the orderly lattice structure of ice, which makes it less dense than liquid water, allowing it to float. It also introduces the hydrophobic effect, which is central to the structure of macromolecules in biochemistry, such as DNA, proteins, and lipid membranes. The hydrophobic effect results from the interaction of nonpolar molecules with water, leading to the aggregation of these molecules away from water, a principle that is essential for understanding biological structures.
đ” Interruption in the Script
This section of the script is an interruption marked by the [Music] tag, indicating a pause or transition in the video. There is no substantial content to summarize, as it serves as a placeholder for musical interludes or editing purposes within the video.
Mindmap
Keywords
đĄBiochemistry
đĄWater
đĄColligative properties
đĄElectronegativity
đĄHydrogen bond
đĄHydrophobic effect
đĄVan der Waals radius
đĄPolar molecule
đĄIce
đĄBenzene
Highlights
Water is the solvent of all biochemistry, essential for understanding biochemical molecules.
Biochemistry can be considered a subset of organic chemistry that occurs in water.
The structure of water is crucial for understanding its properties as a solvent.
Water's electronegativity and the resulting partial charges are fundamental to its behavior.
Hydrogen bonds are a key feature of water molecules and many biological molecules.
The unique property of water allows it to form up to three hydrogen bonds simultaneously.
Ice floats because its highly ordered lattice structure makes it less dense than liquid water.
The hydrophobic effect is central to the structure of macromolecules in biochemistry.
Hydrophobic molecules interact with water in ways that influence biological structures.
Benzene's planar structure with delocalized electrons exemplifies hydrophobic interactions.
The hydrophobic effect is responsible for a significant portion of biological macromolecular structure.
Understanding water's properties is the first step toward understanding biochemical molecules.
The van der Waals radii are always present and play a role in the interactions between water molecules.
The movement of water molecules at the molecular scale is more violent than commonly perceived.
The structure of water as a solvent is dynamic, with molecules constantly forming and breaking hydrogen bonds.
The properties of water are shared with biochemical molecules, making water a biochemical molecule itself.
The salt concentration of cytoplasm is similar to that of seawater, highlighting the importance of water in life.
Transcripts
[Music]
hello I'm Professor Paul Bingham and
this is biochemistry 1 our goal in this
segment is take the first steps toward
Mastery of an understanding of water the
solvent of all biochemistry and in this
segment we're going to particularly talk
about the structure of water how it
dissolves things salvation as it's
called and something called colligative
properties which we'll come to at the
end of the segment so remember the
status of biochemistry it's the missing
piece of the jigsaw puzzle that unifies
the chemical and physical world with the
biological world and water as we've said
is the solvent in which virtually all
biochemistry goes on we won't talk any
more about it today but the the the
tools that that organisms build pro
mostly proteins can occasionally create
a little tiny micro sequestered
environment away from water and allow an
organic reaction action to go on in the
absence of water as needed but in fact
that's a fairly rare uh event most
biochemistry is goes on in in an aquous
environment in in fact we can talk about
biochemistry mostly As the as a specific
subset of organic chemistry that goes on
in water so let's talk first about the
structure of water and as we talk about
the structure of water as a solvent
there's a tendency to think of the
solvent is kind of Fading Into the
background and the interesting stuff
going on in the solvent uh and to some
extent that's true but also the
properties of water turn out to be
properties shared with the biochemical
molecules that we're going to care a lot
about later so as we understand the
property of water as a solvent we're
also taking the first step toward
understanding biochemical molecules in
fact in a very real sense water is a
biochemical molecule as you'll see over
and over again going forward so this
diagram is just to emphasize to you that
that water we live on a water Planet uh
the vast majority of the surface of the
planet is covered by water life evolves
in water and so it's not at all
surprising that the uh that most
biochemical reactions are designed to go
on in water and in fact in seawater so
we won't talk about it today but the the
salt concentration of the cytoplasma
cells is remarkably similar to the Salt
concentration of seawat again not a big
surprise all right so this is a diagram
of the whole picture of a water molecule
in the center is this traditional ball
and stick uh diagrams to emphasize the
spatial relationships of molecules and
then surrounding the clouds in blue and
red blue for hydrogen in this case red
for oxygen are the uh so-called vandor
walls radi these are the um the uh
dimensions of the electron shell such
that when two water molecules approach
their electron shells uh uh when they
get to the point that the electrostatic
repulsion between their electron shells
is over is overwhelming stopping further
U migration together you have
encountered that is the definition of
the Vander walls
radi in most of the diagrams
subsequently we're going to look at ball
and stick um diagrams of water molecules
but remember that the the Vander walls
radi are Al are already there or always
there and we'll call them back from time
to time where they're relevant so this
is a a step toward a ball and stick
model this is a water molecule with the
U um electrons in the bonding external
bonding orbitals diagrammed so there's a
there there's six in the external uh uh
orbitals of uh oxygen so to create the
magic number of eight U they can share
one electron with each of two hydrogen
atoms is diagrammed here at the bottom
and then they have two unbonded electron
pairs diagrammed at the top here and
let's go through that so oxygen is
strongly
electronegative what that means is that
it tends to attract electrons to itself
and away from the less electronegative
atoms to which it is bound of which
hydrogen is a dramatic and specific
example again let me emphasize something
I said a moment ago this property of
electro negativity pulling electrons to
one atom in a bonded molecule and away
from another is a generic property of
many many biological molecules so as we
stud it in water we're learning also
Concepts that we're going to apply over
and over again and then again this here
are the unbonded electrons boxed in
green at the top so let's look now at
the consequences of water to the
structure of water as a solvent of the
strong electr negativity of oxygen uh uh
kind of uh
um holding on disproportionately to
electrons in water molecules so here are
two water
molecules water molecules are polar as
we've said here are the two oxygen in
the molecule so this is a slightly
simplified diagram compared to the one
you saw a moment ago here are the
unbonded electron pairs that you saw
again a moment ago and these green
arrows represent the pulling of
electrons toward the oxygen atom and
away from the hydrogen atoms because
again of the electro negativity of
oxygen that creates therefore small
partial positive charges on hydrogen and
small partial negative charges on oxygen
in a water molecule okay so as a result
of that water molecules have the
capacity to form what is called a
hydrogen bond it is essentially like an
ionic bond a small positive charge is
attracted to a small negative charge but
the hydrogen uh atom is particularly
efficient at providing at at at um in
becoming involved in this kind of bond
and therefore it's often referred to as
a hydrogen bond again for the third time
hydrogen bonds are formed by many
biological molecules they are Central as
we'll see to the structure of biological
molecules so while we're learning about
water today we're also learning about
some principles that are going to be
crucial to the understanding of
biological molecules as well as you'll
see several other of the abundant
elements in organisms specifically
nitrogen and sulfur are also
electronegative Like Oxygen and so in
fact biological molecules that have
oxygen nitrogen or sulfur will often
form hydrogen bonds under the
appropriate circumstances more about
that in later segments today our focus
is oxygen and water
okay that is a hydrogen bond between two
water molecules in fact water molecules
can often form as many as three hydrogen
bonds simultaneously and understanding
that in turn helps us understand a great
deal about the properties of water as a
solvent let's first consider solid water
and the fact that ice floats and that's
a little surprising right in general
when we drop a solid object of some sort
into a glass of water usually expect it
to sink water ice does not it floats why
because in fact ice is lighter the solid
form is lighter than the liquid form how
does that work well in fact ice the
water molecules in ice form a highly
orderly lattice structure so liquid
water the molecules are moving around in
ways that we'll talk about in a moment
as you withdraw thermal energy from them
by cooling them you eventually Traverse
the freezing point and they collapse
into this lce structure diagrammed on
the image that you're looking at on the
screen at the moment uh that highly
orderly structure has some air in it so
to speak some space in it uh uh the
orderly molecules are held apart from
one another a little bit uh beyond their
Vander wals radi uh on average because
of the formation of these highly ordered
structures if we start pumping more heat
energy back in the molecules start
vibrating more rapidly and eventually
when the melting point is reached they
break apart and they form liquid water a
little bit of that is diagrammed here
individual water molecules form and
break hydrogen bonds with their
neighbors but they're now doing it in
kind of an insane three-dimensional
square dance where they form and break
hydrogen bonds with their neighbors very
rapidly in fact on a
nanoscale uh time scale so these uh
movement of molecules at even at room
temperature at the molecular scale is
quite more violent than we're used to
thinking of that will rarely concern us
here directly but it's it's a kind of
interesting fact to know so as liquid
molecules now are going through this
three-dimensional Square Dan forming and
breaking in real-time hydrogen bonds
with one another it means that at
certain moments in time two water
molecules can bump closer than they
would if they were fully hydrogen bonded
in a lattice bumping up against their
vandals radi and therefore liquid water
is about 9% denser than ice and ice
floats which is a useful thing in a
number of contexts our concern at the
moment though is now how liquid water
acts as the solvent in which virtually
all biochemistry occurs and we're going
to start by looking at the how water
interacts with things that don't like to
go into solution of water the so-called
hydrophobic effect we'll come back later
to hydrophilic molecules that like to go
into solution in water but let's begin
with hydrophobic we do this because the
physical chemistry is interesting U more
generally but more importantly because
the hydrophobic effect a very simple
effect the interaction of a molecule
with water is responsible for a enormous
fraction of the structure of the macro
molecules and biological systems so the
structure of DNA the structure of
proteins the structure of lipid
membranes for example are all dependent
on the interaction of those molecules
with water and particularly with the
so-called hydrophobic effect so as we go
through this if it seems a little
esoteric or beside the point precisely
to the contrary is true this is the
hydrophobic effect is Central to all
macromolecular structure in Biochemistry
so let's start with a simple case this
is a a diagram of a Benzene molecule you
remember that Benzene the some of the
bonding electrons delize around the ring
and so you get a rigidly planer
structure in which the carbons and the
surrounding hydrogen molecules are
pulled into this rigid plane notice also
that carbon and hydrogen are comparably
electr negative so carbon is not pulling
I say again not pulling electrons off of
oxygen I'm sorry Alp of
[Music]
[Music]
hydrogen
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