Biochemistry Water, PH and Buffers Part 1 tutorial

Summary

In 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

• 🧬 Water is the solvent in which most biochemistry occurs, playing a crucial role in the structure and function of biological molecules.
• 🌐 The structure of a water molecule includes two hydrogen atoms and one oxygen atom, with the oxygen being more electronegative, attracting electrons towards itself.
• 🔗 Water molecules can form hydrogen bonds due to the polarity created by the electronegative oxygen and the partial positive charges on hydrogen.
• ❄️ 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.
• 🌡 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.
• 💧 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.
• 🚫 Hydrophobic molecules, like benzene, do not interact well with water due to their nonpolar nature and comparable electronegativity between carbon and hydrogen.
• 🔬 The study of water's properties as a solvent helps in understanding biochemical molecules, as water itself can be considered a biochemical molecule.
• 🌍 Life evolved in water, and the biochemical reactions of cells are designed to occur in an aqueous environment, similar to seawater's salt concentration.
• 🔍 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.
• 🔬 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

00:00

🌊 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.

05:01

🧊 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.

10:07

🎵 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.

Keywords

💡Biochemistry

Biochemistry is the study of the chemical processes and substances that occur within living organisms. In the video, it is emphasized as the missing piece that unifies the chemical and physical world with the biological world, highlighting the importance of understanding biochemical processes in the context of water as the solvent.

💡Water

Water is described as the solvent of all biochemistry, meaning it is the medium in which most biochemical reactions take place. The video discusses the unique properties of water that make it essential for life and the focus of the segment is to understand its structure and its role in dissolving substances and supporting biochemical reactions.

💡Colligative properties

Colligative properties are a set of chemical properties that depend on the ratio of the number of solute particles in a solution, not on their nature. Although not deeply explained in the script, the mention of colligative properties suggests they will be relevant to understanding how solutes affect the properties of water.

💡Electronegativity

Electronegativity is a measure of the tendency of an atom to attract a bonding pair of electrons. In the context of the video, oxygen's high electronegativity is crucial in forming water's polar nature, which influences its ability to dissolve other substances and form hydrogen bonds.

💡Hydrogen bond

A hydrogen bond is a type of dipole-dipole attraction between a hydrogen atom covalently bonded to an electronegative atom (like oxygen) and another electronegative atom. The video explains that water molecules can form hydrogen bonds, which is central to the structure of water and many biological molecules.

💡Hydrophobic effect

The hydrophobic effect refers to the tendency of hydrophobic molecules to aggregate in an aqueous solution and exclude water. The video script discusses this effect as a fundamental principle in the structure of biological macromolecules, such as proteins and lipid membranes.

💡Van der Waals radius

The Van der Waals radius is the distance from the nucleus of an atom at which the electron density is low enough that another atom's electron cloud can approach without significant repulsion. In the video, this concept is used to describe the spatial relationships between water molecules and how they interact.

💡Polar molecule

A polar molecule is a molecule that has a permanent dipole due to the uneven distribution of electron density. The video explains that water is a polar molecule because of the difference in electronegativity between oxygen and hydrogen, which leads to the formation of partial charges.

💡Ice

Ice is the solid state of water. The video script explains the surprising fact that ice floats on water because it has a lower density than liquid water due to the highly ordered lattice structure of ice, which includes spaces between the water molecules.

💡Benzene

Benzene is a chemical compound with a ring of six carbon atoms, each bonded to hydrogen atoms. In the script, benzene is used as an example of a hydrophobic molecule, which has a planar structure and does not interact favorably with water, illustrating the concept of the hydrophobic effect.

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