Word of the day…

excogitate (verb): to study intently in order to

comprehend something fully; to think out, devise, invent.

 Pick a half-sheet of paper from the front of the class.

 You won’t need your clickers today.
@UBCWellnessCentre
Introduction to Macromolecules
Introduction to Macromolecules
Learning Objectives
 List the four major categories of macromolecules in cells.
 For each of the macromolecules, List and identify the
monomers, types of covalent bonds linking the monomers
together, the directionality of the macromolecules, and the
reason for the directionality.
 Explain and relate the importance of functional groups to
macromolecule polymerization and directionality.
 Recognize the general structure, chemical properties and
functional groups of monomers that make up each type of
macromolecule.
 Introduction to Macromolecules

Lipids, proteins,
Have a container
and carbohydrates
Gather raw materials
Gather or make parts Proteins
Gather and transform energy

Have a set of instructions DNA

Pass instructions to replicas Proteins and DNA

Mechanism to read the instructions Proteins and RNA

Copyright © 2018, Jared L. Taylor

 Introduction to Macromolecules
There are four groups of macromolecules that we
will consider in Biol 112:
1) Lipids: cell/organelle membranes
2) Proteins: enzymes, structure
3) Carbohydrates: structure, energy
4) Nucleic acids: DNA, RNA

Copyright © 2018, Jared L. Taylor

 Extra Post-class Notes
 Of the four macromolecules listed on the previous
page, we will really only focus on three of them in
Biol 112.
 Carbohydrates as macromolecules won’t be
discussed much more beyond what is shown in the
following slides. You should still be familiar with
this information.

Copyright © 2018, Jared L. Taylor

 Cell Biology and Macromolecules

Component Cell Makeup*

Ions (Na+, K+, Mg2+, etc) ~1%
Proteins 45 - 55% Over 80% of a
Nucleic Acids (DNA, RNA) 15 - 20% cell’s dry weight
Carbohydrates 10 - 15% comes from
Lipids ~5% macromolecules!
Small organic molecules 10 - 20%
*dry weight, not including water

You don’t need to remember these numbers!

Copyright © 2018, Jared L. Taylor

 Which of the following is quite
different from the others?
A) Lipids

B) Proteins

D) Nucleic
Acids

C) Carbohydrates
 Which of the following is quite
different from the others?
A) Lipids

B) Proteins

D) Nucleic
Acids

C) Carbohydrates
What characteristics do each of
these have in common?

nucleotides monosaccharides

amino acids
 Extra Post-class Notes
 Lipids are unusual in that they don’t follow the
usually monomer-to-polymer type of synthesis
(they do to a certain degree but it is limited).
 They are also largely non-polar (hydrophobic) and
tend to be almost completely lacking in functional
groups.
 Directionality and polarity (discussed in the
following slides) also have little meaning for lipids
and cells do not “look” at lipids in this way.

Copyright © 2018, Jared L. Taylor

 Extra Post-class Notes
 Other than carbohydrates (which aren’t really
discussed much after today), everything covered in
the following slides is simply meant as an
introduction to what we will go over in detail over
the coming lectures.

Copyright © 2018, Jared L. Taylor

Monomers
 Except for lipids, each macromolecule types is
composed of a series of repeating monomer units
(individual but related molecules).

nucleotides monosaccharides

amino acids
Extra Post-class Notes
 Macromolecules are polymers that are assembled
from their respective monomers using both
covalent bonds and non-covalent interactions.
Proteins

Macromolecular
polymerization assembly
DNA helix
covalent non-covalent
bonds interactions
Lipid bilayer
(mostly)
Asymmetrical Monomers
Polarity and Directionality
 The monomers are joined together in a very
particular manner, using the same connection
points each time.

Next monomer in the

chain is added here.
 Polarity and Directionality
This gives protein, carbohydrates, and nucleic acids
two important characteristics:
1) Polarity (very unfortunate terminology): the
two ends of the macromolecule chain are
distinct from each other chemically.
2) Directionality: you (and cells) can determine
which end you are moving towards by
observing the polarity of the units as you move
past them (i.e. you know what direction you
are moving in).

Copyright © 2018, Jared L. Taylor

 Extra Post-class Notes
 Just to be clear, “polarity” as used here for
macromolecules has nothing to do with bond
polarity (due to electronegativity differences),
which can be confusing at times.
 Please keep this in mind. In the context of
macromolecules as large molecules, “polarity”
refers to them being asymmetric with two
chemically distinct ends.
 The fact that they are also molecules that tend to
comprise many polar bonds can be confusing
(biologists, it seems, often conscript terms from
chemistry and apply them in confusing ways).

Copyright © 2018, Jared L. Taylor

 Polarity and Directionality
Tea pot analogy:

handle spout

The teapot exhibits polarity: two

distinct ends with different functions.

If we line up a bunch of tea pots in the same direction, you could

describe which end you start at and the direction you are moving!
 Introduction to Macromolecules
 The post-class slides will include some self-study
slides to some introductory details about the four
types of macromolecules. Please read these over
by Friday.

Copyright © 2018, Jared L. Taylor

The following 12 slides are self-study slides. Please
read over them before Friday’s class. We will be
talking about Lipids, Proteins, and Nucleic Acids
again in details so these slides are simply meant as a
brief introduction.
Lipids
 Lipids are a very loose and diverse group of
macromolecules that are based on one of more
long chains of carbon and hydrogen (C-C and C-H
bonds).
 For the purposes of Biol 112 their defining feature
is a hydrophobic region (tail) connected to a
hydrophilic (head).
 Lipids
 Some lipids are formed of smaller lipids called fatty
acids (much like the molecule shown on the
previous slide).
 In this case the monomer could be referred to as
the fatty acid.
 These lipids use ester linkages to hold the fatty
acids in place.
 Fatty acids and ester linkages are used to form
phospholipids, as shown on the next slide.

Copyright © 2018, Jared L. Taylor

Lipids
 In Biol 112, the most
important type of lipid
is the phospholipid.

Ester linkage
 Proteins
 Proteins are complex molecules comprising a long
chain of amino acids.
 The amino acids are joined together using a
peptide bond.
 The critical aspect of proteins is their 3D shape,
which is defined by the sequence of amino acids.
 The protein chain is characterized by an amino end
(N-terminus; the end with the nitrogen group) and
a carboxyl end (C-terminus; the end with the
carbon group).

Copyright © 2018, Jared L. Taylor

Proteins

N-terminus
C-terminus
 Carbohydrates
 Carbohydrates are long chains of cyclic sugar
molecules (monosaccharides).
 The monosaccharides are linked together by a
glycosidic bond.
 In Biol 112, carbohydrates are most important for
structural support in cell walls, and their ability to
be rigid and cross-linked are their most important
features.

Copyright © 2018, Jared L. Taylor

Carbohydrates
 Carbohydrates
 Other than mentioning carbohydrates here and
there as part of other aspects of the course, this is
the only time we will really talk about them.

Copyright © 2018, Jared L. Taylor

 Nucleic Acids
 Nucleic acids are primarily used by cells to encode
and translate their genes (instructions).
 The storage/encode function is handled by
deoxyribonucleic acid (DNA).
 The translate function is handles by ribonucleic acid
(RNA). In this role, RNA acts as both a delivery
service and an enzyme.
 The most important aspect of nucleic acid is the
order of its nucleotides that are joined together
using a phosphodiester bond.

Copyright © 2018, Jared L. Taylor

Nucleic Acids
 Extra Post-class Notes
 For practice I suggest filling out and becoming
familiar with the following table. I will use these
terms a lot and you need to be familiar with them.

Macromolecule Monomer name Covalent bond name

Protein

Nucleic acid (DNA/RNA)

Carbohydrate

Lipid

Copyright © 2018, Jared L. Taylor

 Extra Post-class Notes

Macromolecule Monomer name Covalent bond name

Protein Amino acid Peptide bond

Nucleic acid (DNA/RNA) Nucleotide Phosphodiester bond

Carbohydrate Monosaccharide Glycosidic bond

Lipid Fatty acid Ester linkage

Copyright © 2018, Jared L. Taylor

End of self-study slides.
 More chemistry discussion…
 Before we discuss lipids and membrane structure,
we need to discuss some basic thermochemistry
concepts.
 These same concepts will be applicable to protein
and nucleic acid structures.

Copyright © 2018, Jared L. Taylor

 Half-sheet question…
 Discuss the following terms with your neighbours
and write a definition of each on your half-sheet:
1) Enthalpy
2) Entropy
3) Free Energy

Copyright © 2018, Jared L. Taylor

 Enthalpy
 Potential energy related to the strength of bonds or
interactions.
 Change in enthalpy: we will simplify this and
describe it as the change in system energy due to
breaking and making bonds or interactions
between/within molecule (or atoms).
 Making stronger bonds or interactions decreases
enthalpy, releasing energy and increasing system
stability.
 A negative change (a decrease) in enthalpy
increases system stability.

Copyright © 2018, Jared L. Taylor

 Entropy
 Potential energy related to degrees of freedom.
 Change in entropy: the change in system energy
due to increasing or decreasing degrees of freedom
of molecules (atoms).
 “Degrees of freedom” can be though of as the
motional freedom of molecules or the number of
possible arrangements.
 Often simplified as the “randomness” within a
chemical system (poor definition).
 A positive change (increase) in entropy increases
system stability.

Copyright © 2018, Jared L. Taylor

 Free Energy and Stability
 Free energy is the total system potential energy.
 Change in Free energy is referred to as the change
in system energy when you combine the change in
enthalpy and entropy.
Free energy = (Denthalpy) – (temp)(Dentropy)
DG = DH - TDS
 If the free energy change for a system (reaction,
process, change in interactions) is negative, the
system has lost energy and become more stable.
 Processes that have a negative free energy are said
to be spontaneous (favourable).
Copyright © 2018, Jared L. Taylor
Which of the following could represent
a spontaneous process or reaction?
Free energy = (Denthalpy) – (temp)(Dentropy)

A. Enthalpy > 0 and entropy > 0

B. Enthalpy < 0 and entropy < 0
C. Enthalpy > 0 and entropy < 0
D. Enthalpy < 0 and entropy > 0
E. All of the above could be spontaneous.

Note: assume that the temperature

is the same for all cases.
Which of the following could represent
a spontaneous process or reaction?
Free energy = (Denthalpy) – (temp)(Dentropy)

A. Enthalpy > 0 and entropy > 0

B. Enthalpy < 0 and entropy < 0
C. Enthalpy > 0 and entropy < 0
D. Enthalpy < 0 and entropy > 0
E. All of the above could be spontaneous.

Note: assume that the temperature

is the same for all cases.
 Enthalpy and Entropy Cheat Sheet

Change of > 0 Change of < 0 System stability

Relates to…
means… means… increases when…

Weaker bonds or
Stronger bonds or
interactions have
Strength of interactions have
been replaced by Change in enthalpy
Enthalpy bonds or been replaced by
Stronger bonds or is < 0.
interactions. weaker bonds or
interactions.
interactions.

Molecules in the Molecules in the

Motional
system have system have lost Change in entropy
freedom or
Entropy gained more some of their is > 0.
arrangements
motional freedom motional freedom
(“disorder”).
or arrangements. or arrangements.

Copyright © 2018, Jared L. Taylor

 Free Energy Cheat Sheet

Resulting
DEnthalpy… DEntropy… Overall Result…
DFree Energy…

Spontaneous only if the change in

Depends (could go
>0 >0 entropy is big enough to overpower
either way).
the unfavourable change in enthalpy.

Spontaneous only if the change in

Depends (could go
<0 <0 enthalpy is big enough to overpower
either way).
the unfavourable change in entropy.

<0 >0 <0 Spontaneous process

Non-spontaneous process (requires
>0 <0 >0
input of energy to proceed).

Free energy = (D enthalpy) – (temp)(D entropy)

Copyright © 2018, Jared L. Taylor
 Spontaneous Process
 The big take away, and what you need to always
keep in mind, is that if something (process,
reaction, etc.) happens spontaneously then energy
has been released. Note the this tell us nothing
about the speed of the process.
 Conversely, if energy input is required to drive
something forward, the process is non-
spontaneous (i.e. the backwards direction releases
energy).
 This is a very important concept to understand in
biology and biochemistry.

Copyright © 2018, Jared L. Taylor

 Extra Post-class Notes
 Thermochemistry (part of thermodynamics):
• Studying the stability of chemical systems.
• Deals with the likelihood of reactions occurring.

 Energetically favourable process = spontaneous.

• Likely to happen in this direction.
• Reaction moves from less stable to more stable.

 Energetically unfavourable process = non-spontaneous.

• Requires energy input to happen in this direction.
• Reaction moves from more stable to less stable.

Copyright © 2018, Jared L. Taylor

 Extra Post-class Notes
 Eventually, you should be able to (in general terms)
compare two system states and indicate:
• Which state is more or less stable.
• Which direction is spontaneous or non-spontaneous.
• Which direction releases free energy or requires and
input of free energy.
• Which state is more or less strongly bonded (enthalpy).
• Which state is more motionally free or motionally
restricted (entropy).

Copyright © 2018, Jared L. Taylor

 Thermochemistry and the Cell
 OK, let’s talk about some practical situations that
are important to cells.

Copyright © 2018, Jared L. Taylor

Diffusion
 The graphs to the right
show a computer
simulation of cream
added to coffee.
 The cream molecules
quickly diffuse
through the coffee.
 Extra Post-class Notes
 As stated shortly in the slides, diffusion is the result
of the random kinetic motion of the particles and
entropy.

Copyright © 2018, Jared L. Taylor

Diffusion
 What contributes to this? Enthalpy? Entropy?
Something else? Discuss with your neighbours.
Assuming perfect elasticity, which of
the following will affect the rate (speed)
at which each particle diffuses?
1. The mass of the diffusing particle.
2. The size of the space the particle is diffusing through.
3. The number of molecules that are in the middle initially.
4. The temperature of the system.
5. The characteristics of the space the particle is diffusing
through.
A. All 5 characteristics
B. Only 2 and 4
C. Only 1, 3 and 5
D. Only 1, 4 and 5
E. Only 2, 3 and 4
Assuming perfect elasticity, which of
the following will affect the rate (speed)
at which each particle diffuses?
1. The mass of the diffusing particle.
2. The size of the space the particle is diffusing through.
3. The number of molecules that are in the middle initially.
4. The temperature of the system.
5. The characteristics of the space the particle is diffusing
through.
A. All 5 characteristics
B. Only 2 and 4
C. Only 1, 3 and 5
D. Only 1, 4 and 5
E. Only 2, 3 and 4
 Extra Post-class Notes
 I know that the answers on the previous slide can
be a bit confusing.
 The size of the space is essentially irrelevant to how
fast a particle is moving. A smaller space does
mean the particle will change direction more often,
but speed does not. [Note: in this case we are
assuming perfect elastic collisions. It is true that
more collisions with something will transfer energy
and slow a particle down, but only to a certain
point due to the surrounding temperature.]

Copyright © 2018, Jared L. Taylor

 Extra Post-class Notes
 Likewise, more particles does not mean a change in
speed of any given particle, although it does mean
it will collide more often and change direction
(again, assuming perfect elasticity).

Copyright © 2018, Jared L. Taylor

 Homework for Friday
 Please try the homework worksheet that will be
posted later today before Friday.

Copyright © 2018, Jared L. Taylor