Chapter 5  The Structure and Function of Large Biological Molecules
Student Guided Notes
Overview: The Molecules of Life

Within all cells, small organic molecules are joined together to form larger molecules.

All living things are made up of four main classes of macromolecules: ________________________,
___________________________, ____________________________, and __________________________.

These large macromolecules may consist of thousands of covalently bonded atoms.
Concept 5.1 Macromolecules are polymers, built from monomers

Three of the four classes of macromolecules—carbohydrates, proteins, and nucleic acids—form chain-like
molecules called polymers.
○ A polymer is _________________________________________________________________________
____________________________________________________________________________________
○ The repeated units are small molecules called _____________________________.
○ Some of the molecules that serve as monomers have other functions of their own.

The chemical mechanisms which cells use to make and break polymers are similar for all classes of
macromolecules.
○ These processes are facilitated by enzymes, ________________________________________________
____________________________________________________________________________________

Monomers are connected by ________________________________ bonds that form through the loss of a
___________________________ molecule. This reaction is called a _______________________________
reaction.
○ When a bond forms between two monomers, each monomer contributes part of the water molecule that is
lost. One monomer provides a _________________________________________, while the other
provides a ________________________________________.
○ Cells invest energy to carry out dehydration reactions.

The covalent bonds that connect monomers in a polymer are disassembled by hydrolysis, a reaction that is
_______________________________________________________________________________________.
○ In hydrolysis, bonds are broken by ______________________________________________________
____________________________________. A ______________________________ atom attaches to
one monomer, and a __________________________________ group attaches to the adjacent monomer.
○ The process of _________________________________ is an example of hydrolysis within the human
body.
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Concept 5.2 Carbohydrates serve as fuel and building material

Carbohydrates include ________________________________ and their polymers.
○ The simplest carbohydrates are ____________________________________________, or simple sugars.
○ Disaccharides, or _______________________ sugars, consist of two monosaccharides joined by a
_________________________________________.
○ ________________________________________ are polymers of many monosaccharides.
Sugars, the smallest carbohydrates, serve as fuel and a source of carbon.

Monosaccharides generally have molecular formulas that are some multiple of the unit _______________.
○ For example, glucose has the formula ___________________________.

Monosaccharides have a ______________________ group (>C=O) and multiple
______________________________ groups (—OH).
○ Depending on the location of the carbonyl group, the sugar is an ________________________ (aldehyde
sugar) or a _______________________________ (ketone sugar).
○ Most names for sugars end in -____________.

Monosaccharides are also classified by _______________________________________________________.

Although glucose is often drawn with a linear carbon skeleton, most sugars (including glucose) form
______________________ in aqueous solution.

Monosaccharides, particularly ___________________________, are major nutrients for cellular work.
○ Cells extract energy from glucose molecules in the process of ___________________________________.

Two monosaccharides can join with a ____________________________________________ to form a
__________________________________________ via dehydration.
○ _______________________, malt sugar, is formed by joining two ______________________ molecules.
○ ________________________________, table sugar, is formed by joining ________________________
and _______________________________. Sucrose is the major transport form of sugars in plants.
○ Lactose, ________________________________, is formed by joining glucose and __________________.
Polysaccharides, the polymers of sugars, have storage and structural roles.

Polysaccharides are _____________________________________________________________________
______________________________________________________________________________________

______________________________ is a storage polysaccharide composed entirely of
_________________________________________________. (STARCH = PLANT STORAGE)
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
Plants store surplus glucose as starch granules within _________________________________, including
chloroplasts, and withdraw it as needed for energy or carbon.

Animals store glucose in a polysaccharide called __________________________. (GLYCOGEN =
ANIMAL STORAGE)
○ Humans and other vertebrates store a day’s supply of glycogen in ______________________________
__________________________, hydrolyzing it to release glucose to meet the body’s demand for sugar.

Cellulose is a major component of the ______________________________________________________.
(CELLULOSE = PLANT STRUCTURE)

Like starch, cellulose is a polymer of glucose. However, the glycosidic linkages in these two polymers differ.
o Starch is a polysaccharide of __________________________ glucose monomers.
o Cellulose is a polysaccharide of ________________________ glucose monomers, making every other
glucose monomer upside down with respect to its neighbors. Animals cannot digest ______________
glucose chains, and therefore cannot digest cellulose.
o Many eukaryotic herbivores, from cows to termites, have symbiotic relationships with cellulose-digesting
prokaryotes and protists, providing the microbes and the host animal access to a rich source of energy.

Another important structural polysaccharide is chitin, found in ___________________________________
___________________ (including insects, spiders, and crustaceans). (CHITIN = ANIMAL STRUCTURE)
○ Pure chitin is leathery but can be hardened by the addition of ___________________________________.
○ Chitin also provides structural support for the cell walls of many ___________________________.
Concept 5.3 Lipids are a diverse group of _________________________________________________

Unlike other macromolecules, lipids do not form polymers.

The unifying feature of lipids is that they have little or no affinity for water because they consist of mostly
___________________________________, which form nonpolar covalent bonds.
Fats store large amounts of energy.

Although fats are not strictly polymers, they are large molecules assembled from smaller molecules via
_____________________________________________ reactions.

A fat is constructed from two kinds of smaller molecules: ____________________________ and
_________________________________________.
○ Glycerol is a three-carbon ________________________________ with a ________________________
group attached to each carbon.
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○ A fatty acid consists of a _________________________________ group attached to a long carbon
skeleton, often ________________________ carbons long.
○ The many __________________________ C—H bonds in the long hydrocarbon skeleton make fats
______________________________________.

In a fat, three __________________________________ are joined to __________________________ by an
__________________________________, creating a _______________________________, or triglyceride.
o The three fatty acids in a fat can be the same or different.

Fatty acids vary in length (number of carbons) and in the number and locations of double bonds.
○ If the fatty acid has no carbon-carbon double bonds, then the molecule is a _______________________
fatty acid, saturated with hydrogens at every possible position.
o Straight Chain (because no _____________________________ bonds)
o ______________________________ Fats (Butter or Lard)
o ______________________________ at Room Temperature
○ If the fatty acid has one or more carbon-carbon double bonds formed by the removal of hydrogen atoms
from the carbon skeleton, then the molecule is an ___________________________________ fatty acid.
o Kinks in chain wherever there is a double bond
o ___________________ Fats (Vegetable or Olive Oil) (also ________ fats are unsaturated)
o __________________ at Room Temperature

The phrase “hydrogenated vegetable oils” on food labels means that ________________________________
_______________________________________________________________________________________
_______________________________________________________________________________________
○ ____________________________________ and ______________________________ are hydrogenated
to prevent lipids from separating out as oil.

The major function of fats is ______________________________________.
○ A gram of fat stores ___________________________________________________________________
as a gram of a polysaccharide such as starch.

Humans and other mammals store fats as long-term energy reserves in _____________________________
cells that _______________________________________________________________________________
_______________________________________________________________________________________.
○ Adipose tissue also functions to _________________________________________, such as the kidneys.

A layer of fat can function as ______________________________. (ex. Whales, seals, et.)
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Phospholipids are major components of _________________________________________.

Phospholipids have _______________ fatty acids attached to __________________________ and a
_____________________________________________ at the third position.

The interaction of phospholipids with water is complex.
○ The fatty acid tails are ______________________________________, but the phosphate group and its
attachments form a ________________________________ head.

Phospholipids are arranged as a ____________________________________ at the surface of a cell.
○ The hydrophilic heads are on the outside of the bilayer, in contact with the _____________________
_____________________, and the hydrophobic tails point ___________________________________
_____________________________________________.
○ The phospholipid bilayer forms a barrier between the cell and the external environment.
○ ______________________________________ are the major component of all cell membranes.
Steroids include cholesterol and certain hormones.

__________________________________ are lipids with a carbon skeleton consisting of _______________
______________________________________________________.

Different steroids are created by varying the functional groups attached to the rings.

_________________________________, an important steroid, is a component in animal cell membranes.
Concept 5.4 Proteins include a diversity of structures, resulting in a wide range of functions

Proteins account for more than 50% of _______________________________________________________.
They are instrumental in almost everything an organism does.
○ Protein functions include structural support, storage, transport, cellular communication, movement, and
defense against foreign substances.
○ Most important, protein enzymes function as ____________________________ in cells, regulating
metabolism by selectively accelerating certain chemical reactions without being ___________________.

All proteins are unbranched polymers constructed from __________________________________________
____________________________________.

Polymers of amino acids are called _______________________________________.

A protein is ___________________________________________________________________________
______________________________________________________________________________________
______________________________________________________________________________________.
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Amino acids are the monomers from which proteins are constructed.

Amino acids are organic molecules with both ________________________ and ________________ groups.

At the center of an amino acid is an ___________________________________ carbon atom called
_____________________________________________________

Four components are attached to the α carbon: a __________________________________ atom, a
_______________________________________ group (acid), an ____________________________ group
(base), and a variable ____________________________________ (or side chain).
○ Different R groups characterize the 20 different amino acids.
○ An R group may be as simple as a hydrogen atom (as in the amino acid glycine), or it may be a carbon
skeleton with various functional groups attached (as in glutamine).

The physical and chemical properties of the R group determine the ________________________________
______________________________________________________________________________________

Amino acids are joined together when a ________________________________________ reaction removes
a _______________________________ group from the ________________________________ end of one
amino acid and a _________________________________ atom from the _____________ group of another.
○ The resulting covalent bond is called a _______________________________________.

Repeating the process over and over creates a polypeptide chain.

Polypeptides range in size from ____________________________________________________________.

Each polypeptide has a unique _____________________________________________________________.
Protein conformation determines protein function.

A functional protein consists of one or more polypeptides precisely _______________________________
______________________________________________________________________________________

It is the _____________________________________________________________________ that
determines the three-dimensional structure of the protein under normal cellular conditions.
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
A protein’s specific structure determines its function.

Many proteins are __________________________________ (roughly spherical), while others are
__________________________________ (long fibers) in shape.

In almost every case, the function of a protein depends on ______________________________________
_____________________________________________________________________________________

The function of a protein is an emergent property resulting from its specific molecular order.

Three levels of structure ______________________________, ____________________________, and
___________________________________ structures—organize the folding within a single polypeptide.
○ ___________________________________ arises when two or more polypeptides join to form a protein.

The primary structure of a protein is its unique _______________________________________________.

Even a slight change in the primary structure can affect a protein’s conformation and ability to function.
Example – Sickle-cell disease (an inherited blood disorder) is caused by a change in ONE amino acid

__________________________ and ____________________________ in the polypeptide are referred to as
the ______________________________________ structure and result from _____________________
bonds between the ______________________________________________________________________.
○ Each hydrogen bond is __________________________, but the sum of many hydrogen bonds stabilizes
the structure of part of the protein.
○ The two main types of secondary structure are an ___________________________________ or a
_______________________________________________. See pictures on pg. 80.

Tertiary structure is determined by interactions among _________________________________________.
○ These interactions include hydrogen bonds between polar and/or charged areas, ionic bonds between
charged R groups, and hydrophobic interactions and van der Waals interactions among hydrophobic R
groups.
○ Although these three interactions are relatively ______________________________, their cumulative
effect helps _________________________________________________________________________.
○ Strong covalent bonds called _____________________________________________ that form between
the sulfhydryl groups (SH) of two ________________________________ monomers act to rivet parts of
the protein together.

Quaternary structure results from the aggregation of __________________________________________
______________________________________________________.
○ ________________________________________ is a fibrous protein made up of three polypeptides that
are supercoiled into a larger ___________________________________ helix.
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○ ____________________________________ is a globular protein with quaternary structure.

A polypeptide chain with a given amino acid sequence can spontaneously arrange itself into a threedimensional shape determined and maintained by the interactions responsible for secondary and tertiary
structure.
○ The folding occurs ____________________________________________________________________.

Protein structure also depends on the ______________________________ and
_________________________________ conditions of the protein’s environment.
○ Alterations in ___________, ______________________ concentration, __________________________,
or other factors can unravel or _______________________________________ a protein.
○ Because it is misshapen, a denatured protein is biologically ____________________________________.

Most proteins become denatured if they are transferred from an ___________________________________
environment to a _______________________________________________.
○ The polypeptide chain refolds so that its ______________________________________________ face
outward, toward the solvent.

Denaturation can also be caused by __________________________.
○ This explains why extremely high fevers can be fatal. Proteins in the ___________________________
become denatured by the high body temperatures.

Some, but not all, proteins can return to their functional shape after denaturation.
○ This suggests that the information for building a specific shape is intrinsic to the protein’s primary
structure.

The folding of many proteins is assisted by ________________________________, or chaperone proteins.
○ Chaperonins do not specify the ________________________________________________________ but
rather work to segregate and protect the polypeptide while it folds ______________________________.
o Molecular systems in the cell interact with chaperonins, marking incorrectly folded proteins for refolding
or for destruction.

Accumulation of incorrectly folded polypeptides is associated with many diseases, including ____________
______________________, __________________________________, _____________________________,
and ______________________________ disease.
Concept 5.5 Nucleic acids store, transmit, and help express hereditary information

The amino acid sequence of a polypeptide is programmed by ______________________________________
_______________________________________________________________________ known as a gene.
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
A gene consists of ___________________, a polymer known as a _________________________________.
o Nucleic acids are made of monomers called ________________________________________.
There are two types of nucleic acids: ______________________ and _______________________.

The two types of nucleic acids are ribonucleic acid (RNA) and deoxyribonucleic acid (DNA).

RNA and DNA are the molecules that enable living organisms to reproduce their complex components from
generation to generation.
o DNA provides directions for ____________________________________________________________.
o DNA also directs _____________________________________ and, through RNA, controls _________
_________________________________; this entire process is called ____________________________.

Organisms inherit DNA from __________________________________________.
○ Each DNA molecule is very long, carrying _____________________________________ or more genes.
○ Before a cell reproduces itself by dividing, its DNA is copied. The copies are then passed to the next
generation of cells.

Although DNA encodes the information that programs all the cell’s activities, it is not directly involved in
the day-to-day operations of the cell.

Each gene along a DNA molecule directs the synthesis of ________________________________________
_______________________________________________________________________________________
○ The mRNA molecule interacts with the cell’s protein-synthesizing machinery to direct the ordering of
amino acids in a ______________________________________________.

The flow of genetic information is _________________  __________________  __________________.

Protein synthesis occurs on cellular structures called ___________________________________.

In eukaryotes, DNA is located in the _______________________________, but most ribosomes are in the
_______________________________________.
○ mRNA functions as an intermediary, moving genetic instructions for building proteins from the
_________________________________ to the _______________________________.

Prokaryotes lack nuclei but still use __________________________ as an intermediary to carry a message
from __________________________ to the ______________________________________.
A nucleic acid strand is a polymer of nucleotides.

Nucleic acids are polymers made of ____________________________________________ monomers
organized as ___________________________________________.
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
Each nucleotide consists of three parts: a ___________________________________ base, a
_________________________________ sugar, and one or more ___________________________ groups.

The nitrogenous bases are rings of carbon and nitrogen that come in two types: purines and pyrimidines.
○ Pyrimidines:

___________________ ring structure

Three different pyrimidines: ______________________________, _______________________ ,
and ____________________________________.
o _______________________________________ is found only in DNA and
_____________________________ is found only in RNA.
○ Purines:


_____________________ ring structure

The two purines are _______________________________ and _________________________.
The pentose (sugar) joined to the nitrogenous base is _______________________________ in RNA and
___________________________________ in DNA.
○ The combination of a pentose and a nitrogenous base is a ____________________________________.

The addition of a ________________________________________ creates a ________________________.

The bonds in the sugar-phosphate backbone of DNA are called phosphodiester linkages
o

They are covalent bonds between the sugar of one nucleotide and the phosphate of the next
The two free ends of DNA are distinct.
○ One end has a ____________________________________ attached to a 5 carbon; this is the 5 end.
(Think: Five – Phosphate)
○ The other end has a _______________________________________ on a 3 carbon; this is the 3 end.

The sequence of bases along a DNA or mRNA polymer is unique for each gene.
Inheritance is based on replication of the DNA double helix.

DNA molecules have two polynucleotide strands that spiral around an imaginary axis to form a __________
___________________________.

The sugar-phosphate backbones of the two polynucleotides are on the _____________________ of the helix.
○ The two backbones run in ______________________________________________________________
____________________________, an arrangement referred to as ______________________________.

The two strands of DNA are held together by _____________________ bonds between the nitrogen bases.

Because of their shapes, only some bases are compatible with each other.
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○ Adenine (A) always pairs with ________________________________________ and guanine (G) with
____________________________________.
o In RNA, adenine (A) pairs with _______________________________; thymine is not present in RNA.

Another difference between RNA and DNA is that DNA almost always exists as a double helix, whereas
RNA molecules are more variable in shape.
Concept 5.6 Genomics and proteomics have transformed biological inquiry and applications

Genomics is an approach of addressing problems by analyzing __________________________________
______________________________________________________________________________________.

Similar to genomics, __________________________________ is the approach that analyzes large sets of
protein sequences.
We can use DNA and proteins as tape measures of evolution.

Genes (DNA) and their products (proteins) document the hereditary background of an organism.

Because DNA molecules are passed from parents to offspring, siblings have _________________________
______________________________________________________________________________________
_______________________________________________________________________________________

Two species that appear to be closely related based on fossil and molecular evidence should also be more
similar in DNA and protein sequences than are more distantly related species.
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