Building blocks of life study guide (part 2 of 2) 

Chapters 5, 8.4 and 8.5, 37, 41 

 
Chapters 5 / 8.4 – Structures & functions among 4 classes of macromolecules 
Vocabulary:  
monomer vs. polymer, dehydration synthesis vs. hydrolysis, monosaccharide vs. polysaccharide,
glycogen vs. starch, cellulose, phospholipid, polypeptide vs. protein, amino acid (and amino vs.
carboxyl ends), peptide bond, levels of protein structure (primary, secondary, tertiary,
quaternary), “R” group, denaturation, (also from 8.4 – enzyme vs. catalyst, substrate, active vs.
allosteric site, cofactor vs. coenzyme, competitive vs. noncompetitive inhibitors), DNA vs. RNA,
deoxyribose vs. ribose, nucleotide, nitrogen base, adenine, thymine, guanine, cytosine, uracil,
double helix, antiparallel (and 5’  3’ directionality) 
 
Concepts by section: 
Overview: 
--macromolecules can be organized into 4 major groups … these are found in all living cells
that  
make up all living organisms (and as we’ll see, even some nonliving things like viruses) 
        Carbohydrates              protiens                           lipids                      nucleic acids  
 
 
5.1 – Building blocks 
--the general term for any basic building block is _monomer … when we put a bunch of  
them together, we get a  polymer (note the prefixes there) 
 
--any time two building blocks are combined (overall process called dehydration synthesis ,  
Water is also released (joins countless other molecules in solution) (fig. 5.2a) 
 
--conversely, macromolecules can be split into smaller pieces – a molecule of water is also split,
and the process is called hydro lysis( water, break) (note prefix, suffix) (fig 5.2b) 
 
--read “diversity of polymers” carefully – different combinations of monomers lead to polymers  
with different 3-D shapes – this shape is crucial to molecule’s function (more below) 
 
5.2 – Carbohydrates 
--generic name for carbohydrate monomer monosaccharide (glucose is just one of these) 
 
--structure of carbohydrates: (note: you do NOT need to memorize molecular structures like
5.3)  
--carbohydrates are made of the atoms oxygen, hydrogen, and carbon
 
--carbohydrates are polar due to a lot of O-H bonds (figures 5.3 / 5.4)  
(think about what groups are polar and nonpolar) 
 
--many (though not all) carbohydrates end with the suffix –ose 
 --note how different polysaccharides have different monomers (ex: fig. 5.5)  
or same monomers combined in different orientations (ex: fig. 5.7 b vs. c) 
 
(for example, we humans have the enzymes to fit and break down starch,  
but not cellulose, which is a different shape – p. 71)Page Break 
--functions of carbohydrates:  
1) quick energy (p. 69) – breaking up glucose to make cell energy = cellular respiration
--organisms store glucose by combining them to make storage polysaccharides –  
plants = cellulose while animals = glycogen
 
2) structural support – for example, plant cell walls are made of cellulose
 
3) (not mentioned in chapter 5) identification markers on the outside of cell membranes
–  
glycolipids and glycoproteins (briefly ready p. 128-129 and see fig. 7.7d – green  
is carbohydrate mounted on a purple protein) 
glycoproteins serve as identification tags recognized by membrane proteins in other cells.
 
5.3 – Lipids (fats) 
--structure of lipids:  
--lipids are very diverse in both structure and function, so we will be very broad here 
 
--though they contain the same atoms as carbohydrates above, lipids are very nonpolar  
because there are many more C - H bonds than in carbohydrates (see fig. 5.9b) 
 
--use this nonpolar, hydrophobic lipid structure to explain at the molecular  
level why oil and water separate (bottom p. 72) 
 because the hydrogen bonds between the water molecules form and exclude the fats, causing
them to group together.
 
 
 
--functions of lipids: 
1) major function: energy storage(p. 74 bottom left) 
 
2) cushions organs and insulates the body (p. 74 top right) 
 
3) key component in cell membrane structure (fig. 5.14, much more to come in ch. 7) 
--these lipids are called phospholipids because an additional polar  
part is added on to the traditional lipid structure 
 
draw a basic model of one (fig 5.11c is fine for a model)  
 
 
label which parts of the model above are hydrophilic and hydrophobic 
 
--draw the phospholipid bilayer sketch from fig 5.11d 
  
 
 
 
--explain why this bilayer self-assembles into that shape (p. 75 top left) 
  the by-layer assembles itself in that shape because the polar heads are
attracted to the water, so it faces towards the water, this groups together
the nonpolar tails away from the water, and forms the membrane.
 
 
 
4) signaling cells to change their activity (steroid hormones like testosterone are a  
communication molecule that binds at another cell’s protein receptor … we’ll  
discuss in the signaling unit) (you could briefly preview fig. 11.9 if you want) 
Page Break5.4 – Proteins 
--functions of proteins = immense (preview fig. 5.13, though I like my list of protein types and  
functions from my own video better) 
Class of protein  Broad function of this type of protein 

Enzyme (p. 75)  Accelerates chemical reactions 

 Defensive Protects against disease(antibodies) 
 Storage  Storage of amino acids
 transport Transport items(in the cell membrane ect.) 
 Hormonal Manages organisms activities(Insulin) 
--most importantly, each protein has a unique 3-D shape to do a unique function in the cell (see  
fig. 5.16) – here, we want to explore how each protein is built to have a unique shape 
 
structure of proteins: 
--atoms that make up proteins: C, H, O, N (unlike carbs / fats) and S (unlike nucleic
acids)           (look at any structure on p. 77)      (look at cysteine or methionine, p. 77) 
 
--I have recreated the diagram of the basic monomer of proteins from the bottom left of p. 75 –  
this is a generic amino acid
 1)Amine group 2)carboxyl group 3)R-group
 
 
 
 
 
 
 
 
 
 
 
--proteins get a unique 3-D shape when these monomers are combined together in a particular  
order to create a unique series of bonds that hold the protein in that shape (p. 80 – 81) 
 
Summary of the levels of protein structure: 
Level  What regions interact?  Bond(s) formed 
Carboxyl end and amino end groups of next
primary  door neighbors (fig. 5.15)  (p. 78)  dehydration
 
Hydrogen and oxygen groups that used to be
secondary  (p. 80) hydrogen bonds
far away in backbone 

(p. 81)  hydrogen, ionic,

tertiary  Rgroups (or side chains) of amino acids 
vender walls, and disulfide

(not in book – same as

quaternary*  multiple polypeptides
tertiary) 
More detail about the levels of protein structure: 
primary – at this point, there is just a “necklace” of amino acids linked together – we call this
a polypeptide chain because it is not a folded 3-D protein yet 
 
--note that when amino acids are combined in figure 5.15, we also produce a water
molecule (because this is an example of dehydration synthesis from 5.1) 
 
--this order of linear amino acids is important because they are all structurally different  
(p. 77), and thus this order will determine secondary / tertiary / quaternary
interactions below that ultimately result in a unique 3-D shape 
 
secondary –regular interactions at certain parts of any protein will create two major types of  
shapes – helical and the pleated sheet (p. 80) 
 
tertiary – different shaped 3-D pockets or ridges might form depending on which R groups are  
interacting and where they are relative to each other 
 
 
 
 
 
 
 
 
 
 
 
 
  
 
 
8.4 – Enzyme activity and speed of enzyme activity (do not read 8.1 – 8.3 for this unit) 
--start on p. 151 – note the term “catalyst” is broader than “enzyme” (all enzymes are catalysts,  
not all catalysts are enzymes) 
 
--skip “the activation energy barrier” and “how enzymes lower the EA barrier” for now, read  
“substrate specificity” through the rest of the section (pgs. 153 - 157) 
 
--enzymes often (but not always) have the suffix -ase(top right p. 155) 
 
--protein regions specific to enzymes: enzymes must have a certain 3-D shape to fit a specific  
chemical in a region of the enzyme called the active site 
 
--other proteins have specific binding site regions as well for the molecules they interact  
with, but we reserve the name above just for enzyme proteins 
 
--fig. 8.16 depicts enzymes / substrates / products, though some enzymes do hydrolysis 
(fig. 5.13 p. 76 top left – 1 substrate cut to make 2 products) while other enzymes
do synthesis (fig. 17.19 p. 350 step 2, 2 substrates combined to make 1 product) 
 
 
 
--bottom of p. 154 discusses the speed (or rate of enzyme activity): 
--brief math review – any rate is just some unit per (or divided by) another unit (for us,  
time), so a rate can be calculated on any graph that has time on the X-axis by  
finding Δy-axis / Δ x-axis 
          (whatever the units are / whatever the units are) 
 
--for example, look at enzyme data top right p. 155 … calculate the rate of enzyme  
activity between 10 and 15 minutes (and what would the units of the final rate  
calculation be?)  18umol/mL/min
 
 
--many factors can change the rate of enzyme activity in cells (very important for cells to
control  
enzyme activity rate to maintain homeostasis) … pgs. 154 – 156 and pgs. 82 – 83
discuss  
this to some extent, but we will also explore in investigation 13 
 
1. initial concentration of substrate (also read about enzyme saturation p. 154) 
discuss at molecular level why enzyme activity rate changes: 
 
 if there is too many substrates and not enough enzymes, more products will not be created.
 
 2. initial concentration of enzyme (we will see how cells regulate protein production later
in  
the year … same molecular level explanation as above) 
 
3. temperature changes 
--if solution is made colder than optimal temperature, what happens to enzyme  
activity rate? ___________________ (faster / slower / zero) 
--why? (molecular-level explanation involving enzyme and substrate molecules) 
 If particles are moving faster, then more reactions occur, increasing the activity, therefore if
particles are moving slower, there is less activity.
 
 
 
--if solution is heated well above optimal temperature, what happens to enzyme  
activity rate? ____________________ (faster / slower / zero) 
--why? (molecular-level explanation involving bonds within enzyme protein) 
 The enzyme becomes denatured, and its shape changes meaning the protein unravels and no
substrates can fit.
 
 
4. pH changes 
--if solution is much more acidic / basic than enzyme’s optimal pH, what
happens  
to enzyme activity rate? __________________ (faster / slower / zero) 
--why? (molecular-level explanation involving bonds within enzyme protein) 
 Bonds between the secondary and tertiary structures will breack and then the protein unravels,
meaning substrates cannot fit anymore.
 
 
 
 
-- any time bonds break to cause an enzyme to lose its shape (and therefore, function) we call it  
enzyme denaturation (cells work hard to prevent this) 
 
 
5. DNA code changes (we’ll discuss mutations more in the molecular genetics unit),  
causing incorrect amino acids to be placed in the polypeptide chain 
 
--from our class discussion, what are MANY possible effects if one amino acid
is  
switched for another based on our folding activity? 
 
 
 
-the proteins will fold wrong, causing the substrate to not be able to fit into the enzyme anymore,
and it can cause the protein to not fold properly affecting the function- this can be caused
because a nonpolar is replaced with a polar ect.
 
 
--briefly read about two interesting examples of mutations affecting protein  
function – negatively (sickle cell disease p. 82) and positively (bacteria
breaking down a new food source p. 157) 
 
6. presence of inhibitors or activators (also read section 8.5) 
 
--protein regions that ALL proteins have: inhibitor or activator molecules bind at allosteric
sites to alter a protein’s shape (which therefore affects its level of activity) 
 
--sometimes, proteins are “off” until an activator molecule binds (fig. 8.20a top) 
--draw what the protein might look like at right after its activator molecule binds 
 
 
 
 
 
 
 
 
--other proteins are “on” until an inhibitor molecule binds (fig. 8.20a bottom) 
--it might look the reverse of what you drew above (when inhibitor binds) 
 
--read about feedback inhibition – often, the product is the  
allosteric inhibitor that binds to a protein and stops the production process 
 
--an inhibitor binding at the allosteric site is an example of noncompetitive  
inhibition – so what is competitive inhibition by contrast? 
 
 Competitive inhibition is when a inhibitor binds directly to the active site, blocking the
substrate.
 
 
--briefly note top p. 157 that the deadliest poisons are usually irreversible  
inhibitors of crucial proteins 
 
5.5 – Nucleic acids (just an introduction here, more to come in molecular genetics unit) 
--structure of nucleic acids: 
--they contain atoms C, H, O, and N (like proteins), but also P (unlike  
proteins) (see figure 5.24 b and c for help) 
 
--monomer that repeatedly combines to make nucleic acid polymers = nucleotide
 --three components make up each monomer:  
 
 Nitrogenous base, 5 carbon sugar, phosphate group
 
 
--of these 3 components, nitrogenous base serve as the code for proteins  
--in both DNA and RNA, C pairs with G , in DNA only, A pairs with T 
whereas in RNA only, A pairs with U
 
--the other two non-coding components serve as the “backbone” of the nucleic acid 
--RNA and DNA have slightly different backbones – RNA is made of the  
Ribose sugar while DNA is made of deoxyribose sugar 
 
--overall shape of DNA is a double helix
--DNA strands are antiparallel … show understanding by filling in the complementary  
strand below (p. 86 middle right will help, or go to fig. 16.7b p. 317) 
 
given strand:    5’  GTTACTCGAA   3’ 
 
complementary strand:  3’CAATGAGCTT 5’
 
 
 
--functions of nucleic acids: 
1) DNA and RNA – instructions for building proteins workers correctly 
(fig. 5.23 - more in molecular genetics unit) 
 
2) ATP – delivering phosphorus often to proteins (p. 64 – an RNA “A”  
nucleotide with three phosphates instead of one – more in the metabolism unit) 
 
Chapter 37 – Plants obtaining the macromolecules discussed above 
Vocabulary: nitrogen fixing bacteria, mycorrhizae 
from ch. 35 – vascular tissue (xylem(water to leaves) and phloem(sugar from leaves to roots)) p.
757, stomata pores on epidermis(regulate evaporation)and guard cells(regulate opening and
closing of stomata)p. 764 
 
--to start, read just pg. 185-6 and clearly define autotroph (producer) and heterotroph
(consumer)  -make their own food by photosynthesis ect.
 -consume other living organisms for energy
 
--we will study plant autotrophs, though see figure 10.2 p. 186 to note other autotrophs  
 
 
37.1 –  good to skim, especially “organic components” subsection to see how soil is really a  
complex community of species, but nothing specific to know for this unit 
 
37.2  – How plants get needed nutrients (CHONSP and other atoms) 
--first go to fig 36.2 p. 779 to see where plants obtain the materials needed to build the 4  
different types of macromolecules in their cells 
 -water and minerals from the group; CO2 from the air
--we’ll begin thinking about macromolecule production by studying how plants build simple  
carbohydrate monomers through photosynthesis (more to come in metabolism unit) 
 
6 CO2+6 H2O = C6H12O6 + 6 O2 
 
 
 
 
 
 
 
--table 37.1 – the vast majority (~90%) of a plant’s biomass (not water mass, but the mass of all  
its macromolecules in dry tissue) comes from what source?  Carbon dioxide
 
--what happens to the carbohydrates that are produced? 
1) some used for cellular respiration (more to come in metabolism unit) 
2) some used to build important carbohydrate polymers (cellulose, starch, etc.) 
3) some are converted by enzyme pathways to other monomer types (see below) 
 
--if a carbohydrate is going to be converted to an amino acid or nucleotide, then they are also  
going to need sources of nitrogen
 
--this is a challenge because most of this element is in the air (review fig. 37.10 without  
memorizing details), and plants cannot fix this from the air as they can CO2 gas 
 
--so they have to get this nutrient (along with every other macro and
micronutrient  
listed in table 37.1) from the ground… fortunately, these compounds are
all very polar (see table 37.1) and dissolve in water well 
 
--there are also tiny amounts of other elements that plants take up from the soil in table 37.1 –
do  
NOT memorize all these elements, but note that many of them serve as cofactors – go
back to chapter 8.5 (p. 156) and define the purpose of these 
 -co-factors are loose molecules, inorganic and organic (co-enzymes) that parts of
enzyme or substrate and increase activity.
 
 
37.3 – Mutualistic relationships to increase access to nutrients for plants 
--the only type of organisms that have the enzyme pathways to take N2 gas out the air and  
convert into soil nitrogen are certain species of nitrogen fixing bacteria 
 
--the Rizobium plant family often works mutualistically with these nitrogen fixers 
by inviting them in to their roots (see fig. 37.11, but no details / vocabulary needed) 
(these plants produce fruits / vegetables with lots of protein)  
 
--what do the plants provide to these organisms to make the relationship mutualistic? 
 Sugars, amino acids, organic compounds
--another mutualism: mycorrhizae (this names the overall relationship, not an organism) 
--this relationship is between (basically ALL) plants and species of fungi.
--what does the plant provide? Phosphate and other minerals from the soil, growth factors
and antibiotics from the fungi, greater surface area for water intake.
--what does the other species provide? 
 -nutrient transfer between the fungus and the plant. In arbuscular, oval vesicles may form in the
hyphae serving as food storage for the fungus.
--another interesting plant adaptation – carnivorous plants (p. 799, 812) … these plants are not  
considered heterotrophs because they are not digesting the insects for all their  
macromolecules, but instead just to obtain more minerals in particular 
 
Chapter 41 – Heterotrophs obtaining the macromolecules discussed above 
Vocabulary: stomach, villi, small vs. large intestine (or colon) 
 
Concepts: 
--identify the three purposes of taking in food (in title of 41.1) 
1) 2)3) chemical energy for cellular processes, organic building blocks for
macromolecules, essential nutrients.
 
41.1 – Making and storing energy 
--which of the 4 macromolecules can be used in cell respiration to make ATP energy? (p. 893) 
1)2)3) carbs, protiens, and lipids
 
--so we often assume glucose is burned in a respiration chemical equation, but
organisms  can really burn multiple sources of fuel 
 
--good to skim section about essential nutrients, but nothing to memorize there 
 
41.2 – Different strategies heterotrophs use to digest and absorb food nutrients 
--food has to be digested before absorbed into cells, but organisms also want to prevent
digestion  of their own cell components – so digestion occurs in a separate area, including: 
a. inside the cell – for example, heterotrophic protists and sponges have specialized
organelles called intracellular digestion that have many types of digestive enzymes 
 
b. in body compartments outside cells – discuss an advantage of a gastrovascular cavity
over just digesting in each cell as in a) above, and discuss an advantage of a complete digestive
tract that most animals have 
-an advantage of a gastrovascular cavity is that the body can digest much larger food
particles than which can enter the cell with phagy-or pinocytosis.
  -a complete digestive tract allows food to be digested in a stepwise fashion, and allows
for an organism to be eating food while still digesting.
 
 
c. go briefly to 31.1 left p. 649 and discuss how fungi digest food outside of their cells
(noting that fungi are heterotrophs too) 
 -fungi digest food outside their body by releasing enzymes into their environment. These
enzymes either break down the molecules into compounds in the environment, or penetrate into
the walls of these cells and absorb the nutrients.
 
 
 
41.3 -  the textbook goes into too much detail about the mammalian digestive system – I just
want  to hit the basics (so you can skim whole section or just go to targeted notations below) 
 
 
 
--first goal after ingestion: break up food into smaller pieces for more efficient absorption 
breakdown #1: physical breakdown – starts in the oral cavity
(large chunks  smaller pieces) and finishes in the esophagus
(small pieces  liquid slurry) 
 
breakdown #2: chemically breaking down larger polymers into monomers (called  
chemical digestion generally in 5.1) – different enzymes are released into the
mouth, stomach, and beginning of the small intestine
 
also during breakdown, a lot of water is secreted by bordering cells to  
dissolve the monomers (to spread them out even more) … however,  
nonpolar tryglycerides do not dissolve in water, so lipase is released to
help them dissolve (fig. 41.14 caption) 
 
--p. 904 – with breakdown complete, the vast majority of nutrients are absorbed in the  
Small intestine 
--animals have evolved to maximize absorption in this organ 
1. sheer length and twisting quality of the organ (note the comparison of total surface  
area size on p. 904) 
 
2. the inside is full of little tiny hair-like extensions called villi that  
consist of many cells – this creates a high surface area for contacting the food
slurry and pulling in nutrients (p. 904 and fig. 41.13) 
 
--p. 904 – nutrients that have been successfully absorbed first travel to the liver to  
be stored / modified before going to body cells by systemic circulation 
 
--this organ is made of cells with many different enzymes to convert certain monomers  
into other monomers and neutralize toxic chemicals 
 
--p. 905 – anything not absorbed stays in the digestive system and travels to the  
Small intestine where water is reabsorbed that  
was secreted by body cells earlier in the digestive system (this is crucial as diarrhea and  
resulting dehydration is a major cause of death around the world) 
 
--anything not absorbed into the bloodstream at this point is released from the body as feces.
 
41.4 – Adaptations to increase nutrient digestion and absorption 
--identify some brief adaptations that carnivores and herbivores have to increase access
to  nutrients in the food they consume 
 -carnivores are sufficient with short digestive tracts because their stomach can expand
bigger to digest big species of animals.
-herbivores have longer digestive tracts and bigger surface areas. This is because more
surface area is needed to digest the tough cell walls of plants.
--read about mutualistic intestinal bacteria – what do they do to benefit us?  what do we  
do to benefit them? 
 -they supply our daily intake of vitamins often when taken into the bloodstream.
-intestinal bacteria regulates intestinal epithelium, and helps with functions of the immune
system.
-we give them a place to live
 
 
(we will read 41.5 in a later unit – can skip for now)