chapter 5 biology - sept 2025

what are ¾ of the four important classes of biological molecules

macromolecules that are polymers

polymers

long chains of monomer subunits linked by covalent bonds 

carbohydrates

a source of energy and provide structural support

proteins

a wide range of functions, such as catalyzing reactions and transporting substances into & out of cells

nucleic acids

store genetic information & function in gene expression

what is the fourth class that are not polymers or macromolecules

lipids

lipids

group of diverse molecules that do not mix well w/ water
key functions include providing energy, making up cell membranes, and acting as hormones 

macromolecules

carbohydrates, proteins & nucleic acids
huge size
chain-like molecules called polymers

enzymes

specialized macromolecules (usually proteins) that speed up chemical reactions
the chemical mechanisms by which cells make polymers (polymerization) and break down down are facilitated by enzymes

condensation reaction

reaction in which two molecules are covalently bonded to each other with the loss of a small molecules
if a water molecules is lost, it is known a dehydration reaction
one of the reactants provides a -—OH and the other provides a —H

hydrolysis

the process in which polymers are disassembled to monomers, reverse of dehydration
means: water, breakage
the bond between monomers is broken by the addition of a water molecules, with a hydrogen from water attaching to one monomer & the hydroxyl group attaching to the other
example: process of digestion since bulk of organic material in our food is in the form of polymers that are too large to enter our cells; enzymes attack the polymers, speeding up hydrolysis; released monomers are then absorbed into the bloodstream for distribution to all body cells

why are there differences between human siblings?

due to the inherited differences between close relatives reflected small variations in polymers particularly DNA & proteins
molecular differences between unrelated individuals are more extensive & those between species greater still

what is the basis for such diversity in life’s polymers?

constructed from 40-50 common monomers & some others that occur rarely
arrangement of sequence that the units follow 

proteins: 20 kinds of amino acids arranged in chains that are typically hundreds of amino acids long

carbohydrates 

serve as fuel and building material
include sugars & polymers of sugars
simple carbohydrates are the monosaccharides or simple sugars — monomers 
disaccharides — double sugars, two monosaccharides joined by a covalent bond
carbohydrate macromolecules are polymers called polysaccharides

monosaccharides molecular formula

some multiple of the unit CH2O

glucose (C6H12Og) is the most common monosachharide
- carbonyl group C=O 
- and multiple hydroxyl groups —OH
depending on the location of the carbonyl group, a monosaccharide is either an aldose (aldehyde sugar) or a ketose (ketone sugar) 

aldoses vs. ketoses

glucose — aldose

fructose — ketose

size of carbon skeleton for monosaccharides

3-7 carbons long
trioses
pentoses

hexoses (glucose, fructose) 

asymmetric carbon

carbon attached to four different atoms or groups of atoms
for example, glucose & galactose

what is the difference between glucose & galactose

the placement around one asymmetric carbon

what shape do sugars form?

rings!

cellular respiration

cells extract from glucose molecules by breaking them down in a series of reactions since monosaccharides are major fuel for cellular work & their carbon skeletons serve as raw material for the synthesis of other types of small organic molecules such as amino acids and fatty acids
monosaccharides not immediately used are incorporated as monomers into disaccharides or polysaccharides

disaccharide

two monosaccharides joined by a glycosidic linkage, a covalent bond formed between two monosaccharides by a dehydration reaction (glyco refers to carbohydrate)

lactose intolerance

humans who lack lactase, the enzyme that breaks down lactose, which is instead broken down by intestinal bacteria causing formation of gas & cramping
(avoided by taking lactase)

polysaccharides

polymers with a few hundred to thousand monosaccharides joined by glycosidic linkages
some serve as storage material, hydrolyzed as needed to provide monosaccharides for cells
other serve as building material for structures (architecture and function determined by its monosaccharides & position of glycosidic linkages)

starch

storage polysaccharide in plants
polymer of glucose monomers, as granules within cellular structures known as plastids (include chloroplasts)
synthesizing starch enables the plant to stockpile surplus glucose
represents stored energy and can be withdrawn by hydrolysis
potato tubers & grains are major sources
most of the glucose monomers are joined by 1-4 linkages like in maltose

simplest form- amylose is unbranched
amylopectin - branched w/ 1-6 linkages at branch points
all glucose molecules are in alpha configuration

glycogen

storage polysaccharide in animals
like amylopectin but more branched
vertebrates store in liver & muscle cells
glycogen stores depleted in about a day unless replenished by eating (issue of low carb diets - weakness & fatigue)

cellulose

structural polysaccharide in plants
component of cell walls
most abundant organic compound on Earth
polymer of glucose w/ 1-4 glycosidic linkages
all glucose monomers are in beta configuration
straight as opposed to the helical shape of starch
never branched & some hydroxyl groups on its glucose monomers hydrogen bond with the hydroxyls of other cellulose molecules lying parallel to it
parallel cellulose molecules held together in this way are grouped into units called microfibrils (strong building material) - paper & cotton
enzymes that digest starch are unable to hydrolyze beta linkages of cellulose due to the different shapes of these two molecules
most organisms cannot digest cellulose (abrades the wall of the digestive track & stimulates lining to secrete mucus) - insoluble fiber
cows & termites & fungi

chitin

carbohydrate used by arthropods to build their exoskeletons
embedded in layers of protein
also found in fungi (use this instead of cellulose to build their cell walls)
similar to cellulose due to beta linkages but the glucose monomer of chitin has a nitrogen-containing attachment

lipids

the one class of large biological molecules that does not include true polymers & are generally not big enough to be called macromolecules
are all hydrophobic
mostly C—H bonds

fats

glycerol molecules joined to three fatty acids
glycerol - alcohol
fatty acid - long carbon skeleton of 16 or 18 carbon atoms in length, the carbon at the end is part of a carboxyl group
ester linkage - bond between a hydroxyl group & a carboxyl group 
other names for a fat are triacylglycerol & triglyceride
fatty acids can all be the same or 2 or 3 types
major function is energy storage (hydrocarbons similar to gasoline molecules), cushions organs, insulation

saturated vs unsaturated

unsatured fatty acid — has double bonds between some carbons — liquid
double bonds in naturally ocurring fatty acids are cis-double bonds
most animal fats are saturated, can be packed tightly — solid because they have no kinks from the cis-bonds 
most plants are unsaturated (have kinks & bending from the cis bonds)
hydrogenation — making liquid unsaturated fats saturated so they become solid at room temperature (such as peanut butter)
atherosclerosis — deposits called plaques develop within the walls of blood vessels, causing inward bulges
trans fats — trans double bonds that contribute to coronary heart disease (common in processed & baked goods) 

phospholipids

part of cell membranes
only two fatty acids and the third hydroxyl group is attached to a phosphate group
another molecule (small or polar) molecule is linked to the phosphate group
hydrocarbon tales are hydrophobic
the phosphate group & its attachments are hydrophilic head
arranged in a bilayer (heads outside, tails inside)

steroids/cholesterol

steroids - four fused rings
distinguishable by particular chemical groups attached to the rings
cholesterol - a type of steroid , animal cell membranes & precursor from which other steroids are synthesized 
synthesized in the liver and obtained from diet 
atherosclerosis - high level of cholesterol 

protein

account for than 50% of the dry mass of most cells
catalysts - enzymatic proteins that speed up chemical reactions without being consumed & can function over & over again (workhorses)
same set of 20 amino acids
bond between them is called a peptide bond (polymer is called a polypeptide)

amino acid

organic molecules w/ both an amino group & a carboxyl group
in the middle is an asymmetric carbon called the alpha carbon

types of proteins

enzymatic - selective acceleration of chemical reactions
digestive
storage - storage of amino acids
casein the protein of milk is a major source of amino acids for baby mammals
ovalbumin is the protein of egg white
hormonal - coordination of an organism’s activities
insulin secreted by the pancreas, causes other tissues to take up glucose
contractile & motor - movement
undulations of cilia & flagella, actin & myosin proteins
defensive - protection against disease
antibodies
transport proteins - transport of substances
hemoglobin
receptor proteins - response of cell to chemical stimuli
receptors built into the membrane of a nerve cell detect signaling molecules
structural - suport
keratin, collagen, elastin

polypeptides

joined by dehydration reaction and the bond is called a peptidebond

polypeptide backbone is the repeated sequence of atoms, different R chains extend from the backbone

structure of proteins

globular proteins : spherical

fibrous proteins : long fibers

primary - sequence of amino acids (20 possible types)

secondary - H bonds between the repetitive constituents of the backbone (not the side chains), O atoms have negative & H atoms attached to the nitrogen have a positive 

alpha helix - coil every fourth amino acid

b - pleated sheet connected by parallel segments

tertiary - stabilized by side chain interactions (R groups) 

hydrophobic interaction - amino acids with nonpolar side chains end up in clusters at the core of the protein, out of contact with water (van der waals interactions)

h bonds & ionic bonds between side chains happen too

covalent bonds called disulfide bridges may further reinforce the shape (between sulfhydryl/thiol groups —-S—-S—-) rivets parts of the protein

quaternary structure - more than 2 polypeptide subunits (globular protein w/ a quaternary structure is hemoglobin)

sickle cell disease

substitution of one amino acid valine for the normal one glutamic acid at the position of the sixth amino acid in the primary structure of hemoglobin, causing blood cells to aggregate into chains/sickles

impedes blood flow
Many diseases—such as cystic fibrosis, Alzheimer’s, Parkinson’s, and mad cow disease—are associated with an accumulation of misfolded proteins.

denaturation

proteins lose shape (transferred out of aqueous into a nonpolar solvent) - chloroform

 X-ray crystallography

 X-ray crystallography, which depends on the

diffraction of an X-ray beam by the atoms of a crystallized mol-

ecule. Using this technique, scientists can build a 3-D model

that shows the exact position of every atom in a protein mol-

ecule

intrinsically disordered proteins

have an indefinite structure until they interact with a target protein or other molecule

gene

discrete unit of inheritance

nucleic acids

polymers made of monomers called nucleotides

DNA & RNA

deoxyribonucleic acid
ribonucleic acid
gene expression - DNA replicates, DNA directs RNA synthesis, RNA controls protein synthesis

mRNA

interacts with the cell’s protein-synthesizing machinery to direct production of a polypeptide which folds into proteins

ribosomes

sites of protein synthesis which receive messages from mR

nucleotides

three parts:

• five carbon sugar (pentose) - in DNA deoxyribose, in RNA ribose

• nitrogenous base

• 1-3 phosphate groups (beginning has three but two are lost during the polymerization process) 

portion of a nucleotide without any phosphate groups is called a nucleoside 
pyrimidine: 6-membered ring of carbon & nitrogen atoms
UTC
purine: larger 60member ring or carbon to a 5-member ring
AG

Uracil is only in RNA 
TA
CG
UA

attach one of the three phosphate groups to the 5’ carbon of the sugar
5’ & 3’

double helix & antiparallel

yk

tRNA

transfer RNA

brings amino acids to the ribosome

80 nucleotides in length