Chapter 3 & 4
Synthesis of macromolecules
What are macromolecules? Most macromolecules are made from single subunits, or
building blocks, called monomers. The monomers combine with each other using
covalent bonds to form larger molecules known as polymers. In doing so, monomers
release water molecules as byproducts. This type of reaction is dehydration synthesis,
which means “to put together while losing water.” Monomers Polymers done by
DEHYDRATION SYNTHESIS.
2 glucose molecules undergoing dehydration to form the disaccharide, maltose.
*Dehydration synthesis = simple molecules to more complex (anabolic rxn, but not all
rxns in cells are this) AKA biosynthetic. Rxn requires energy!
*HYDROGEN of 1 monomer combines with a HYDROXYL GROUP of the other monomer.
C6H12O6 + C6H12O6 àC12H22O11 + H20 **H20 was removed, see changes in amount of H&O’s
*Hydrolysis is the opposite; Polymers break down into monomers when H20 is added
across the bond. During these reactions, the polymer breaks into two components: one
part gains a hydrogen atom (H+) and the other gains a hydroxyl molecule (OH–) from a
split water molecule. *Digestion*
Each of these reactions require energy(dehydration)/release energy(hydrolysis).
They are catalyzed rxns. **Hydrolysis is catabolic, Dehydration is anabolic**
Carbohydrates (Carbon,Water)
Þ Functions: Energy source, Energy storage, structure/support specifically cellulose
Þ # of C in carbs
3 C’s= Triose 5=Pentose 6=Hexose (Glucose, Galactose, Fructose)
**Most monosaccharide names end with the suffix -ose. If the sugar has an aldehyde
group (the functional group with the structure R- CHO), it is an aldose, and if it has a
ketone group (the functional group with the structure RC(=O)R'), it is a ketose.
*The carbonyl group is in different spot. Know this!!
3 Subtypes of Carbs: monosaccharides, disaccharides, and polysaccharides.
*Disaccharides: two monosaccharides undergo a dehydration reaction. During this
process, one monosaccharide's hydroxyl group combines with another
monosaccharide's hydrogen, releasing a water molecule and forming a covalent bond. A
**glycosidic bond= a type of covalent bond that joins a carbohydrate molecule to
another group, which may or may not be another carbohydrate. -O*Monosaccharides, in aqueous solutions, are usually in ring forms
*We classify monosaccharides based on the position of their carbonyl group and the number of
carbons in the backbone.
Polysaccharides: long chains of monosaccharides linked by glycosidic bonds. Examples=Starch,
cellulose, glycogen (storage form of glucose in humans), chitin.
**Alpha and Beta Glucose: H-OH is flipped! difference between starch (Alpha) and
cellulose(Beta).
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Lipids
Þ Non-polar molecules are hydrophobic (“water fearing”), fatty acid, carboxyl group
HO-C=O (C is reactive).
Þ Functions: energy storage, homeostasis, cell membranes, hormones. Lipids
include waxes, phospholipids, and steroids.
Þ Glycerol + Fatty acid chain(3)=Triglyceride – Bonded
together by Ester linkage. 3 H20’s are released
(Dehydration synthesis).
Þ Saturated Fats have NO C=C bonds! Hydrogens in every
position!(Straight)
Þ Unsaturated Fats DO HAVE C=C bonds, bent structure
because of it.
**Cis and trans indicate the configuration of the molecule around the double bond. If
hydrogens are present in the same plane, it is a cis fat. If the hydrogen atoms are on two
different planes (one up,one down), it is a trans fat. The cis double bond causes a bend
or a “kink” that prevents the fatty acids from packing tightly, keeping them liquid at
room temperature.
Þ Phospholipids= major plasma membrane constituents that comprise cells'
outermost layer. Hydrophilic head=phosphate and glycerol group. Hydrophobic tails
(2)= saturated and unsaturated fatty acids.
Þ If a drop of phospholipids is placed in water, it spontaneously forms a structure that
scientists call a micelle, where the hydrophilic phosphate heads face the outside and
the fatty acids face the structure's interior.
Steroids= All steroids have four linked carbon rings and several of them, like cholesterol,
have a short tail. Many steroids also have the –OH functional group, which puts them in
the alcohol classification (sterols).
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Proteins
Functions: Digestive, hormones, transport (hemoglobin), defense, structural, etc.
*Different arrangements of the same 20 types of amino acids comprise all proteins.
• Enzymes= catalysts in biochemical rxns. *Catabolic=break down (think of catsnegative) *Anabolic=build up (Think of letter A being at top). *Catalytic= speed
up a rxn without being changed (think of car and catalytic converter,car=speed
up)
Amino Acids
*The monomers that comprise proteins
*these acids contain both amino group and carboxyl-acidgroup in their basic structure
NON-POLAR R GROUPS=C&H’s, phobic
*TYROSINE= Polar because OH
*PROLINE= Non-Polar
Þ The Aminos are BASES (picking UP H+), -COO
ACID (donating H+)
*PEPTIDE BOND= the covalent bond that attaches to aminos
Þ One amino acid's carboxyl group and the incoming amino acid's amino group
combine, releasing a water molecule. The resulting bond is the peptide bond
Protein Structure
1. Primary= Amino acids' unique sequence in a polypeptide chain. 2 distinct ends.
Terminal End/N-Terminal=free amino group. C-Terminal end has free carboxyl.
2. Secondary=local folding of the polypeptide in some regions… α-helix and βpleated sheet structures form because of hydrogen bonding between carbonyl
and amino groups in the peptide backbone. Hydrogen bonds!
3. Tertiary= interactions among R groups create the protein's complex threedimensional tertiary structure-Basic R group (+), Acidic R group (-) variety of
chemical interactions determine the proteins' tertiary structure-hydrophobic
interactions, ionic bonding, hydrogen bonding (polar), and disulfide linkages.
4. Quaternary = The shape of multiple proteins that are forming a functional unit.
proteins form from several polypeptides, or subunits, and the interaction of these
subunits forms quaternary.
*Changes in protein structure, will alter its function* Sickle Cell example= an amino acid
(glutamic switched to valine) switch in hemoglobin causes the RBC to become
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deformed. Denaturation: losing its shape w/out losing its primary sequence, can
sometimes be reversed.
Central Dogma of molecular biology: an explanation of the flow of genetic information
within a biological system. DNA makes RNA and RNA makes proteinà DNA dictates the
structure of mRNA in a process scientists call transcription, and RNA dictates the
protein's structure in a process scientists call translation.
Nucleic Acids
*deoxyribonucleic acid (DNA) and ribonucleic acid (RNA): Deoxyribose is similar in
structure to ribose, but it has an H instead of an OH at the 2ʹ position
*cell's entire genetic content is its genome. *DNA and RNA are comprised of monomers
that scientists call nucleotides. The nucleotides combine with each other to form a
polynucleotide, DNA or RNA. Three components comprise each nucleotide: a
nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group
**Deoxyribose or Ribose structure= 1’: Nitrogenous base. 2’: H in deoxyribose, or OH in
ribose. 3’: -OH…important to DNA synthesis.
5’: Phosphate group
Bases= Purines: double ring structure &
pyrimidines: single ring
Nitrogenous bases= have amino group that can
take up H’s/decrease H in environment, making it basic.
Þ DNA contains A, T, G, and C; whereas, RNA contains A, U, G, and C.
*The phosphate residue attaches to the hydroxyl group of the 5ʹ carbon of one sugar
and the hydroxyl group of the 3ʹ carbon of the sugar of the next nucleotide, which forms
a 5ʹ–3ʹ phosphodiester linkage. --formation involves removing two phosphate groups
Þ Double Helix structure= sugar and phosphate lie on the outside of the helix,
forming the DNA's backbone. The nitrogenous bases are stacked in the interior,
like a pair of staircase steps.
*antiparallel orientation : helix's two strands run in opposite directions, meaning
that the 5ʹ carbon end of one strand will face the 3ʹ carbon end of its matching
strand. Important in replication and nucleic acid interactions.
RNA: Ribonucleic Acid. protein synthesis under the direction of DNA.
-comprised of ribonucleotides that are linked by phosphodiester bonds.
-Ribonucleotide contains: ribose (the pentose sugar), one of the four nitrogenous bases
(A, U, G, and C), and the phosphate group.
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**4 types of RNA** messenger
RNA (mRNA), ribosomal RNA (rRNA),
transfer RNA (tRNA), and microRNA
(miRNA).
Type of
molecule
Carbohydrates
(CnH2nOn)
Lipids
Monomers
Monosaccharides
Proteins
Amino Acid
Nucleic Acids
Nucleotides
-Glycerol & 3 Fatty
Acids
-Glycerol & 2 Fatty
Acids. Phosphate
“head”…Amphipathic:
hydrophobic AND
hydrophilic
Polymers
Held together by…
Polysaccharides— Glycosidic
starch, cellulose
bonds/linkages
-Triglycerides
Ester Linkage
-Phospholipid
Protein
(Peptide—short
protein)
DNA & RNA
Peptide bonds
(Dehydration)
Phosphodiester –
forming between 5’
phosphate of one
nucleotide, and 3’ OH
of another nucleotide
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Chapter 4
unified cell theory=states that one or more cells comprise all living things, the cell is the
basic unit of life, and new cells arise from existing cells
*Cells share 4 common components= 1) Plasma membrane 2) Cytoplasm 3) DNA
4) Ribosomes
Þ Prokaryotes: No nucleus, but has nucleoid region where DNA is found.
-Ribosomes= protein synthesis (translation)
-Cell membrane= allows for selective permeability. Cholesterol helps to strengthen
membrane. Non-polar aminos in membrane…proteins-transport, sense environment,
energy production, ID tags, and anchors help build tissues.
-Cell wall= isn’t selective permeable, rigid and strong to protect from lysis.
-Capsule= allows bacteria to attach to surfaces **Biofilms
-Pili= hair like structures on outside, used for bacterial “mating”/replicating. Genetically
distinct cells in the end, but technically they’re non-reproductive. This is what causes
antibiotic resistant strains. Plural: Pilus
-Flagellum= “tail”àmovement
Prokaryotes
Eukaryotes
1 protein (flagellin)
Multiple proteins
No membrane
Enclosed by membrane
Small size
Larger
Spinning movement
Whips
Proton motive force for
ATP for energy
energy- H+ movement
Convergent evolution: process whereby organisms not closely related
independently evolve similar traits as a result of having to adapt to similar
environments or ecological niches. 2 structures in different organisms.
Þ Endosymbiosis= a cell engulfing another cell, not destroying it, and both working
together. Mitochondria example: if it is killed, the cell cannot make another one.
There are also double membranes surrounding the new cells, suggesting that the
new cell took on the OG cell’s membrane when it was engulfed. New cell has its
own DNA and ribosomes to make its own proteins.
Eukaryotic Cells
Cell size
SA/V
SA:V ratio gets smaller as the cell becomes larger. If cell grows beyond a certain limit,
not enough material will be able to cross the membrane fast enough to accommodate
the increased cell volume…this is why cells are so small!
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SA: how much cell membrane Membrane: exchange of nutrients and wastes w/
environment.
Volume: amt. of space occupied by cell-nutritional or energy needs.
*What was the independent variable in cell lab? Surface to volume ratio
*Dependent? Changing cell size
Volume= length x width x height x # of cubes (mm3)
SA= length x width x 6 sides x # of cubes (mm2)
Structure & Organelles
*Plasma Membrane: Phospholipid bilayer
controls the passage of organic molecules,
ions, water, and oxygen into and out of the
cell. Also wastes (such as carbon dioxide
and ammonia). -membranes that specialize
in absorption fold into microvilli.
*Cytoplasm: organelles suspended in the
gel-like cytosol, the cytoskeleton, and
various chemicals. Many metabolic reactions,
including protein synthesis, take place in the
cytoplasm.
*Nucleus: The nucleus stores chromatin (DNA plus
proteins) in a gel-like substance called the
nucleoplasm. The nucleolus is a condensed chromatin
region where ribosome synthesis occurs. We call the
nucleus' boundary the nuclear envelope. It consists of
two phospholipid bilayers: an outer and an inner
membrane. The nuclear membrane is continuous with
the endoplasmic reticulum. Nuclear pores allow
substances to enter and exit the nucleus.
**Nucleolus is NOT the nucleus; Ribosomes are
assembled there. aggregates the ribosomal RNA with
associated proteins to assemble the ribosomal subunits that are then transported out
through the pores in the nuclear envelope to the cytoplasm.
*Histone proteins are like a spool. DNA wraps around them in the nucleus (DNA
packing). DNA + Histones= Chromatin. Condenses into visible chromosomes and helps
the DNA divide.
**Transcription can increase when its DNA is not tightly associated with histones.
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*Chromatin: protein-DNA complex that serves as the chromosomes' building material,
describes the material that makes up the chromosomes both when condensed and
decondensed.
*Ribosomes= responsible for protein synthesis, makes peptide
chains (primary structures DNA). consist of two subunits, large and
small. àReceive orders from nucleus where the DNA transcribes
into mRNA, travels to the ribosomes, which translates the code
provided by the sequence of the nitrogenous bases in the mRNA
into a specific order of amino acids in a protein. Amino acids are the
building blocks of proteins.
*Mitochondria= ATP production, uses oxygen and carbon dioxide is
a waste product. muscle cells have a very high concentration of mitochondria that
produce ATP. Double membrane. Inner layer has folds called cristae, area surrounded by
the folds the mitochondrial matrix. ATP synthesis takes place on the inner membrane.
*Peroxisomes= carry out oxidation reactions that break down fatty acids and amino
acids. They also detoxify many poisons that may enter the body. (Many of these
oxidation reactions release hydrogen peroxide, H2O2, which would be damaging to
cells; however, when these reactions are confined to peroxisomes, enzymes safely break
down the H2O2 into oxygen and water.)
*Vesicles and vacuoles are membrane-bound sacs that function in storage and
transport.
* centrosome is a microtubule-organizing center, important in mitosis and meiosis.
Þ Cytoskeleton= network of protein fibers within the cell, Maintains cell’s shape,
secures organelles in specific positions, allows cytoplasm and vesicles to move
within cell, and enables unicellular organisms to move independently
Consists of…
*Microtubules: made of tubulin, largest of 3, hollow. MOTILITY, because they’re
the building blocks of flagella and cilia. Also involved in separating chromosomes
during mitosis and meiosis. 9+2 arrangement is shared by cilium and flagellum.
**Dyein proteins cause flagellum to have whipping movement
*Microfilaments: smallest, composed of 2 strands of ACTIN protein strands.
Muscle contraction (+ myosin protein), cell motility (Phagocytosis), and cell
division.
*Intermediate filaments: Medium size. Example: keratin proteins help to anchor
the organelles, maintain shape of cells, and waterproofing outside of cells.
*Lysosome: the cell’s “garbage disposal.” In plant cells, the digestive processes take
place in vacuoles. Enzymes within the lysosomes aid in breaking down proteins,
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polysaccharides, lipids, nucleic acids, and even worn-out organelles. These enzymes are
active at a much lower pH than the cytoplasm's. Therefore, the pH within lysosomes is
more acidic than the cytoplasm's pH.
*Endoplasmic Reticulum (ER): network of membranes
responsible for manufacturing and modifies proteins and synthesizes
lipids. *Rough ER: Ribosomes making membrane proteins and
secreted proteins (antibodies). Smooth ER: SER functions include
synthesis of carbohydrates, lipids, and steroid hormones;
detoxification of medications and poisons; and storing calcium ions
(muscle cell contractions).
*Golgi body: refines materials from ER, tags molecules so they
make it to destination (post office of cell). Polar organelle= cis & trans
face. Cis receives from ER (Closest), Trans face gets final active form of
molecules, transport vesicles carry to plasma membrane.
Plant cells= chloroplasts: carry out photosynthesis… carbon dioxide,
water, and light energy to make glucose and oxygen= 6CO2 + 6H2OàC6H12O6 + H2O.
Reverse that= aerobic respiration. Product of Endosymbiosis.
Central Vacuole= filled w/water, keeps plant
Animals only
Plants only
hydrated, why plants wilt if dehydrated.
Lysosome Cell Wall
Centrosome Plasmodesmata
Central vacuole
Chloroplast
Cell communication
*most abundant protein is collagen. Collagen fibers are interwoven with
proteoglycans, which are carbohydrate-containing protein molecules. Collectively, we
call these materials the extracellular matrix.
*Cells have protein receptors on their plasma membranes' extracellular surfaces. When a
molecule within the matrix binds to the receptor, it changes the receptor's molecular structure. The
receptor, in turn, changes the microfilaments' conformation positioned just inside the plasma
membrane. These conformational changes induce chemical signals inside the cell that reach the
nucleus and turn “on” or “off” the transcription of specific DNA sections, which affects the associated
protein production, thus changing the activities within the cell.
*Plasmodesmata (Plasmodesma,singular): Plant cells only. Numerous channels
that pass between adjacent plant cells' cell walls connect their cytoplasm, and enable
transport of materials from cell to cell.
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*Tight junction: Animal cells only. Watertight seal between two adjacent animal
cells. Proteins (predominantly two proteins called claudins and occludins) tightly hold
the cells against each other. Found in epithelial tissues that line internal organs and
cavities, and comprise most of the skin. Desmosomes: act like spot welds between
adjacent epithelial cells
**Gap junctions in animal cells are like plasmodesmata in plant cells in that they
are channels between adjacent cells that allow for transporting ions, nutrients, and
other substances that enable cells to communicate
*The Endomembrane System: group of membranes and organelles in eukaryotic
cells that works together to modify, package, and transport lipids and proteins. nuclear
envelope, lysosomes, vesicles, endoplasmic reticulum, Golgi apparatus, and plasma
membrane.
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Chapter 14 & 17
**Father of genetics? Gregor Mendel=through his work on pea plants, discovered the
fundamental laws of inheritance. He deduced that genes come in pairs and are inherited
as distinct units, one from each parent.
**Friedrich Miescher= discovered nucleic acids (called them nuclein).
**Griffith’s Transformation experiment= Injected mice w/ live “S” strain-death.
Injected mice with live “R” strain-survived. Injected w/ heat killed “S” strain-survived.
Injected w/heat killed S AND live R= death.
Why? The S retained what R cells had…concluded there must be info transfer from dead
S cells to live R cells= Transformation.
Þ Oswald Avery, Colin MacLeod, and Maclyn McCarty: took Griffith’s experiment
and found that when DNA was degraded, the resulting mixture was no longer able
to transform the bacteria, whereas all of the other combinations were able to
transform the bacteria. This led them to conclude that DNA was the transforming
principle. **Purified 4 organic molecules (lipids, proteins, carbohydrates, and
nucleic acids), added the strains, injected and found the mice died only when DNA
was added w/ S strain.
*Chase & Hershey= used radioactive S35 (labels proteins, DNA does NOT have Sulfur so
it’s easily identified) and P32(labels nucleic acids) to study
bacteriophage (bacteria eaters/viruses). They found DNA
DOES go inside bacteria so therefore DNA must have
genetic info!
*Chargoff= DNA exhibits molecular diversity. He analyzed
DNA from different organisms and found that the base
composition varied from species to species. Rules=1:1
ratio (base Pair Rule) of pyrimidine and purine bases and,
more specifically, that the amount of guanine should be
equal to cytosine and the amount of adenine should be
equal to thymine.
*Rosalind Franklin= x-ray diffraction photograph of DNA
*Crick and Watson= suggested that there were 3 replication models: semi-conservative,
conservative, and dispersive. They also determined the structure of DNA was double
helix (partly based off of stolen data from Franklin).
*Meselson & Stahl= DNA replication, E. Coli experiment, confirmed semi replication.
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Meselson-Stahl à
Þ Building blocks of DNA are nucleotides… nucleotides combine with each other to
produce phosphodiester bonds.
Þ phosphate residue attached to the 5' carbon of the sugar of one nucleotide forms
a second ester linkage with the hydroxyl group of the 3' carbon of the sugar of the
next nucleotide, thereby forming a 5'-3' phosphodiester bond. In a
polynucleotide, one end of the chain has a free 5' phosphate, and the other end
has a free 3'-OH. These are called the 5' and 3' ends of the chain.
Þ 5’à3’ direction ONLY (leading strand)
Order of DNA replication
-Origin of replication: replication starts here, A-T rich, 2H bonds break
-Helicase breaks hydrogen bonds between base pairs and “unzips” double helix.
-Single-strand binding (SSB): binds to the single strands to keep them separated.
-Topoisomerase (Gyrase): prevents super-coiling by breaking, swiveling, and re-joining
strands. Controlled breakage!
-Primase (RNA polymerase): creates starting point for DNA Pol III to get started. Adds at
5’ end of leading strand AND at each Okazaki fragment on the lagging strand.
-DNA Polymerase III : adds nucleotides one-by-one to the growing DNA chain that is
complementary to the template strand. Covalently adds nucleotides to free 3’-OH’s end.
WORKHORSE!! *Cannot make DNA w/out 3’-OH* Can also proofread and fix
-DNA Polymerase I: Removes RNA primer (nucleotides) from 5’ end and replaces w/
DNA nucleotides.
-Okazaki fragments: On lagging strand…needs a primer for each new fragment. Need
phosphodiester bonds.
-DNA Polymerase II: repairs base pairs
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-Telomerase: The ends of the linear chromosomes are known as telomeres: repetitive
sequences that code for no particular gene. These telomeres protect the important
genes from being deleted as cells divide and as DNA strands shorten during replication.
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