Law of Thermodynamics

1st energy is conserved

2nd - Increased disorder
3rd at absolute zero, entropy is zero

Reactions
Exergonic reaction release of free
energy. Spontaneous
Endergonic require free energy from
outside

Metabolism
The key to survival
The total of all the life activities required to
sustain life.
Each process is chemical (metabolic) in
nature
Anabolism is a constructive activity
Catabolism is a destructive process

Homeostasis
The key to the quality of life
Life functions are carried out in an
integrated way that results in the
maintenance of a stable internal
environment (internal dynamic equilibrium)
This maintenance is known as
homeostasis

Water
Polar. Solvent.
Density highest at 4oC. Leads to fall & spring
overturn.
High heat of vaporization
Water absorbs heat in phase change

High heat capacity (specific heat)- can absorb

lots of heat with only minimal changes in
temperature
Hydrogen bonds
Dissipates heat when broken
Prevents sudden temperature change

Lab 1 Diffusion and Osmosis

Dialysis bag of sucrose (solution) was
placed in distilled water. Water moved into
the bag. There was a higher water
potential outside the bag. Water moves
toward a more negative water potential.
The bag is hypertonic to the distilled water.
The water is hypotonic to the sugar solution
in the bag.

Lab 1 Cont.
Adding sugar to the distilled water
decreases the water potential there.
Water potential is represented by psi
= p + pi symbol
At equilibrium the pressure (turgor) of the
cell wall will balance out the negative
potential of the solutes out of the cell.

pH etc
pH scale is used to show relative amounts of H+
and OH- ions
pH of 7 = neutral (equal amounts of H+ and OHions)
Acid (pH 0-7) a compound that dissolves in
water to yield H+; a proton donor
Base (pH 7-14) a compound that dissolves in
water to yield OH-; a proton acceptor
pH = 1/ log[H+] = -log[H+]

Organic Compounds
Contain both the elements carbon and
hydrogen

Macromolecules
Carbohydrates (sugars and starches)
Lipids (fats, oils, and waxes)
Proteins (functional and structural)
Nucleic Acids (RNA and DNA)

Carbohydrates
Consist of C, H, and O (2:1 ratio)
Monomer monosaccharide
Pentose sugar has 5 carbons

Lipids, Protein and Nucleic Acid

Lipids
Saturated fatty acid no double bonds
saturated with hydrogen!

Protein
- Monomers are amino acids

Nucelic Acid
Monomers are nucelotides
(sugar, phosphate, and nitrogenous base)

Proteins
Monomer amino acids
20 commonly found
4 levels of structure

Primary structure
Number, type, and sequence of amino acids

Secondary Structure
Due to hydrogen bonding
A twist: alpha helix, or pleat: beta pleat

Tertiary Structure
3D folding pattern due to interactions between the amino acids
and their various charges

Quaternary
The way two or more folded subunits fit together (hemoglobin
structure)

Enzymes

Organic Catalysts
Protein nature all enzymes are either all protein or protein with non-protein
parts known as coenzymes. Coenzymes are often vitamins.
Active site Enzyme molecules are usually much larger than the molecule
they interact with.
Enzyme substrate complex with induced fit.
Factors influencing enzyme action
Temperature:
In general as temperature increases, action increases
Most efficient temperature is optimum temperature
At high temperature enzyme denatures

Relative amounts of enzyme and substrate:

Rate of enzyme action varies with the amount of available substrate molecules.
When an excess of substrate is added to a system with a fixed concentration of
enzymes, the rate of enzyme action tends to increase to a point then remain fixed as
long as the enzyme concentration remains constant.

pH:
Ranges and optimums differ

Enzyme Catalysis Lab #2

In this lab you used the enzyme catalase

to convert hydrogen peroxide (H202) to
water and oxygen gas.
The slope of the graph line in the early,
constant period is called the initial velocity.
It is the same for an enzyme and
substrate when conditions are the same. It
is used to compare one reaction with
another. It is constant because at the
beginning of the reaction, the number of
substrate molecules is usually large
compared to the number of enzymes.
Increasing the substrate concentration will
increase productive collisions.
Rate of reaction pick any two points on
the straight line portion. Divide the
difference in product by the difference in
time.

uMoles2 uMoles1 30 -20

t2 - t1
180 -120

10
60

0.17 umoles/sec

Mitosis and Meiosis Lab

You calculated the relative duration of the phases of mitosis.

Prophase was found to have the longest relative length (50 + %)
Telophase was the shortest (~12%)
You looked at meiosis and mitosis in the formation of ascospores within the asci of
Sordaria fimicola.
Meiosis reduces the chromosome number. It starts out 2n and ends up n. (n is the
number of different chromosomes you have. In humans your n number is 23 and you
have two of each (2n) for 46 total.)
2n is called diploid
n is haploid
Sordaria is usually haploid. It is diploid only when the mycelia of 2 strains fuse to form
a diploid nucleus. It must undergo meiosis to return to its haploid state.
Meiosis (chromosomes double then divide, leaving one n)
is followed by
Mitosis two of each of the 4 cells from meiosis. Resulting in 8 haploid ascospores in
a sac called an ascus (plural asci). Many asci are in a fruiting body called a
perithecium.
Synapsis (coming together) and crossing over frequency can be calculated because
the alleles are independently expressed in the haploid state.

DNA
In Progress

Central Dogma: DNA-RNA-Protein

Replication: DNA to DNA (semi-conservative)
Transcription: DNA to RNA
Primary Transcript-result of translation
Must be processed
Introns-Clipped out (think intervening)
Exons-stuck together

Translation: RNA to Protein

3 nucleotides = 1 amino acid

DNA Replication
1. Start at origins
2. DNA Polymerase adds nucleotides
3. Nucleotides are only added to the 3 end.
Grows in the 5 to 3 direction.
4. Have a leading strand and a lagging strand.
5. DNA ligase joins the lagging or Okazaki
fragments together.
6. Chains must be started with an RNA primer
added by the enzyme primase.

Lab 6 Molecular Biology Part I

There are 3 ways to move genes between
bacteria:
Conjugation (mating)
Transduction (virus transfer the genetic
material)
Transformation (direct uptake of DNA by cells)

We did a lab on transformation.

Lab 6 Molecular Biology Part I

Transformation with pGlo
We made the cells
competent- able to take up
environmental DNA.
We mixed the competent
E.coli with plasmids.
The plasmids we used were
already made and carried

Bacteria
Big ring of DNAone circular
chromosome
The little ring
of DNA is a
plasmid.

1. a gene for antibiotic

resistance.
2. pGlo gene

We could tell if our transformation worked because we grew the bacteria on plates
full of ampicillin. They could only grow there if they contained the plasmid with the
antibiotic gene (therefore the plasmid). If the sugar arabinose was present it
turned on the gene which made the glow in the dark protein.
Positive Control LB+ Negative Control LB/Amp- (+ or the plasmid)

Lab 6 Molecular Biology Part II

Restriction Enzyme Cleavage
DNA can be cut with restriction enzymes. These
have been isolated from bacteria and protect
them from viral invasion.
They recognize palindromes. Many leave sticky
ends. These allow different pieces of DNA cut with
the same restriction enzyme to combine due to base
pairing.

In this lab DNA from the bacteriophage (virus)

lambda was cut with three different restriction
enzymes. The results were electrophoresed (is
that a word?)

Eco RI

HIND III

No Enzyme

Number of Base Pairs (log)

Lab 6 Molecular Biology Part II

Restriction Enzyme Cleavage

Distance Cm

Plot
the
known,
say
HIND
III

If one of the enzymes produced pieces of known

size (Like HIND III- data was given), the size of
pieces cut with a different restriction enzyme can
be determined. To find the size of pieces cut with
ECO RI measure the bands and find the base
pairs from the intersecting line (See the red

line).

Respiration

Glycolysis-No oxygen needed

1.
2.

Glucose is broken into 2 pyruvate molecules.

Nets 2 ATP molecules by phosphorylation .
2 molecules of NAD+ are reduced to NADH
In fermentation pyruvate is converted to lactate,
ethanol, etc.
Occurs in the cell cytoplasm.

3.
4.

Respiration (Cellular)
1.
2.

Occurs in mitochondria
Pyruvate (See last slide) goes into the Krebs cycle
(AKA the Citric Acid Cycle).
In a series of steps enzymes transfer electrons to
coenzyme acceptors NAD+ and FAD, CO2 released.
Electron Transport Chain

3.
4.

The electron energy from NADH and FADH2 is retrieved and

stored in ATP.
ETC is made of a series of pigment containing cytochrome
compounds that serve as electron carriers.
Cytochromes are embedded in the inner membrane of the
mitochondria.
Making ATP from ADP this way is oxidative Phosphorylation.

Respiration (Cellular)
ATP Ledger
Glycolysis

Krebs
Chemiosmosis

3 per NADH

4 ATPs -2 ATP
2 ATPs
34 ATPs
2 from glycolysis*
2 from Acetyl CoA
6 from Krebs cycle

2 per FADH2 2 from Krebs cycle

=
=

2
2

=
=
=
=

4
6
18
4
36

2 ATP needed to move NADH from glycolysis across the

mitochondrial membrane.
*

Respiration (Cellular)
Mitchell Hypothesis
Chemiosmotic coupling hypothesis:
Movement of electrons through the ETC is
accompanied by a protein pumping mechanism
that sets up an energy gradient consisting of
hydrogen ions (protons) across the inner
mitochondrial membrane. These are pumped
from the inner mitochondrial matrix to the outer
compartment. As they flow back through the
molecule known as ATP Synthase, free energy is
released and conserved as ATP.

Lab 5
Cell Respiration

In this lab you compared germinating with non-germinating peas and their
rate of repiration. You also looked at the effect of temperature.
As plants respire they use up oxygen. You measured how fast they used it
up.
Non-germinating seeds are alive but dormant.
To take CO2 out of the equation a CO2 absorbent was used (KOH)
Germinating
25

O2

10

Consumed

Non-germinating
Colder-slower respiration

ml

25
10
5
Time (minutes)

Warmer-faster respiration
Germinating- faster respiration
Dormant- Slower

Photosynthesis

Light hits chlorophyll (strikes the antenna complexes on thylakoids in the chloroplast-photons
are funneled to the reaction center of the photosystem).

1.
2.

First occurs in the P680 reaction center in Photosystem II.

Water is cleaved to replace the excited electrons which leave the reaction center. Oxygen is
released.
The electrons move down the ETC. ATP is made.
Last acceptor is P700 reaction center in Photosystem I.
Photons boost electrons again. 2e- are energized and reduce NADH + forming NADPH.
NADP+ is reduced to NADPH. (OIL RIG)

3.
4.
5.

Steps 1-5 is the light reaction.

ATP and NADPH will be used in the dark reaction.
Photophosphorylation is the term for making ATP from the movement of electron excited by light, as
they move down the electron transport chain.
Remember there is also Substrate level phosphorylation and oxidative phosphorylation. They all
involve adding a phosphate. Substrate is a direct transfer, oxidation is when the energy comes
from breaking down food.

Photosynthesis
Light-Independent: AKA Calvin-Benson cycle: AKA
Dark Reaction (in the stroma)
1.
2.
3.
4.

CO2 is converted to carbohydrate.

CO2 is fixed as it reacts with ribulose
biphosphate( RuBP).
The above is catalyzed by the enzyme ribulose.
RuBP is regenerated so the cycle may continue.

Photorespiration-an inefficient form of the dark reaction; O 2 os

fixed instead of CO2. No carbohydrates are produced.
C3- typical plant
C4- thrive in arid conditions (less photorespiration due to
special leaf anatomy)
CAM-also thrive in arid conditions