Phospholipids: diglyceridew with a phosphate group

Phosphate: electronegative or polar

Amphipathic molecule: has one side that is hydrophobic (the tail portion) and another
that is hydrophilic (the head)

The bilayer insulates the hydrophobic tail from water

Peptide bonds are covalent

R Groups: Groups containing C and H are hydrophobic

Primary Structure of Proteins: amino acid sequence starting from NH2 end

Secondary Level: Alpha helices or beta pleated sheets held together by hydrogen bonds

Tertiary Level: secondary structure and coils fold into a three dimensional shape
connected by hydrogen bonds, disulfidge bridges, ionic interactions, hydrophobic, and
van der waals interactions

Quaternary Structure: the joining of 2 or more polypeptide chains to form a complete

functional protein

Lambert Beer Law: absorbance is directly proportional to the concentration of solute

molecules

Spectrophotometry: used to identify and quantify colored solutions based on their light
absorbing properties

Proteins and nucleic acids absorb light (240 to 200 nanometers), pigments and dyes (400
to 770 nanometers), infrared energy as in organic compounds (above 770 nanometers)

Microscopes:

ocular lens: adjustable eyepieces which you can set at the appropriate interpupillary
distance

objective lens: close to the specimen can be set at: (4x, 10x, 40x, 100x) which becomes
anywhere from 40x to 1000x level of magnificatio

the ocular lens has adjustable eyepieces and is attached to the turtet which can be turned
to get a different magification level

stage: area where the specimen is placed for viewing

base
focus adjustment knob

arm

reflective light source: located beneath the stage and can be turned on or off

zoom magnification adjustment

steeper slope indicates greater enzyme activity

Light has a wave and particle duality according to Maxwell light is electromagnetic
radiation which is a self propagating oscillating transverse wavelength an electric
component and a magnetic component

when a charged particle oscillates it creates an electric field

electric and magnetic fields are perpendicular to the direction that the light is oscillating

The Nature of Energy:

Einstein discovered the photoelectric effect

E = hv he concluded that energy is proportional to the frequency where Planck's constant

h is 6.626 x 10-34 Joules x seconds

A laser emits a monochromatic beam of light at 4.69 x 1014 m/s

E = 1.3 x 10-2 Joules number of photons

The wavelength of light c is a universal constant 3.00 x 108 meters per second

All electromagnetic radiation travels at the same velocity

Therefore c = wavelength λ x velocity v

x rays have a very high frequency which is damaging to the bodily tissues

If we know the frequency, we can calculate the wavelength. Similarly, if we know the
measurement of wavelength, we can determine the frequency

Black body radiation:

Photoelectric effect (discovered by Max Planck and Albert Einstein)

Emission Spectrum

heating iron goes from red (infrared radiation) to white (emitting of all the radiation in
the visible light spectrum 400 to 700 nanometers) white is a mixture of all seven colors
and can be separated out through a prism

Photons are tiny particles of light. The radiation is emitted as a packet of energy

Purple is left on the visible light spectrum at 400 nanometers

Red is to the right of the visible light spectrum at 750 nanometers

The visible light spectrum is considered continuous

The wave nature of light does not explain how an object can glow when its energy
increases. Max Planck explained this by assuming that energy comes in packets called
Quanta

E = hv

h (Planck's constant) 6.626 x 10-34

units: Joules (unit for energy) multiplied by seconds

What is a gene?

chromosomes 46 chromosomes 2n diploid

gametes 23 n haploid

RNA is genetically unstable

Primase synthesizes the primer in the 5 prime to 3 prime direction

DNA polymerase has a free 3 prime hydroxyl

helicase opens up DNA to create a replication fork

replaces ribonucleotides with deoxynucleotides

DNA polymerase I cannot seal the final gap

DNA ligase seals gap completing phosphodiester between the 2 nucleotides

replacing RNA primer from okazaki fragment #1

Topoisomerase relieves the strain on the DNA strands

DNA Ligase forms a phosphodiester linkage between okazaki fragments

The leading strand undergoes continuous replication

The lagging is synthesized discontinuously due to its okazaki fragments

Helicase: unwinds the parental double helix at replication forks by breaking the hydrogen
bonds

single stranded binding protein: binds to and stabilizes single stranded DNA until it can
be used as a template (prevents complementary DNA base strands from reforming
complementary base pairs) coats the 2 unzipped strands

Topoisomerase: relieves the tension (overwinding strain) ahead of the replication fork

Primase: synthesizes an RNA primer at the 5 prime end of the leading strand and of each
Okazaki fragment of the lagging strand (each Okazaki fragment needs a primer) Replaced
by DNA Polymerase I. DNA Polymerase III extends off of the primer

DNA Ligase: Joins 3 prime end of DNA that replaces primers to rest of leading strand
and connects Okazaki fragments of the lagging strand. It functions similarly to a glue

shine delgarno sequence: GGAGGA

DNA Polymerase I: replaces RNA nucleotides of primers with DNA nucleotides. DNA
Polymerase I leaves a gap in the sugar phosphate backbone after replacing the last RNA
nucleotides of the primer

Ribosomal RNA: is part of the ribosome

Guanine cap: after transcription is completed, a G cap is added

The polyadenylation sequence is found in the mRNA

signified by AAUAAA

There are approximately thirty to 100 Adenines added to the 3 prime end

The polyadenylation sequence signals an end to eukaryotic transcription

intron splicing:

what reasons exist for introns?

regulatory: prevents protein from being produced

variability: getting variable proteins from a specific gene

biological principles and definitions:

cells and their environment

how do cells communicate?

cells communicate through a mechanism called cell fusio

gene: a segment of DNA that transmits information from parent to offspring. One section
of DNA has thousands of genes

chromosome: a rod shaped structure, forms when DNA ad its associated proteins coil
tightly before cell division.

why must DNA coil? to fit into a cell

chromatids: 2 copies of each chromosome

homologues: 2 copies of each chromosome. 2 homologues of each chromosome (diploid

quantity)

alterations in chromosome structure:

mutations:

deletion: deletion of less that than 3 nucleotides results in a frameshift mutation

duplication: 2 copies of a certain set of genes

inversion: reattaches in a reverse orientation

translocation: gene fragment joins a nonhomologous chromosome

Mitosis and Cell Division:

why is cell division necessary?

the size of the cell is a signal for it to divide

Eukaryotic cells undergo nuclear division

(protists, fungi, plants, and animals) have a more complex structure, nucleus, organelles

cell cycle: repeating sequence of growth and division

G1 ---> S ---> G2 ---> M ---> C

G1 (Growth Phase) ---> S (Synthesis: DNA is copied) ---> G2 (Mitochondria replicates

and microtubules are assembled) ---> M (Mitotic phase. Nucleus is divided into 2 each
with the same number and types of chromosomes) ---> C (cytokinesis, the cytoplasm
divides, represented by a cell plate: in plants; cleavage furrow in animals)

G1 ---> S ---> G2 are collectively labeled interphase

Growth, chromosomes are loosely wound, genes are being used to make enzymes to
direct cell activity

Forming spindle fibers:

chromosomes condense in prophase

enzymes in the cell break down the nuclear envelope

animal cell: centrioles separate (move to opposite poles of the cell) a spindle fiber forms
in berween (spindle fibers are made up of microtubules) plant cells lack spindles. cell
division ensures the transfer of an organism's information to new cells

terminator sequence: sequence of nucleotides in prokaryotes that marks the end of a gene
and signals RNA polymerase to release the newly made RNA molecule to detach from
the DNA

point mutations:

nonsense mutation: Truncation of protein product due to a premature stop codon: AUG
---> UAG terminates translation. Truncates after one amino acid

a missense mutation is the most likely to be advantageous (it provides a selective

advantage)

nonsense mutations are the most likely to be deleterious to an orgaism

a single base pair insertion or deletion always causes a frameshift mutation

all of the amino acid sequences are changed downstream as a result of an insertion or
deletion

a frameshift mutation is deleterious and renders the protein nonfunctional

these DNA changes only apply to DNA changes within an open reading frame

N-Terminus AUG AAA GUU UGG CUA A C-Terminus

MET LYS VAL TRP LEU now has no stop codon

Multiple Base Pair Mutations

the removal of a codon does not result in a frameshift mutration (only one amino acid is
missing) in a three base pair deletion

the rest of the protein remains the same, anything that is not a multiple of three will cause
a frameshift mutation
inversion: cut out, inverted, and replaced into the DNA

Adenosine and Thymine form a double hydrogen bond

Cytosine and Guanine for triple hydrogen bonds

the RNA polymerase falls off at the end of Transcription

In eukaryotic termination, endonuclease binds to the polyadenylation signal in the RNA.

Once synthesized (polyadenylation signal)

Questions:

For what purpose(s) do multicellular organisms undergo mitosis?

What is meant by the term sister chromatids?

What is the differences between a plant cell and an animal cell undergoing cytokinesis?

How is the cell cycle regulated? What conditions affect the cell cycle?

What strucutre is responsible for cell elongation during telophase and cytokinesis?

The non-kinetochore microtubules lengthen thereby elongating the cell

Regulation of Gene Expression

Not all genes are expressed

Genes are expressed (Transcribed and Translated) when required

Genes involved in the breakdown of certain molecules present in food (and produce the
correct catabolic enzyme) will only be expressed if that type of molecule is present

Two Mechanisms Are Used to Orchestrate Metabolic Processes

Regulation of Gene Expression

Regulation of Enzyme Activity

Result: More effective at the point of transcription (energy is conserved)

Mutations are any change in the DNA sequence of an organism; usually bad for an
organism because they result in non-functional proteins; mutations are a necessary elemet
of evolution because evolution requires variation in the characteristics of an organism and
selection of the fittest characteristics

Definitions:
Promoter: a specific nucleotide sequence in DNA that binds to RNA polymerase
positioning it to start transcribing RNA at the appropriate place

Mutation: a change in the nucleotide sequence of an organism's DNA; ultimately creating

genetic diversity

Mutagen: a chemical or physical agent that interacts with DNA and causes a mutation

DNA Ligase: a linking enzyme essential for DNA replication. DNA Ligase catalyzes the
covalent bonding of the 3 prime end of one DNA fragment such as an Okazaki fragment
to the 5 prime end of another DNA fragment such as a growing DNA chain

DNA Polymerase: an enzyme that catalyzes the elongation of new DNA at a replication
fork by the addition of nucleotides to the 3 prime end of an existing chain

Mitosis:

Primase: an enzyme that joins RNA nucleotides to make the primer using the parental
DNA strand as a template

Interphase: a period in the cell cycle when the cell is not dividing. Cellular metabolic
activity is high. Chromosomes and organelles are duplicates and the cell size increases.
Interphase accounts for ninety percent of the cell cycle

Prophase: Prophase is the first step in Mitosis. The chromatin condenses. Mitotic spindle
forms. Nucleolus disappears but the nucleus remain intact

Metaphase: Third stage, spindle is complete, chromosomes attach to microtubules at their

kinetochores. All are aligned at the metaphase plate (which is like the cellular equator)

Anaphase: Fourth stage in Mitosis. Chromatids have separated. Daughter chromosomes

move to opposite poles of the cell

Telophase: Final Stage. Daughter nuclei are forming. Cytokinesis has begun

Cytokinesis: Process of cytoplasmic division to form 2 separate daughter cells

Mitosis: is the process of nuclear division in eukaryotic cells. It conserves chromosome

number by allocating replicated chromosomes equally to each of the daughter nuclei

Kinetochore: attaches to centromere. Links each sister chromatidto the mitotic spindle

Centrosome: Houses microtubules

Centromere: The center where the chromosomes attach

Codon: a sequence of three nucleotides of DNA or mRNA that specifies a particular

amino acid or termination sequence. Comprises the basic unit of the genetic code

Anticodon: A nucleotide triplet at one end of a tRNA molecule that recogizes a particular
complementary codon on an mRNA molecule

Transcription: the synthesis of DNA using an RNA Template

Translation: the synthesis of a polypeptide using genetic information encoded in an

mRNA molecule. There is a change in language from nucleotides to amino acids

Transfer RNA: (tRNA) Transfer RNA functions as an interpreter between nucleic acids
and the protein language by picking up specific amino acids and recognizing the
appropriate codons in the mRNA

Ribosomal RNA: most abundant (Together with proteins make up ribosomes)

Messenger RNA: synthesized using a DNA template. Attaches to ribosomes in the

cytoplasm and specifies the primary structure of a protein

RNA Polymerase: links ribonucleotides to a growing RNA chain during transcription

Gene: a unit of hereditary information consisting of a specific nucleotide sequence in

DNA

degenerate codon: indicates redundancy but not ambiguity of the genetic code. For
example many different codons code for Glutamate but they do not code for any other
amino acids

Okazaki Fragments: short segments of DNA synthesized away from the replication fork
on a template strand during DNA replication many of which are formed together to make
the lagging strand of the newly synthesized DNA

An inversion mutation involves breaking and reforming phosphodiester bonds

Missense: altered function of protein. May be good, evolutionarily advantageous (as well
as duplications and translocations) Results from the change of a single amino acid within
a protein sequence. GGC ---> AGC (Glycine to Sarine) however the rest of the protein
sequence will remain identical. If this mutation occurs in the active site of an enzyme is
may alter the protein function. It ca have a good, bad, or neutral effect (if it is in part of
the amino acid that is not critical for protein function)

Silent Mutations: as the name implies, these have no effect, silent mutations are silent
because there is no change in the protein sequence due to degeneracy in the amino acid
codons (GGC ---> GGU) Glycine results in the same protein function usually occurs at
the third nucleotide of a codon (because that is where the degeneracy occurs)

Inversion:

5--CGTAC--3

3--GCATG--5

Results in a sequence that is flipped both vertically and horizontally inverted and then
reattached to the DNA

5--GTACG--3

3--CATGC--5

Duplication: a region of the DNA is duplicated

5 -- CTCTTG -- 3

3 -- GAGAAC -- 5

Becomes:

5 -- CTCTTGCTCTTG -- 3

3 -- GAGAACGAGAAC -- 5

What causes mutations?

Replication errors, alterations of base pairs directly (doesn't involve replication)

Mutations can be spontaneous or induced

Spontaneous Mutations result from the normal error rate of the replication machinery

Induced Mutations result from the presence of a chemical or physical change called a
mutagen (ex: a carcinogen)

Homology: 2 proteins that are similar can take on different functions

Rearrangement: Translocation Mutation

results in the breakage of the chromosome (phosphodiester bonds break) and reattach
elsewhere (in the same chromosome or on another chromosome)

Will have a definite effect on the characteristics of an orgaism

Replication is a high fidelity process. If mistakes are not proofread or fixed, they can be
made permanent within the organism's DNA
Mutations arising in gametogenesis are the most harmful (happen within the zygote)
because they affect every cell and lead to birth defects

A mutation within a skin cell ca lead to cancer

A mutagen that leads to cancer becomes a carcinogen

DNA Polymerase creates more errors when this happens