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Instructor Name
Islam & Five Pillars
Islam is a world religion found by 7 th century. It is the
youngest of the three monotheistic religions of the world. There
are more than 1 billion Muslims worldwide. Qur’an is the holy
book of Muslims and is the core of the religion. They believe in
the five pillars of the religion which are namely;
( Shahadat,
( Salat,
( Zakat,
( Saw, &;
( Hajj.
The belief of Muslims is the final reward and punishment. The
ethos of Islam is in its disposition toward Allah: to His will
Muslims submit; Him they laud and commend; and in only him
they trust. In any case, in prevalent or people types of Islam,
Muslims solicit intervention from the holy people, prophets, and
blessed messengers, while protecting the refinement amongst
Creator and creature. Islam sees the Message of Muhammad as
the continuation and the satisfaction of lineage of predictions.

(Online Research Library, November)
Shahadat
The declaration of faith is stating with conviction, "La ilaha illa
Allah, Muhammadur rasoolu Allah." This expression signifies
"There is no true Allah (god) however Allah (Allah),1 and
Muhammad is the Messenger (Prophet) of Allah." The initial
segment, "There is no true Allah yet Allah," implies that none
has the privilege to be revered yet Allah alone, and that Allah
has neither accomplice nor child. This declaration of faith is
known as the Shahada, a straightforward recipe which ought to
be said with conviction to change over to Islam. The declaration
of faith is the most critical pillar of Islam.
Salat
Muslims perform five prayers a day. Every prayer does not take
more than a couple of minutes to perform. Prayer in Islam is an
immediate connection between the admirer and Allah. There are
no mediators amongst Allah and the admirer. In prayer, a man
feels internal satisfaction, peace, and comfort, and that Allah is
satisfied with him or her. The Prophet Muhammad said: Bilal,
call (people) to prayer, let us be support by it. Bilal was one of
Muhammad's colleagues who was charged to call the people to
prayers. Prayers are performed at sunrise, twelve, mid-evening,
nightfall, and night. A Muslim may pray anyplace, for example,
in fields, workplaces, production lines, or colleges.
Zakat
All things have a place with Allah, and riches is in this way
held by people in trust. The first significance of the word zakat
is both "refinement" and "development." Giving zakat signifies
'giving a predefined rate on specific properties to specific
classes of poor individuals.' The rate which is expected on gold,
silver, and money finances that have achieved the measure of
around 85 grams of gold and held under lock and key for one
lunar year is more than two percent. Our belonging is

decontaminated by putting aside a little bit for those in need,
and, like the pruning of plants, this reducing parities and
empowers new development. A man may likewise give as much
as he or she satisfies as willful offerings or philanthropy.
Sawm
Consistently in the month of Ramadan, all Muslims quick from
day break until nightfall, declining sustenance, drink, and
sexual relations. Even though the quick is gainful to wellbeing,
it is viewed chiefly as a technique for otherworldly self-
purging. By cutting oneself off from common solaces,
notwithstanding for a brief span, a fasting individual increases
true sensitivity for the individuals who go hungry, and
development in his or her profound life.
Hajj
The annual pilgrimage (Hajj) to Makkah is a commitment rare
for the individuals who are physically and fiscally ready to
perform it. Around two million individuals go to Makkah every
year from each edge of the globe. Although Makkah is
constantly loaded with guests, the yearly Hajj is performed in
the twelfth month of the Islamic schedule. Male explorers wear
extraordinary straightforward garments which strip away
refinements of class and culture with the goal that all stand rise
to before Allah.
The ceremonies of the Hajj incorporate circumnavigating the
Kaaba seven times and going seven times between the hillocks
of Safa and Marwa, as Hagar did amid her hunt down water. At
that point the explorers stand together in Arafa and approach
Allah for what they wish and for His absolution, in what is
regularly considered as a set of the Day of Judgment. The end
of the Hajj is set apart by a celebration, Eid Al-Adha, which is
praised with prayers. This, and Eid al-Fitr, a devour day
recognizing the end of Ramadan, are the two-yearly celebrations
of the Muslim schedule.

The hajj Arabic for "journey" is a five-day religious journey to
Makkah and adjacent heavenly destinations in Saudi Arabia that
all Muslims who are physically and monetarily capable must
perform in any event once in their lives. It is one of the five
pillars, or obligations, of Islam, alongside the calling of faith in
the one Allah and Mohammed as his prophet, prayer, altruistic
giving, and fasting amid the blessed month of Ramadan. The
hajj happens just once per year, in the twelfth and last month of
the Islamic lunar date-book; journeys to Makkah made at
different times in the year are supported however don't consider
the hajj. Since the Islamic lunar date-book is around 11 days
shorter than the 365 days of the standard Gregorian date-book,
the planning of the hajj goes in reverse every year.
Over the five days of the hajj, pioneers play out a progression
of ceremonies intended to symbolize their solidarity with
different adherents and to pay tribute to Allah. On the most
recent three days of the hajj, explorers and every single other
Muslim around the globe observe Eid al-Adha, or the Festival of
Sacrifice. This is one of the two noteworthy religious occasions
Muslims praise each year. The other is Eid al-Fitr, which comes
toward the end of Ramadan.
Toward the end of the hajj, pioneers return home and are
regularly given the honorific "hajji," which means one who has
played out the hajj. One fascinating note here: During the Iraq
War, US troops much of the time utilized the expression "hajji"
as a critical term for any Iraqi, Arab, or other individual of
Middle Eastern or South Asian plummet. Along these lines,
although they surely didn't mean it thusly, and it probably
wasn't taken along these lines by the individual on the less than
desirable end of the slur, US troops were accidentally applying
a term of regard and respect to these people. Individuals might
be amazed to discover that the hajj has almost no to do with the
Prophet Mohammed. Or maybe, it for the most part honors
occasions in the life of the Prophet Ibrahim.

Allah told Ibrahim, as a trial of faith, to take Hagar and the
baby Ismail out to a fruitless forsake zone situated between the
two slopes of Safa and Marwah in Makkah, and allow them
there to sit unbothered with just fundamental arrangements.
Eventually the water ran out, and the undeniably wild eyed
Hagar kept running forward and backward from slope to slope
seven times looking for water for her dry youngster. At that
point a supernatural occurrence happened: A well, later called
the Zamzam well, sprang from the beginning, both. The
narrative of how the well was found varies: Some records say it
was the child Ismail's troubled kicking of his feet that scratched
away the soil and revealed the water source. Different records
hold that the Jibril (AS) tipped his wing into the soil to reveal
the well.
Abraham and Ismail later went ahead to construct the Kaaba,
the dark cuboid structure in Makkah that Muslims confront
when they pray together, as a position of love of the one Allah.
Not long after they manufactured the Kaaba, convention holds,
Allah told Abraham to broadcast a journey to the site as it were,
the hajj to all humankind with the goal that they can meet up in
one place to demonstrate their commitment to Allah.
Eid-al-Fitr
Eid al-Fitr falls on the main day of Shawwal, the month which
takes after Ramadan in the Islamic calendar. It is an opportunity
to give in philanthropy to those in need, and celebrate with
family and companions the fulfillment of a month of favors and
delight.
Prior to the day of Eid, amid the most recent few days of
Ramadan, every Muslim family gives a decided sum as a gift to
poor people. This gift is of actual nourishment rice, grain,
dates, rice, and so forth to guarantee that the penniless can have

an occasion meal and take an interest in the festival. This gift is
known as Sadaqah al-Fitr.
Upon the arrival of Eid, Muslims accumulate at a young hour in
the morning in open air areas or mosques to play out the Eid
prayer. This comprises of a sermon took after by a short
congregational prayer. After the Eid prayer, Muslims usually
scramble to visit different family and companions, give
blessings especially to youngsters, and make telephone calls to
inaccessible relatives to give well-wishes for the occasion.
These exercises traditionally proceed for three days. In most
Muslim nations, the whole 3-day time frame is an official
government/school occasion. Eid al-Fitr is an occasion devoted
to devouring and serves as the promising end to present
circumstances following a long and troublesome month of
fasting and declining. Eid-al-Fitr marks the end of Ramadan,
when Muslims break their month-long quick. The date of Eid-al-
Fitr, which is also known as the Lesser Eid, is dictated by the
affirmed locating of the new moon. Islamic sacred writing
advises how Allah directed Ibrahim to sacrifice his child as a
trial of his commitment.
Works Cited;
Abuznaid, S. (2006). Islam and management: what can be
learned?. Thunderbird International Business Review, 48(1),
125-139.
Esposito, John L. Islam: The straight path. Vol. 4. New York:
Oxford University Press, 1998.
El Azayem, Gamal Abou, and Zari Hedayat-Diba. "The aspects
of Islam: Basic principles of Islam and their corollary." The
International Journal of Religion 4.1 (1994): 41-50.
Lippman, T. W. (1995). Understanding Islam: An introduction
to the Muslim world. New York: Meridian.
Nasr, S. H. (2003). Islam: Religion, history, and civilization.
HarperOne.
"List of Books and Articles About Islam | Online Research
Library: Questia | Online Research Library: Questia,

www.questia.com/library/religion/islam/islam. Accessed Nov.
Cellstructures.ppt
Cell theory - originated in mid-1800s
Every organism is composed of one or more cellsThe cell is the
smallest unit having the properties of lifeNew life comes from
growth and division of single cells
2 major types of cells:
1. Prokaryotic - evolved first
2. Eukaryotic - evolved from prokaryotic cells
Prokaryotic Cell - autotrophic bacteria
Cyanobacteria
Eukaryotic cell - Overview of a plant cell

Eukaryotic single-celled autotroph
(Plant-like Protist)
Euglena
Single-celled
Colonial
Filamentous
Green Algae - Types
Large Complex
Eukaryotic cell - Overview of an animal cell
Eukaryotic single-celled heterotrophs
(Animal-like protists)
Paramecium
Stentor
The detailed structure of an animal cell’s plasma membrane, in
cross section
Passive and active transport compared
The three types of endocytosis in animal cells

Amoebas use phagocytosis
to obtain food
The nucleus and its envelope
Ribosomes
Endoplasmic reticulum (ER)
The Golgi apparatus
Lysosomes
The formation and functions of lysosomes
part2.doc
BI 101E Ocean Life Foundations
Knelly
Exam 2

NAME___________________
Multiple choice: Circle the letter of the most correct answer.
Ask me if questions (24 pts)
1) Nucleic acids function as:
a. structure and support
b. transporters of energy
c. information storage
d. reaction catalyst
2) In unsaturated fats, fatty acid tails have one or more:
a. single covalent bonds between neighboring Carbon atoms
b. double covalent bonds between neighboring Carbon atoms
c. single covalent bonds between neighboring Hydrogen atoms
d. double covalent bonds between neighboring Hydrogen atoms
3) The basic unit of carbohydrates is:
a. fatty acids
b. monosaccharides
c. amino acids
d. nucleotides
4) ___________________ are to carbohydrates as

______________ are to lipids.
a. sugars; fatty acids
b. sugars; proteins
c. amino acids; fatty acids
d. amino acids; nucleotides
5) The cell membrane is composed of a double layer of:
a. phospholipids
b. monosaccharides
c. amino acids
d. triglycerides
6) Membrane-bound organelles:
a. include the Golgi apparatus and the endoplasmic reticulum
b. are typical of eukaryotic cells, not prokaryotic cells
c. create compartments in which certain chemical reactions
occur
d. all of the above are features of membrane bound organelles
7) Cells of many plants and fungi, but not animals, commonly
have:
a. mitochondria

b. a plasma membrane
c. ribosomes
d. a cell wall
8) Unlike eukarytoic cells, prokaryotic cells:
a. lack a plasma membrane
b. have RNA, but no DNA
c. do not have a nucleus
d. all of the above
9) A chemical reaction is:
a. making of chemical bonds
b. breaking of chemical bonds
c. forming new molecules
d. all of the above
10) What are autotrophs?
a. photosynthetic producers
b. consumers
c. chemosynthetic producers
d. both a and c
11) What is the key step in the first stage (light reaction) of

photosynthesis that directly results in the formation of the
oxygen that we are breathing?
a. carbon fixation
b. capture of energy with chlorophyll
c. photolysis splits H2O
d. sugar formation
12) Chemical reactions are facilitated by:
a. lipids
b. carbohydrates
c. nucleic acids
d. enzymes
13) The Calvin cycle (dark reaction) produces predominantly
a. free oxygen
b. CO2
c. ATP
d. sugar
14) Anaerobic respiration is completed in the:
a. nucleus

b. mitochondria
c. plasma membrane
d. cytoplasm
15) Aerobic respiration is completed in the:
a. nucleus
b. mitochondria
c. plasma membrane
d. cytoplasm
16) Which of the following is the most important food energy
source for heterotrophs?
a) sunlight
b) CO2
c) nucleic acids
d) carbohydrates and lipids
17) Osmosis is the diffusion of
a) salts across a semi-permeable membrane

b) gases across a semi-permeable membrane
c) cytoplasm across a semi-permeable membrane
d) water across a semi-permeable membrane
18) A cell is ____________ if the concentration of solutes is the
same inside and outside the cell.
a) hypertonic
b) hypotonic
c) isotonic
d) gin and tonic
19.
Before the onset of mitosis & meiosis I, all chromosomes are
____________________.
a. condensed
b. duplicated
c. destroyed
d. both a and b

20.
Interphase is the part of the cell cycle when _______________.
a. a cell ceases to function
b. a cell goes through mitosis
c. a cell grows and duplicates its DNA
d. cytokinesis occurs
21.
In a chromosome, a _______________ is an un-replicated
region that holds together sister chromatids and is the location
where microtubules attach.
a. chromatid
b. cell plate
c. centromere
d. centriole
22.
Sexual reproduction requires ________________.
a. meiosis
b. gamete formation
c. fertilization
d. all of the above
23.
Which is NOT a nucleotide base in DNA?

a. adenine
b. guanine
c. uracil
d. thymine
24.
Generally, a pair of homologous chromosomes
_______________________.
a. carry the same genes
b. has the same length and shape
c. interact to form a tetrad during meiosis
d. all of the above
Matching:
1) Match each cell component with its function: Don’t forget
the chart handout. (6 points)
Component:Function:
_________mitochondria
a. site of protein synthesis
_________chloroplast
b. controls passage of materials into and out of cell
_________ribosome
c. synthesis, sorting and shipping of materials

_________ER
d. photosynthesis
_________Plasma membrane
e. site of ribosome manufacture and storage
_________cytoskeleton
f. storage of genetic information
_________nucleolus
g. formation of ATP
_________Golgi apparatus
h. isolate ‘digestive’ enzymes from the rest of cell
_________lysosomes
i. moving the cell from place to place
_________centriole
j. provide shape, support & allow for movement
_________cilia and flagella
k. provides large surface for chemical reactions
_________chromatin
l. organize microtubules into spindle fibers
2) Match each term with its best description (some may have
more than one answer) (8 points)
______ kinetic

a. energy of motion
______ potential
b. produced as a result of respiration
______hydrogen bonds
c. largest portion of liquid water on earth
______eukaryotes
d. contain phosphates
______ATP
e. component of proteins & nucleic acids
______oceans
f. stored energy
______phospholipids
g. evolved from prokaryotes
______nitrogen
h. join DNA strands
Fill in the blank: (5 points)
1) During the process of diffusion across a semi-permeable
membrane, molecules tend to move from an area of
____________________ concentration to an area of
__________________ concentration.
2) Photosynthetic autotrophs use _________________________
from the air as a carbon source and ___________________ as
their energy source.

3) ________________ __________ is the anaerobic respiration
by-product that causes sore muscles when you run too much.
Short answer: (9 pts total)
1) List 3 differences between DNA & RNA. (3)
2) a. Summarize photosynthesis as a symbolic chemical
equation. (1)
b. Summarize aerobic cellular respiration as a symbolic
chemical equation. (1)
3) If plants can make ATP from sunlight during the first stage
of photosynthesis, then why do they bother to make glucose and
then break that glucose down through the process of cellular
respiration? (1 point)
4) List 3 differences between mitosis and meiosis (from packet
notes, lab, & PP). (3 points)
Powerpoint answers: (7 points)
1. a.
b.
c.
2. a.
b.
3. a.
b.
c.
d.

e.
f.
4. a.
b.
c.
- 1 -
part1.ppt
a.
b.
c.
1. Label the 3 parts of a nucleotide in DNA. (3 points)
a.
b.
2. Name each organelle: (2 points)
3. Label what happens at each stage of the cell cycle. (use
cell cycle/ division Powerpoint)

d.
e.
f.
a.
b.
c.
4. Label the type of tonicity of each cell.
a.
b.
c.
cell_division.ppt
Importance of cell division: GrowthMaintenanceRepair
2 kinds of cell division:
Mitosis - body cells with full set of chromosomes (diploid)
Meiosis - sex cells (sperm & egg) with 1/2 set chromosomes
(haploid)
What is a chromosome (from DNA notes)?
What is a gene (from DNA notes)?
Genes on 1 chromosome are different from genes on
another chromosome.
Genes on each chromosome arranged in a specific order.
Every organism has a fixed number of chromosomes.

Loosely organized DNA - chromatin
In a non-dividing cell (each thread is a chromosome)
Condensed
chromosome
Loosely organized
chromatin coils
around proteins
In a dividing cell:
Humans have 2 pairs of 23 different chromosomes
(46 chromosome total)
Chromosomes occur in homologous pairs (diploid)
Cell cycle - all cells have same life cycle but vary in the
amount of time they spend in the different stages (fig 8-1)
Stages to life cycle of eukaryotic cells:
Interphase - not dividing; metabolic activities; longest
1. G1 - 1st growth phase; RNA, ribosomes, enzymes
& other cell components produced
2. S - synthesis phase (DNA replication-each
chromosome is now composed of 2 sister chromatids)
3. G2 - 2nd growth phase (protein synthesis for spindle

formation)
Mitosis - division of nucleus (4 stages)
Cytokinesis - division of cytoplasm
G0: some cells enter dormant stage (ex. nerve cells)
Cell Cycle
Condensed
chromosome
Loosely organized
chromatin
Interphase - G1, S, G2
Centrioles
Chromatids
Nuclear
membrane
Nuclear
pores
Nucleolus
What happens?
Mitosis - Prophase (1st stage)
Spindle

fibers
Centromere
Sister
chromatids
What happens?
Centrioles
Nucleolus
Metaphase
What happens?
Spindle fibers
Poles
Anaphase
Daughter chromosomes
What happens?
Telophase
Cleavage
furrow
Daughter
chromosome
What happens?
Cytokinesis
Daughter cells
Animal cells

Mitosis in Plants
Cell plate formation instead of cytokinesis
What is cancer?
Tumor - mass of cells not normally found in body; tumors are
harmful because they require lots of nutrients from the
body and can interfere with the normal functioning of
the body
Benign tumor - a cell mass that does not fragment & spread
beyond the original area
Malignant tumor - a cell mass that spreads or invades other
areas of the body; cells that move (metastasize) can
form other colonies in the body
Cancer - any abnormal growth of cells that has a malignant
potential
Meiosis - division of reproductive cells (gametes) in which the
number of chromosomes is reduced in half through a 2-stage
nuclear division process
most body (somatic) cells are diploid (2N) where N = # of
different chromosomes
2 copies of each chromosome - 1 from mother, 1 from father
this pair is called homologous chromosomes

gamete cells haploid (1N) only 1 chromosome of each type
gametes must be haploid so that when 2 gametes join to
form new organisms in sexual reproduction the # of
chromosomes will equal the # in the somatic (body) cells of
the parents (2N)
Purpose: sexual reproduction
Meiosis and sexual reproduction
Sources of variation:
Mutation - point (change in DNA nucleotide results in
production of a different protein); chromosomal (genes are
re-arranged)
Crossing-Over - exchange of parts of chromatids between
homologous pairs of chromosomes (fig 9-16)
Segregation - splitting of homologous pairs & movement to
opposite poles; may produce offspring with different traits

Independent assortment - how the pair of chromosomes
arrange at the equator is determined by chance
Fertilization - millions of genetically different sperm & eggs
can produce infinite combinations
Independent assortment
Problems in Meiosis
Non-disjunction:
a pair of homologous chromosomes don’t segregate
properly in Meiosis I
both copies end up in the same daughter cell when fertilized
this results in Trisomy (3 copies) Trisomy of chromosome 21 =
Downs syndrome
the other daughter cell is missing a chromosome
completely when fertilized this results in Monosomy (1 copy)
For review of mitosis - p. 145 table 8.1
For review of meiosis - p. 161 table 9.2
For comparison of mitosis & meiosis - p. 168 table 9.3

PLEASE NOTE: WE WILL NOT DO LABS ON
P. 59 - P. 68 IN PACKET PART A
Also we will not be reading or discussing
Mendelian genetics
DNA.ppt
DNA Structure & Replication
Protein synthesis from genetic code
DNA - deoxyribonucleic acid = chain of nucleotides
each nucleotide contains
+ 5 carbon sugar
+ phosphate group
+ base
- purines (A-adenine; G-guanine)
- pyrimidines (C-cytosine; T-thymine)
1953 - The double helix x-ray diffraction photo - Rosalind
Franklin
Watson & Crick deduced twisted ladder theory from this.
What makes up the backbone of DNA ladder?
How do the two halves connect? What bases match? Bonds?

Purines
Pyrimidines
always bonds with
or
Nitrogen containing bases
2 H bonds
between A & T
3 H bonds
between G & C
NOW YOU BUILD YOUR OWN MODEL OF
A DNA MOLECULE USING THE KITS
PROVIDED (FOLLOW THE DIRECTIONS
IN EACH KIT)
ANSWER THE QUESTIONS
ON LAB P. ???
YOU HAVE 1/2 HOUR TO COMPLETE

Definitions:
Chromosome = 1 DNA molecule & many proteins
intimately associated with it
Gene = particular stretches of a chromosome
1) Get a sheet of lined paper
2) Write STRAND 1 on the top left hand side of the paper
and STRAND 2 on the upper right hand side of the paper
3) Choose one of the two strands in your DNA molecule
4) Write down the order of the bases (A,T,G or C) in this strand
under STRAND 1 - starting at the top and going to the
bottom
of the DNA molecule. Write the bases under the word
STRAND 1 moving down vertically one line at a time
Strand 1 Strand 2
5) Do the same for the other strand in your DNA molecule
6) Draw in the hydrogen bonds that hold your base pairs
together.
7) Turn this paper in for individual lab credit along with p.66-
68
in packet when finished with all of it.
2 important points about your DNA molecule:
Sequence of bases tells specific genetic informationMust be
preserved to maintain integrityChange in sequence causes
mutationIf no mistakes ever occurred no variation in gene
sequence would result & evolution would halt
Sequence of 1 strand will always indicate sequence
of complementary strand

a) Allows copies (replications) to be exact
DNA replication
Before a cell can divide and make two cells that are identical
to each other; the cell must first replicate its DNA to make
two copies that are exactly the same. One copy will go to
each cell
How to make an exact copy of DNA: Replication
1. Break Hydrogen bonds
2. Unwind old strands
3. Base Pair free nucleotides
4. Create a new backbone - using DNA polymerase
(enzyme)
5. Form new Double helix - this happens for both old
strands
creating two double helixes
This is the first half of exercise on p.?? of homework
DNA Replication
Old strand
New strand
New strand
Old strand

Old strand
New strand
New strand
DNA is the storage molecule for genetic information (genes),
but for that information to actually be used to make organisms
and to direct the function of those organisms,
that genetic information must be used to make proteins.
This process is called protein synthesis Remember that proteins
are composed of subunits called
amino acids. The ordering of amino acids in a protein is
determined
by the ordering of nucleotides in DNA
The Central Theme of Biology
Protein synthesis occurs in to two parts
DNA -- > RNA in a process called transcription
(coding strand is the side made into RNA;
the non-coding side has the complementary sequence)

- responsible for carrying this sequence information
from the storage area in the nucleus to the protein
manufacturing area in the cytoplasm (the ribosome)
RNA
DNA
always bonds with
always bonds with
Sugar = Ribose
Sugar = Deoxyribose
Has one less oxygen
RNA
DNA
Transcription
mRNA being transcribed from coding strand
Non-coding strand
of DNA
Coding strand
of DNA

The Genetic Code
mRNA contains a code that corresponds to different amino acids
– 3 bases in a row correspond to 1 amino
acid
- Base Triplets are called codons
20 different amino acids, but there are 43 or 64 codons.
- So many amino acids have more than one codon AUG
codes for methionine and it is the START codon. All amino
acid sequences must start with AUG UAA, UAG, and UGA do
not code for an amino acid –
they signal the end of the amino acid sequence
(STOP codons)
START
Protein synthesis occurs in to two parts
2. RNA -- > Protein in a process called translation
The ribosome attaches to the mRNA at the rRNA siteInitiation:
The ribosome attaches the first amino acid
– always Met – when it reads the start codon
– each codon
lines up with matching transfer RNA (tRNA) segments
with amino acids attachment sites
Termination: When the ribosome comes to a STOP codon

- so the amino acid chain is released from the ribosome
as a completed protein
a. This new protein may stay in the cytoplasm or
enter the rough ER
Translation
Non-coding strand
Coding strand
mRNA
Protein
Homework: finish worksheets p.???
EnergyNutrients.ppt
Everything in nature is either matter or energy.
Neither can be created, and neither can be destroyed.
But matter can be turned into energy: E = mc2.

So all energy and matter in life comes from somewhere
and goes somewhere. (Remember potential & kinetic?)
Life requires energy and raw materials (nutrients) to function.
A great deal of the interaction (ecology) between life forms
and their environments is to obtain these items.
First, energy: Different species get energy in different ways,
so there are trophic levels, different levels in the food web
that species can occupy .
Autotrophs = make food = producers
Heterotrophs = eat food = consumers
Simplified Arctic Food Web
Grouped into categories
according to their trophic level
About 10% energy transfers from one level to the next,
the rest is detritus, non-living particulate organic matter
(made of DOM = dissolved organic matter)
This is eaten by detritovores = decomposers (bacteria).
Net primary production = organic matter (fixed Carbon)
left over after autotrophic respiration; Leads to biomass
About 170 billion tons of plant material per year.
Phytoplankton-> DOM -> bacteria -> protozoans -> zooplankton
1/2 of primary production is Dissolved Organic Matter (DOM)
Microbial loop

Limitations to primary production:Light
(photosynthesis)Nutrients
a) Nitrogen from (NO3)-1
b) Iron from weathering & detritus
c) Phosphorous from (PO4)-3
3. Seasonal patternsOverturnUpwelling (caused by
Ekman transport)
4. Geographic patterns
(shallow/deep)
Many organic particles (detritus) sink out of epipelagic
Surface waters are nutrient poor & phytoplankton growth
limited
Upwelling helps redistribute the nutrients that fall to bottom
Open ocean nitrate & phosphate
Seasonal overturn of
cold and warm H2O
leads to seasonal
cycles of primary
productivity
Energy (E = mc2)
Important: all changes of energy form lead to some
energy lost as heat.
Ultimately, all the energy coming into an ecosystem is turned
into heat and dissipated, lost to space at night.
This is not the case for nutrients (chemicals).

These are recycled through the ecosystem.
Water Cycle
Evaporation (especially from oceans) and
evapotranspiration (production of water as a result of
respiration) put water into atmosphere.
Precipitation leads to run-off and aquifers of fresh water.
Also allows absorption and drinking.
Returns to sea.
http://observe.arc.nasa.gov/nasa/earth/hydrocycle/hydro3.html
H2O Budget
H2O Cycle
Carbon Cycle
Atmospheric CO2
CaCO3 from sediments
Dissolves in H2O
Used in photosynthesis
Released in respiration
Decomposition of detritus
C2 in all organic
macromolecules
Man has increased
atmospheric CO2
Global warming?

(p.394-395 Castro)
Nitrogen cycle
Atmospheric N2 --> Nitrates
Fixation by cyanobacteria,
other bacteria, & archae
Iron (Fe) is important in fixation
Lightning causes fixation also
Most of cycle is local :
Through wastes & decomposition
Human fertilizers, sewage
What macromolecules contain
N2?
Proteins & Nucleic Acids
Phosphorous Cycle
Enter as phosphates:
Small amount from atmosphere
Most from river runoff weathering of rocks bird guano
fertilizers recycling through detritus
Phosphates are one of the
chemical functional groups.
What macromolecules contain
phosphates?
Lipids (Phospholipids)
photo_respiration-1.ppt

Properties of life:
Capture & use energy & raw materialsSensing & responding to
the environmentCapacity to reproduce itselfTo reproduce must
contain DNA
2 types of energy capture in organisms:
Auto-trophic - use photosynthesis or chemosynthesis
to produce their own food
Hetero-trophic - must obtain (eat) food
Importance of primary production by autotrophs
Cells and energy:
Energy = capacity to do work (kinetic or potential)
Energy in the biological world comes from the SUN
Chemical reactions transfer energy with electrons in making
and breaking bonds (oxidation-reduction = redox reactions)
Energy is required to initiate reactions
Enzymes (proteins) catalyze (jump-start) reactions in cells
sensitive to temperature & pH coenzymes also affect enzyme
activity
In mitochondria and chloroplasts chemical or photosynthetic
energy is harnessed to form ATP.

ATP is used to drive the living activities of the cell
Photosynthesis - making sugar from sunlight
Occurs in chloroplasts in eukaryotic plant cells,
single-celled algae, and phytoplankton (also in cyanobacteria,
but not in a chloroplast)
6CO2 + 12H2O + solar energy --> 1C6H12O6 + 6O2 + 6H2O
The LIGHT REACTIONS: Capturing energy using pigments
(chlorophyll)Photosystems in grana excite electronsElectron
transport chain used to move electronsH+ in thylakoid spaces
make NADPH from NADP+
2. Using the energy to make ATPPhotolysis splits H2O - source
of atmospheric oxygenH+ replaced in stroma via channel
12H2O + solar energy --> 6O2 + 18ATP + NADPH + 12H+
Structure of a Chloroplast
Outer membrane
Inner membrane
thylakoid

space
Structure of a Chloroplast
Electron Transport
The DARK REACTION - Calvin Cycle using CO2 & ATP to
make Sugar
Location: chloroplast stroma
Steps:Carbon fixation using RuBP (enzyme)Carbon from CO2 is
added to 5 C sugar in ATPSugar formation (1/2 of a glucose
molecule)Newly formed 6 C sugar splits into two 3 C
sugarsRegeneration of RuBP Some 3 C sugars rebuild 5 C
sugarSome 3 C sugars combine to form glucose
Cycle:
these three steps occur 2 times to generate 1 glucose
molecule
Calvin Cycle - using CO2 + ATP to make sugar

CO2
Unstable (6 carbon)
PGA (3 carbon)
ATP (energy)
NADPH (hydrogens)
PGAL (3 carbon)
PGAL (3 carbon)
ATP (energy)
RuBP (5 carbon)
The synthesis part of photosynthesis
1
2
3

Review of photosynthesis
6CO2 + 12H2O + solar energy --> 1C6H12O6 + 6O2 + 6H2O
Photosynthesis
Respiration
Cellular Respiration = Opposite of photosynthesis
Overview of aerobic respiration - oxidation of food
C6H12O6 + 6O2 ----->6CO2 + 6H2O + 36 ATP
Cellular Respiration occurs in 4 stages
Stage 1: Glycolysis - Splitting sugar in cytoplasm of cell
- no O2 required
- phosphorylation to creat pyruvates
- one of earliest biochemical processes
Stage 2: 1st step of oxidation
- pyruvate goes into the mitochondria
- split into 2 acetyl-CoA with NAD + CoA
- channeled into fat synthesis (lipid storage) or
ATP production in Krebs cycle

Structure of a Mitochondria - occur in plant & animal cells
Intermembrane
space
Evolved from free-living bacteria p.75 Castro
Stage 3: Krebs cycle 2nd step in oxidation
- occurs in mitochondrial matrix
- 3 steps
- Breaks down C compounds to release H+ and e-s
- small amount of CO2 + ATP produced
At the end of Part 3 (after two full cycles):
2 Acetyl CoA ----
Krebs Cycle
Acetyl CoA
6 carbon)
CO2
ATP (energy)
NADH (hydrogens)
4 carbon
OXA (4 carbon)

NADH
(hydrogens)
FADH2
(hydrogens)
1
2
3
Stage 4: Electron Transport - Makes lots of ATP
- occurs in mitochondrial inter-membrane space “cristae”
- electron transport chain moves H+ into space
- channels in membrane passes H+ through to matrix
- chemi-osmosis through proton pumps(facilitated diffusion)
- ATP formed in matrix
Fig. 4.6 Castro

Fermentation - Anaerobic respiration
Or, how to extract a little bit of ATP (2, to be precise)
out of glucose when O2 is not present!
Production of ATP without the help of oxygen
One of two waste products typically result:
1. Plants: Ethanol: wine, beer, etc
2. Animals: Lactic acid: sore muscles after exercising
Not a lot of energy, but better than nothing!
Net primary production = organic matter left after autotroph
respiration
PhotosynPigments.ppt
In the ocean: light absorption depends on
clarity (transparency) and depth of the water

Many chemicals other than CO2 &
H2O are necessary for effective use
of available sunlight. This is why
overturn (downwelling & upwelling) is
especially important to ocean algae &
phytoplankton.
The wavelength of light determines its color.
For example, The wavelength of red is about 700 nm and the
wavelength
of blue light is about 470 nm.
Visible light is a part of a larger spectrum of radiation called
the
electromagnetic spectrum.
Pigments are chemical compounds which reflect only certain
wavelengths
of visible light.
This makes them appear "colorful". Flowers, corals, and even
animal skin contain pigments
which give them their colors.
More important than their reflection of light is the ability of
pigments
to absorb certain wavelengths.
There are three basic classes of pigments.

1. Chlorophylls are greenish pigments which contain a
porphyrin ring.
There are several kinds of chlorophyll, the most important being
chlorophyll "a".
All plants, algae, and cyanobacteria which photosynthesize
contain chlorophyll "a".
A second kind of chlorophyll is chlorophyll "b", which occurs
only in "green algae”
and in the “true” plants.
A third form of chlorophyll which is common is (not
surprisingly) called chlorophyll "c",
and is found only in the photosynthetic members of the
Chromista as well as the
dinoflagellates.
2. Carotenoids are usually red, orange, or yellow pigments, and
include the familiar compound carotene, which gives carrots
their color.
They do not dissolve in water, and must be attached to
membranes within
the cell.
Carotenoids cannot transfer sunlight energy directly to the
photosynthetic pathway,
but must pass their absorbed energy to chlorophyll. For this
reason, they are called
accessory pigments. One very visible accessory pigment is
fucoxanthin the brown pigment which colors kelps and other

brown algae as well as the diatoms.
Diatoms
3. Phycobilins are water-soluble pigments, and are therefore
found in the cytoplasm, or
in the stroma of the chloroplast. They occur only in
Cyanobacteria and Rhodophyta.
2 types: a. Bluish pigment phycocyanin, which gives the
Cyanobacteria their name.
b. Reddish pigment phycoerythrin, which gives the red algae
their common name.
When a photon of light strikes a photosynthetic pigment, an
electron in an atom contained within
the molecule becomes excited.
Energized electrons move further from the nucleus of the atom.
The excited (energized) molecule can pass the energy to another
molecule or release it
in the form of light or heat.
Without photosynthesis our atmosphere would not contain
oxygen, and
the huge diversity of life on earth would revert back to
anaerobic bacteria.

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