Biology
Exam Review
Subjects covered this session
• The science of Biology
• Biology Basics
• Branches of Biology
• Ecology
• The Biosphere
• Ecosystems and Communities
• Populations
• Cells
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Cell Structure
Photosynthesis
Cell Respiration
Cell Growth and Division
• States of Matter
• DNA and RNA
The Science of Biology
• Natural Science studying life and living organisms:
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Structure
Function
Growth
Evolution
Distribution
Taxonomy
Biology
• Cell – The basic unit of life
• Genes – basic unit of heredity
• Evolution – synthesis and creation of new species
The Science of Biology
• Branches of Biology
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Biochemistry
Molecular Biology
Botany
Cellular Biology
Physiology
Evolutionary Biology
Ecology
What are the scientists called?
What are they studying?
Why are they studying this?
Biochemistry
• Biochemistry, sometimes called biological chemistry, is the study of chemical
processes within and relating to living organisms.
• Today, the main focus of pure biochemistry is in understanding how biological
molecules give rise to the processes that occur within living cells, which in turn
relates greatly to the study and understanding of whole organisms.
• Much of biochemistry deals with the structures, functions and interactions of
biological macromolecules, such as proteins, nucleic acids, carbohydrates and
lipids, which provide the structure of cells and perform many of the functions
associated with life. The chemistry of the cell also depends on the reactions of
smaller molecules and ions. These can be inorganic, for example water and metal
ions, or organic, for example the amino acids which are used to synthesize
proteins.
• The findings of biochemistry are applied primarily in medicine, nutrition, and
agriculture.
Molecular Biology
• Study of the molecular basis of biological activity between the various
systems of a cell, including the interactions between the different types of
DNA, RNA and proteins and their biosynthesis, and studies how these
interactions are regulated.
• Studies the processes of replication, transcription, translation, and cell
function. The central dogma of molecular biology where genetic material is
transcribed into RNA and then translated into protein,.
• Much of the work in molecular biology is quantitative, and recently much
work has been done at the interface of molecular biology and computer
science in bioinformatics and computational biology.
• As of the early 2000s, the study of gene structure and function, molecular
genetics, has been among the most prominent sub-field of molecular
biology.
Botany
• Also called plant science(s) or plant biology, is the science of plant life and a branch of biology.
• A botanist or plant scientist is a scientist who specializes in this field of study.
• Traditionally, botany has also included the study of fungi and algae by mycologists and phycologists
respectively. Nowadays, botanists study approximately 400,000 species of living organisms[4] of which some
260,000 species are vascular plants and about 248,000 are flowering plants.
• Botany originated in prehistory as herbalism with the efforts of early humans to identify – and later cultivate
– edible, medicinal and poisonous plants, making it one of the oldest branches of science.
• Efforts to catalogue and describe their collections were the beginnings of plant taxonomy, and led in 1753 to
the binomial system of Carl Linnaeus that remains in use to this day.
• In the 19th and 20th centuries, new techniques were developed for the study of plants, including methods
of optical microscopy and live cell imaging, electron microscopy, analysis of chromosome number, plant
chemistry and the structure and function of enzymes and other proteins. In the last two decades of the 20th
century, botanists exploited the techniques of molecular genetic analysis, including genomics and
proteomics and DNA sequences to classify plants more accurately.
• Botanical research has diverse applications in providing staple foods and textiles, in modern horticulture,
agriculture and forestry, plant propagation, breeding and genetic modification, in the synthesis of chemicals
and raw materials for construction and energy production, in environmental management, and the
maintenance of biodiversity.
Cellular Biology
• Cell biology - formerly called cytologiy and otherwise known as molecular
or cell biology, is a branch of biology that studies the different structures
and functions of the cell and focuses mainly on the idea of the cell as the
basic unit of life.
• Cell biology explains the structure, organization of the organelles they
contain, their physiological properties, metabolic processes, signaling
pathways, life cycle, and interactions with their environment. This is done
both on a microscopic and molecular level as it encompasses prokaryotic
cells and eukaryotic cells.
• Knowing the components of cells and how cells work is fundamental to all
biological sciences it is also essential for research in bio-medical fields such
as cancer, and other diseases. , research in cell biology is closely related to
genetics, biochemistry, molecular biology, immunology, and developmental
biology.
Physiology
• Physiology is the scientific study of the normal function in living systems.
• A sub-discipline of biology, its focus is in how organisms, organ systems,
organs, cells, and bio-molecules carry out the chemical or physical
functions that exist in a living system.
• Given the size of the field it is divided into, among others, animal
physiology (including that of humans), plant physiology, cellular physiology,
microbial physiology, bacterial physiology, and viral physiology.
• In medicine, a physiologic state is one occurring from normal body
function, rather than pathologically, which is centered on the abnormalities
that occur in animal diseases, including humans.
Evolutionary Biology
• Evolutionary biology is a subfield of biology concerned with the study
of the evolutionary processes that produced the diversity of life on
Earth.
• Someone who studies evolutionary biology is known as an
evolutionary biologist.
• Evolutionary biologists study the descent of species, and the origin of
new species.
Ecology
• The scientific analysis and study of interactions among organisms and their
environment. It is an interdisciplinary field that includes biology and Earth
science. Ecology includes the study of interactions organisms have with
each other, other organisms, and with abiotic components of their
environment.
• Ecologists seek to explain:
• Life processes, interactions and adaptations
• The movement of materials and energy through living communities
• The successional development of ecosystems
• The abundance and distribution of organisms and biodiversity in the
context of the environment.
Biosphere
• Global sum of all ecosystems
• Closed system that self regulates
Biome
• Formation of plants and
animals that have
common characteristics
due to similar climates
and can be found over a
range of continents.
• Biomes are distinct from
habitats, because any
biome can be comprised
of a variety of habitats.
Ecosystems
• Each ecosystem is made up of the following parts
• Producers – Make their own food (energy)
• Plants
• Small organisms
• Consumers – Cannot make their own food.
• Primary Consumers - Eat Producers (Herbivores)
• Secondary Consumers – Eat primary Consumers and / or Producers (carnivores,
omnivores)
• Decomposers – Break down dead or decaying organisms
• Bacteria, Fungi, Earthworms
Food Chain
• Direct line from plant (bottom) to largest or most advance (top) entity
in an ecosystem.
Food Web
• Lines go in several
directions
• Connected food chains
• Shows everything
within an ecosystem
and what it eats or
what eats it
Populations
• Group of organisms, which live in a particular area and can interbreed
• Interbreeding is generally more common than cross-breeding with
individuals from other areas
• Populations are affected by Environmental Impacts
• Wars
• Drops in childbirths, production of products and crops
• Baby booms
• Diseases
• Water, Crop, or food product issues
• Natural Disasters
Cell Structure
Plant
Cell
Animal
Cell
Photosynthesis
• What three things are reactants (are used) in the photosynthetic
process?
• sunlight, carbon dioxide, and water
• What two substances are products (get made) in the photosynthetic
process?
• oxygen and glucose
Photosynthesis
• There are two phases in photosynthesis.
• light-dependent reactions
• the Calvin cycle
• The Calvin cycle is the principal mechanism that leads to the conversion of carbon dioxide into sugars by
plants, algae, photosynthetic bacteria, and certain other bacteria that use chemicals as an energy source
instead of light.
The Calvin cycle, also known as the Calvin Benson cycle, is an integral part of the process of
photosynthesis in plants, algae, and photosynthetic bacteria. Named after its discoverer, Melvin Calvin of
the University of California at Berkeley, its principal product is a three-carbon compound called
glyceraldehyde 3-phosphate, or PGAL. Sugars are synthesized using PGAL as a starting material.
Light, absorbed by chlorophyll, is used to synthesize the high-energy compounds adenosine triphosphate
(ATP) and reduced nicotinamide adenine dinucleotide phosphate (NADPH). Chlorophyll and the enzymes
that are used for synthesis of ATP and NADPH are associated with internal membranes in all
photosynthetic cells.
The ATP and NADPH, once formed, are released from the membrane-bound enzymes and diffuse into
the surrounding solution inside the cell. The Calvin cycle takes place in this solution, using the ATP and
NADPH molecules as a source of energy to drive the conversion of carbon dioxide into PGAL.
Calvin Cycle
Photosynthesis
• The light-dependent
reactions use
sunlight energy and
water. The water is
obtained through the
roots. (Reminder:
water enters through
the roots, and travels
through the xylem to
the rest of the plant)
• Xylem - The basic
function of xylem is
to transport water,
but it also transports
some nutrients.
Photosynthesis
• The light-dependent reactions produce oxygen and energy. The
oxygen leaves the leaf through the stomata.
• Stomata - The stomata are pores in leaves. They are responsible for gas
exchange. Carbon dioxide enters through the stomata.
• The light-dependent reactions happen in the thylakoids of the
chloroplast.
• The thylakoid membranes of a chloroplast is an internal system of
interconnected membranes, that carry out the light reactions of
photosynthesis. They are arranged into stacked and unstacked regions called
grana and stroma thylakoids, respectively
Photosynthesis
• The Calvin cycle uses the energy from the light reactions, as well as
the input of carbon dioxide The big product of following the Calvin
cycle is glucose, which has the chemical formula C6H12O6.
• The Calvin cycle happens in the stroma of the chloroplast.
• This is the complete balanced equation for photosynthesis.
• 6 COs + 6 H2O + energy  C6H12O6 + 6 O2
• carbon dioxide + water + sunlight  glucose + oxygen
Photosynthesis
• What is the primary pigment responsible for absorbing the light
energy for photosynthesis?
• chlorophyll is the primary pigment
• Why do most plants appear green?
• Chlorophyll reflects green light, and absorb other colors like red, blue, and
violet. We see what is reflected from objects.
• Chlorophyll is contained in disc-shaped structures in the chloroplasts
called thylakoids. A stack of these discs is called a granum.
Photosynthesis
Photosynthesis
• Gas exchange is necessary for photosynthesis. How does carbon
dioxide gas get in and oxygen gas get out of the leaves?
• The gases move in an out through the stomata, which are tiny holes on the
bottom side of leaves.
• What layers of cells in the leaf perform photosynthesis?
• the mesophyll layers – palisade mesophyll and spongy mesophyll
Cellular Respiration
• Cellular respiration is the set of metabolic reactions and processes that take place in the cells of
organisms to convert biochemical energy from nutrients into adenosine triphosphate (ATP), and
then release waste products. The reactions involved in respiration are catabolic reactions, which
break large molecules into smaller ones, releasing energy in the process, as weak so-called "highenergy" bonds are replaced by stronger bonds in the products. Respiration is one of the key ways
a cell gains useful energy to fuel cellular activity. Cellular respiration is considered an exothermic
redox reaction which releases heat. The overall reaction occurs in a series of biochemical steps,
most of which are redox reactions themselves. Although technically, cellular respiration is a
combustion reaction, it clearly does not resemble one when it occurs in a living cell due to slow
release of energy from the series of reactions.
• Nutrients that are commonly used by animal and plant cells in respiration include sugar, amino
acids and fatty acids, and the most common oxidizing agent (electron acceptor) is molecular
oxygen (O2). The chemical energy stored in ATP (its third phosphate group is weakly bonded to
the rest of the molecule and is cheaply broken allowing stronger bonds to form, thereby
transferring energy for use by the cell) can then be used to drive processes requiring energy,
including biosynthesis, locomotion or transportation of molecules across cell membranes.
States of Matter
Gas
Evaporation
Sublimation
Solid
Condensation
Liquid
Melting
Freezing
DNA and Genes
What is DNA?
• Our genes are located on
chromosomes.
• Chromosomes are made
of DNA deoxyribonucleic acid.
• DNA contains the
instructions for making
proteins.
Structure of DNA
• DNA is a long
polymer of repeating
subunits called
nucleotides.
• Nucleotides –
deoxyribose (sugar),
phosphate group, and
a nitrogen base.
• Four possible
nitrogen bases:
adenine (A), guanine
(G), cytosine (C),
thymine (T).
The Four Bases
– The four bases can be
broken down into two
groups:
– Pyrimidines
• Thymine
• Cytosine
– Purines
• Adenine
• Guanine
Structure of DNA cont.
• Nucleotides join together to
form long chains, with the
phosphate group of one
bonding to the sugar of the
next.
• Backbone – sugar and
phosphate groups
• Middle (rungs) – base pairs
held together by hydrogen
bonds
Structure of DNA cont.
• Adenine always pairs
with thymine.
• Cytosine always
pairs with guanine.
• Two chains of DNA
join together to form
a double helix
(twisted ladder).
Discovering DNA’s Structure
• Chargaff
determined basepairing in 1949.
• Franklin & Wilkins
discovered helical
structure in 1952.
• Watson & Crick
built first 3-D
model in 1953.
Base Pairing
– Ex: ATTGCTATCGGCA
TAACGATAGCCGT
• Try writing a match for the following
strand:
GTACGCTAGCTAGCT
_ _ _ __ __ _ _ _ __ _ _ _
The answer:
GTACGCTAGCTAGCT
CATGCGATCGATCGA
Nucleotide Sequence
• All organisms contain DNA made of
nucleotides with the same four bases.
• Differences between organisms come
from the sequence of the four bases
along the DNA strand.
• Nucleotide sequence is the unique
genetic information of an organism.
• The closer the relationship between
two organisms, the greater the
similarity in their DNA.
Replication of DNA
• DNA Replication – process that copies the
DNA in the chromosomes.
• Occurs during interphase, before cell
division.
• Each single strand of DNA serves as a
template to reconstruct the other strand.
How DNA Replicates
• Hydrogen bonds between bases are
broken and the DNA molecule is
unwound and “unzipped” by DNA
helicase.
• Free nucleotides bond to the exposed
single strands by base pairing and are
linked together by DNA polymerase.
• This continues until the whole molecule
has been unzipped and replicated.
How DNA Replicates cont.
• Each new DNA molecule formed contains
one parent strand and one newly synthesized
strand.
RNA
• RNA – ribonucleic acid
• Three major differences between
RNA and DNA:
- RNA is a single strand
- RNA’s sugar is ribose
- RNA contains the base uracil
(U) instead of thymine (T)
RNA vs DNA
RNA cont.
• RNA molecules are responsible
for protein synthesis.
• There are three types of RNA:
- Messenger RNA (mRNA)
- Ribosomal RNA (rRNA)
- Transfer RNA (tRNA)
Central Dogma
• In order to make protein, DNA must be
transcribed into mRNA.
• mRNA leaves the nucleus and is
translated into protein in the cytoplasm.
Transcription
• First the DNA “unzips”, just like during
replication.
• Free RNA nucleotides match up with the
exposed DNA nucleotides by base
pairing. (A – U, G – C)
• The completed mRNA molecule breaks
away and the DNA molecule “zips” back
together.
• mRNA can leave the nucleus, carrying
instructions to the cytoplasm.
• Transcription Animation
RNA Genetic Code
• mRNA carries the
instructions for building a
protein.
• Instructions are written in
three-letter words called
codons.
• Each codon stands for
one of twenty amino acids.
• Proteins are chains of
amino acids in the order
coded on the mRNA
RNA Genetic Code
Translation
• Translation – process of converting
the information in a sequence of
nitrogen bases in mRNA into a
sequence of amino acids in a protein.
• Takes place at the ribosomes (rRNA)
in the cytoplasm.
• As the ribosome moves down the
mRNA strand, transfer RNA (tRNA)
brings in the appropriate amino acid.
Translation
Translation cont.
• Each tRNA has an
anticodon of three
nitrogen bases.
• The tRNA
anticodon matches
with a mRNA
codon.
• tRNA also carries
an amino acid to
add to the growing
protein.