All chapter notes

Chapter 1

Biology- the scientific study of life

Cells- the structural and functional units of life

There are seven characteristics of life:

1. Order- life is categorized by highly ordered structures

2. Response to the environment- All organisms respond to stimuli from their environment

3. Regulation- Organisms have mechanisms to maintain homeostasis

4. Growth and development- The DNA organisms inherit controls their pattern of growth. Organisms get bigger and change

5. Energy processing- Organisms take in energy and use it to power their activities

6. Evolutionary adaptation- Traits evolve over generations to help live their environments better

7. Reproduction- Organisms reproduce with their own kind

Homo sapiens- Wise man

Taxonomy- Branch of bio that names and classifies species

Hierarchy of life

• kingdom

• phylum

• class

• order

• family

• genus

There are five kingdoms:

1. bacteria

2. protist

3. plants

4. fungi

5. animal

There are three domains

1. Bacteria

2. Archaea

3. Eukarya includes:

   • protists

   • plants

   • fungi

   • animals

Hierarchic of organizations of life

• Organelle

• Celle

• Tissue

• Organ

• Organ system

• Organism

• Population

• Community

• Ecosystem

• Biosphere

Science- an approach to understanding the natural world

Data- the evidence that is used to base a scientific question

Hypothesis- a proposed explanation for a set of scientific questions

Experiment- a scientific test

Theory- A broader scope of hypothesis supported by a large body of evidence

Controlled experiment- an experiment where one of the experimental group is compared to a control group.

Independent variable- the factor manipulated by the researcher

Dependent variable- affected by the independent variable

Variable- any condition that may cause change in the system that is being studied

Feedback mechanisms- used by organisms to maintain or amplify chemical systems

Two types:

1. Positive feedback

   • increases stimulus

2. Negative feedback

   • Decreases stimulus

   • maintains homeostasis

Stimulus- triggers a reaction

Signal- communication usually between 2 systems

Response- how something reacts to a stimulus

Evolution- the idea that living species are descendants of ancestral species that were different from the present day ones

Natural selection- A process in which certain inherited traits are more likely to survive and reproduce than the individuals that don’t have those traits

Humans affect evolution intentionally or unintentionally

Artificial selection- the selective breeding of domesticated plants and animals to promote the occurrence of specific traits

The processes of life depend on the transmission and use of information.

Genes- A discrete unit of hereditary Information consisting of a specific nucleotide sequence in DNA

Gene expression- The process where genetic information flows from genes to make a protein

In biology structure (the shape of something) and function (what it does) are related and are used to give information about each other

The activities of life require energy

Vital parts of the ecosystem are small animals, fungi and bacteria in the soil that decomposes water.

The input and conversion of energy form one form to another make life possible

Energy flows though a system in one direction: entering as light and exiting as heat

Life depends on the interactions within different systems

System- the complex organization of the components of life.

Systems biology- An approach to studying biology that aims to model the dynamic behavior of biological systems based on a study of their interactions among their parts

Life is categorized by interconnections and interactions

Chapter 2

Matter- Anything that occupies space and has mass

Element- A substance that can’t be broken down with any ordinary chemical means

Compound- Two or more elements combined in a fixed ratio

A compounds properties are different from the elements that make it up

Trace elements- elements that are essential to life but are found in minute quantities in the human body

Atom- The smallest unit of matter that still retains properties of elements and life

Sub-atomic particles- proton, neutron, electron

Nucleus- An atom’s core or center

Proton and neutron are found inside the nucleus and electrons are found in electron shells surrounding the nucleus

Proton- positive change

Electron- negative charge

Neutron- no charge

You can tell atoms apart by their atomic number.

Atomic number- number of protons

Atomic mass- proton + neutron

Isotopes- An atom having the same number of proton but different number of neutrons

Radioactive isotope- An isotope whose nucleus decays randomly giving off particles and energy. They can be helpful in dating fossils and diagnosing diseases

Electron shell- A level of electrons characterized by their distance from the nucleus

Atoms to make their electron shell full will:

• Share electrons

• Give up electrons

• Accept electrons

Chemical bond- Atoms being held close together held by attraction

3 types of Chemical bonds:

1. Ionic bond

   • Transfer of electrons

   • attractions between oppositely charged ions

2. Covalent bond

   • Atoms sharing a pair of electrons

   • Strongest chemical bond

   • Atoms don’t always share the electrons equally

   • Can be single, double of triple bonds

     
     

Electronegativity- The measure of an atoms attraction for shared electrons

2 types of covalent bods:

A. Non-polar covalent bond- two atoms having the similar electronegativity and sharing electrons equally.

B. Polar covalent bond- two atoms having different electronegativity. causes partial charges. the atom that most of the shared electrons is partially negative while the atom the gets less of the shared electrons is partially positive.

Oxygen is one of the most electronegative elements.

Molecules- Atoms held together by covalent bonds

3. Hydrogen bonds

   • Weakest chemical bond

   • Formed between 2 individual water molecules between the partially negative region of the first molecule and the partially positive region of the second molecule

Chemical reaction- The making and breaking of chemical bonds leading to changes in the composition of matter

Reactant- The starting material in a chemical reaction

Product- The final material in a chemical reaction

Chemical reactions don’t create of destroy matter so they have to be balanced

Properties of water

• Cohesion- When a water molecule sticks to another water molecule

• Adhesion- When a water molecules sticks to other surfaces

Surface tension- The measure of how difficult it is to stretch or break the surface of a liquid. Water has high surface tension because of the hydrogen bond holding the molecules together

Water’s hydrogen bonds moderate temperature

Thermal energy- heat that comes from kinetic energy

Temperature- The measure of the average thermal energy

Heat- Thermal energy in transfer from one body of matter to another

Evaporative cooling- The process when the surface becomes cooler during evaporation. A result of molecules with the greatest energy changing from liquid to gas.

Ice floats because it is less dense than water

• Water is less dense as a solid because of hydrogen bonds

• The freezing of water make the hydrogen bonds distant making it decrease in density

Water is the solvent of life

Solution- A liquid consisting of a uniform mixture of two or more substances

Solvent- The dissolving agent is the solvent

Solute- substance that is dissolved is a solute

Aqueous solution- Aqueous solution is one in which water is the solvent.

In aqueous solutions some water will break into ions. those ions are the hydrogen ion(H+) and hydroxide ion(OH-).

The chemistry of life is sensitive to acidic and basic conditions

Acid-A substance that releases hydrogen ions to solutions. From 0-6.9 on the PH scale

Base-A substance that releases hydroxide ions to solutions. From 7.1-14 on the PH scale

PH scale-Used to describe how acidic or basic a solution is

PH scale increases by 10 at every level

Bluffers-chemical substances that minimize changes in pH

Chapter 20

An animals structure isn’t perfect, its just good enough to function

A structure of an ancestral organism can be modified to function in a descendant organism

Structure fits function at all levels of organization

Anatomy - The study of the form of an organism’s structure

Physiology - The study of the functions of those structures

Hierarchy of life

1. Cells - building block of life

2. Tissues - a group of cells that serve a similar functions

3. Organ - made up of 2 or more tissues to perform a specific task

4. Organ System - made up of multiple organs to perform on or more vital body function

5. Organism - made up of multiple organ systems each for different tasks

Types of tissues

Epithelial tissues - closely packed cells that cover organs and cavities

Helps as a protective barrier, secretion, exchanging materials and nutrient absorbtion

One side is attached to a dense mat of protein and the other side is what faces the outside and is aka Apical surface

They are organized by their cell shape and size

Ex: skin, tube in kidney, blood vessels, lining in intestines

Connective tissues - sparse population of cells scattered throughout a matrix

Form the framework of the bods, bind and support other tissues

Ex: blood, cartilage, bone

Muscle tissues - made up of long cells known as muscle fibers

Help with movement

Ex: skeletal muscle, cardiac muscle, smooth muscle

Nervous tissues - senses stimuli and rapidly transmits info

Also transits biological information

Main unit of the nervous tissue is the Neuron which is a tissue that is uniquely specialized to conduct electrical impulses

Ex: brain, spinal cord, nerves

Chapter 30

Respiratory and Circulatory Functions

Circulatory system - Heart and three types of blood vessels, arteries, veins and capillaries, Transportation network for blood

Circulation is maintained in the veins by the activity of skeletal muscles

Heart - A muscular pump that keeps blood moving to every part of the body

Arteries

• Strong and flexible blood vessels that carry blood away from the heart to the rest of the body

• Carry O2 rich blood

• Smaller arteries (arterioles) connect arteries to capillaries

Veins

• Larger diameter and thinner wall

• Blood vessels that carry blood from the rest of the body to the heart

• Carry O2 poor blood

• Has valves to prevent blood from flowing backwards

• Smaller veins (venues) connect the veins to capillaries

Capillaries

• A system that connects arteries and veins

• Only one cell thick

• Easy for materials to diffuse into and out of them

Main function of Circulatory system

• Transport blood and other materials

• Bring supplies to cells

• Carry cell’s waste

• Keep O2 poor blood and O2 rich blood from mixing

• Maintain body temperature by distributing/ conserving internal heat

Blood and blood pressure

Blood pressure - The measure of the force in which blood pushes against the artery wall

Systolic pressure - Measures pressure in the artery after the left ventricle has contracted, numerator

Diastolic pressure - Measures pressure after the left ventricle has relaxed, denominator

Blood - made up of plasma, red blood cells, white blood cells and platelets

Plasma

• Mostly water and makes up 55% of blood

• Contains proteins, amino acids, hormones, vitamins…

• Movement of these materials helps maintain homeostasis

• Contains proteins that help stabilize blood volume and control bleeding

Red blood cells

• Transports O2 to cells and carry CO2 away from them

• Binds to Hemoglobin that gives it its reddish color

• Has protein markers that defines a persons blood type and rh factor

It is Important to know a person’s blood type and rh factor because if it isn’t the correct blood type the white blood cells will attack it which will cause the blood to clump

White blood cells

• Defend the body against infections

• Remove foreign materials and dead cells

• Don’t contain hemoglobin

• They are not limited to the circulatory system

• Are considered part of the immune system

Platelets

• Cell fragments that help control bleeding

• Form a net around an injury and release clotting factors to stop bleeding and create a seal around a wound

• Hemophilia- a genetic disorder, inability to create clotting factors

Circulatory diseases

They mainly affect the heart and arteries

Arteriosclerosis - Artery walls become thick and inflexive

Atherosclerosis - Blood flow is partially or fully blocked by plaque that is collected on the walls of arteries

Both diseases can lead to a stroke, heart attack or kidney damage

Hypertension - Permanently high blood pressure

Respiratory system - Nose/Mouth | trachea | bronchi | bronchioles | alveoli

Mechanics of Breathing - muscles of the ribcage and diaphragm

Inhale - low pressure in the lungs | diaphragm flattens and moves downward

Exhale - high pressure in the lungs | diaphragm relaxes and rises

Main function of Respiratory system

• Exchange gases

• Bring O2 into the body

• Expel CO2 and water vapor

Both systems work together to maintain homeostasis

Main goal - increase surface area for gas exchange

Gas exchange

Alveoli and capillary is the only place where gas exchange with the atmosphere takes place.

Gas exchange of the lungs have three principles

• O2 and CO2 are carried by the lungs

• Gas moves by diffusion | from high to low concentration

• Lining of the alveoli must be moist to her gasses diffuse

Capillaries surround alveoli

1. Blood in the capillaries have lower concentration of O2 compared to alveoli so O2 diffuses from the alveoli to the capillaries and binds with Hemoglobin

The blood in capillaries contain Red blood cells, a type of cells that picks up O2 from the lungs to the body cells

The O2 molecules in red blood cells bind to Hemoglobin, an iron rich protein that gives blood it’s reddish color

2. CO2 concentration in the blood is higher compared to alveoli so CO2 diffuses from capillaries to the alveoli

CO2 is expelled from the body with some water vapor

Gas exchange and the nervous system

Gas exchange is an automatic function regulated by the brainstem

These centers monitor dissolved gasses in the blood especially CO2 concentration

When u exercise the CO2 concentration increase which makes the blood acidic which makes sensors in the respiratory and circulatory system send signals to the brainstem

The brainstem send signals to stimulate the diaphragm and rib cage muscles to work harder

Respiratory Diseases

Damage to the respiratory system makes gas exchange more difficult

Emphysema

• Caused mainly by smoking

• Destroys the alveoli and reduces surface area for gas exchange

• Has no cure

Asthma

• Causes bronchioles to constrict due to muscle spasms

• Makes it hard to move air in and out the lungs

• Can be relieved by taking medicine

Cystic fibrosis

• Genetic disease that causes the lungs to produce mucus

• Mucus blocks airways and allows microorganisms to thrive in lungs

• Causes lung infections

• Treatment does exist

The heart and Circulation

The hear has four chambers

Atrium - Smaller chambers, receive blood into the heart, upper half | two sides left and right

Ventricles - Larger chambers, send blood away from the heart, lower half | two sides left and right

Septum - A thick wall of tissue that separates the left and right ventricles

Valves - The heart’s flaps that prevent blood from flowing backward, opens when the atria of ventricles contract and close when they relax

Heartbeat

The first heartbeat takes place in the atria and then in the ventricle

The first contraction starts at the SA node aka the pacemaker which make the atrium contract

The signal from the SA node spreads and stimulates the AV node which makes the ventricles contact

Blood flow in the heart

1. O2 poor blood enters the right atrium which contracts and sends blood into the right ventricle

2. The right ventricle contracts and sends blood into the pulmonary artery which carries it to the lungs for gas exchange

3. O2 rich blood returns to the heart through the pulmonary vein and enters the left atrium. Atrium contracts and sends blood to left ventricle

4. Left ventricle contracts and sends blood out of the heart to the rest of the body through the aorta

Types of Circulation

1. Pulmonary circulation- occurs between the heart and lungs, its main function is to carry O2 poor blood to the lungs and O2 rich blood to the heart

2. Systematic circulation- its main function is to carry O2 rich blood to body cells and O2 poor blood back to the heart

Homeostasis is maintained by matching respiration with the O2 needs of the body.

Chapter 3

Carbon

Carbon based molecules are called Organic compounds

Carbon’s valance is 4

Valance- An atoms need for electrons to be stable

Carbon can bond to four other atoms by sharing electrons

One of the simplest organic compound is Methane

Compounds only composed of Carbon and Hydrogen are called Hydrocarbons

Carbon Skeleton- a chain of carbon atoms

Carbon skeletons can:

1. vary in length

2. be branched or unbranched

3. have double bonds

4. be arranged in rings

Isomers- compounds with the same formula but different arrangements

Polymers- forms that are made from identical building blocks

Macromolecules- another word for polymer

Monomers- building blocks of polymers

Micromolecule- another word for monomer

Dehydration synthesis- process that linked up monomers to make polymers by removing water from the joint molecules

Hydrolysis- A process that separates polymers into different monomers by adding water into the compound

Enzymes- A substance used to speed up chemical reactions

Organic compounds

All life depends on the properties and reactions of the 4 organic compounds

Carbohydrates

Monomer- Monosaccharides(simple sugar)

• Monosaccharides contain a hydroxyl group(-OH) and a carbonyl group(C=O)

• Sugars dissolve in water because the hydroxyl group forms hydrogen bonds with water

• Made up of Carbon, Hydrogen and Oxygen

• Always in a 1:2:1 ratio

• 2 monosaccharides can form disaccharides like maltose and sucrose by a dehydration synthesis

• In an aqueous solution sugars from ring like shapes

• The bond created when sugars are joined together is called a Glycosidic linkage

Food sources

1. sugar

2. bread

3. pasta

4. cereal

Function

1. instant energy

2. can be used to make cellulose and parts of the cell membrane

3. stores energy as glycogen in animals and starch in plants

Polysaccharides

• Are polymers composed of thousands of monosaccharides

• Are usually Hydrophilic (water loving)

Function

• Serve as storage molecules

• Serve as structural compounds

Examples

• Starch

• Glycogen

• Cellulose

• Chitin- used by insects to build an exoskeleton

Lipids

Monomer- Glycerol and Fatty acids

• Is hydrophobic (water fearing)

• Contains twice the amount of energy as polysaccharides

• Made up of Carbon, Hydrogen and Oxygen linked together by non polar covalent bonds

Function

• Long term energy storage

• Thermal regulation

• Cushions vital organs

Types of Lipids

1. Fats- One glycerol linked to three fatty acid chains by dehydration synthesis

   • They are often called Triglycerides because of their structure

   • The bond between fatty acids and glycerol is called an Ester Bond

   • Fatty Acids- Can be Saturated or Unsaturated

   • Saturated- Dripping wet with hydrogen

     No carbon carbon (C=C) bond

     Solid in room temperature

     Mostly animal fat like butter and red meat

     Bad for a person’s health

   • Unsaturated- Forms a kink from its carbon carbon (C=C) bond

     Liquid in room temperature

     Mostly plant fat like corn and olive oils

     Good for a person’s health

   • An unsaturated fat can be turned into a solid or semisolid by Hydrogenation

   • Hydrogenation creates Trans fats which are associated with health risks

2. Phospholipids- One glycerol attached to two fatty acid chains. The Glycerol is attached to a phosphate group.

   • The phosphate group and glycerol make up the Hydrophilic heads

   • The fatty acid chains make up the Hydrophobic tails

   • Phospholipids cluster into a bilayer of phospholipids

   • The hydrophilic heads are in contact with the water of the environment and the hydrophobic tails are in the center of the bilayer

3. Steroids- Lipids where the carbon skeleton contains four fused rings

   • Makes up our hormones

4. Cholesterol- A common component in animal cell membranes

5. Anabolic steroids- Synthetic variations s of testosterone that can cause buildup of muscle and bone mass.

   • Often prescribed to treat anemia

   • Abused by some athletes

   • Consequences include: violent mood swings, depression, liver damage, cancer etc

Protein

Monomer- Amino acids

• Contains Carbon, Hydrogen, Oxygen and Nitrogen

• Are involved in every dynamic function in our body

• Amino Acids

  • Made up of - an animo group(H-N-H)

    - a carboxyl group(O=C-OH). It makes amino acids acid

    - A central carbon that is bonded to hydrogen and the R group

  • Amino acids always have an N-C-C structure

  • The R group gives amino acid its chemical properties

  • Amino acids are classified as either hydrophobic or hydrophilic

  • When two amino acids are being bonded the carboxyl group of one amino acid joins the animo group of the other amino acid form bonds known as Peptide bonds

  • More amino acids can be added to create a chain of Polypeptides

  • Dipeptide- two amino acids bonded by dehydration synthesis

• The shape of a protein determines its function

• The shape of a protein is caused by the amino acid sequence

• If a shape of a protein is altered, it can no longer function

• Denaturation- a process where a protein

  • unravels

  • loses its shape and

  • loses its function

• Proteins can be denatured by:

  • Changes in salt concentration

  • Changes in PH

  • High heat

Function

• Acts as an enzyme

• Include antibodies of the immune system

• Transmit signals to cells

• Serve as a source of amino acids for developing embryos

Nucleic Acid

Monomer- Nucleotide

• Consists of Carbon, Hydrogen, Oxygen, Nitrogen and Phosphorus

• Nucleotides- have three parts

  1. Sugar

  2. Phosphate group

  3. Nitrogen base

  • Nucleotides are the monomers of DNA and RNA

• A nucleic acid polymer aka polynucleotide is formed by the dehydration synthesis that bonds the phosphate group of one nucleotide to the sugar of the next nucleotide.

• This bond creates a sugar-phosphate backbone with protruding nitrogen bases

Function

• store genetic Information

• transmit genetic information

An amino acid sequence of polypeptides are programmed by a unit of inheritance called Genes

Genes- consists of DNA that is inherited from an organism’s parents

DNA

• Provides directions for its own replication

• programs a cell’s activities by directing proteins

• DNA doesn’t build proteins directly

• DNA→RNA→Protein

• In DNA, the sugar that makes up the nucleotide is a five carbon sugar called deoxyribose

• DNA’s nitrogen bases are

  1. A

  2. T

  3. C

  4. G

• A→T

• C→G

• The letters in DNA that go together are called Base pairs

• Two strands of polynucleotides that form a double helix

RNA

• A single polynucleotide strand

• In RNA, the sugar that makes up the nucleotide is a five carbon sugar called ribose

• RNA’s nitrogen base has

  1. A

  2. C

  3. G

  4. U

Chapter 4

Cell- is the simplest collection of matter that is alive

They were first observed by Robert Hooke in 1665

Microscopes were developed for a clearer view of cells and cellular structures

There are 2 major types

Light microscopes

• most frequently used microscopes

• can magnify up to 100x

• can’t provide the details of a small cell’s structure

• can’t show organelles other than the nucleus

• Is safer and keeps cells alive

Electron microscope

• uses a beam of electrons

• used to view the ultra structure of cells

• can magnify up to 100,000 times

• Cells are dead

• 2 types

  1. Scanning electron microscope- used to scan and study cell surface

  2. Transmission electron microscope- used to study internal cell structure

Magnification- The increase in the size of an object

Resolution- The measure of the clarity of an image

Cell theory

• all living cells are composed of cells

• all cells come from other cells

• refutes the concept of spontaneous generation- life force in the air

Measurements

Most organelles are between 10-100nm

The external differences between eukaryotic and prokaryotic cells can be seen between 1-100µm

Cells must be able to

• be large enough to hold DNA, protein and other structures

• be small enough to allow a surface to volume ratio that allows enough exchange with the environment

* The smaller the cell the faster the rate of osmosis will be

Volume = (l)(w)(h)

Surface area = (l)(w)(number of sides)

Plasma membrane- forms a flexible boundary between a cell and its surrounding

Phospholipids form a two layer sheet called a Phospholipid bilayer that has:

• hydrophilic heads that are exposed to the environment

• hydrophobic tails that are inward shielded from water

The duality between the heads and tails controls what goes in and out

Membrane proteins- are either

• attached to the membrane surface

• embedded in the phospholipid bilayer

• There are two types

  1. Passive transport- tunnels that shield ions and other hydrophilic molecules as they pass through the center of the bilayer

  2. Active transport- serve as pumps that use energy to actively transport molecules in and out of the cell

Active and Passive Transport: Red Rover Send Particles Over ...

There are two types of cells

1. Prokaryotic

   • No nucleus

   • Bacteria and Archaea

   • No true organelles

   • No membrane bound organelles

   • No mitochondria

   • Has a plasma membrane

   • Has ribosome

   • Has DNA chromosomes in the Nucleoid

   • The surface of prokaryotic cells may

     • be surrounded by a cell wall

     • have a capsule surrounding the cell wall

     • Have short projections called Fimbriae that help attach it to other cells

     • Have longer projections called Flagella that help the cell move efficiently

2. Eukaryotic cells

   • Has a nucleus

   • Plant, Animal, Fungi and Protista

   • Has membrane bond organelles

   • Has a mitochondria

   • Has a plasma membrane

   • Has a ribosome

   • Has DNA in the Nucleus

The structure of the organelles in eukaryotic cells have four basic functions

1. Genetic control and reproduction

2. Manufacture, distribution and breakdown of molecules

3. Energy processing

4. Structural support

The internal membranes of eukaryotic cells partition into compartments

Cellular metabolism- The many chemical activities of cells, occurs within organelles

Differences between plant and animal cells

• Animal cells have lysosomes and plant cells don’t

• Animal cells have centrioles and animal cells don’t

• Plant cells have a mitochondria and chloroplast but animal cells only have a mitochondria

• Plant cells have a rigid cell walls and animal cells don’t

• Plant cells have chloroplast and animal cells don’t

• Plant cells have a central vacuole and animal cells don’t

Organelles and their functions

Nucleus

• DNA replication

• RNA synthesis

• Assembly of ribosomal subunits

Ribosomes

• Protein synthesis

Rough ER

• Lipid and protein synthesis

• Synthesis of secretory proteins

• Synthesis of hydrolytic enzymes

• Formation of transport vesicles

Smooth ER

• Lipid synthesis

• Detoxification(in liver cells)

• Calcium ion storage(in muscle cells)

Golgi apparatus

• Modification and sorting of ER products

• Formation of lysosomes and transport vesicles

Lysosomes

(found in some protists and animal cells)

• Digestion of ingested foods

• Recycling of a cell’s damaged organelles

Vacuoles

• Storage of food

• Storage of waste products for removal

Peroxisomes

• Detoxify alcohol(in liver cells)

• Cholesterol synthesis

• Breakdown hydrogen peroxide

Mitochondria

• Conversion of chemical energy from food to the chemical energy of ATP (Cellular respiration)

Chloroplast

• Conversion of light energy to the chemical energy of sugars (Photosynthesis)

Cytoskeleton

(microfilaments, intermediate filaments and microtubules)

• Maintenance of cell shape

• Supports plasma membrane and other organelles

• Helps in cell movement ex: movement of the cilia and flagella

Plasma membrane(Cell membrane)

• Regulate what goes in and out of the cell

Extracellular matrix(animal only)

• Support and regulate cellular activities

Cell junctions

• Help in communication between cell

• Helps in binding of cells in tissues

Cell wall(plant only)

• Support and protect cells

• Helps in binding of cells in tissues

*In-depth descriptions of organelles

*The Nucleus, it’s parts and the Ribosome can be grouped as the Genetic control group

Nucleus

• It contains most of the cell’s DNA

• Controls cellular activities

• Also known as “the cell’s genetic control center”

• Directs protein synthesis by making mRNA(Messenger RNA)

Chromosomes- Protein structures associated with DNA

Nuclear envelope-

• Double membrane

• Has pores to let materials flow in and out the nucleus

• Attached to the Endoplasmic Reticulum(ER)

Chromatin-

• Mixture of DNA and proteins

• Used to package DNA into small capsules so that it fits in the nucleus

Nucleolus-

• An important structure in the nucleus

• The place where ribosomal (rRNA) synthesis takes place

Ribosomes

• Involved in protein synthesis

• Synthesized from rRNA produced in the nucleolus

• Large amount of protein synthesis = large number of proteins

• There are two types

  1. Free ribosomes

     • Suspended in the cytoplasm

     • Involved in making proteins that function within the cytoplasm

  2. Bound ribosomes

     • Attached to the ER

     • Associated with the nuclear envelope

     • Associated with proteins packed in organelle or exported form the cell

Cytoplasm- A liquid found in cells that is bound by the cell membrane and made up of water, enzymes, organelles and salts.

The Endocrine System

• Most of Eukaryotic cell’s organelles are a part of the endocrine system

• All the organelles are made up of a phospholipid bilayer

• Some of them are physical connected and others are related by the transfer of membrane segments by vesicles

• Many of these organelles work together in the synthesis, storage and export of molecules

• Includes:

  • Nuclear Envelope

  • Endoplasmic reticulum (ER)

  • Golgi apparatus

  • Lysosomes

  • Vacuoles

  • Plasma membrane

Vesicle- small sacs that are made of membrane

Endoplasmic Reticulum(ER)

• Two types:

  1. Smooth ER:

     • Lacks attached ribosomes

     • Produces enzymes important in lipid, oil, phospholipid and steroid synthesis

     • Produces enzymes that process drugs and alcohol

     • Helps store calcium ions

  2. Rough ER:

     • Has ribosomes attached to it

     • Site of protein synthesis

     • Lines the outer layer of membranes

     • Produces additional membranes for itself

     • Produces proteins used for secretion

     • Functions in protein folding, sorting and transporting to their destinations

• Smooth and Rough ER are physically connected

Golgi apparatus

• Functions as the finishing factory for products made in the ER

• Products travel From the ER to the Golgi apparatus through vesicles

• One side of the Golgi apparatus acts as a receiver and the other as a sender

• Products are modified as they go from one side to the other then they travel through vesicles to other sites

Lysosomes

• The digestive compartments within a cell

• Enzymes and membranes are produced in the ER→ goes to the Golgi apparatus for further processing→ lysosomes separate the Important enzymes from the rest of the cell

• Help digest food engulfed by the cell

  • Food vacuole binds with lysosome→ Enzymes in lysosome digests it→ nutrients are released into cell(cytosol)

• Help remove or recycle damaged parts of a cell

  • Damaged organelle gets enclosed in a vesicle→ lysosome fuses with the vesicle→ lysosome dismantles its content and breaks it down

Lysosomal Storage Disease

Taysach disease

• Lysosomal disorder

• Can be inherited

• Leads to non functioning lysosomes

• Often seen in infants

• Unavoidable death

Vacuoles

• Large vesicles that vary in function

• Function in protists → Eliminate water from protist

• Function in plants → Digestive function, contain pigment, contain poisons that protect the plant

• The function of vacuoles can be generalized as food and waste storage

Energy converting group

Mitochondria

• Carry out cellular respiration in eukaryotic cells

• Has two internal compartments

  1. Inter-membrane space- The narrow region between the inner and outer membranes

  2. Mitochondrial matrix-

     • Contains the DNA of the mitochondria

     • Contains ribosomes

     • Contains enzymes that catalyze some of the reactions in cellular respiration

• Has Cristae- The folds in the inner- membrane

Cellular respiration- Conversion of the chemical energy from foods to the chemical energy of ATP

Chloroplast

• Photosynthesizing organelles in all photosynthesizing eukaryotes

• Portioned into compartments

  • Thin inter-membrane space between the outer and inner membrane

  • Inside the Inner-membrane there is:

    • Stroma- A thick fluid that contains chloroplast DNA, ribosomes and many enzymes

    • Thylakoids- A network of connected sacs

    • Granum- A stack of connected thylakoids, the place where chlorophyll molecules trap solar energy

Endosymbiosis-

The mitochondria and chloroplast have DNA and ribosomes unlike the other organelles

The Structure of the DNA and ribosomes are very similar to that of prokaryotic cells

Endosymbiosis means one prokaryote being engulfed by another prokaryote for the mutual benefit of both prokaryotes

Endosymbiont theory- A theory that states that Mitochondria and chloroplast were once small prokaryotes and that they began living in larger cells

Cytoskeleton group

Cytoskeleton- A network of protein fibers that function in structural support and movement

Movement and cellular regulation result in the cytoskeleton interacting with proteins Called Motor proteins

Cytoskeleton is composed of three kinds of fibers

1. Microfilament- Support the cells shape and are involved in movement

2. Intermediate filament- Reinforce that cells shape and anchors organelles

3. Microtubules- Provide the inability the cell to be bent or forced out of shape and serve as tacks in organelle movement

Cilia and Flagella

• Protists have a flagella and cilia that are important in movement but other multicellular organisms have them of different reasons

• Cells that sweep mucus of of the lung have cilia

• Animal sperms have a flagella

• Flagellum are longer than cilia and move in a whiplike motion

• Cilia moves in rowing motion

• Both cilia and flagella are made of microtubules that are wrapped in an extension of the plasma membrane

• A ring of nine microtubule doubles surround the central pair of microtubules in a 9+2 pattern

• Both cilia and flagella move by bending motor proteins called Dynein feet

  • The feet attach and exert a sliding force on an adjacent doublet

  • The arms then releases and reattach a little further along and the process is repeated

  • This causes the microtubules to bend

Extracellular matrix(only in animal cells)

• Helps hold tissued together

• Protect and support the plasma membrane

• It is attached to a cell through intergrins- glycoproteins that bind to membrane proteins

• Intergins span the plasma membrane and connect to the microfilaments of the cytoskeleton

Cell junctions

• Helps adjacent cells communicate and interact

• Three types(only in animal cells)

  1. Tight junctions- Prevent leakage of extracellular fluid across a layer of epithelial cells

  2. Anchoring junctions- Fastens cells together into sheets

  3. Gap junctions- Channels that allow molecules to flow between cells

• Plasmodesmata(only in plant cells)- Serves in communication between plant cells

Cell wall(only in plant cells)

• Protects and provides skeletal support

• Keeps the cell upright against gravity

• Primarily composed of cellulose

Chapter 5

Bioluminescence- the process where organisms use energy converting reactions to produce light

Used by marine animals to hide from predators

Many of the cell’s reactions take place in the organelles and use membrane embedded in the membranes of these organelles

5.1

The cell membrane is constructed in a structure called fluid mosaic

The cell membrane is called a fluid mosaic because its components float in a cytoplasmic fluid

Membranes are made of:

• A phospholipid bilayer

• Proteins

  • Glycoprotein

  • Transport protein

    • Carrier protein

    • Channel protein

  • Surface protein

• Cholesterol (embedded)

• Cytoskeleton(on the inside of the cell)

• Extra cellular matrix(on the outside of the cell)

• Intercellular junction

• Lipids

Cholesterol

In animal cell membranes they help:

• Stabilize membranes at warmer temperatures

• keep the membrane fluid at a lower temperatures

Proteins

Membrane proteins have many functions like

1. Help maintain cell shape and coordinate changes inside and outside the cell

2. Act as receptors for chemical messages from other cells

3. Function as enzymes

4. Help in cell-cell recognition, ie glycoproteins

5. Help in intercellular junctions that attach adjacent cells together

6. Transport molecules in and out of the cell

Glycoprotein

In membranes they are used to:

• Cell-cell recognition- recognize other cells as familiar or foreign

• Cell adhesion- help cells attach to other cells

Surface proteins

• function in communication between a cell and its environment

Membranes are selectively permeable- allow some substances to cross more easily that others

5.2

Phospholipids

Are made up of:

• A polar phosphate head

• 2 non-polar fatty acids chains that are unsaturated and have kinks

The kinks prevent phospholipids from packing tightly together and keeps them in liquid form

Phospholipids are the key components in cell membranes

Phospholipids spontaneously self-assemble into simple membranes because of their duality

The formation of membrane enclosed collections of molecules was a critical step in the evolution of the first cells

5.3

Passive transport- transportation of molecules that doesn’t require energy.

Diffusion- the tendency for particles to move from areas of high concentration to areas of low concentration

Diffusion is a type of passive transport

Concentration gradient- the difference in concentration of a substance for one point to another

*During diffusion molecules move down their concentration gradient until they reach equilibrium

The original kinetic energy from molecule’s constant random motion causes them to diffuse

Water is one of the most important substances that crosses the cell membrane

Osmosis- the diffusion of water across a selectively permeable membrane

Osmosis is a type of passive transport

*if a membrane is permeable to water but not a solute and separates the solutions with different solute to solvent ratio

1. Water will move across the membrane and move down its concentration gradient

2. Move until the solute concentration(solute to water ratio) on both sides is equal

5.5

Tonicity- the ability of a solution to cause a cell to gain or lose water

tonicity depends on the concentration of a solute on both sides of the membrane

Types of solutions

1. Hypertonic solution- High concentration of solute. Low concentration of water.

Water needs to enter to make in isotonic

2. Isotonic solution- Equal concentration of solute and solvent. water enter and exits in the same rate.

3. Hypotonic solution- Low concentration of solute. High concentration of water.

Water needs to go out to make it isotonic

Plants and Animal cells in different types of solutions

Animal cells in an isotonic solution- cell volume stays the same cuz water molecules enter and exit in the same rate

Animal cells in a hypotonic solution- cells swell and burst lysis cuz water enters quicker than it exits

Animal cells in a hypertonic solution- cell shrivel and dies crenate cuz water exits quicker than it enters

Plant cells in an isotonic reaction- cell volume will decrease but won’t die flaccid

Plant cells in a hypotonic solution- cell will swell but not burst turgid/ normal b/c of their rigid cell wall

Plant cells in a hypertonic solution- cell will shrivel and die plasmolyze

For animal cells to survive in a hypertonic or hypotonic environment they engage in osmoregulation- the regulation of the movement of water into and out of the cell

EX: the contractile vacuole in a paramecium

Plant cells, prokaryotic cells and fungi have their own adaptation of osmoregulation:

• Hypotonic environment- the cell wall of these cells exerts pressure that prevents the cells from taking too much water and bursting

• Hypertonic environment- cells will shrivel(includes animal cells)

5.6

Molecules that can easily diffuse across the cell membrane

• hydrophobic/ non-polar substances

• small molecules like O2 and CO2

• small lipids

Molecules that don’t easily cross the cell membrane

• hydrophilic/ polar substances

• charged molecules ie ions

Facilitated diffusion- transport proteins helping move molecules that can’t diffuse easily

• It doesn’t require energy

• Relies on the concentration gradient

Transport proteins help in facilitating diffusion by:

• becoming a tunnel for ions aka Channel protein ,only transports water soluble things

• binding to the molecules and shooting them out on the other side aka Carrier protein , transports water soluble and insoluble things

In both of these situations the protein is specific to their substrate just like enzymes

*Water is polar so its diffusion thorough the membrane is slow

Aquaporin- a very rapid diffusion of water that’s made possible by a protein channel

5.7

Aquaporins were discovered by Dr. Peter Agre

His research on the Rh protein used in blood typing led to this discovery

5.8

In active transport a cell

• uses energy in the form of ATP

• moves a solute against its concentration gradient

• In active transport the transport proteins have specific solutes that they can pump

EX: the sodium potassium pump

Steps for active transport

1. Solute binds with the transport protein

2. ATP phosphorylates the protein and ATP becomes ADP

3. Protein changes shapes and shoots solute on the other side

4. Protein reverses shape and dephosphorylates

5.9

A cell has two mechanisms to move large molecules like proteins and carbs across the cell membrane

1. Exocytosis- used to export bulky molecules

   Ex: Cells exporting protein

   Steps in exocytosis

   A. Molecules inside the vesicle move towards the cell membrane

   B. The vesicle docks on the membrane

   C. The vesicle fuses with the cell membrane and releases the molecules out

2. Endocytosis- used to import substances that are useful to the cell

   Ex: A prokaryotic cell taking in a mitochondria

   Steps in endocytosis

   A. Cell membrane makes a pocket filled with fluid for the molecule to come

   B. Molecules come into the pocket and the membrane folds inwards

   C. the membranes connect forming a vesicle or vacuole then moves into the cell

Endocytosis and exocytosis are both active transports but they don’t require a protein

Endocytosis and exocytosis both change the shape of the cell membrane for a short period of time before the phospholipids come back together because of their duality

Types of Endocytosis

1. Phagocytosis- engulfement of a particle by forming a vacuole:

   • AKA cell eating

   • also used for digesting waste

2. Pinocytosis- engulfment of fluids by forming a vesicle

   • Aka cell drinking

3. Receptor-medicated endocytosis- used receptors in a receptor coated pit to interact with a specific protein and form a vesicle

5.10

Cells- small units that house chemical reactions.

Cells use chemical reactions for

• cell maintenance

• creation of cellular parts

• cell replication

A cell can’t be a cell without chemical reactions

Energy- the capacity to cause change or to perform work

There are two kinds of energy

1. Kinetic energy- the energy of motion

2. Potential energy- the energy of location or structure

   In bio potential energy is found in

   • the arrangement of atoms in molecules

   • the covalent bonds that holds molecules together

   Making and breaking these bonds release the potential energy

Heat or thermal energy- a type of kinetic energy associated with random movements of atoms or molecules

Light- a type of kinetic energy that can be harnessed from the sun and be used to power photosynthesis

Law of conservation of energy- energy can’t be created nor destroyed

Chemical energy- the potential energy(found in the covalent bonds of a molecule) that is available for release in a chemical reaction

It is the most important type of energy for living organisms to power the work of cells

Thermodynamics- the study of energy transformations that occur in a collection of matter

Scientists use the words

• System - what they study. ex: a single cell

• Surroundings- the environment of the system. ex: blood stream

Laws of thermodynamics

First law- energy in the universe is constant aka can’t be created or destroyed

Second law- energy conversions increase the disorder of the universe

Entropy- the measure of disorder or randomness

*The universe leans towards disorder

*Humans are endothermic and endergonic

Cellular respiration- The transfer of energy from the chemical energy of the food we eat and the oxygen we breathe to the chemical energy of ATP.

This reaction is very controlled and releases energy slowly

In this reaction the oxygen we breath is used as a key component

5.11

Types of chemical reactions

Exergonic-

• Releases the energy in Covalent bonds of the reactants

• Easier for cells to accomplish compared to endergonic reaction

• Downhill reaction

• Spontaneous

• EX: Burning wood, Cellular respiration, hydrolysis

• Macromolecules → Monomers

Endergonic-

• Requiere a constant input of energy

• Uphill reaction

• Not spontaneous

• EX: dehydration synthesis, protein, carb, nucleic, lipid synthesis and photosynthesis

*All chemical reactions require:

1. An enzyme

2. ATP

3. Addition or removal of water

Metabolism- The total number of an organisms chemical reaction

Metabolic pathway- A series of chemical reactions that

• Builds a complex molecule or

• Breaks down a complex molecule

Energy coupling- Uses the energy released in exergonic reactions to fuel endergonic reactions.

Usually uses the energy stored in ATP molecules

5.12

ATP(Adenosine triphosphate)-

• Powers all terms of cellular work.

• Is renewable source of energy

• Energy form an exergonic reaction goes into an endergonic reaction to produce ATP

ATP consists of:

• Nitrogenous base Adenine

• Five carbon sugar Ribose

• Three phosphate groups

Phosphorylation- A hydrolysis reaction that releases energy by transferring its third phosphate group to some other molecule

Most cellular work depends on ATP energizing molecules by phosphorylating them

* There are three main types of cellular work

1. Chemical

2. Mechanical

3. Transport

ATP drives all three of them

• ADP + P → ATP

• ATP gives away the last phosphate group and becomes ADP

• ADP + P → ATP

5.13

Although biological molecules contain a lot of potential energy, It is not released spontaneously

An energy barrier must be overcome before a chemical reaction can begin called Activation Energy

Activation energy is the energy needed for a reactant molecule to move up hill to a higher but unstable energy before the rest of the reaction happens

One way to speed up a reaction is Adding heat but that kills our cells

Enzymes

• Organic catalysts that are safe and can be used in living organisms to speed up a chemical reaction.

• Reduces the Activation energy barrier

• Increases the rate of the reaction without being consumed into the reaction

• Usually proteins and sometimes RNA molecules

• Does not add or remove energy of the final product

• Very selective and has a shape that determines the enzyme specifically

• Enzymes are specific because their active site fits only specific types of substrate

Substrate- The specific reactant to an enzyme

Active site- The space where the enzyme and substrate connect

5.14

Every enzyme has optimal conditions where its most effective

Most human enzymes work best at 35-40*C

Denaturation- happens when the PH, Salinity or Temperature is too high. It changes the shape of an enzyme making it not function

Most enzymes require a Non-protein helpers called cofactors

Cofactors-

• Binds to the active site and functions in catalysis

• Some are inorganic like zinc, iron and copper

Coenzyme-

• An organic cofactor

• Always vitamins

5.15

Inhibitor-

• A chemical that interferes with an enzymes activity

• Important in regulating cell metabolism

Enzyme inhibition- An inhibitor that prevents the enzyme from doing its work

Competitive inihibitor

• Block the substrate from entering an enzymes active site

• Reduces an enzyme’s productivity

Noncompetitive inhibitor-

• Binds to an enzyme somewhere other that the active site

• Changes the shape of the active site

• Prevents the substate from binding

*Both competitive and non competitive prevent the substrate from bonding with the enzyme

Feedback inhibition- When the product acts as an inhibitor of one of the enzyme’s in the pathway that produced it

5.16

Many beneficial drugs act as enzyme inhibitors including

• Ibuprofen- inhibits the production of prostaglandins

• Blood pressure medicines

• Antidepressants

• Antibiotics

• Protease- inhibitors used to fight HIV

Enzyme inhibitors have also been developed as pesticides and deadly poisons for chemical warfare

Chapter 6

Life requires energy

Energy ultimately comes from the sun

Cellular respiration takes place in mitochondria and photosynthesis takes place in mitochondria

Respiration- an exchange of gases aka breathing

Cellular respiration- the Aerobic- oxygen requiring harvesting of energy from food molecule

Cellular respiration is an exergonic reaction that transfers energy from the bonds in glucose to form ATP

Each glucose molecule produces 32 ATP molecules

Other organic molecule can also be used as the energy source

C6H12O6 + O2 → 6CO2 + 6H2O + ATP(heat)

The human body uses energy from ATP to fuel all its activities

Kilocalorie(kcal) - the quantity of heat required to raise the temperature of 1 kg of water by 1 degree celsius

The energy needed for life can be found in the arrangement of electrons in the chemical bonds that hold organic molecules together

When the Carbon-hydrogen bonds in glucose are broken electrons get transferred to oxygen because of its tendency to attract electrons

Energy can be released from glucose by simply burning it but the energy dissipated as heat and light isn’t available to living organisms

Cellular respiration is the controlled breakdown of organic molecules

Energy is:

a. gradually released in small amounts

b. captured by a biological system and

c. stored in ATP

Redox reaction(oxidation-reduction)- the movement of electrons from one molecule to another.

Oxidation- the loss of electrons

Reduction- the addition of electrons to one substance

In cellular respiration:

• Glucose loses its hydrogens and becomes oxidized to CO2

• Oxygen gains hydrogen atoms and becomes reduced to H2O

Enzymes are necessary to oxidize glucose and other foods

NAD+

• important enzymes in oxidizing glucose

• accepts electrons and

• becomes reduced to NADH

There are other electron carrier molecules that function like NAD+

They form a staircase where the electrons pass from one to the next down the staircase. They are called Electron transport chain

As electrons are moved down the staircase ATP is generated

Cellular respiration can be divided into 3 stages

• Glycolysis

• Pyruvate oxidation and citric acid cycle

• Oxidative phosphorylation

1.Glycolysis

• occurs in the cytoplasm

• begins cellular respiration

• breaks down glucose into two molecules of 3 carbon compound called pyruvate

• Releases 2 ATP molecules

Glucose→ 2 pyruvate

NAD+ → NADH

FAD+→ FADH2

2.Pyruvate oxidation and citric acid cycle/ krebs cycle

• occurs in the mitochondria

• oxidizes pyruvate into 2 carbon compounds

• Supplies the third step with electrons

• Releases 2 ATP molecules

2 pyruvate → CO2

NAD+ → NADH

FAD+ → FAD2

3.Oxidative phosphorylation

• Occurs in the mitochondria

• Uses O2 to phosphorylate ADP → ATP

• Involves the electron transport chain and Chemiosmosis- Generating ATP through oxidative phosphorylation

• Releases 28 ATP molecules

NADH + FADH2 + O2 → H2O + ATP

Aerobic- requires O2, glycolysis→ citric acid cycle→ Oxidative phosphorylation

Anaerobic- doesn’t require O2, glycolysis→ fermentation

Fermentation- a way of harvesting chemical energy that doesn’t require oxygen (Anaerobic). Main function is to oxidize NADH back to NAD+

Fermentation

• takes advantage if glycolysis

• Produces 2 ATP molecules for every glucose molecule

• reduces NAD+ to NADH

The trick of fermentation is to provide an anaerobic path for recycling NADH back to NAD+

Your muscle cells and certain bacteria can oxidize NADH through Lactic acid fermentation.

Lactic acid fermentation:

• NADH is oxidized to NAD+

• Pyruvate is reduced to lactate

Lactate is carried by the blood to the liver where it’s converted back to pyruvate and oxidized in the mitochondria of liver cells

The dairy industry uses lactic acid fermentation by bacteria to male cheese and yogurt

Other microbial fermentation turn

• Soybeans→ soy sauce

• Cabbage→ sauerkraut

The baking and winemaking industries use Alcohol fermentation to harvest chemical energy

In this process Yeast( single celled fungi)

• Oxidize NADH back to NAD+

• Convert pyruvate to CO2 and ethanol

Obligate anaerobes vs. Facultative anaerobes

Obligate anaerobes:

• Are poisoned by oxygen requiring anaerobic conditions

• Live in stagnant ponds and deep soils

Facultative anaerobes:

• Includes yeasts and many other bacterias

• Can make ATP by fermentation or Oxidative phosphorylation

Chapter 7

Plants, algae and certain prokaryotes convert light energy to chemical energy and store it in sugar

Autotrophs:

• make their own food through the process of photosynthesis.

• sustain themselves

• don’t usually consume organic molecules from other organisms

Photoautotrophs- use the energy of light to produce organic molecules

Chemoautotrophs- prokaryotes that use inorganic molecules as their energy source

Heterotrophs- are consumers that feed on plants, animals. they decompose organic material

Photosynthesis in plants:

• takes place in chloroplast

• converts CO2 and water into organic molecules

• releases O2

Chloroplast are the major sites of photosynthesis in green plants

Chlorophyll

• and important light absorbing pigment in chloroplast

• makes plants green

• plays a major role in converting solar energy to chemical energy

Chloroplast are concentrated in the cells of the mesophyll- the green tissue in the interior of the leaf

stomata- tiny pores in the leaf that allow the CO2 to move in and O2 to exit

Veins in the leaf deliver H2O absorbed by the roots

Chloroplast consists of an envelope of two membranes that:

• enclose the inner compartment with a thick fluid called stroma

• contain a system of interconnected membranous sacs called thylakoids

Thylakoids

• are often concentrated into stacks called grana

• have an internal space called thylakoid space

• thylakoid membrane also have most of the machinery that converts light energy to chemical energy

Chlorophyll molecules are:

• built into the thylakoid membrane

• capture light energy

Photosynthesis is a redox (oxidation- reduction) process

• CO2 becomes reduced to sugar as electrons from H2O are added to it

• Water molecules are oxidized when they lose electrons along with hydrogen ions

6CO2 + 6H2O → C6H12O6 + 6O2

In photosynthesis

1. light energy is captured by chlorophyll molecules to boost the energy of electrons

2. light energy is converted to chemo energy

3. chemical energy is stored in the chemical bonds of sugars

Photosynthesis occurs in two stages

1. Light reactions- occurs i. the thylakoid membranes

• H2O→ O2

• ADP + P → ATP

• NADP+ → NADPH by using light to excite the electrons

the NADPH produced by the light reactions provides the electrons for reducing carbon in the carbon cycle

2. Calvin cycle- occurs in the stroma of the chloroplast

• Uses CO2 and ATP to assemble sugar molecules

• Carbon fixation- a process that incorporates CO2 into organic compounds

• After carbon fixation enzymes of this cycle make sugars by further reducing the carbon compounds

• AKA light independent reaction

Sunlight contains energy called electromagnetic energy

Visible light is only a small part of the electromagnetic spectrum

Electromagnetic energy travels in waves

Wave length- the distance between the crests of two adjacent waves

Light behaves as discrete packets of energy called photons

Photon- a fixed quantity of light energy

*the shorter the wavelength the greater the energy

Pigments absorb light and are built into the thylakoid membrane

Plant pigments absorb some wavelengths of light and reflect or transmit others

*we see the color of wavelengths that are transmitted

Chloroplast contains several different pigments that absorb different wavelengths

chlorophyll a - absorbs blue, violet, red and reflects green

chlorophyll b - absorbs blue and orange and reflects yellow and green

carotenoids -

• broaden the spectrum of colors used for photosynthesis

• provide photoprotection- absorbing or getting rid of excess light energy that would have damaged the chlorophyll or interacted with O2 to create reactive oxidative molecules

Most plants use CO2 directly from the air and carbon fixation occurs when the enzyme rubisco adds CO2 to RuBP. These plants are called C3 plants.

they are called C3 plants because the first product of carbon fixation is a 3 carbon compound, 3- PGA

in hot and dry weather C3 plants:

• close their stomata to reduce water loss

• prevent CO2 from entering the leaf and O2 from leaving

• as O2 builds up in a leaf, rubisco adds O2 instead of CO2 to RuBP, and a two-carbon product of this reaction is then broken down in the cell. This process is called Photorespiration because it occurs in the light, consumes O2 and releases CO2

• Photorespiration uses ATP instead of producing it

C4 plants evolved in the means of:

• carbon fixation that saves water during photosynthesis and

• optimizes the Calvin cycle

C4 plants are called C4 plants because they fix CO2 into a four carbon compound

In hot and dry weather C4 plants keep their stomata mostly closed to conserve water

CAM plants- plants like pineapples and cacti

Conserve water by opening their stomata and admitting CO2 only at night

CO2 is fixed into a four carbon compound that:

• banks CO2 at night and

• released it into the Calvin cycle during the day

Chapter 8

A key characteristic of life is reproduction

Cell division

• reproduction at the cellular level

• duplicates the chromosomes and sorts the new sets into daughter cells

Cell division is used for:

• reproduction of unicellular organisms

• growth and development of multicellular organisms

• replacement and repair of cells

• sperm and egg production

There are two methods of reproduction

1. Asexual reproduction

• produces offsprings that are identical to the original organism

• involves the inheritance of all genes from one parent

2. Sexual reproduction

• produces offsprings that are similar to the parents but vary in traits

• involves the inheritance of unique sets of genes from two parents

Prokaryotes aka bacteria and archaea reproduce by binary fission

Cell division of prokaryotic cells is faster that cell division in eukaryotic cells

The chromosome of a prokaryote is

• a single circular DNA molecule associated with proteins

• a lot smaller that eukaryotic chromosome

Stages of binary fission in prokaryotic cells

1. duplication of the chromosome and separation of the copies

2. elongation of the cell and movement of the copies

3. division into daughter cells

Eukaryotic cells

• are larger and more complex compared to prokaryotic cells

• have more genes

• store most of their genes on multiple chromosomes inside the nucleus

Eukaryotic chromosomes are made of Chromatin consisting of:

• one long DNA molecule

• Proteins that help maintain its structure and control the activity of the genes

When preparing for division the Chromatid becomes compact and visible under a light microscope

Before eukaryotic cell division the cell duplicates its chromosome making:

• two copies called sister chromatids

• joined at the waist called the centromere

When the cells divide the sister chromatids

• separate from each other now called chromosomes and

• sort into separate daughter cells

Cell cycle- an ordered sequence of events that extends from a cells that’s first formed from dividing until its own division

The cell cycle consists of two stages:

1. Interphase - duplication of cell contents

   • G1 - growth, increases the cytoplasm

   • S - duplication of chromosomes

   • G2 - growth, preparing for division

2. Mitotic phase - division

   • Mitosis - division of the nucleus

   • Cytokinesis - division of the cytoplasm

Mitosis occurs in a series of stages:

1. Prophase

2. Pro-metaphase

3. Metaphase

4. Anaphase

5. Telophase

Cytokinesis occurs at the same time as telophase

Prophase

a. Chromatin fibers become more tightly coiled and folded, forming discrete chromosomes that can be seen with the light microscope

b. The duplicated chromosomes appear as two sister chromatids

c. The mitotic spindle begins to form as microtubules rapidly grow out from the centrosomes

Pro-metaphase

a. The nuclear envelope breaks and disappears

b. Microtubules from the centrosomes extend and reach the chromosomes

c. Some of the microtubules attach to the kinetochore- a protein structure within the centromere

d. Other microtubules make contact with the microtubules coming from the opposite pole

Metaphase

a. At this phase the mitotic spindle is fully formed

b. The chromosomes line up on the metaphase plate- an imaginary plane equidistant between the two poles of the spindle

c. The centromeres of all chromosomes are lined up on the plate. For each chromosome, the kinetochores of the two sister chromatids are attached to microtubules from opposite poles

Anaphase

a. The sister chromatids separate at the centromere

b. Daughter chromosomes are moved to opposite poles

c. The cell elongates

Telophase

a. The elongation of the cell continues

b. The nuclear envelopes form around the now separated chromosomes

Basically reverse prophase

c. The chromatin fibers uncoil and the mitotic spindle disappears

Cytokinesis

a. The cytoplasm is divided into separate cells

Cytokinesis differs in animal and plant cells

Cytokinesis in animal cells

1. A Cleavage furrow forms a contracting ring of microfilaments, interacting with myosin, and

2. The cleavage furrow deepens to separate the contents into two cells

Cytokinesis in plant cells

1. A Cell plate forms in the middle, form vesicles containing cell wall material

2. The cell plate grows outward to reach the edges, dividing the contents into two cells

3. Each cell now possesses a plasma membrane and a cell wall

The cells within an organism’s body divide and develop at different rates

The rate of cell division is determined on what the cell does for the body

Cell division is controlled by:

• The presence of essential nutrients

• Growth factors

• Density- dependent inhibition

• Anchorage dependence

Growth factors - proteins that are released by a near by cell and stimulate cell division when taken in by a cell

Density- dependent inhibition - Cells divide until the presence on the cell touching shuts down cell division

Anchorage dependence - The need for cells to be in contact with a solid surface to divide. In humans its the bloodstream

The Cell cycle control system is a cycling set of molecules in the cell that

• triggers and

• coordinates key events in the cell cycle

Checkpoints in the cell cycle can

• stop an event

• signal on event to proceed

There are 3 major checkpoints in the cell cycle

1. G1 checkpoint

   • allows entry to the S phase or

   • Causes the cell to leave the cycle, entering a non dividing G0 phase

2. G2 checkpoint

3. M checkpoint

Cells in G0 maybe injured and won’t divide ever again

Cancer currently claims the lives of 20% of the people in the US

Cancer cells escape controls on the cell cycle

Cancer cells:

• divide rapidly, often in the absence of growth factors

• spread to other tissues through the circulatory system

• grow without being inhibited by other cells

Cancer cells violate all of the cell cycle control system

Tumor - an abnormally growing mass of body cells. There are 2 types

1. Benign tumor - remain at the original site. Can be removed by surgery

2. Malignant tumor - spread to other locations called Metastasis

Metastasis- The spreading of cancer cells from their origin to other parts of the body. The newly spread cancer is identical in genetic makeup to the original cancer cell

The bloodstream/ circulatory system and the Lymphatic system/ immune system touches every cell in the human body.

Cancers are named are the organ/tissue it comes from

Carcinomas - arise in external or internal body coverings

Sarcomas - arise in supportive and connective tissue

Leukemias and Lymphomas - arise from blood- forming tissues

Localized tumors can be:

• removed surgically

• treated with concentrated beams of high-energy radiation

Chemotherapy is used for metastatic tumors

Cancer cells have the ability to release molecules that command the cells in the bloodstream to move towards them and feed them when cancer cells aren’t in direct contact with the bloodstream

In humans Somatic cells - body cells, have:

• 22 pairs of homologous chromosomes known as Autosomes that are the same size and genetic makeup

• Sex chromosomes- X and Y chromosomes that differ in size and genetic makeup

XX → Female

XY → Male

Homologous chromosomes are matched in:

• length

• centromere position

• gene locations

Homologous chromosomes have the same gene position but not the same allele

Locus- the position of a gene

A pair of homologous chromosomes are called a Tetrad

An organisms life cycle is a sequence of stages leading from the adults of one generation to the adults of the next

Humans and many animals and plants are Diploids with body cells that have

• two sets of chromosomes

• one from each parent

Ploidy- the number of copies of the genome

Meiosis is a process that converts a diploid into haploid

Diploid cells - have two homologous sets of chromosomes

Haploid cells - have one set of chromosomes NO HOMOLOGOUS SETS

Meiosis occurs in sex organs producing gametes- sperm and egg cells

Fertilization- the union of sperm and egg cells. forms a zygote. Occurs in the Fallopian tube

Zygote- has a diploid chromosome number one set from each parent

Meiosis has to happen to offset fertilization

All sexual life cycles alternate between a diploid stage and a haploid stage

In meiosis the cell goes from a diploid → haploid with sister chromatids → haploid with one set of chromosome

Meiosis has one cycle of duplication and two cycles of cell division

Stages of Meiosis

Meiosis 1

Prophase 1

• Chromosomes coil and compact

• Homologous pairs come together as pairs by synapsis

• Non-sister chromatids exchange genetic makeup by Crossing over

Metaphase 1

• Tetrads align at the cell equator

Anaphase 1

• Homologous pairs separate and move towards the opposite poles of the cell

Telophase 1

• A nuclear envelope re-forms around chromosomes in some species

• Duplicated chromosomes have reached the poles

Meiosis 2

Prophase 2

• Chromosomes coil and become compact (if uncoiled after telophase 1)

• Nuclear envelope, if re-formed, breaks up again

Metaphase 2

• Duplicated chromosomes align at the cell equator

Anaphase 2

• Sister chromatids separate

• Chromosomes move toward opposite poles

Telophase 2

• Chromatids have reached the poles of the cells

• A nuclear envelope forms around each set of chromosomes

With Cytokinesis four haploid cells are produced

Origins of genetic variation

• Independent orientation at metaphase 1

• Crossing over

• Random fertilization

Independent orientation at metaphase 1

• Each pair of chromosomes independently aligns at the cell equator

• There’s an equal probability of maternal or paternal chromosome facing a given pole

• The number of combinations for chromosomes packaged into gametes in 2^n where n = the haploid number of chromosomes

Random fertilization

• The combination of each unique sperm with each unique egg increases genetic variability

Separation of homologous chromosomes during meiosis can lead to genetic differences between gametes

• Homologous chromosomes may have different versions of a gene at the same locus

• One version was inherited from the maternal parent and the other from paternal parent

  • Since homologues move to opposite poles during anaphase 1, gametes will receive either the maternal or paternal version of the gene

Genetic recombination- The production of new combinations of genes due to crossing over

Crossing over- an exchange of corresponding segments between separate (non-sister) chromatids on homologous chromosomes

• Non-sister chromatids join at the Chiasma- The site of attachment and crossing over

• Corresponding amounts of genetic material are exchanged between maternal and paternal (non-sister) chromatids

Aneuploidy- Not a good set of genes 2n = 45 or 2n = 47

Karyotype- Images of a person’s chromosomes in pairs

Karyotypes are produced from dividing cells arrested at metaphase of mitosis

Karyotypes allow the observations of

• homologous chromosomes

• chromosome numbers

• chromosome structure

Amniocentesis- Diagnostic test that shows the chromosomes of an unborn child

Trisomy 21/ Down syndrome- inheriting 3 copies of the 21st chromosome

Down syndrome is the most common human chromosome abnormality

The characteristic set of symptoms for down syndrome include:

• mental retardation

• short stature

• circulatory defects

• susceptibility to respiratory diseases, leukemia and alzheimer’s

• shortened life span

• characteristic facial features

The incidence of down syndrome increases with the age of the mother

Non disjunction- failure to separate during anaphase 1 or anaphase 2

• Anaphase 1- all the gametes have incorrect chromosome numbers

• Anaphase 2- there’s a 50/50 chance that a gamete with the right number of chromosomes will be fertilized

Fertilization after non disjunction yields zygotes with altered number of chromosomes

Abnormalities in sex chromosomes tend to be less severe because of:

• the small size of the Y chromosome

• the X chromosome inactivation

A single Y chromosome is enough to produce maleness even in combination with several X chromosomes

The absence of a Y chromosome yields femaleness

Errors in mitosis or meiosis may produce polyploid species with more than two chromosome sets

The formation of polyploid species are more observed in plant species compared to animals

chromosome breakage can lead to rearrangements that produces:

• genetic disorders/ birth defects

• if changes are in somatic cells then cancer

Rearrangements that changes the DNA sequence that changes the product includes:

Deletion- the loss of chromosome segment

Duplication- the repeat of a chromosome segment

Duplication usually of crossing over where one chromosome takes both copies of the segment inserted of exchanging segments

Inversion- the reversal of a chromosome segment

Translocation- when a segment of a chromosome separates and reattaches itself to a different chromosome

Chronic myelogenous leukemia (CML)

• is one of the most common leukemias

• affects cells that give rise to white blood cells (leukocytes)

• results from the translocation between the 22nd and 9th chromosomes

• the translocation creates a cancer causing gene called the philadelphia chromosome

Chapter 9

Pan-genesis, a concept made up by Hippocrates around 400BCE, was an early explication for inheritance that suggested that:

• particles called pan-genes came from all parts of the organism to incorporated into eggs/sperm

• characteristics aquifers during the parents lifetime could be transferred of the offspring

Aristotle rejected the idea and suggested that instead of particles, the potential to produce the traits was inherited

The idea that hereditary materials mix in forming offspring is called the bending hypothesis. it was:

• suggested in the 19th century by a scientist studying plants

• later rejected because it didn’t explain how traits that disappear in one generation can reappear in later generations

Heredity- the transmission of traits from one generation to the next

Genetics- is the scientific study of heredity

Gregor Mendel:

• began the field of genetics in the 1860s

• deducted the principles of genetics by breeding garden peas

• relied upon the background of math, physics and chemistry

In 1866, Mendel

• correctly argued that parents pass on to the offspring discrete heritable factors

• stressed that the heritable factors today called genes retain their individuality generation after generation

Character- a heritable feature that varies among individuals, ex: flower color

Trait- each variant of a character, ex: purple or white flowers

True breeding varieties result when self fertilization produces offspring all identical to the parent

Hybrids are offsprings of two different varieties

The cross fertilization is a hybridization or genetic cross

O generation- true breeding parental plants

F1 generation- the hybrid offsprings of gen p

F2 generation- the cross of F1

Monohybrid cross- the cross between two individuals different in a single character

Mendel performed a monohybrid cross between with and purple flowers:

• the F1 produced all purple flowers

• the cross of F1 with each other made an F2 generation with ¾ purple and ¼ white flowers

The F1 generation didn’t produce any light purple flowers as predicted by the bending hypothesis

Mendel developed four theories based on his experiments:

1. Alleles- are alternative versions of genes that account for variations in inherited characters

2. For each characteristic an organism inherits two alleles one from each parent. The alleles can be the same or different

   • Homozygous- genotype has identical alleles

   • Heterozygous- genotype has two different alleles

3. If the alleles are heterozygous one will be dominant (determine the appearance) and one will be recessive (no noticeable effect)

   • phenotype- the appearance of a trait

   • genotype- the genetic makeup of a trait

   • The same phenotype may be determined by more than one genotype

4. The law of segregation- a sperm or egg carries only one allele for each character because the allele pairs segregate during gamete production

Mendel’s hypothesis also explains the 3:1 ratio in the F2 generation

Punnet square- shows the four possible combinations of alleles that could occur when the gamete combine

Locus(loci)- the specific location of a gene along a chromosome

Homozygous individuals have the same allele on both homologues

Heterozygous individuals have a different allele on each homologues

Dihybrid cross- a mating of parental varieties that differ in their characters

After his dihybrid cross, Mendel needed to explain why the F2 gen

• had new no parental combinations of traits

• and a 9:3:3:1 phenotype ratio

Mendel suggested that:

• the inheritance of one character has no effect on the inheritance of another

• the dihybrid cross is equivalent to two monohybrid crosses

• Called this The law of independent assortment

Testcross- the mating between and individual with unknown genotype and homozygous recessive individual

A testcross can show whether the unknown genotype includes a recessive allele

Mendel used testcrosses to verify that he had true breeding genotypes

Many inherited disorders in humans are controlled by a single gene

1. Recessive inheritance:

   • two recessive alleles need to show disease

   • heterozygous parents are carriers of the disease causing allele

   • the possibility of inheritance increases with inbreeding

2. Dominant inheritance:

   • one dominant allele is needed to show disease

   • dominant lethal alleles are usually eliminated from the population

The most common fatal genetic disease in the US is Cystic fibrosis

The CF allele is recessive and carried by 1 in 31 Americans

Dominant human disorders include:

• Achondroplasia- results in dwarfism

• Huntington’s disease- caused by a late acting lethal dominant allele, degenerative disorder of the nervous system

Technology offers ways to obtain genetic information:

• before conception

• during pregnancy

• after birth

Genetic testing can identify potential parents who are heterozygous carriers of certain diseases

Technology used before birth

Amniocentesis- extracts samples of amniotic fluid containing fetal cells and allows

• karyotyping

• biochemical tests for other conditions like taysachs

Chronic collusion sampling- removes a sample of chorionic villus tissue from the placenta and allows karyotyping and biochemical tests

Chronic collusion sampling takes shorter to produce results

Fetal imaging allows the physical to examine a fetus directly for anatomical deformities

The most common form of fetal imaging is ultrasound imaging

Newborn screening can detect diseases that can be prevented by special care and precautions

Ethical considerations of the technologies

• confidentiality and potential use of results of genetic testing

• time and financial costs

• determining what, if anything, should be done as a result of testing

Variations on Mendel’s Laws

Complete dominance- when the offspring always looked like on of the parental varieties

Incomplete dominance- when the phenotype of the offspring falls between the two parental varieties:

• Neither allele is dominant over the other

• Both alleles are expressed and results in a 3rd intermediate phenotype

A heterozygote expressing an intermediate phenotype= incomplete dominance occurred

Incomplete dominance does not support the bending hypothesis because the original parental phenotypes reappear in the F2 generation

ex Incomplete dominance in humans:

hypercholesterolemia

• extremely high levels of cholesterol occurs in blood

• heterozygotes have intermediately high cholesterol levels

Although an individual can carry at most 2 different alleles for a particular gene, more that two alleles can exist in the wider population

The human ABO blood group phenotype has three alleles for a single gene

The four blood groups A,B,AB,O are phenotypes resulting from the two alleles

A and B are both expressed in heterozygous individuals in Codominance

In Codominance:

• neither allele is dominant over the other

• both alleles are expressed in distinct phenotypes

EX: Type AB blood

difference between codominance and incomplete dominance: codominance doesn’t have intermediate phenotypes

Mendel knew that the rules of mathematical probability affected:

• The segregation of allele pairs during gamete formation

• The re-forming of pairs at fertilization

The probability scale ranges from 0 to 1

• certainly has the probability of 1

• certainly not has the probability of 0

Probability of a specific event- the number of ways that event can occur out of the total possible outcomes

When determining the probability of individual events use the rule of multiplication where the product is the probabilities for each event

The probability that an event can occur in two or more alternative ways is the sum of the separate probabilities called rule of addition

Wild-type traits- traits that aren’t necessarily specified by dominant alleles

Some dominant and recessive traits

• Freckles are dominant over no freckles

• Widows peak is dominant over straight hairline

• Free earlobe is dominant over attached earlobe

The inheritance of human traits follows Mendel’s laws

A Pedigree is used to:

• Show the inheritance of a trait in a family through multiple generations

• demonstrates dominant or recessive inheritance

• can be used to deduce genotypes of family members

• can be used on both autosomal and sex linked traits

Even though a person can carry at most 2 alleles of one gene more that 2 alleles can exist in the wider population

The human blood group phenotypes have 3 alleles for a single gene

The phenotypes: A, B, AB, O

A and B are codominant

In Codominance:

• One allele isn’t dominant over the other

• both phenotypes are expressed in distinct phenotypes

Pleiotropy- when one gene influences many characteristics

ex: sickle cell - affects:

• affects the shape of red blood cells

• causes anemia and organ damage

• makes a person resistant to malaria

• sickle cell is co-dominant to normal cell

Polygenic inheritance- when a single phenotypic character results from the combined effects of two or more genes

ex: skin color, height, weight, hair color, eye color

Epistasis- When one unrelated gene can affect the expression of all of the other genes for that trait

Ex: albino genes, gene for baldness

Many characters are products of heredity and environment

ex:

• skin color is affected by sunlight exposure

• susceptibility to cancer has both hereditary and environmental factors

• identical twins show some differences

Only genetic influences are inherited

The Chromosome theory of inheritance states that:

• genes take up specific loci on chromosomes

• Chromosomes segregate and independently assort during meiosis

Mendel’s laws correlate with chromosome separation in meiosis

• the law of segregation depends on homologous chromosomes in anaphase 1

• the law of independent assortment depends on alternative orientations of chromosomes in metaphase 1

Bateson and Punnett studied plants that didn’t show a 9:3:3:1 ratio in the F2 generation and accidentally discovered linked genes

linked genes- genes on the same chromosome

They tend to be inherited together

The closer in proximity the genes are the greater the likelihood that they’re inherited together

Linked genes don’t follow Mendel’s laws of independent assortment

Even with crossing over, some traits are almost always inherited together

Crossing over between homologous chromosomes produces new combinations of alleles in gametes

Linked genes that are separated by crossing over form recombinant gametes

The percentage of recombinant is the recombination frequency

recombinants- offsprings whose genotypes don’t match the parents

Recombination frequency (%) = recombinants / total number of offspring

Geneticists use crossover data to map genes

The more genes are farther away from each other the higher the rate of crossover can occur

Recombination frequencies can be used to map the relative location of genes on chromosomes

ex: if 2 genes that cross over 20% of the time are 20 map units apart

Many animals have a pair of sex chromosomes

In mammals:

• males have and XY chromosomes

• females have and XX chromosomes

The Y chromosome contains SRY genes that code for testosterone, all the male reproductive systems and sex characteristics like deep voice, facial hair, larger muscles

The absence of Y chromosomes allows the female reproductive system to develop

The X chromosome is much larger and carries additional traits that are not connected to biological sex

different animals have different ways of determining biological sex

ex:

• Grasshoppers, roaches and some other insects have an X-O system where O stands for the absence of a sex chromosome

  • Females are XX

  • Males are XY

• In some fishes, butterflies and birds the sex chromosomes are Z and W

  • Females are ZW

  • Males are ZZ

• Some organisms lack sex chromosomes all together

  ex:

  • Females are diploid

  • Males are haploid

• In some animals environmental temperature determines biological sex

  ex:

  • In some species of reptiles the biological gender is determined by the temperature at which the eggs are incubated at during a period of development

  • Global climate change heavily impacts the sex ratio of the species

Sex linked genes- genes located on either of the sex chromosomes

Sex linked traits- traits inherited on the X chromosome

Males and females will express sex linked traits differently

• Males are more likely to express a sex linked disorder compared to females

• Males can’t be carriers of sex linked disorders, they either have it or not

The X chromosomes carries many genes that are not related to biological sex

Most sex linked human disorders are:

• caused by recessive alleles

• mostly seen in males

A male will have the disorder if he receives a recessive allele from his mother

A female will have the disorder if she receives a recessive alleles from both parents

Examples of recessive sex linked disorders

• hemophilia- lack of proteins needed for blood clotting

• red-green color blindness- a malfunction of light sensitive cells in the eyes

• Duchenne muscular dystrophy- the progressive weakening of the muscle and loss of coordination

The Y chromosome provides clues about human male evolution because:

• Y chromosomes are passed intact from father to son

• mutations in the Y chromosome can reveal data about recent shared ancestry

Chapter 10

10.1

Until the 1940s scientists believed that protein served as genetic material was stronger than DNA

• Proteins were made from 20 different amino acids

• DNA was just made from four kinds of nucleotide

Studies of bacteria and viruses

• helped in molecular biology- the study of heredity at a molecular level

• revealed the role of DNA in heredity

In 1928, Frederick Griffith discovered that a “transforming factor” could be transferred into a bacteria cell

He discovered that:

• when a heat killed pathogenic(disease causing) bacteria is exposed to a harmless bacteria, some harmless bacteria would be converted to disease-causing bacteria

• the disease causing characteristic was inherited by the descendants of the transformed cells

In 1952, Alfred Hershey and Martha Chase used bacteriophages to show that DNA is the genetic material of T2(a virus that infects that bacterium E. coli)

• Bacteriophages (phages)- are viruses that infect bacteria cells

• Phages were labeled with radioactive sulfur to detect proteins or radioactive phosphorus to detect DNA

• Bacteria were infected with either type of phages to determine which substance was injected into the cell and which remained outside the cell

• The sulfur labeled protein stayed with the phages outside the bacteria cell and the phosphorus labeled DNA was detected inside cells

• Cells with phosphorus labeled DNA produced new bacteriophages with radioactivity in DNA but not in protein

10.2

DNA and RNA are nucleic acids and are polymers of nucleotides

DNA polynucleotide- A nucleotide chain. One of the two strands of DNA

A Nucleotide is made of

• nitrogen base

• five carbon sugar called deoxyribose

• phosphate group

Nucleotides are joined to one another by a Sugar phosphate backbone

There are four nitrogen bases that can make up a DNA nucleotide

1. Adenine (A)

2. Cytosine (C)

3. Thymine (T)

4. Guanine (G)

RNA is different from DNA in that it has:

• the sugar ribose instead of deoxyribose

• RNA has a nitrogen base uracil (U) instead of thymine

10.3

After the Hershey-Chase experiment there was a race on to

• describe the structure of DNA

• explain how the structure on properties of DNA can account for its role in heredity

In 1953, James D. Watson and Francis Crick deduced the secondary structure of DNA using

• X-ray crystallography data of DNA from the work of Rosalind Franklin and Maurice Wilkins

• Chargaff’s observation that in DNA

  • the amount of adenine was equal to the amount of thymine

  • the amount of guanine was equal to the amount of cytosine

Watson and Crick reported that DNA consisted of two polynucleotide strands wrapped into a double helix

• the sugar-phosphate backbone is on the outside

• the nitrogenous bases are perpendicular to the backbone in the interior

• specific pairs of bases give the helix a uniform shape

  • A pairs with T forming two hydrogen bonds

  • G pairs with C forming three hydrogen bonds

In 1962, the Nobel prize was awarded to

• James D. Watson, Francis Crick and Maurice Wilkins

• Rosalind Franklin probably would’ve received the prize as well but she died in 1958

The Watson-Crick model gave new meaning to the words genes and chromosomes. The genetic information in a chromosome is encoded in the nucleotide sequence of DNA

10.4

In their description of DNA, Watson and Crick noted that the structure of DNA suggests a possible copying mechanism

DNA replication is Semiconservative

1. the two strands separate

2. each strand is used as a template to produce a complementary strand using the base pairing rule

3. each new DNA helix has one old and one new strand

10.5

DNA replication begins at the origin of replication where:

• DNA unwinds at the origin to produce a “bubble”

• replication proceeds in both directions from the origin

• replication ends when products from the bubbles merge with each other

DNA replication occurs in the 5’ to 3’ direction adding new nucleotides to the 3’ end

• Replication is continuous (leading) on the 3’ to 5’ template

• Replication is discontinuous (lagging) on the 5’ to 3’ template, forming short segments

The key enzymes involved in DNA replication

1. Hilacase- separates the parent DNA strand

2. Primase- initializes the process of replication (made of RNA)

3. DNA polymerase- adds new nucleotides to the growing chain based on the parent template, proofreads and corrects incorrect base pairings

4. Ligase- connects the Okazaki fragments (lagging strands)

DNA polymerase and Ligase also repair DNA damaged by harmful radiation and toxic chemicals

DNA replication ensures that all the somatic cells in a multicellular organism carry the same genetic information

10.6

DNA specifies traits by dictating protein synthesis

The molecular chain of command is from

• DNA in the nucleus to RNA and

• RNA in the cytoplasm to protein

Transcription- the synthesis of RNA under the directions of DNA

Translation- the synthesis of protein under the directions of RNA

The DNA genotype os expressed as proteins which provide the molecular basis for phenotypic traits

The connections between genes and proteins

• The initial one gene - one enzyme hypothesis was based on studies of inherited metabolic diseases

• One gene - one enzyme hypothesis was expanded to include all proteins

• Recently the one gene - one polypeptide hypothesis recognizes that some proteins are composed of multiple polypeptides, also recognizes that genes code for many proteins not just enzymes

10.7

Genetic information written in codons is translates into amino acid sequences

The sequence of nucleotides in DNA provides a code for constructing a protein

• protein construction needs a conversion of a nucleotide sequence to an amino acid sequence

The flow of information from gene to protein is based in a triplet code called codons

• Translation involves switching from the nucleotide language to amino acid language

• Each amino acid is specified by a codon

  • 64 codons are possible

  • some amino acids have more than one possible codon

10.8

The genetic code dictates how codons are translated into amino acids

Characteristics of the genetic code

• Three nucleotides specify one amino acid

  • 61 codons correspond to amino acids

  • AUG codes for Methionine and signals the start of transcription, codes for an amino acid

  • 3 stop codons signal the end of translation, they don’t code for an amino acid

The genetic code is

• Redundant- more than one codon for some amino acids

• Unambiguous- any codon for one amino acid doesn’t code for any other amino acid

• Nearly universal- the genetic code is shared by most organisms

• Without punctuation- codons are adjacent to each other with no gaps in between

10.9

Transcription produces genetic messages in the form of RNA

RNA synthesis resembles the synthesis of DNA during DNA replication

• RNA nucleotides are linked by the transcription enzyme RNA polymerase

• Specific sequences of nucleotides along the DNA mark where transcription begins and ends

• The start transcribing signal is a nucleotide sequence called a prompter

There are 3 phases in RNA synthesis

1. Transcription begins with initiation as the RNA polymerase attaches to the prompter

2. During the second phase elongation the RNA grows longer

   As the RNA peels away, the DNA strands rejoin

3. In the third phase termination the RNA polymerase reaches a sequence of bases in the DNA template called a terminator which signals the end of the gene

   The polymerase molecule detaches from the RNA molecule and the gene

RNA is synthesized in a 5’ to 3’ direction

10.10

Eukaryotic RNA is processed before leaving the nucleus as mRNA

mRNA

• encodes for amino acid sequences

• conveys genetic messages from DNA to the translation machinery of the cell which in:

  • prokaryotes- occurs in the same place that mRNA is made

    • transcription and translation happens at the same time

    • leads to more errors

  • eukaryotes- mRNA must exit the nucleus via nuclear pores to enter the cytoplasm

    • more sequenced and accurate

Eukaryotic mRNA has

• introns- interrupting sequences that separate exons

  • Non coding segments

• exons- the coding regions

Eukaryotic mRNA undergoes RNA processing before leaving the nucleus

RNA processing/ RNA splicing

• removes introns and joins exons to produces a continuous coding sequence

• A cap and tail of extra nucleotides are added to the ends of the mRNA to:

  • facilitate the export of the mRNA from the nucleus

  • protect the mRNA from attack by cellular enzymes

  • help ribosomes bind to the mRNA

10.11

transfer RNA molecules serve as interpreters during translation

tRNA- molecules function as a language interpreter

• converting the genetic messages of mRNA

• into the language of proteins

tRNA molecules perform this interpreter task by

• picking up the appropriate amino acid

• using a special triplet of bases called anticodon, to recognize the appropriate codons in the mRNA

tRNA has 2 binding sites

1. anticodon- binds with the mRNA codon

2. amino acid- the amino acid product exits

10.12

Ribosomes build polypeptides

Translation occurs on the surface of the ribosome:

• Coordinate the functioning mRNA and tRNA and ultimately the synthesis of polypeptides

• have two subunits: small and large

• each subunit is made of rRNA and proteins

• ribosomal subunits come together during translation

• ribosomes have binding sites for mRNA and tRNAs

10.13

Translation can be divided into the same three phases as transcription:

1. initiation

   • brings together

     • mRNA

     • a tRNA bearing the first amino acid

     • the two subunits of a ribosome

   • establishes where translation will begin

   • occurs in two steps:

     • mRNA molecule binds to a small ribosomal subunit and the first tRNA binds to the mRNA at the start codon

       • the start codon reads AUG and codes for methionine

       • the first tRNA has the anticodon UAC

     • A large ribosomal subunit joins the the small subunit allowing the ribosome to function

       • the first tRNA occupies the p site, which will hold the growing peptide chain

       • the a site is available to receive the next tRNA

2. Elongation

   • adds amino acids one by one to the polypeptide chain

   • Each cycle of elongation has three steps

     • codon recognition- the anticodon of an incoming tRNA molecule carrying its amino acid pairs with mRNA codon in the A site of the ribosome

     • peptide bond formation- the new amino acid is joined to the clan

     • translocation- tRNA is released from the P site and the ribosome moves tRNA from the A site into the P site

   • Elongation continues until the termination stage of translation when,

     • the ribosome reaches a stop codon

     • the completed polypeptide is freed from the last tRNA

     • the ribosome splits back into its separate subunits

3. Termination

   • ends translation

10.15

4 major processes

1. replication- DNA to DNA

2. transcription- DNA to RNA transcript

3. RNA processing- produces mRNA

4. translation- mRNA to protein

10.16

Mutations can change the meaning of genes

A mutation is any change in the nucleotide sequence of DNA

mutations can involve

• large chromosomal regions or

• just a single nucleotide pair

Mutations can be divided into two general categories

1. Substitution

   • involves the replacement of one nucleotide with another

   • may not effect at all- silent mutation

   • changes the amino acid coding which produces a different amino acid- missense mutation

   • lead to a base substitution that produces an improved protein that enhances the success of the mutant organism and its descendants

   • change an amino acid into a stop codon, produces a nonsense mutation

2. Deletions/ insertions

   • may alter the reading frame (triplet grouping) of the mRNA so that nucleotides are grouped into different codons

   • lead to significant changes in amino acid sequence downstream of the mutation

   • produce a nonfunctional polypeptide

Mutagenesis- the production of mutations

Mutations can be caused by

• spontaneous errors that occur during DNA replication or recombination

• mutagens, includes

  • high energy radiation such as X rays and ultraviolet light

  • chemicals

Chapter 13

Evolution- Change in allele frequency over time

• driven by natural selection

• only populations/ species evolve

Allele- Version of a trait

Natural selection- The mechanism that allows evolution to take place

Easier to occur with sexually reproducing organisms

Requirements for natural selection include:

• Variation must exist

• Limited resources

• Competition

• Some organisms with genes that are better adapted to survive (determined by DNA)

• Survival→Reproduction→Pass on trait

Organisms that don’t have the beneficial traits die off and decrease their allele frequency and over time the population changes

Fossils- the imprints or remains of organisms that lived in the past

Jean Baptiste Lamarck’s proposal

• organisms evolve by the use and disuse of body parts

• the acquired characteristics are passes on to their offspring

Lyell’s Principles of Geology

• natural forces gradually changed earth

• natural forces are still operating today

During his voyage, Darwin realized that

• The earth is very old

• Over time, present day species have arisen from ancestral species by natural processes

Darwin published On the Origin of Species by Means of Natural Selection

Main ideas of the book:

• it presents a logical explanation of descent with modification and evolution by natural selection

• organisms accumulate various adaptations that fit their environments

• exploring adaptations of organisms to their environment

• discussed examples of natural selection

• recognized the connection between natural selection and the capacity to over reproduce

Key points of evolution by natural selection

1. Individuals don’t evolve, they either survive or die

2. Natural selection can only amplify or diminish only heritable traits not acquired characteristics

3. Evolution doesn’t lead to perfection, favorable traits as environments change

Main points about natural selection

1. Natural selection is more of an editing process that a creative mechanism

2. Natural selection is contingent on time and place

Fossil record- the sequence in which fossils appear within strata(layers of sedimentary rocks)

Paleontologist- scientists who study fossils

Scientist have found that prokaryotic cells→eukaryotic cells→multicellular eukaryotic cells

Biogeography- the geographic distribution of species

Comparative embryology- the comparison of early stages of development among different organisms. It reveals homologies not visible in adult organisms

Vestigial structures- remnants of features that served important functions in an organism’s ancestors

Molecular biology- used to reveal evolutionary relationships by comparing DNA and amino acid sequences between different organisms

Darwin was the first to represent the history of life as a tree

Homologous structures can be used to determine the branching sequences of an evolutionary tree. This includes:

• anatomical structure

• molecular structure

Population- a group of individuals of the same species and living in the same place at the same time

Populations maybe isolated from one another with interbreeding

Gene pool- the total collection of genes in a population at any one time

Microevolution- a change in the relative frequencies of alleles in a gene pool over time

Population genetics- studies how populations change genetically over time

Modern synthesis- connects Darwin’s theory with population genetics

Organisms typically show individual variation

The Origin of Species couldn’t explain:

• the cause of variation among individuals

• how variations were passed down from parents to offspring

Mutations:

• changes in the nucleotide sequence of DNA

• the ultimate source of new alleles

Chromosomal duplication is an important source of genetic variation

Sexual reproduction shuffles alleles to reproduce new combinations in three ways:

1. Independent assortment

2. Crossing over

3. Random fertilization

Hardy-Weinberg principle- within a sexually reproducing diploid population allele and genotype frequencies will remain in equilibrium unless outside forces act to change those frequencies

The conditions of Hardy-Weinberg

1. A very large population

2. No gene flow between populations

3. No mutations

4. Random mating

5. No natural selection

Genotype frequencies- p² + 2pq + q² = 1

Alleles- p + q = 1

The Hardy-Weinberg equation is useful in public health science

The three main causes of evolutionary change aka microevolution

1. Natural selection

2. Genetic drift

3. Gene flow

Genetic drift:

• a change in the gene pool of a population due to change

• in a small population it may lead to the loss of genetic diversity

bottleneck effect: leads to a loss of genetic diversity when a population is greatly reduced

founder effect: when a few individuals colonize a new habitat

Relative fitness: it makes to the gene pool of the next generation relative to the contribution of other individuals

Natural selection can affect the distribution of phenotypes in a population

1. Stabilizing selection- favors intermediate phenotype, against extreme phenotypes

2. Directional selection- acts against individuals to one end of the phenotypic extremes

3. Disruptive selection- favors individuals at both extremes, against intermediate phenotypes

Sexual selection- a form of natural selection where individuals with certain characteristics are more likely to obtain mates

Sexual dimorphism- the different appearances if male and female species

Intersexual selection(b/n same sex)- competition for mates, usually by males

Intersexual selection(b/n sexes) aka mate choice- when individuals of one sex(usually females) are choosy in piking their mates and often select flashy or colorful mates

What prevents natural selection from eliminating unfavorable genotypes

1. Natural selection attacks phenotypes not genotypes so heterozygous individuals survive

2. Balancing selection- maintains stable frequencies of two or more phenotypes in a population

3. Heterozygous advantage

4. Frequency-dependent selection- a type of selection that maintains two different phenotypes in a population

Chapter 37

Biological community:

• an assembly of all the population of organisms living close enough together for potential interaction

• described by its species composition

Interspecific interactions:

• relationship with individuals of other species in the community

• greatly affect population structure and dynamics

• can be categorized according to their effect on the interacting populations

Interspecific competition:

• occurs when populations of two different species compete for the same limited resource

Mutualism- both populations benefit

Predation- one organism kills and eats the other organism

Herbivory- an animal consumes plant parts or algae

Parasitism- the host plants or animals are victimized by parasites or pathogens

Ecological niche- the sum of an organisms’s use of the biotic and abiotic resources in its environment

Interspecific competition occurs when the niches of two populations overlap

Competition lowers the carrying capacity of competing population b/c the resources used by one population aren’t available to the other population

Predication leads to diverse adaptations in prey species like:

• camouflage

• mechanical defenses

• chemical defenses

Herbivores and plants undergo coevolution

Coevolution- a series of reciprocal evolutionary adaptations in two species in which change in one species acts as new selective force on another

Herbivory leads to diverse adaptations in plants

Parasites and pathogens can affect Community composition

Parasite- lives in or in a host from which it obtains nourishment

Pathogens- disease causing microscopic parasite that include

• bacteria

• viruses

• fungi

• protists

Non-native pathogens can have rapid and dramatic impacts

Non-native pathogens can cause a decline of the ecosystem

Trophic structure- pattern of feeding relationships within a community

Food chain- the sequence of food transfer up the trophic levels

Producers- autotrophs that support all the other trophic levels

Consumers- heterotrophs

1. Primary consumers

2. Tertiary consumers

3. Quaternary consumers

Detritiviores- get the energy from detritus(the dead material produced at all trophic levels)

Decomposers- have enzymes that digest organic materials and convert them into inorganic forms in the process of decomposition. mainly prokaryotes and fungi

10% rule- only 10% of the energy from one tier gets transferred from one level to the next

Food web- a network of interconnecting food chains

• consumers may eat more than one type of producer and several species of consumers may feed on the same species of producer

Species diversity: defined in two components

1. species richness, the number of species in a community

2. relative abundance , the proportional representation of a species in a community

Keystone species- a species whose impact on its community is larger than its biomass or abundance indicates and occupies a niche that holds the rest of its community in place

keystone species have a disproportionate impact on diversity

Disturbances: events that damage biological communities. the frequencies and severity may vary from community to community

Communities change drastically following a severe disturbance that:

• strips away vegetation

• removes significant amount of soil

Ecological succession- results from colonization by variety of species whisch are replaced by a succession of other species

Primary succession- begins in a lifeless area with no soil

Secondary succession- occurs when a disturbance destroys an existing community by leaves the soil intact

Invasive species- organisms that have bben introduced into non-native habitats by human actions

Invaisive species establish themselves at the expense of native communities

The absence of natural enemies → rapid growth of invaisive species

Ecosystem- consists of all the organisms in a community and the abiotic envrionment with the organisms interact

Energy flow- moves through the components of an ecosystem

Chemical cycling- the transfer of materials within the ecosystem

Terrarium- represents the components of an ecosystem and illustrates the fundamentals of energy flow

Primary production:

• carried out by producers

• the amount of solar energy converted to chemical energy by an ecosystem’s producers for a given area

• produces biomass-the amount of living organic material in an ecosystem

Ecosystems vary in their primary production and contribution to the total production of the biosphere

Energy supply limits the length of food chains

Chemicals are cycled between organic matter and abiotic reservoirs

Ecosystems get their energy from:

• the sun

• the earth’s core

Biogeochemical cycles: include

• biotic components

• abiotic components

• abiotic reservoirs- where a chemical accumulates outside of living organisms

Biogeochemical cycles can be local or global

Carbon cycle

Carbon is found in

• the atmosphere

• fossil fuels

• dissolved in carbon compounds in the ocean

The return of CO2 to the atmosphere by respiration closely balances its removal by photosynthesis

The carbon cycle can be affected by things like:

• burning wood

• burning fossil fuels

Steps of the Carbon cycle

1. Carbon enters the atmosphere

2. Plants absorb CO2

3. Carbon enters the food chain

4. Carbon reenters the atmosphere

Sources of carbon to the atmosphere:

• burning

• decomposition

• respiration

Phosphorus cycle

The phosphorus cycle doesn’t have an atmospheric component

Rocks are the only source of phosphorus for ecosystems

Plants absorb phosphorus ions in the soil and build them into organic compounds

Phosphorus are returned ti the soil by decomposers

Phosphorus levels in aquatic ecosystems are typically low enough to be a limiting factor

Nirtogen cycle

nitrogen has 2 abiotic reservoirs

1. the atmosphere

2. soil

Nitrogen fixation:

• converts N2 compounds of nitrogen that can be used by plants

• is carried out by some bacteria

Decomposers- use their enzymes to change the dead living organims into Ammonium by using the process of decomposition

Denitrifiers- converts nitrate and nitrite in the soil into nitrogen gas that enter the atmosphere by using the process of denitrification

Nitrifying bacteria- converts the ammonia into nitrate by using the process of nitification

In aquatic ecosystems, primary production is limited by low levels of:

• Phosphorus

• Nitrogen

A rapid inflow of nutrients degrades aquatic ecosystems

Over time standing water ecosystems

• gradually accumulate nutrients from the decomposition of organic matter

• primary production increases in a process known as Eutrophication

Eutrophication depletes oxygen levels and decreases species diversity

Phosphate pollution leading to eutrophication comes from:

• fertilizers

• pesticides

• sewage treatment facilities

• runoff of animal waste

• feedlots

Although we depend on agricultural ecosystems we also get resources from natural ecosystems

Examples of natural ecosystems:

• supply of freshwater and some foods

• recycling nutrients

• decomposition of waste

• regulation of climate and air quality

A rapid increase of food production comes in the expense of natural ecosystems and the resources they produce

Human activities also threaten many ecosystems and their products