AP Biology

Study Guide

Created by Science National Honor Society 2017-18

Cheongna Dalton School


Table of Contents

  1. BioChemistry [pg. 2-21]
  2. Cell [pg. 22-27 ]
  3. Genetics [pg. 28-47]
  4. Virus [pg. 47]
  5. Evolution [pg. 48-53]
  6. Plants [pg. 54-56]
  7. Immune System [pg. 57 - 63]
  8. Nervous System [pg. 64-67]
  9. Endocrine System [pg. 68]
  10. Excretory System [pg. 69-70]
  11. Ecology [pg. 71-79]

BioChemistry

Type of Bond

Explanation

Ionic

These bonds result from transfer of electrons. An atom that gains electrons becomes an anion (a negative ion) and an atom that loses electrons becomes a cation (a positive ion).

Covalent

These bonds form when atoms share electrons. The resulting structure is called a molecule. Can be either single, double, or triple, depending on how many electrons the two atoms are sharing.

Nonpolar

This is a type of a covalent bond where the electrons are shared equally between two identical atoms. This type of bond occurs in diatomic molecules, such as H2 and O2.

Polar Covalent

This is a type of a covalent bond where the electrons are shared unequally. This type of bond occurs between any two different atoms.

Type of Bond

Explanation

London/ Dispersion

The attraction between temporary dipoles. This type of bond occurs between nonpolar molecules and the strength of the attraction is low.

Dipole-dipole

The attraction between permanent dipoles. This type of bond occurs between polar molecules and the strength of the attraction is medium.

Hydrogen

The attraction between a hydrogen atom and a highly electronegative atom such as nitrogen, oxygen, or fluorine. This type of bond occurs between polar molecules and the strength of the attraction is medium-high.

Ion-dipole

The attraction between a full ion and a dipole. This type of bond occurs between polar molecules and the strength of the attraction is high.

Property of Water

Explanation

Water is asymmetrical and highly polar.

The oxygen atom in a molecule of water exerts a greater pull on the share electrons than do the hydrogen atoms. Hence, one side of the molecule has a negative charge and the other side has a positive charge.

Water has a high specific heat.

Since molecules of water is connected by strong hydrogen bonds, it takes a lot of energy to increase the temperature of the water. As a result, water can resist changes in temperature and provide a stable environmental temperature for the organisms.

Water has a high heat of vaporization.

It takes a great amount of heat to evaporate water. As a result, the evaporation of sweat significantly cools the body surface.

Water is a universal solvent.

Since water is highly polar, it can dissolve all polar and ionic substances.

Water exhibits strong cohesion tension.

Water molecules tend to attract one another, allowing water to move up without the expenditure of energy, which is often referred to as transpirational-pull cohesion tension.

Ice floats on water.

Even though ice is a solid form of water, it is less dense than water, allowing it to float on the surface of water. This allows floating ice to insulate the liquid water below it, allowing living organisms to survive beneath the frozen surface during winter.

(1) short term energy storage

(2) structural support

Type

Explanation

Examples

Monosaccharides

Contain a single polyhydroxy aldehyde or ketone unit and tend to have the formula C6H12O6

Glucose

Galactose

Fructose

Disaccharides

Consist of two monosaccharide units linked by a covalent bond and tend to have the formula C12H22O11

Sucrose

Maltose

Lactose

Oligosaccharides

Contain 3 to 10 monosaccharide units

Raffinose

Polysaccharides

Contain very long chains of hundreds or thousands of monosaccharide units, which may be either in straight or branched chains

Cellulose

Glycogen

Starch

Chitin

Peptidoglycan

Type

Structure

Explanation

Fat

Most lipids consist of 1 glycerol and 3 fatty acids. Glycerol is an alcohol. A fatty acid is a hydrocarbon chain with a carboxyl group at one end.

Also known as triglycerides, fats can be distinguished by several categories.

If there are NO double bonds in the fatty acids then it is a saturated fat. If there is one or more double bonds in the fatty acid, then it is an unsaturated fat.

Trans fats are mostly artificial fats which are made by filling unsaturated fats with hydrogen through a process called hydrogenation.

Steroid

Steroids consist of four fused rings unlike other lipids.

Steroids are lipids that do not have the same general structure as other lipids. Some common steroids are cholesterol, testosterone, and estradiol.

Phospholipid

Phospholipids are modified lipids in which one of the fatty acids is replaced by a phosphate group. The fatty acids that are attached to the glycerol backbone form hydrophobic “tails”. The third hydroxyl group attaches to a phosphate group, which is charged and therefore hydrophilic.

When phospholipids are added to water, they assemble into a double-layered structure called a “bilayer”. The phosphate is outside and it shields the hydrophobic tails from water. The lipid bilayer is the structural basis of all plasma membranes.

Level

Bonds Involved

Explanation

Primary

1) Peptide bonds between amino acids

Primary structure is a unique linear sequence of amino acids. The slightest change in the sequence can have major consequences.

Secondary

1) Hydrogen bonding within the polypeptide molecule

Secondary structure consists of hydrogen bonds within the polypeptide chains that cause it to either coil in an alpha helix or fold into a beta pleated sheet.

Tertiary

1) Hydrogen bonding between R-groups

2) Ionic bonding between R-groups

3) Hydrophobic interactions

4) Van der Waals Interactions

5) Disulfide bonds between cysteine amino acids

Tertiary structure is the intricate three-dimensional shape or conformation of a protein that is superimposed on its secondary structure. Tertiary structure determines the protein’s specificity, which is the ability of a protein’s binding site to bind specific ligands.

Quaternary

1) Hydrogen bonding

2) Disulfide bonds

3) Hydrophobic interactions

4) Ionic bonding

Quaternary structure refers to proteins that consist of more than one polypeptide chain. Not all proteins possess a quaternary structure.

Stage

Type

Reactants

Products

Glycolysis

Both

1 molecule of glucose, 2 NAD+, 2 ADPs

2 molecules of pyruvate or pyruvic acid, 4 ATPs (Net gain of 2 ATPs), and 2 NADHs.

Glycolysis is the first step of cellular respiration. It is a 10-step process that occurs in the cytoplasm and releases ATP without using oxygen. The process requires 2 ATPs to activate and produces 4 ATPs, hence net gain of 2. ATP is produced through substrate level phosphorylation, which is a direct enzymatic transfer of a phosphate to ADP.

Oxidation of Pyruvate

Aerobic

2 molecules of pyruvate, 2 NAD+, and 2 coenzyme A

2 molecules of acetyl co-A, 2 NADH, 2 CO2

This process involves the conversion of pyruvate into a form that can enter the citric acid cycle. The produced CO2 is a waste product and it is exhaled.

Citric acid cycle or Krebs cycle

Aerobic

2 molecules of acetyl co-A, 2 FADs, 2 ADPs, 6 NAD+

4 molecules of CO2, 2 FADH2s, 2 ATPs, 6 NADHs

The Krebs cycle is a cyclical series of enzyme-catalyzed reactions, which takes place in the matrix of mitochondria and requires pyruvate, the product of glycolysis. The cycle occurs twice for each molecule of glucose, since 2 pyruvates are produced for each glucose during glycolysis. Each cycle produces 1 ATP by the process of substrate-level phosphorylation. Citric acid cycle is a multistep process.  

  1. Acetyl co-A combines with oxaloacetic acid and produces citric acid.
  2. Citric acid is converted into isocitrate by removing a water molecule and then placing it in a different location.
  3. Isocitrate is converted into an intermediate along with reduction of 1 NAD+ and then the intermediate is converted into alpha-ketoglutarate by removing a carbon dioxide molecule.
  4. Alpha-ketoglutarate is converted into succinyl-CoA by replacing another carbon dioxide with coenzyme A. This step also involves the reduction of another NAD+ into NADH.
  5. The coenzyme A in succinyl-CoA is replaced by a phosphate group and the resulting molecule is attached to GDP to form GTP, which results in a molecule called succinate.
  6. Succinate is turned into fumarate by removing 2 hydrogen atoms. Those atoms are used to reduce 1 FAD to FADH2.
  7. Fumarate is converted into L-malate by adding a water molecule to it.
  8. Finally, L-malate is oxidized to produce oxaloacetate, thus allowing the process to repeat. This final step also involves the reduction of another NAD+ to NADH.

Electron transport chain

Aerobic

10 NADHs, 2 FADH2, 6CO2

10 NAD+, 2 FAD, 6 H2O

The electron transport chain (ETC) is a proton pump in the mitochondria that combines an exergonic and an endergonic reactions. It uses energy released from the exergonic reaction to pump protons against a gradient from the matrix to the outer compartment, which results in the formation of proton gradient. The ETC carries electrons delivered by NAD and FAD to oxygen, which is a final electron acceptor. This process doesn’t produce any ATP, but it sets up everything for the final step of aerobic respiration.

Oxidative phospho- rylation

Aerobic

32 ADP

32 ATP

This process is also known as chemiosmosis and it occurs in mitochondria. It involves the oxidation of the NADH and FADH2 molecules and the energy from the proton gradient to phosphorylate ADP into ATP. In this step, oxygen acts as the final hydrogen acceptor. It forms water, which is a waste product that is excreted.

Alcoholic fermentation

Anaerobic

2 molecules of pyruvate and 2 NADHs

2 molecules of ethanol, 2 CO2, 2 NAD+

If there is no oxygen available, then the cell cannot perform the citric acid cycle and chemiosmosis. However, glycolysis can be repeated over and over as long as there is an adequate supply of glucose and NAD+. Fermentation allows to regenerate the NAD+ by oxidizing NADH, so glycolysis can be continued. Alcoholic fermentation is one type of fermentation. The beer, liquor, and wine industry depends on yeasts to ferment sugar into ethyl alcohol.

Lactic acid fermentation

Anaerobic

2 molecules of pyruvate and 2 NADHs

2 molecules of lactic acid, 2 NAD+

Lactic acid fermentation is the other type of fermentation, which results in the product of lactic acid and regeneration of NAD+. Lactic acid fermentation occurs in human skeletal muscles during extensive exercise since the body is unable to supply enough oxygen.

Step

Explanation

Photosystem II - P680

Light energy is absorbed by P680. Electrons from the double bonds in the head of chlorophyll a become energized and move to a higher energy level. They are captured by a primary electron acceptor.

Photolysis

During this step, water is split into two electrons, two protons, and one oxygen atom in order to provide electrons to replace those lost from chlorophyll a in P680. The oxygen atoms combine into O2 and are released from the cell as waste.

ETC

The electrons from P680 travel along an ETC, which consists of several molecules including cytochromes. The final destination of the electrons is P700. The flow of electrons is exergonic and provides energy for the next steps.

Chemiosmosis

The protons from water are pumped into the thylakoid space called lumen. These protons diffuse down the gradient from lumen through ATP synthase channels into the stroma. This produces ATP that will be used to power the Calvin cycle. The protons are eventually picked up by NADP that gets reduced to NADPH. NADPH carries those protons to the calvin cycle and they will be used to make sugar.

Photosystem I - P700

Energy is absorbed by P700. Similarly to P680, the electrons from the head of chlorophyll a become energized and are captured by a primary electron acceptor. The released electrons are replaced by electrons from P680 and this produces NADPH instead of ATP.


Cells

Eukaryotic Cells

Prokaryotic Cells

Differences

  • Larger
  • Have organelles
  • Mostly multicellular
  • Linear chromosome
  • Smaller
  • X membrane bound organelles
  • Unicellular
  • Circular chromosome

Similarity

  • Surrounded by plasma membrane
  • Contain cytoplasm and chromosome
  • Have ribosomes

Prokaryotes

Component

Function

Cell wall

  • Maintains cell shape
  • Provides physical protection
  • Prevents cell from bursting

Capsule

  • Covers and protects cell wall of some prokaryotes

Flagella

  • Allows movement

Cytoplasm/cytosol

  • Fills the cell
  • Gives a cell its shape
  • Keeps organelles in their place

Nucleoid

  • Chromosome is housed

Ribosomes

  • Protein synthesizers

Bacterial chromosome

  • Contains DNA

Plasmids

  • Contains genes for adaptations

F Plasmids

  • Forms sex pilus
  • Gives the cell ability to have fertility
  • Allows DNA donation

R Plasmids

  • Gives antibiotic resistance

Sex pili

  • Allows bacteria to transfer genetic information from one cell to another

Fimbriae

(type of pili)

  • Allows attachment to other cells
  • inanimates objects

Surface Area to Volume Ratio

Small cell size

Large cell size

Increased surface area to volume ratio

Decreased surface area to volume ratio

Performs chemical reactions slower but it has a easier time getting nutrients in and waste out

Performs chemical reactions faster but it has a harder time getting nutrients in and waste out

Eukaryotic cells are mostly larger than prokaryotic cells. In order to increase efficiency in the larger cell, eukaryotes evolved organelles.

Organelles are bacterium-sized, specialized structures within a living cell.

Eukaryotes

Component (Organelle)

Function

Nucleus

  • Contains DNA
  • Controls cell activity
  • Directs protein synthesis from DNA
  • Assembles ribosomes
  • Copies DNA instructions into RNA
  • Enclosed by nuclear envelope, which has nuclear pores that help the nucleus communicate with other parts of the cell

Lysosomes

  • Break down macromolecules and damaged organelles for recycling

Ribosomes

  • Produce proteins and enzymes

Peroxisomes

  • Contain enzymes that transfer hydrogen atoms from certain molecules to oxygen
  • Produces hydrogen peroxide as a by-product

Mitochondria

  • Cellular respiration
  • Produces ATP
  • Regulates cellular metabolism

Vacuoles

  • Digestion
  • Storage
  • Waste disposal
  • Water balance
  • Plant cell growth and protection

Smooth endoplasmic reticulum

  • Synthesis of lipids and metabolism of carbohydrates
  • Detoxification of drugs and poisons (therefore, liver cells have huge amounts of smooth ER)

Rough endoplasmic reticulum

  • Adds carbohydrates to proteins to make glycoproteins
  • Aids in synthesis of secretory and other proteins from bound ribosomes
  • Produces new membrane

Chloroplasts

  • Photosynthesis
  • Convert light energy into energy for later use
  • Food producers

Golgi apparatus

  • Modification of proteins
  • Synthesis of many polysaccharides
  • Sorting of Golgi products, which are then released in vesicles

Animal cell

Plant cell

Mitochondria

Chloroplast

Endomembrane system includes the following organelles: nucleus, rough and smooth endoplasmic reticulum, golgi apparatus, and lysosomes. It makes proteins and ships it to its final destination in the cell membrane or outside the cell.

Cytoskeleton

  • Provides structural support
  • Involved in various types of cell movement and motility
  • Made up of
  • Microfilaments
  • Actin filament → cytokinesis (cell division)
  • Intermediate filaments
  • Nuclear lamina → structural support and gives shape to nucleus
  • Microtubules
  • Flagella and cilia → movement
  • Spindle fiber → cell division

Extracellular matrix

  • Provides structural support to the cells
  • Anchorage
  • Cellular healing
  • Separates tissues from one another
  • Regulates cellular communication

The Evolution of Eukaryotes (Endosymbiotic Theory)

Mitochondria and chloroplast have their own DNA, their own ribosomes, a double cell membrane, and self-replicate, so there is a theory that states that the mitochondria and chloroplast were once free-living prokaryotes that got taken up by another prokaryote.

Plasma membrane

Structure

Function

  • Phospholipid bilayer
  • Proteins are embedded
  • Selective permeability
  • Protection
  • Structural support

Transport across plasma membrane

Passive transport

Active transport

Bulk transport = Active

Diffusion is the spontaneous movement of a substance down its concentration gradient.

Osmosis is the diffusion of water.

  • Hypertonic: solution outside has a higher solute concentration than the cytosol
  • Hypotonic: cytosol has a higher solute concentration
  • Isotonic: concentrations are equal

In facilitated diffusion, a transport protein speeds the movement of water or a solute across a membrane down its concentration gradient.

*No energy investment

*Uses energy

Specific membrane proteins use energy, usually in the form of ATP, to move solutes against their gradients.

Exocytosis: cell secretes certain biological molecules

Endocytosis: cell takes in molecules and particulate matter

  • Phagocytosis: a cell engulfs a particle
  • Pinocytosis:  a cell “gulps” droplets of extracellular fluid
  • Receptor-mediated endocytosis: a type of pinocytosis in which the receptor proteins enable the cell to gulp specific substances

Cell Signaling is the process in which cells interact with their environment and other cells around them.

4 Types of Cell Signaling:

  1. Endocrine → long distance
  2. Autocrine → cell sends signals to itself
  3. Juxtacrine → cell to cell contact

Junction

Animal

Plant

Transfer molecule (signal)

Gap

Plasmodesmata

Prevent leakage

Tight

Fasten 2 cells together

Desmosome

  1. Paracrine → short distance

There are receptors on the plasma membrane that can detect signals. Hormones are often used as cell signaling molecules for long-distance signaling by animal and plant cells. Signaling molecules that bind to membrane receptors trigger a three-stage cell-signaling pathway:

2 Types of Receptor:

  1. Membrane bind receptor
  1. GPCR
  1. GTD binds to G-protein → active
  2. GDP binds to G-protein → inactive
  1. RTK → triggers multiple transduction pathways at once
  2. Ligand-gated ion channel
  1. Intracellular receptor

  1. Reception: a signaling molecule binds to a receptor protein , causing the protein to change shape.
  2. Transduction: the signal is converted into a different form, which commonly involves a change in a protein’s shape.
  1. Apoptosis is programmed cell death.
  1. Death signaling ligand
  2. DNA damage in nucleus
  3. Protein misfolding in ER → prions → Alzheimer & madcow
  1. Crosstalk = one signal transduction pathway activate/inhibit another
  2. Second messenger
  1. CAMP made by adenylyl cyclase
  2. Calcium ions, which need additional second messengers (IP3 and DAG)
  1. Response: the regulation of transcription in the nucleus or of an activity in the cytoplasm

Genetics

<Key Words>

Word

Definition

gene

It is where our genetic information is coded; a form of hereditary unit

gametes

Reproductive cells in animals and plants

Somatic cells

All the cells of the body except the games

Locus

A gene’s specific location along the length of a chromosome

Karyotype

Ordered display of chromosomes

Sex chromosomes

X and Y chromosomes

Autosomes

All the other chromosomes except X and Y chromosomes

Diploid cell

Any cell with two chromosome sets (2n)

** zygote is diploid which contains both maternal gene and paternal gene

Haploid cell

Cell that contains a single set of chromosomes (n)

 

** eggs and sperms are haploid

Fertilization

The union of gametes; egg and sperm coming together

zygote

A form after egg and sperm gets fertilized

<Sexual and Asexual Reproduction>

Sexual Reproduction

Asexual Reproduction

Definition: two parents give rise to offspring that have unique combination of genes inherited from the two parents

3 sources of genetic variation

  • Independent assortment
  • Crossing over
  • Random fertilization

Definition: a single individual passes copies of all its genes to its offspring without the fusion of gametes

4 types of asexual reproduction

  • Binary fission
  • Budding
  • Fragmentation
  • Vegetative propagation        

Advantages and Disadvantages of Asexual and Sexual Reproduction

Asexual

Sexual

Advantage

Faster & save energy for finding mate

Genetic variation

Disadvantage

No genetic variation

Slow & energy consuming

<Cell cycle>

3 stages

<Interphase>

G1

1. Cells grow 2. Organelles replicate

S

DNA replication **Chromosome becomes chromatid

G2

Preparation, more cell growth

<M-Phase>

Mitosis

Meiosis I

Prophase

Chromatin becomes chromosome

Nuclear envelope dissolve

Spindle fibers form

Prophase I

Chromatin becomes chromosome

Nuclear envelope dissolve

Spindle fibers form

Synapsis: homologous chromosomes pair up

Crossing over: genetic recombination occurs at chiasmata and between non sister chromatids

Metaphase

Sister chromatids align at metaphase plate

Metaphase I

Homologous chromosomes align at metaphase plate

Anaphase

Sister chromatids move to opposite poles

** involves motor proteins

Anaphase I

Homologous chromosomes move to opposite pole and separate

Telophase

Chromosome becomes chromatin

Nuclear envelope forms

Spindle fibers dissolve

Telophase I

Chromosome becomes chromatin

Nuclear envelope forms

Spindle fibers dissolve

Meiosis II

** no interphase

Prophase II

Chromatin becomes chromosome

Nuclear envelope dissolve

Spindle fibers form

Metaphase II

Sister chromatids align at metaphase plate

Anaphase II

Sister chromatids move to opposite poles

** involves motor proteins

Telophase II

Chromosome becomes chromatin

Nuclear envelope forms

Spindle fibers dissolve

<Cytokinesis>

Physical separation of cell occurs

plant

animal

  • Cell plate
  • Vesicle forms
  • Cleavage furrow forms
  • Actin filaments + motor proteins pinch and divide the cell in half


<Mendel>

Genotype: genetic makeup of organism

Phenotype: physical appearance

Mendel’s 3 Laws

P

P

p

PP

Pp

p

Pp

Pp

Phenotype: 100% purple

Self fertilizes = Pp x Pp

P

p

P

PP

Pp

p

Pp

pp

Phenotype: 75% purple 25% white

Phenotypic ratio = 3:1

Genotypic ratio = 1:2:1

YR

YR

YR

YR

yr

YyRr

YyRr

YyRr

YyRr

yr

YyRr

YyRr

YyRr

YyRr

yr

YyRr

YyRr

YyRr

YyRr

yr

YyRr

YyRr

YyRr

YyRr

Phenotype: 100% Yellow Round

Self fertilizes = YyRr x YyRr

YR

Yr

Ry

yr

YR

YYRR

YYRr

YyRR

YyRr

Yr

YYRr

YYrr

YyRr

Yyrr

Ry

YyRR

YyRr

yyRR

yyRr

yr

YyRr

Yyrr

yyRr

yyrr

Phenotypic ratio = 9:3:3:1

Genotypic ratio = It’s all the alphabet combination up above

<Mendel’s Punnett Square>

Punnett Square: a device for predicting allele composition of all offspring resulting from cross between individuals of known genetic make up

<Rule of Probability> = multiplication method

[EX] YyRr x YyRr

** Y=yellow  y=green  R=round  r=wrinkled

YyRr x YyRr

Y

y

Y

YY

Yy

y

Yy

yy

YY and Yy= yellow

yy= green

R

r

R

RR

Rr

R

Rr

rr

RR and Rr= round

rr= wrinkled

Look at the traits separately and multiply those chances

¾ = yellow

¼ = green

¾ = round

¼ = wrinkled

  1. Yellow round = ¾ X ¾ = 9/16
  2. Yellow wrinkled = ¼ X ¼ = 3/16
  3. Green round = ¼ X ¼ = 3/16
  4. Green wrinkled = ¼ X ¼ = 1/16

<Character vs. Trait>

Character: a heritable feature that varies among individuals

ex) eye color

Trait: each variant for a character

ex) blue, brown, black

Test cross: a method to determine unknown genotype by crossing Dominant phenotype and homozygous recessive

[Ex] Is this flower PP (dominant) or Pp (Dominant recessive)??

        

PP

Pp

  1. Cross the flower with pp
  2. If the results shows 100% dominant phenotype, then the flower is PP
  1. Cross the flower with pp
  2. If the result shows 75% dominant and 25% recessive, then the flower is Pp

<Exceptions of Mendel’s law>

Blending Hypothesis

Mendelian Hypothesis

R= red

r= white

R

r

R

RR

Rr

r

Rr

rr

R= red

r= white

R

r

R

RR

Rr

r

Rr

rr

Codominance

Multiple allele

IA

IB

IA

IAIA

IAIB

Type A

Type AB

i

IAi

IBi

Type A

Type B

IA

i

IA

IAIA

IAi

Type A

Type A

i

IAi

ii

Type A

Type O

**Heterozygous advantage

b= brown

P= pigment controlling gene

p= no pigment

BP

Bp

bP

bp

BP

BBPP

BBPp

BbPP

BbPp

Bp

BBPp

BBpp

BbPp

Bbpp

bP

BbPP

BbPp

bbPp

bbPp

bp

BbPp

Bbpp

bbPp

bbpp


<Pedigree>

Dominant - it can’t skip generations

Recessive - can skip generations

Autosomal         v.s.         Sex linked

                Even distribution between                 More males are related

affected male and females

Morgan’s experiment

<Linked genes>

  1. Sex-linked recessive patterns
  1. [P] parental generation = XRXR x XRY    XR=Red        Y=White

[F1] 1st Filial Generation

XR

XR

XR

XRXR

XRXR

Y

XRY

XRY

Phenotype: 100% Red

  1. [F2] 2nd Filial Generation

XR

Xr

XR

XRXR

XRXr

Y

XRY

XrY

Phenotype: 75% red 25% white

Phenotypic ratio = 3:1

Recessive r showed white drosophila (fruit fly)

                Found that x-chromosomes carry recessive disorders

                Y chromosomes carry SRY gene

                        i) SRY gene - secondary sex male characteristics

Most characteristics derive from X because X chromosome is bigger than Y chromosome

Sex-linked disorders

                        X inactivation

  1. Linked genes

                2 requirements

  1. Close together
  2. On the same chromosome

GN

GN

GN

GN

gn

GgNn

GgNn

GgNn

GgNn

gn

GgNn

GgNn

GgNn

GgNn

gn

GgNn

GgNn

GgNn

GgNn

gn

GgNn

GgNn

GgNn

GgNn

Phenotype: 100% Gray Normal

Test cross  = GgNn x GGNN

GN

Gn

gN

gn

gn

GgNn

Ggnn

ggNn

ggnn

gn

GgNn

Ggnn

ggNn

ggnn

gn

GgNn

Ggnn

ggNn

ggnn

gn

GgNn

Ggnn

ggNn

ggnn

Parental  Non-parental                        

Phenotypic ratio = 1:1:1:1 expected

                      1:1:0:0 observed

Complete linkage  Incomplete linkage

<Recombination theory>

        = Nonparental

                Total

→ Dominantly inherited disorder

→ Recessively inherited disorders

Sex-linked disorders

X inactivation

Multifactorial disorders

<Genetic Disorders>

Alteration of chromosome number

Nondisjunction: the members of a pair of homologous chromosomes do not separate properly→ Error during Anaphase I and II of meiosis

Alteration of chromosome structure

Inversion

A chromosomal fragment attach in the reverse orientation

Translocation

A segment of gene move to another chromosome

Addition

An extra segment of sister chromatid due to duplication

Deletion

A chromosomal fragment is lost

DNA

History of DNA (+ Experiments)

  1. Griffith - Transformation
  1. When Griffith injected a S strain into the mouse, it died.
  2. When Griffith injected a R strain into the mouse, it lived.
  3. When Griffith injected a heat-killed S strain into the mouse, it lived
  4. When Griffith injected a combination of a heat-killed S strain and a R strain into the mouse, it died.
  5. Griffith concluded that something in the heat-killed S bacteria TRANSFORMED the hereditary properties of the R bacteria.
  1. 2 strains: a virulent S strain and a non-virulent R strain
  2. Transformation - change in genotype and phenotype due to assimilation of foreign DNA
  1. Avery - Transforming substance was DNA
  1. Hershey and Chase - DNA contained genetic material
  1. Bacteriophage - virus that infect bacteria
  1. Chargaff
  1. DNA composition varies within species
  2. Amount of A equals T, and C equals G (A=T, C≡G; Hydrogen Bond)
  3. Chargaff rule - one purine to one pyrimidine

i) Purine - double ring (A,G)

ii) Pyrimidine - single ring (T,C)

  1. Rosaline Franklin - x-ray crystallography
  1. Picture of DNA
  1. Watson and Crick - DNA is a double helix
  2. Meselson and Stahl - Semiconservative model
  1. During DNA replication

DNA Replication

  1. DNA helicase - unzip DNA
  2. RNA primase - make RNA primer for DNA polymerase III
  1. 5’ to 3’ direction
  1. DNA polymerase III - add new nucleotides
  2. DNA polymerase I - proofread, remove RNA primer
  3. DNA ligase - connect okazaki fragment (glue)
  4. Topoisomerase - prevent over-wiring of DNA (make loose)
  5. Single binding protein - stabilizing single-strand DNA

* Replication towards = favorable = leading fragment

* Replication against = unfavorable = lagging fragment

* Leading = no okazaki, Lagging = okazaki

6 types of RNA

  1. mRNA - carries information from DNA to ribose
  2. tRNA - help translation/help carry amino acids & anticodon to ribose
  1. Anticodon - complementary codons in mRNA
  1. rRNA - functional building blocks of ribosomes
  2. miRNA - degrade mRNA, block translation
  3. siRNA - degrade mRNA, block translation
  4. piRNA - induce heterochromatin

Gene expression

Central Dogma - DNA ➡ RNA ➡ protein

Transcription and translation always occurs from 5’ to 3’

        Transcription (3 stages)

  1. Initiation - RNA polymerase binds to promoter
  1. TATA box is included in promoter
  1. TATA box - nucleotide sequence only using A,T & less hydrogen bond
  1. Elongation - RNA polymerase slides down and adds complementary mRNA sequence
  2. Termination - transcription ends at terminator

RNA Processing

  1. 5’ cap & 3’ poly A tail
  1. Facilitate the export of mRNA to cytoplasm
  2. Protective mechanism against hydrolytic enzyme
  1. Alternative splicing
  1. Intron (non-coding) & Exon (coding)
  2. pre-mRNA goes through RNA splicing and results in mRNA
  1. Spliced by spliceosomes

Translation (3 stages)

  1. Initiation - ribosome binds to mRNA and slides down to start codon (AUG)
  1. Ribosomes have 2 units
  1. Large - tRNA
  2. Small - mRNA
  1. Elongation - codon recognition (codon of mRNA + anticodon of tRNA), peptide bond formation, translocation
  2. Termination - translation ends at stop codon (UAA, UAG, UGA), release factor

Prokaryote

Eukaryote

  • Cytoplasm
  • Translation occur immediately after transcription
  • Nucleus
  • Pause between transcription and translation

* Transcription and translation always occurs from 5’ to 3’

<Genetic engineering>

        Techniques

  1. Electrophoresis - separate DNA or proteins based on size
  2. Plasmid-based transformation - cut DNA restriction on enzyme at restriction sites and paste it using DNA ligase
  3. Restriction enzyme analysis of DNA - cut plasmid into different fragments
  4. Polymerase Chain Reaction (PCR) - produces many copies of a specific segment of DNA (forensic science) by amplifying DNA

        Products

  1. Genetically modified foods (GMO)
  1. Maximize food production (positive)
  2. Decreases diversity / allergic reaction can be prevented by the food table (negative)
  1. Transgenic animals - animals that carry a foreign gene that has been inserted into its genome
  2. Cloned animals - produce genetically identical animals
  3. Pharmaceuticals, such as human insulin or factor X
  1. Insert plasmid ➡ extract gene of interest ➡ insert to bacteria using plasmid ➡ use for phenotypic selection

Mutation

  1. Nucleotide variability
  1. Substitution (point mutation) ex) sickle cell anemia
  1. Missense - a change in nucleotide leads to a different amino acid
  2. Nonsense - premature stop codon
  1. Codon - triplet mRNA sequence)
  1. Silent - no effect on phenotype
  1. Frame shift (without replacement) - change the reading frame
  1. Addition
  2. Subtraction
  1. Chromosomal alteration

  1. Mutagen
  1. Substance that can cause damage in DNA
  1. Cigar, smoke, alcohol

Regulations of gene expression

Eukaryotic gene regulation

  1. Chromatin modification
  1. DNA methylation (negative)
  2. Histone acetylation (positive)
  1. Adding acetyl group in histone
  2. Loosens up chromatin structure - transcribe gene
  1. Euchromatin                v.s.                Heterochromatin

Loose                                        more coiled

                Gene expression                        no gene expression

  1. piRNA - includes (stimulates) heterochromatin structure
  1. Transcription
  1. Transcription factors
  1. Transcription factors bind
  1. Activator (positive)
  2. Repressor (negative)
  1. General transcription factors
  1. Bind to TATA box
  2. On promotor
  3. Help increase the affinity of RNA polymerase
  1. RNA processing
  1. Alternative RNA splicing - At times exons are treated as introns, vise versa
  2. Limited nucleotide - more opportunity
  3. UTR - untranslated region
  1. Control life span of RNA
  2. More protection
  3. Prevent mRNA to be cleaved

* not in prokaryote

  1. Translation factor
  2. Protein processing & degradation
  1. Post translational mechanism
  1. Chaperonin
  2. ER (golgi) = proteins modified
  3. Mark proteins with ubiquitin and degrade with proteasome

        Prokaryotic gene regulation

Operons

  1. Lac operon (positive)
  1. Inducible operon (on) - catabolism (digest lactose)
  2. Normally off (repressor)
  3. Inducer - lactose
  4. Activator - cAMP and CAP protein
  1. CAP protein - binds to promoter which increases binding affinity of RNA polymerase

                        * Lactose binds to the repressor which detaches to operator

  1. Repressor comes off
  2. Promoter allows RNA polymerase to enter
  3. RNA & proteins
  4. Lactose digested
  1. Trp operon (negative)
  1. Repressible operon (off) - anabolism (synthesize tryptophan protein)
  2. Normally on (repressor)
  3. Corepressor - Trp protein ➡ bind to repressor which binds to operator to turn off transcription
  1. Repressor off
  2. RNA polymerase enter
  3. Protein
  4. Makes more tryptophan

<Cell differentiation>

**Gene regulation results in different gene expression, leading to cell differentiation

Cell Differentiation: the process by which cells become specialized in structure and function

Homeotic genes: regulate development of anatomical structures in various kinds

Apoptosis: a programmed cell death; uses protease and nuclease

Cytoplasmic determinants: Maternal substances in the egg that influences the course of early development

Induction: signal molecules cause transcriptional change in nearby target cells

Virus

Virus = DNA + RNA + Protein “capsid

It’s not living because…

  1. It cannot reproduce on their own
  2. It depends on host to reproduce

2 Life Cycle of a Virus

  1. Lytic cycle → host dies
  2. Lysogenic cycle → host doesn’t die and viral DNA gets integrated into host DNA

2 Bacteriophages

Bacteriophage: a virus that infects and replicates

  1. Virulent phage uses only lytic cycle
  2. Temperate phage uses both lytic and lysogenic cycle

Retrovirus

Evolution

Evolution: the process by which different kinds of living organisms are thought to have developed and diversified from earlier forms during the history of the earth

Darwin

Lamarck

  • Current species are descendants of ancestral species                                                      Evolution: descent with modification
  • Only happens within populations not individuals
  • Fossils: Remains of organisms from the past
  • Resembles living species from the same region
  • Geographic distribution of species
  • Adaptation ←> Origin of new species
  • Fossils of extinct species: Fill in morphological (structure wise) gaps between present-day groups
  • Natural selection
  • Individuals with favorable inherited traits are more likely to survive and reproduce
  • Increases match between organisms & environment
  • Change in environment: adaptation to new conditions of new species
  • Can only increase/decrease heritable traits that vary in population
  • Artificial selection
  • Humans modified other species by selecting & breeding individuals with desired traits
  • Adaptive radiation
  • diversification of a group of organisms into forms filling different ecological niches

  • Species evolve through uses and disuses of body parts and inheritance of acquired characteristics

Evidence of Evolution

5 evidence of evolution

Pros

Cons

Fossils

  • Defect age of fossil
  • Transition fossils
  • Gaps

Comparative anatomy

  • Homologous structure
  • Vestigial structure
  • Analogous structure

Comparative embryology

  • Slow evidence of common ancestor
  • Structures get lost in adult form

Molecular data

  • Accurate
  • No data for extinct species

Biogeography

  • Endemic species
  • Gene flow

Reproductive Isolation

Prezygotic barrier

Postzygotic barrier

  • Before successful mating attempt
  • Habitat isolation
  • Temporal isolation
  • After successful mating attempt
  • Behavioral isolation
  • Mechanical isolation
  • Reproductive organs are incompatible
  • Genetic isolation
  • Gametes do not fuse
  • Hybrid breakdown
  • Eventually offspring of hybrid will be infertile
  • Reduced hybrid viability
  • Offspring dies at young age
  • Reduced hybrid fertility
  • Hybrids are sterile (no offspring)

leads to Speciation

2 types of speciation

Allopatric speciation

Sympatric speciation

  • Physical barrier
  • Natural selection
  • Gene flow
  • Transfer of alleles or genes from one population to another
  • Genetic drift
  • Change of frequency of allele in a population due to random sampling of organisms
  • No physical barrier
  • Polyploidy
  • Multiple sets of chromosome
  • ex) super-sized strawberry
  • Habitat differentiation (different niche)
  • Sexual selection
  • Intrasexual selection
  • Competition
  • Intersexual selection
  • Males - Females

Convergent evolution

Microevolution

  • Evolution of analogous features in distantly related groups
  • Groups independently adapt to similar environments in similar ways
  • Not evidence of evolution
  • Change in allele frequencies in a population over generations

Natural selection

Genetic shift

Gene flow

- Causes adaptive evolution

- Increase in specific alleles for fitness

- Sampling error

- Allele frequencies of a population change over generations due to chance

- Movement of alleles among populations (ex. pollen)

- Reduce genetic variation over time

- May decrease or increase fitness of population

Genetic variation

Formation of new alleles

  • Variations in heritable traits: prerequisite for evolution
  • Phenotypic variations
  • Difference in genes or DNA sequence
  • Gene variability: average percent of loci that are heterozygous
  • Measured at molecular level of DNA as nucleotide availability
  • Natural selection only acts on phenotypic variation
  • Mutation / Gene duplication
  • WITHOUT GENETIC VARIATION, NATURAL SELECTION CANNOT OCCUR!!!!
  • Mutation: Change in nucleotide sequence of DNA
  • Only mutations in cells that produce gametes can be passed to offspring
  • Point mutation: change in one base in a gene
  • Mutations in non-coding regions are harmless
  • Mutations that change phenotype often harmful
  • Mutations in protein production may be beneficial

Rapid reproduction

Sexual reproduction

  • Mutation rates in animals and plants are low
  • Recombination of alleles

Directional selection

Disruptive selection

Stabilizing selection

  • One extreme trait is selected

  • Two traits are selected and selects against one trait

  • Both extreme traits are left difficult to survive

Founder effect

Bottleneck effect

  • Few individuals isolated from population
  • Allele frequencies may be different from parent population
  • Drastic reduce in population due to environmental change

Key points

Relative fitness

Neutral variation

Diploidy

  • Contribution an individual makes to the gene pool of next generation
  • Selection indirectly favors certain genotypes by acting directly on phenotypes
  • Genetic variation that does not confer a selective advantage or disadvantage
  • Hidden recessive alleles
  • Heterozygotes can carry recessive alleles hidden from effects of selection

Balancing selection

Frequency-dependent selection

  • Natural selection maintains stable frequencies of two or more phenotypic forms in a population
  • Heterozygote advantage
  • When heterozygotes have a higher fitness than do both homozygotes
  • ex) sickle cell anemia
  • Fitness of a phenotype declines if it becomes too common in the population


Plants 

Phytochrome is synthesized in the Pr form. When plant is exposed to light, Pr converts to Pfr. In the dark, Pfr converts back to Pr. The concentrations of Pr and Pfr enable the plant to keep track of time.


Immune System

Pathogen: disease-causing agent (bacteria, fungi, viruses, etc.)

Immune system: the body’s defenses against pathogens


<Innate Immunity> - Non-specific

Invertebrates

Vertebrates

-Exoskeletons (insects)

-Lysozymes (enzymes in lysosomes that break down cell walls)

-Immune cells activated by recognition proteins; phagocytosis

  • Hemocytes that release antimicrobial peptides

<First line defense>

Skin, mucous membranes (releases mucus)

  • Contain lysozymes in mucus, saliva, tears, etc.)

Stomach acids


-Toll-like receptors (TLR) bind to molecule fragments to “recognize” pathogens

-Neutrophils (circulate blood) and macrophages (larger) are main phagocytic cells.

-Other phagocytic cells: dendritic and eosinophils, natural killer cells (abnormal array of surface proteins), and lymphatic system


-Interferons inhibits viral reproduction

-Complement proteins circulate blood plasma, only activated by substances on microbes, resulting in lysis of invasive cells


Upon injury/infection, an inflammatory response is triggered:

  1. Cytokines are released to increase blood flow to injury
  2. Mast cells in connective tissue release histamine molecules, making blood vessels more permeable
  3. Complement proteins increase histamine release
  4. More phagocytic cells enter injury
  5. Greater blood flow delivers more antimicrobial peptides
  6. Pus forms.

Other possible responses: fever, increased white blood cells, septic shock, diseases from chronic inflammation, etc.


If pathogens are able to evade the innate immunity, they may cause serious problems like tuberculosis, pneumonia, and meningitis

Adaptive Immunity

Antigen Recognition in B cells

Antigen Recognition in T cells

B cell antigen receptors are Y-shaped proteins of 4 polypeptide chains (2 identical heavy chains and 2 identical light chains).

The chains are paired in their variable and constant regions.

structure of b cell antigen receptor에 대한 이미지 검색결과

Antigen and antigen receptor bind early in B cell activation -> cells secrete antibodies (a.k.a. Immunoglobulin (Ig))

T cell antigen receptors are made of 2 polypeptide chains, α chain and β chain, which also have constant and variable regions. The chains are linked by a disulfide bridge.

structure of t cell antigen receptor에 대한 이미지 검색결과

T cells only bind to fragments of antigens (instead of epitopes like B cells), displayed by host cells’ proteins, called major histocompatibility complex (MHC) molecules.

Pathogen infects host cell -> cell’s enzymes divide antigens to peptides -> peptides/antigen fragments bind to MHC molecule -> MHC molecules are transported to surface to be displayed (antigen presentation)


<The 4 characteristics of Adaptive Immunity>

  1. Generation of B and T cell diversity
  1. The high diversity of B and T cell antigen receptors are mainly dependent of the arrangement of V and J (joining) segments and mutations during their development.
  1. Self-Tolerance
  1. Lymphocytes’ receptors are tested for self-reactivity; self-reactant receptors are rendered non-functional or destroyed by apoptosis.
  1. Proliferation of B and T cells
  1. Antigens and antigen receptors eventually match in their epitopes, activating the lymphocyte
  2. Lymphocyte goes through cell divisions, creating clones
  3. Some clones become effector cells (cells that take immediate action against antigens/pathogens)
  1. Effector cells -> B cells: plasma cells (secrete antibodies); T cells: helper T cells and cytotoxic T cells
  2. The rest -> memory cells (long-lived cells that can create more effector cells)
  1. The process where specific clones are created to fight against these antigens is called “clonal selection
  1. Immunology Memory
  1. The second immune response (2-7 days) is faster than the primary immune response (10-17 days) because B/T memory cells are already reserved after the initial response.

<Adaptive Immunity> — Defense Against Infection

  1. Humoral immune response (produces blood and lymph by facing toxins/pathogens)
  2. Cell-mediated immune response (specialized T cells destroy infected host cells)

T cell

Helper T cells = activate both humoral & cell mediated response


Cytotoxic T cells = destroy pathogen (infected cell)

B cell

Plasma cells = induce immune response (antibodies)


Memory cells = remember pathogen for second exposure

** make sure to know the process THOROUGHLY

Passive immunity

Active immunity

  • Passive immunity is a different type of adaptive immunity, where antibodies in the recipient are produced by another (takes longer because it happens w/o lymphocytes)

[EX] babies borrow mother’s antibodies through breastfeeding

  • Active immunity can be induced artificially via vaccines (made w/ inactivated bacterial toxins, weakened pathogens, genes in microbial proteins, etc.) — immunization — for primary immune response and immunological memory

[EX] vaccines

<Disruptions in Immune System Function>

  1. Allergies
  1. Exaggerated responses to allergens (type of antigens)
  2. Antibodies and allergens interact -> trigger mast cells to release histamine and inflammatory chemicals -> sneezing, teary eyes, etc. (sometimes anaphylactic shock)
  1. Autoimmune diseases
  1. Immunes system active vs. particular molecules in the body (i.e. histones and DNA)
  2. Related diseases: type 1 diabetes, multiple sclerosis, rheumatoid arthritis)
  1. Immune system avoidance
  1. Change in epitopes expressed (antigenic variation) through mutation, such as in influenza
  2. Largely inactive state (latency) before activation, such as in herpes
  1. Human immunodeficiency virus (HIV), the pathogen of AIDS, uses latency. It also mutates frequently and infects helper T cells., and has reduced interactions with antibodies and cytotoxic T cells. Results in AIDS, or impairment of immune responses in the body. HIV is transferred through body fluids such as semen, blood, or breast milk.
  1. Transplant rejection: receiver’s body thinks that transplanted organs are pathogenic

When adaptive immunity is inactivated, certain cancers become more frequent. (15-20% of all human cancers involve viruses)


Nervous System

Neurons: Building blocks of the body’s communication system

Nervous system:network of neurons that allows signals to move between brain and body

3 points of neuron

3 types of Neurons

Sensory Neuron

detects stimuli and transmit info to brain

Interneuron

process and integrate information

Motor Neuron

1) transmit signal

2) send info to effector cells (target)

3) stimulate gland or muscle activity

Nervous System

Central Nervous System

Peripheral Nervous System

Brain

Spinal Cord

Somatic

(voluntary)

Automatic

(involuntary)

Sympatric

(fight or flight)

Parasympathetic

(rest and digest)

<Brain Parts>

Central Nervous System

CNS

- Consists of brain and spinal cord

- Responsible for processing every sensation and thoughts you experience

- Sends message out to the other body parts to control movements, actions, and responses

Peripheral Nervous System

PNS

- Consists of a number of nerves that extend out of the CNS

- Axons from neuron cells

Somatic Nervous System

- Transmits sensory communications and responsible for voluntary action

Autonomic Nervous System

- Responsible for controlling involuntary functions like heartbeats, digestion etc

- Regulate activities of the smooth muscles, cardiac muscles and glands

Sympathetic Nervous System

- Controls the body’s response to emergencies

(fight or flight)

- Makes heartbeats faster

Parasympathetic Nervous System

- Counters the Sympathetic Nervous System

- Calms the body up aroused by sympathetic nervous system

How neurons communicate

Dendrite→ soma→ axon→ axon terminal → synapse→ dendrite ...

             Pre-synaptic neuron                          post-synaptic neuron


Synapse

Key neurotransmitters

Action Potential

action potential graph에 대한 이미지 검색결과

Nerve cells(neurons) communicate each other with electrical signaling. In order to make that, cells use the concentration difference between sodium and potassium ions.

  1. Stimulus: sodium ions out and potassium ions in, using ATP to keep resting membrane potential
  2. Depolarization: sodium channel opens up → sodium inside the cell, increasing voltage from -70mv to 30mv. Passive transport
  3. Action Potential: climax of the depolarization
  1. Definition: A short-term change in the electrical potential on the surface of a cell in response to stimulation, and then leads to the transmission of an electrical impulse that travels across the cell membrane.
  1. Repolarization: potassium channel opens up. Potassium ions goes outside the cell, which decreases the voltage from 30mv to -70mv. Passive transport
  2. Refractory period (hyperpolarization) : potassium channel close too slowly so too much potassium goes out, which cause the voltage to go below -70mv

3 pump/channels involved in dividing action potential

Na+ and K+ Pump

Na+ OUT and K+ IN

Helps neurons maintain at resting potential (-75mv)

Voltage-gated Na+ Channel

<depolarization>

Na+ IN, increase voltage

-75 mV → +35 mV

Voltage-gated K+ channel

<repolarization>

K+ OUT, decrease voltage

+35 mV → -75 mV

After signal reaches axon terminal…

  1. Ca2+ ion channel opens, and Ca2+ ion moves in which stimulate release of neurotransmitters at the synapse
  2. Neurotransmitter released → bind to membrane bound receptor on postsynaptic neuron

After signal passes postsynaptic neuron, 2 mechanisms can take place

  1. Enzymatic breakdown of neurotransmitter in the synaptic area
  2. Reuptake of neurotransmitter by presynaptic neuron

Endocrine System

Hormone: chemical signal that are secreted into circulatory system and communicate via regulatory messenger within the body. In order to communicate, it is essential for a target cell to have a receptor for that particular hormones

Example of hormones: Insulin→ blood glucose level down

                                     glucagon→ blood glucose level up

3 lipid-soluble Hormones

Gland: part of body that produces and secretes hormones


Excretory System

Excretion: the process that rids the body of nitrogenous metabolites and other metabolic waste products

Osmoregulation: the general term for the processes by which animals control solute concentrations and balance water gain and loss

Osmoregulation of a marine fish and freshwater fish

** left is marine fish and right is freshwater fish

Marine Fish

- High osmolarity (total solute concentration) outside than inside

- Fish LOSES water because water flows from where there is low osmolarity (low solute concentration) to high osmolarity (high solute concentration)

- FISH < WATER in terms of solute concentration

Freshwater Fish

- Low osmolarity (total solute concentration) outside than inside

- Fish GAINS water because water flows from where there is low osmolarity (low solute concentration) to high osmolarity (high solute concentration)

- FISH > WATER in terms of solute concentration


 Animal Excretory Process through kidney

1. Filtration: The excretory tubule collects a filtrate from the blood. Water and solutes are forced by blood pressure across the selectively permeable membranes of a cluster of capillaries and into the excretory tubule.

2. Reabsorption: The transport epithelium reclaims valuable substances from the filtrate and returns them to the body fluids.

3. Secretion: Other substances, such as toxins and excess ions, are extracted from body fluids and added to the contents of the excretory system

4. Excretion: The altered filtrate (urine leaves the system and the body

1. Nephron: function unit of a kidney

  1. It is a single long tube with ball of capillaries (glomerulus)

2. Filtration happens at renal artery.

**Renal artery: glomerulus surrounded by Bowman’s capsule

3. As fluid descend along Loop of Henle, reabsorption happens

4. As fluid ascend along Loop of Henle, secretion happens

5. Urine is excreted through distal tube

Ecology

<Population Ecology and the Distribution of Organisms >

What is Ecology? 

It is the scientific study if the interactions between organisms and the environment. It will mainly focus on what controls the distribution of species and their overall densities throughout different environments.

There are different types of ecology systems:

Organismal Ecology- Only concerned an organism’s physical features, and behavior and how they face the environment.

Population Ecology- It includes a group of individuals of same species living in an area. It looks at the overall size of the population and its trend over time.

Community Ecology- It includes a group of population of different species in an area. It looks upon the interactions between species and how competition affects the whole cycle.

Ecosystem Ecology- It includes the whole community of organisms and the interactions within them. The overall energy flow and chemical cycling is an important part.

Landscape Ecology- It is a set  of ecosystems. It examines the factors that control the exchange of energy and materials over several ecosystems.

Global Ecology- Also known as biosphere. It sums up all ecosystems and looks from the biggest scope out of all the other systems.

The most significant influence on the distribution of organisms on land in climate.

Abiotic- Nonliving (Water, Salinity, Temperature, pH, Nutrients, Sunlight)

Biotic- Living (Predation, Parasitism, Competition, Disease)

How large bodies of water and mountain affect climate:

As air flows inland from the ocean or the sea, it will nullify the temperatures over the shoreline and areas that is close. They will travel upwards due to the mountain and will turn into either rain or snow moisturizing one side of the mountain. As water gets lost on one side, the other side will not receive any kind of precipitation and remain dry.

The climate on the distribution of biomes is usually shown with a climograph.

Three important Terrestrial Biomes:

-Tropical Forest

-Savanna

-Desert

Other biomes are not a significant part of the test.

Zonation in a lake:

Oligotrophic lakes: Nutrient-poor and oxygen-rich

Eutrophic lakes: Nutrient rich and oxygen depleted


Dispersal: The movement of individuals away from their area of high population density.

Organisms can move in and out of a community. Moving out is called Emigration while moving in is called immigration.

Dispersion: The pattern of spacing among individuals within the boundaries of the population.

There are three types of Dispersion:

Type of Dispersion

Description

Clumped

Organisms are gathered in groups with a distance.

Uniform

Organisms are spread out evenly.

Random

Organisms are spread out without a pattern.

Survivorship Curve

The graph is a plot of the proportion or numbers in a cohort still alive at each age.

Analysis:

Type I- The organism has a high probability of surviving at its beginning part of its life, but its surviving probability will fall as it gets older. (Human)

Type II- The organism has the same probability of surviving throughout its whole life. (Meerkat)

Type III- The organism has a high risk of dying off at an earlier stage of its life than later on.

<Population>

Change in population size= Births + Immigrants - Deaths - Emigrants

Change in population size/ Change in time= Births- Deaths = R

= r(per capita change in population)N

These equations are usually called upon as exponential and the results essentially are exponential population growth.

With a higher “r” the slope of the exponential graph will be steeper and vice versa.

Carrying Capacity: Usually symbolized as “K”, it shows the maximum population an environment can handle with its resources and space.

A usual population in a niche will look like the following. It will increase at distinct rates but will eventually reach its maximum. When it goes over the carrying capacity, they will run out of resources and eventually move down towards the carrying capacity again.

The Logistic Growth Model

dN/dt = rN [K - N/K]

where dN/dt = change in population size; r = intrinsic rate of increase; N = population size; K = carrying capacity

The Exponential Growth Model

Ex. Zebra Mussels

The overall physical and genetic traits that gave influence to an organism’s reproduction and survival is known as life history.

K-selection (Density-Dependant): Type of organisms where selection for traits are sensitive to population density. They emphasize in variations within an organism rather than number. (Humans)

R-selection (Density-Independent): They try to maximize reproductive success in low densities. In other words, they emphasize in number than variations. (Bacteria)

Density-dependant regulations:

Competition- Populations will compete for space, nutrients, and other growth factors.

Predation- A certain group of organisms will eat up other group of organisms. One will develop in offensive physical traits, while other will develop in defensive traits.

Territoriality- It can limit population density when space becomes the resource for the animals to  survive in an environment.

<Species Interactions>

Interspecific competition: Usual competition that occurs when two populations have to both compete for resources.  

Exploitation: This is when one population will benefit while the other is harmed.

In order to survive, organisms develop several kinds of camouflage skills such as cryptic,  coloration, aposematic coloration, and Batesian mimicry.

Types:

Predation: +/-

Herbivory: +/-

Parasitism: +/-

Mutualism: +/+

Commensalism: +/0

Trophic Structure:

Quaternary consumers

I

Tertiary consumers

I

Secondary consumers

I

Primary Consumers

I

Primary Producers

Energy transfer between trophic levels is typically only 10% efficient.

As energy moves down a level, such as from Secondary consumers to Primary consumers, the amount of energy received will be only 10%.  → 10% rule

When the cycle runs and there is transfer of energy, it is referred to as the food chain.

Dominant species: Strongest in the community

Keystone species: They play a big role in a community by being a part of a crucial cycle and will change the way community runs drastically.

Ecological succession

First an area will be wiped out by a natural disaster, which is called as the primary succession.

When the niche grows back with resources with nutrient-rich soil, it is called the secondary succession.

The niche will eventually grow and proliferate and return to its lush state.

Ecosystems and Energy

Conservation of Energy- Energy in an environment can change its energy forms but is always totally conserved.

Conservation of Mass- The chemical elements are continually recycle, therefore the overall mass in all parts of the environment is conserved.

The primary producers will first receive sunlight and transfer its energy to the primary consumers. Then the energy will be transferred to the secondary/tertiary consumers, Detritus, and lastly microorganisms. Throughout the cycle, energy can be released through heat but is still conserved as other forms of energy.

Gross primary production (GPP)- Amount of energy from light converted to chemical energy of organic molecules.

Net primary production (NPP)- GPP minus autotrophic respiration.

Basically NPP is the real energy amount an organism consumes over time.

Net ecosystem production (NEP)- GPP minus total respiration of all organisms over time.

Eutrophication happen from dead bodies of animals as it can supply the soil with nutrients, provide as a source of food, and natural resources.

Production efficiency= (Net secondary production xv 100%) / (Assimilation of primary production)

For example in a typical caterpillar, if it receives 200J amount of energy, 100J will be part of its waste product, 67J for cellular respiration, and barely 33J for growth.


Nitrogen Cycle:

Water cycle:

Every other cycle is not a big part of the AP.

<Global Ecology and Conservation Biology>

Conservation Biology: Discipline that integrates ecology, physiology, molecular biology, genetics, and evolutionary biology to conserve biological diversity through all scopes.

Three levels of Biodiversity:

-Genetic Diversity

-Species Diversity

-Ecosystem Diversity

Due to such active human activities, it mixes up the environment animals live in which can eventually lead to a threat to biodiversity.

A group of animals can fall into either endangered species or threatened species.

It can also lead to introduced species, which are animals that have been intentionally or accidentally moved to a non-native area.

Overharvesting: Harvesting of wild organisms at rates exceeding the ability of their populations to rebound.

People seek for pure profit and ignore ethical guidelines.

Recently, there has been mitochondrial DNA tests to prevent such practices.

Movement corridors are made to help animals cross man-made infrastructures such as bridges safely.

Smaller populations are more bound to be affected by inbreeding and lead to extinction.

Minimum viable population (MVP)- Estimated computer models that integrate many factors and calculate the amount of animals of a species needed in order to sustain its population.

Effective population size:

When there is a sudden population boom, it will cause a critical load in a certain region and damage the balanced ecosystem.

Biological magnification: It describes a phenomenon of piling up of toxin materials as it moves town the trophic level.