Biology 311C

Big Idea 1

Hierarchy of Life

Biosphere

Ecosystem

Domains of Life

Bacteria

Archaea

Eukarya

Community

Popullation

Organism

Humans

96%

Oxygen

Carbon

Hydrogen

Nitrogen

Calcium

Phosphorous

Potassium

Sulfur

Sodium

Chlorine

Magnesium

Classification

Domain

Kingdom

Phylum

Class

Order

Family

Genus

Species

Organ System

Organ

Tissue

Cell

Organelle

Molecule

Atom

Cell Structure

Prokaryotic

Nucleoid

Plasmid

Ribosome

Granule

Cystoplasm

Pilli

Flagellum

Capsule

Cell Membrane

Eukaryotic

Nucleus

Endoplasmic Reticulum

Smooth E. R.

Rough E. R.

Ribosome

Golgi

Lysosome

Peroxisome

Micro-Fillaments

Microvilli

Centosome

Flagella

Mitochondria

Outer Membrane

Inner Membrane

Inter Membrane Space

Cristae

Matrix

Ribosome

DNA

ATP Synthase Particles

Plant

Nucleus

Ribosome

Vacuole

Plasmodesmata

Mitochondria

Chloroplast

Outer Membrane

Inter Membrane Space

Inner Membrane Space

Stroma

Granum

Thylakoid

Thylakoid Space

Golgi

Plasma Membrance

Microtubuole

Biological Membrane

Phosphlipid Bilayer

Globular Protein

Glycolipids

Cholesterol

Cellular Transportation

Diffusion

Passive Transport

Osmosis

Tonicity

Isotonic

Hypertonic

Hypotonic

Facillitated Diffusion

Aqua Porins

Active Transport

Carrier Proteins

Voltage-Electrical Potential Energy

Membrane Potential

Electrical Potential

Interior Membrane

Exterior Membrane

Electrochemical Gradient

Chemical Force

Electrical Force

Co-Transport

Exocytosis

Biological Molecules

Proteins

Amino Acids

Protein Structure

Primary

Chaperonin

Secondary

Tertiary

Quaternary

Enzymes

Lipids

Nonpolar Molecules

Fats

Phospholipids

Steroids

Carbohydrates

Monosacharides

Nucleic Acids

DNA

Double Strand

2 Carbon & H Group

Amino Acids

Adenine

Guanine

Cytosine

Thymine

RNA

Single Strand

2 Carbon & OH Group

Amino Acids

Adenine

Guanine

Cytosine

Uracil

Big Idea 3

DNA & Replication

Structure

Nucelotide Bases

A=30.4%

Purine

T=30.1%

G=19.6%

C=19.9%

Pyrimidines

Double Helix

James Watson & Francis Crick

Nitrogenous Base

Pentose Sugar Deoxyribose

Phosphate Group

Replication

Models

Conservative

Semiconservative

Dispersive

Parts

Origin of Replication

Specific Sequence of DNA nucleotides

Replication Fork

Where parental strands are being unwound

Helicase

Enzyme unwinds helix to create template strands

Topoisomerase

Breaking, Swiveling, & Rejoining of tangled DNA Strand Upstream

Primer

RNA chain that adds RNA nucleoides

RNA Primase

Enzyme that synthesises RNA Primer Chain

DNA Polymerase 3

Adds DNA nucleotides to RNA primer 5'-3'

Okazaki Fragments

DNA Polymerase 1

Replaces the RNA with DNA

Prokaryotes

Occurs in the Cytosol

Transcription

Prokaryotic

DNA

Shine Dalgarno

RNA Polymerase 2

mRNA

Eukaryotic

DNA

Promoter (TATA Box)

Start Codon

Transcription Factors

RNA Polymerase 2

Pre-mRNA

5' Cap

Start Codon

Stop Codon

Polyadenylation Signal

Poly - A Tail

Exon 1

Intron

Exon 2

snRNPs

Spliceosome

mRNA

Translation

Prokaryotic

Occurs With Transcription

No Cap or Tail

Eukaryotic

5'Cap leads mRNA out of Nucleus

Attaches to Ribosome

tRNA attaches amino acid bases to poypeptide chain

Big Idea 2

Cellular Respiration

Anaerobic

Fermentation

Pyruvate

Alcohol

CO2

Pyruvate loses 2 CO2 to make 2 Acetaldehyde

Acetaldehyde

Acetaldehyde gains 2 H+ ions from the 2 NADH made in Glycolysis to produce 2 NAD+ and the 2 H+ions attach to the 2 Acetaldehyde to make 2 Ethanol

Ethanol

2 ATP

2 NADH

Both used to make Ethanol producing 2 NAD+

2 Ethanol

Lactic Acid

2 Lactate

2 Pyruvate gain 2H+ ions from the 2 NADH made in Glycolysis to make 2 NAD+ and 2 Lactate

Aerobic

Cellular Respiration

Glycolysis occurs in the cytosol and Krebs Cycle occurs within the Mitochondria

Glycolysis (Energy Investment)

Glucose

Reactant: 6 Carbon Glucose Sugar Molecule

Hexokinase

Hexokinase transfers a phosphate group from ATP to glucose, making it unstable (traps glucose in the cell)Molecule becomes: Glucose 6-phosphateEnters enzyme: Phosphogluco-isomeraseconverts Glucose 6-phosphate to its isomerMolecule becomes: Fructose 6-phosphate

Phosphofructokinase

Adds phosphate to Fructose 6-phosphate from ATP in the cell making it very unstable(can be used for regulation)Molecule becomes: Fructose 1,6-bisphosphateEnters Adolase: Makes 2 molecules one of which is converted to be like the other forming 2 molecules of Glyceraldehyde 3-phosphate

Triose Phosphate Dehydrogenase

Enzyme oxidizes molecules transfering the 2 electrons to NAD+ to from 2 NADH (electron carrier: energy carrier)and 2 H+ ionsAttaches a phsphate to make it unstableMolecule becomes: 1,3-bisphosphogylerate

Phosphoglycerokinase

Enzyme uses the phosphates from previous molecule to make 2 ATP (substrate level phosphorylation)A substrate (1,3-bisphophoglycerate) synthesized the production of ATP. Molecule becomes: 3-Phosphoglycerate

Phosphoenol-Pyruvate(PEP)

3-Phosphoglycerate enters phosphoglyceromutase which moves the phosphate group around to make the molecule unstalbeMolecule becomes: 2-phosphoglycerateEnters enolase wich forms a double bond in the R - Group by extracting water making Pohsphoenolpyruvate (PEP) Super unstable and HIGH Energy

Pyruvate

PEP enters the enzyme Pyruvate Kinase which transfers a phosphate from PEP to ADP to make 2 ATP (Another Substrate Level Phosphorylation)Final: 2 molecules of Pyruvate4 ATP produced - 2 used: 2 ATP Yield2 NADH Yield2 Pyruvate

Split: 2 (3) Carbon Sugars

2 ATP

4 ATP Used

Oxidation

2 NADH

2 Pyruvate

Krebs Cycle (Energy Payoff)

Pyruvate

Enters Mitochondrion

Acetyl CoA

Pyruvate cannont enter Krebs CycleIt is converted into Acetyl CoA by removing CO2 and transfering an electron with energy to NAD+ to make NADH. Since 2 pyruvate are formed, 2 NADH are formed and 2 Acetyl CoA are made

Oxaloacetate

Acetyl CoA attaches to Oxaloacetate 1 at a time!!!Produces the molecule Citrate

Isocitrate

Citrate is converted into Isocitrate by dehydration process. Isocitrate loses energy to NAD+ to make NADH. It also loses CO2. Molecule becomes a-KetoglutarateBecomes oxidized, makes another NADH and loses another CO2. Molecule becomes Succinyl CoA.

ATP Generation

The Co-A group is removed By the addition of a phosphate which is then removed to be added to GDP to make GTP which is then transfers it's phosphate to ADP to make ATP.

Oxaloacetate

The remaining molecule after the production of ATP is Succinate which transfers 2 electrons to FAD to make FADH2 becoming Fumarate which gains water to become Malate which is unstable enough to oxidize and make another NADH to end/ start the cycle with another oxaloacetate.

2 Acetyl CoA

2 ATP

1 ATP per Acetyl CoA

6 NADH

3 NADH per Acetyl CoA

2 FADH2

1 FADH2 per Acetyl CoA

Totals

4 ATP

2 FADH2

10 NADH

Photosynthesis

Photosystem 2

Light

Pigment Molecule

P680

Primary Acceptor

Electron Transport Chain

ATP

H2O

Photosystem 1

Energy from ETC in Photosystem 2 transfers to Photosystem 1

ETC Energy Excites P700

Primary Acceptor

Light Replaces P700 Energy

ETC

Cyclic Electron Flow

The plant process switches to Cyclic Electron Flow when enough NADPH is made within the cellThe plant produces ATP

Ferredoxin

Cytochrome Complex

ATP

NADPH