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DNA Structure

Double Helix

Made up of Deoxyribose

Attached to the sugars are the four Nitrogenous bases:

Adenine (A)

Connected by chemical bonds

Cytosine (C)

Guanine (G)

Connected by chemical bonds

Thymine (T)

Made up of Phosphate groups

The strands run antiparallel

5' -> 3'

3' -> 5'

Discovered by James Watson and Francis Crick

Enables a cell molecule to copy itself during cell division

DNA Regulation

Eukaryotes

Transcription Factors

General

(Basal/background) low levels of transcription

Specific

Activators

Increases levels of transcription

Repressors

If there is a high level of transcription, reduces levels

10nm fiber

30nm fiber

300nm fiber

Metaphase Chromosome

Nucleosomes

Control Elements

Proximal

Bind to general transcription factors

Distal

Bind to specific transcription factors (activators/repressors)

Enhancers

Prokaryotes

DNA Expression

Gene Activation

Regulatory Elements

Promoter

Enhancers

Silencers

Transcription Factors

Chromatin Modifications

Histone Acetylation

Remodeling

Transcription (DNA --> RNA)

The process of synthesizing RNA from a DNA template.Enzymes and Factors: Prokaryotes: RNA polymerase.Eukaryotes: RNA polymerase II, general transcription factors, spliceosome (for RNA splicing).

RNA Polymerase

Transcription factors

Elongation

Termination

RNA Splicing

Exons (Expressed)

Introns (Removed)

Experiments

Meselson and Stahl Experiment (1958)

Purpose: To determine the mechanism of DNA replication (conservative, semiconservative, or dispersive). Method: Nitrogen isotopes (¹⁵N, heavy, and ¹⁴N, light) were used to label DNA. Bacteria were grown in ¹⁵N medium to incorporate the heavy isotope into their DNA. They were then shifted to ¹⁴N medium, and DNA was isolated after one and two rounds of replication. The DNA was analyzed using density gradient centrifugation. Results: First generation (after one replication cycle): All DNA had an intermediate density, ruling out conservative replication. Second generation (after two replication cycles): Half the DNA had intermediate density, and half had light density, confirming semiconservative replication. Conclusion: DNA replication follows the semiconservative model, where each daughter molecule contains one original strand and one newly synthesized strand.

Griffith Experiment (1928)

Purpose: To demonstrate the phenomenon of transformation in bacteria. Method: Used two strains of Streptococcus pneumoniae: S strain: Smooth, virulent (caused pneumonia).R strain: Rough, non-virulent. Griffith injected mice with: Live R strain (non-virulent): Mice lived. Live S strain (virulent): Mice died. Heat-killed S strain: Mice lived. Heat-killed S strain + live R strain: Mice died, and live S strain bacteria were recovered from their blood. Results: The non-virulent R strain was transformed into the virulent S strain by a "transforming principle" from the heat-killed S cells. Conclusion: This experiment suggested the existence of a genetic material responsible for transformation, later identified as DNA

Hershey and Chase Experiment (1952)^

Purpose: To confirm that DNA, not protein, is the genetic material. Method: Used bacteriophages (viruses that infect bacteria) and labeled their components with radioactive isotopes: ³²P: Labeled DNA (phosphorus is present in DNA). ³⁵S: Labeled protein (sulfur is present in proteins but not in DNA). The phages were allowed to infect bacteria. After infection: The mixture was agitated in a blender to separate the phage protein coat from bacterial cells. The solution was centrifuged to isolate the bacterial cells. Results: Radioactive ³²P was found inside the bacterial cells, indicating DNA had entered. Radioactive ³⁵S remained outside in the phage coats, indicating protein did not enter. Conclusion: DNA is the genetic material responsible for heredity.

Chargaff's Rule (1950)

Purpose: To analyze the composition of DNA and determine its structural characteristics. Observations: The amount of adenine (A) equals the amount of thymine (T), and the amount of cytosine (C) equals the amount of guanine (G): A = T and G = C A = T and G = C The ratio of purines (A and G) to pyrimidines (T and C) is constant: (A + G) = (T + C) (A + G) = (T + C) Base composition varies between species, suggesting a role in genetic diversity.

mRNA Processing

5' cap

Poly A tail

Splicing

Translation

Translation is the synthesis of a protein from an mRNA template.Enzymes and Factors Ribosomes (small and large subunits).tRNA synthetase for charging tRNAs with amino acids.Elongation factors

DNA Replication

Process by which a cell copies its DNA to produce two identical copies

Initiation of DNA Replication

Enzymes separate the two strands

Topoisomerase breaks, swivels and rejoins parental DNA ahead of replication fork

Relieves the strain caused by unwinding

Single-strand binding proteins stabilize unwound parental strands

Primase synthesizes RNA primers and uses parental DNA as a template

Helicase unwinds and separates parental DNA strands

Next, there is a formation of a daughter strand or a new polymer of DNA

DNA Polymerases

Add complementary base to daughter strand

Need RNA primer to add nucleotides to

Nucleotides added to 3' end of primer

Polymerization occurs in 5' to 3' direction

Need sliding clamp

Converts DNA pol III from being distributive to processive

Two DNA polymerases needed in bacterial replication

DNA Polymerase I

DNA Polymerase III

Synthesis of Leading Strand

After RNA primer is made, DNA pol III starts to synthesize the leading strand

Leading strand is elongated continuously as the fork progresses

Many Okazaki fragments are made at the lagging strand

DNA pol I removes the RNA primer and replaces it with DNA nucleotides

DNA ligase seals gaps

Models of DNA Replication

Dispersive Replication

Each strand of both daughter molecules contains a mixture of old and newly synthesized DNA

Conservative Replication

Two parental strands reassociate after functioning as templates for new strands

Restore the parental double helix

Operon

lac Operon

Operator

Negative Regulation

Repressor bound

No transcription

No repressor

Positive Regulation

Activator bound

Transcription

No Activator

Promoter

Lac L: Regulatory Gene

Operon On

Lactose present

Lactose Present, no glucose

Operon Off

Glucose present

Glucose and lactose present

Nothing Present

Structural genes

Lac Z: B-galactoisdase

Lac A: Trans-acetylase

Lac Y: Permease

Histones

H1

links histones together to form the nucleosome

H2A

Histone Core (Octamer)

H2B

H3

H4

Semiconservative replication

Two strands of the parental molecule separate and function as a template for synthesis of a new, complementary strand

Parental molecule has two complementary strands of DNA

Each base is paired by hydrogen bonding with its specific partner

Two DNA strands are separated

Each parental strand serves as a template for a new complementary strand.

Nucleotides complementary to the parental strand are connected

Form the sugar-phosphate backbones of the new daughter strands

Concept Map 1

Biological Molecules

Lipids

Carbohydrates

Structure

Carbon

Oxygen

Hydrogen

Monosaccharides

Types

Simple

Examples:
- Sugars
- White bread

Quick bursts of energy
due to the body being
able to metabolize quickly

Complex

Examples:
- Starches
- Legumes
- Whole Grains

Raises blood glucose levels
for longer and produce
a more lasting elevation
in energy.

Both provide sources
of energy

They both contribute to
cell structure: Lipids form
the phospholipid bilayer, while carbs contribute to glycoproteins

Nucleic Acids

Subtopic

Proteins

Cells

Eukaryotes

Plant Cells

Cell Wall

Gives structure/support to cell

Chloroplasts

Large Central Vacuole

Plasmodesmata

Key in movement of molecules between cells.

Animal Cells

Lysosomes

Organelle that breaks down things with digestive enzymes.

Centresomes

DNA

Cytoskeleton

Helps maintain cell shape and stability

Mitochondira

Turns glucose into ATP

Vacuoles

Endoplasmic Reticulum

Produce proteins

Smooth ER

Synthesize lipids and helps in detoxification

Rough ER

Rough ER had ribosomes on it, they produce proteins.

Golgi Apparatus

Helps package proteins and lipid molecules

Vesicles

Used in storage and movement of molecules

Prokaryotes

Flagella

Aids in movement

Capsule/Slime Layer

Layer of Protection

Plasma Membrane

Separated the outside and inside of a cell and controls what goes in and out.

Ribosomes

Synthesize Proteins

Cytoplasm

Filling in the cell/hold organelles/components in place

Nucleoid

Area where chromosomes are

Capsules

Pilli/Fimbre

Pilli are hairs that help in movementFimbre stick out and can attach to stuff

Chemical Bonds

A chemical bond refers to a force of attraction between two or more atoms that are held together to form molecules.

Ions

Ions are charged particles.

Ionic Bonds

Bonds formed between ions with opposite charges.

Anions

Negative ions are formed by electron gain.

Cations

Positive ions formed by losing electrons.

Covalent Bonds

Atoms share electrons in covalent bonds.

Nonpolar Covalent Bonds

Two atoms share electrons somewhat equally.

Polar Covalent Bonds

Electrons are unequally shared by atoms.

Electrons spend more time close to one atom rather than another.

Partial Positive Charge

Partial Negative Charge

Hydrogen Bonds

Hydrogen will have a slight positive charge, so it will be attracted to neighboring negative charges.

Van der Waals Forces

Interactions of electrons of nonpolar susbtances.

Intramolecular

Bonds between atoms in molecules.

Some atoms become more stable by gaining or losing an electron.

Cell Functions

Provide Structure and Support

Cell Wall (Plant Cells)

Cytoskeleton (Plant & Animal Cells)

Transport

Passive Transport

Active Transport

Carried out by the Cell/Plasma Membrane

Energy

The take in of nutrients to produce ATP through cellular respiration

Mitochondria

Waste Removal

Breaking down of molecules and defective components

Lysosomes

Main topic

Concept Map 2

Cell Communications

Junctions

Animals

Desmosomes

Gap Junctions

Tight Junctions

Plants

Plasmodesmata

Signalling

Long Distance

Hormal Signalling

Local

Paracrine signalling

Synaptic Signalling

Cell Membranes

Passive Transport

Diffusion

Facilitated Diffusion

Osmosis

Active Transport

Proton Pump

Sodium-Potassium Pump

Ion Channels

Electrogenic Pumps

Contransport

Phospholipid bilayer

A thin, semi-permeable membrane that separates the inside of a cell from the outside environment.

Hydrophilic head

Attracts water into the membrane

Hydrophobic tail

Repels water

Creates selectively permeable membrane

Controls what substances can pass through the cell

Membrane fluidity

Each phospholipid has a specific phase transition temperature.

Below this temperature, the lipid is rigid and in a gel phase.

Above this temperature, the lipid is a fluid and it is in its liquid crystalline phase.

Cell Respiration

Anerobic

Doesn't Require Oxygen

Lactic Fermentation

When oxygen is not present, pyruvate is reduced and forms lactate and recycled back into NAD+ allowing glycolysis to continue. In Lactic Acid fermentation CO2 is not formed.

Alcohol Fermentation

When there is no O2, pyruvate forms acetaldehyde and is reduced to ethanol where CO2 is released.This reduced electrons from NADH allowing glycolysis to continue.

Aerobic

Requires Oxygen

Glycolosis

1st Step:Glucose to Glucose-6-Phosphate with the enzyme hexokinase. 3rd Step:Fructose-6-Phosphate to fructose-1-6-phosphate with the enzyme phosphofructokinase.Output:2 Net ATP2 Pyruvate2 NADH

Pyruvate Oxidation

Pyruvate Oxidation requires oxygen.Pyruvate makes:1 Acetyl CoA 1 NADH

Citric Acid Cycle

Citric Acid Cycle (Krebs Cycle/TCA Cycle)Step 1:Acetyl CoA and Oxaloacetate go together and make Citrate.Step 3:Isocitrate becomes ketoglutarateOutput:1 ATP3 NADH1 FADH2

Oxidative Phospohlation

This process is broken down into two parts, the Electron Transport Chain(ETC) and Chemiosmosis.

Electron Transport Chain

This process includes:Complex IComplex IIComplex IIIComplex IVComplex QCycNADH gives an electron to complex one turning it into NAD+. FADH2 gives electron to Complex 2, turning into FAD. They both give their electrons to Q, from Q to complex III, Complex III to Cyc, then to complex IV and given to oxygen where it makes water(H2O). Complexes I, III, and IV are proton pump which pump out H+ into the intramitochondrial space when the electrons are being passed around.

Chemiosmosis

Once many H+ exits into the intramitochondrial space through the ETC, ATP synthase allows H+ to go back into the matrix in through facilitated diffusion in attempt to even out on both sides. This takes ADP turning it into ATP.

Energy Transfer

Photosynthesis

Cells break down glucose with oxygen to release energy, CO₂, and water.

ATP Production: Energy from respiration is stored in ATP molecules for cellular functions

Energy Loss as Heat: Not all energy is stored; some is lost as heat during metabolic processes.

Organism Level

Hetero and Autotrophs (Individual)

Metabolic rate how much energy an organism uses, affecting energy needs.

Energy Flow in Populations: Individual energy needs impact group energy consumption.

Energy Loss Between Levels (Community): Only about 10% of energy is passed up each trophic level; the rest is lost as heat.

Photosynthesis

Stage One: Light Reactions

Solar Energy --> Chemical Energy

Location: Thylakoid Space

Photosystems

Inputs: Light, ADP, NADP+, H2O

Outputs: ATP, NADPH, O2

Stage Two: Calvin Cycle

Produces sugar from CO2

Location: Stoma

Phase 1: Carbon Fixation

CO2

(+ rubisco): 6C (Short term intermediate, unstable)

3-Phosphoglycerate

(+ 6 Phosphates): 1,3-Bisphoglycerate

(- 6 phosphate due to NADPH): Glyceraldehyde-3-phosphate (G3P)

One G3P leaves, makes sugar, rest back to regen RuBp

Inputs: CO2, ATP, NADPH

Outputs: Sugar, NADP, ADP

Photosystem II

H2O UsedO2 Released through StomataElectrons used from H2OATP Made

Photosystem I

Uses electrons from PSIIMakes NADPH

Non-Cyclic Electron Flow

Products of Non-cyclic:OxygenNADPHATP

Cyclic Electron Flow

When there is too much NADPH, changes to cyclic flow. "Catch-up" on making ATP.

G-Proteins

G-proteins act as molecular switches in the signaling pathways initiated by receptors like GPCRs (G-protein-coupled receptors).

Photorespiration

C4 photosynthesis

PEP Carboxylase (Fix CO2 @ low levels)

Mesophyll cell

Bundle-sheath cell

(CAM)

Stomata closed during day, closed during the night