Kategorier: Alla - replication - dna - enzymes - nucleotides

av Joseph-Hoang Nguyen för 12 dagar sedan

88

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DNA replication is a fundamental process by which a cell duplicates its DNA, resulting in two identical copies. It begins with the separation of the two DNA strands by enzymes such as helicase.

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Photorespiration

(CAM)

Stomata closed during day, closed during the night

C4 photosynthesis

Mesophyll cell
Bundle-sheath cell
PEP Carboxylase (Fix CO2 @ low levels)

G-Proteins

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

Photosystem I

Uses electrons from PSII

Makes NADPH

Cyclic Electron Flow

When there is too much NADPH, changes to cyclic flow.

"Catch-up" on making ATP.

Non-Cyclic Electron Flow

Products of Non-cyclic:


Photosystem II

H2O Used

O2 Released through Stomata

Electrons used from H2O

ATP Made

Concept Map 2

Photosynthesis
Stage Two: Calvin Cycle

Outputs: Sugar, NADP, ADP

Inputs: CO2, ATP, NADPH

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

Stage One: Light Reactions

Outputs: ATP, NADPH, O2

Inputs: Light, ADP, NADP+, H2O

Solar Energy --> Chemical Energy

Location: Thylakoid Space

Photosystems

Energy Transfer
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

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.

Cell Respiration
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 ATP

2 Pyruvate

2 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 ketoglutarate


Output:

1 ATP

3 NADH

1 FADH2


Oxidative Phospohlation

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

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.

Electron Transport Chain

This process includes:

Complex I

Complex II

Complex III

Complex IV

Complex Q

Cyc


NADH 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.

Anerobic

Doesn't Require Oxygen

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.

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.

Cell Membranes
Membrane fluidity

Each phospholipid has a specific phase transition temperature.

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

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

Phospholipid bilayer

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

Hydrophobic tail

Creates selectively permeable membrane

Controls what substances can pass through the cell

Repels water

Hydrophilic head

Attracts water into the membrane

Contransport

Proton Pump

Electrogenic Pumps

Ion Channels

Sodium-Potassium Pump

Osmosis

Diffusion

Facilitated Diffusion

Cell Communications
Signalling

Local

Synaptic Signalling

Paracrine signalling

Long Distance

Hormal Signalling

Junctions

Plants

Animals

Tight Junctions

Gap Junctions

Desmosomes

Concept Map 1

Main topic
Cell Functions
Waste Removal

Breaking down of molecules and defective components

Energy

The take in of nutrients to produce ATP through cellular respiration

Mitochondria

Transport

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Active Transport

Carried out by the Cell/Plasma Membrane

Passive Transport

Provide Structure and Support

Cytoskeleton (Plant & Animal Cells)

Cell Wall (Plant Cells)

Chemical Bonds

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

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

Atoms share electrons in covalent bonds.

Intramolecular

Bonds between atoms in molecules.

Polar Covalent Bonds

Hydrogen Bonds

Van der Waals Forces

Interactions of electrons of nonpolar susbtances.

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

Electrons are unequally shared by atoms.

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

Partial Negative Charge

Partial Positive Charge

Nonpolar Covalent Bonds

Two atoms share electrons somewhat equally.

Ions

Ions are charged particles.

Cations

Positive ions formed by losing electrons.

Anions

Negative ions are formed by electron gain.

Ionic Bonds

Bonds formed between ions with opposite charges.

Cells

Pilli/Fimbre

Pilli are hairs that help in movement

Fimbre stick out and can attach to stuff

Capsules

Nucleoid

Area where chromosomes are

Cytoplasm

Filling in the cell/hold organelles/components in place


Ribosomes

Synthesize Proteins

Plasma Membrane

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

Capsule/Slime Layer

Layer of Protection

Flagella

Aids in movement

Vesicles

Used in storage and movement of molecules

Golgi Apparatus

Helps package proteins and lipid molecules

Endoplasmic Reticulum

Produce proteins

Rough ER

Rough ER had ribosomes on it, they produce proteins.

Smooth ER

Synthesize lipids and helps in detoxification

Vacuoles

Mitochondira

Turns glucose into ATP

Cytoskeleton

Helps maintain cell shape and stability

DNA

Animal Cells

Centresomes

Lysosomes

Organelle that breaks down things with digestive enzymes.

Plant Cells

Plasmodesmata

Key in movement of molecules between cells.

Large Central Vacuole

Chloroplasts

Cell Wall

Gives structure/support to cell

Biological Molecules
Proteins
Nucleic Acids

Subtopic

Carbohydrates

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

Types

Complex

Both provide sources of energy

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

Examples: - Starches - Legumes - Whole Grains

Simple

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

Examples: - Sugars - White bread

Structure

Monosaccharides

Hydrogen

Oxygen

Carbon

Lipids

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

Histones

H4

H3

H2B

H2A

Histone Core (Octamer)

H1

links histones together to form the nucleosome

Structural genes

Lac Y: Permease

Lac A: Trans-acetylase

Lac Z: B-galactoisdase

lac Operon

Operon Off

Nothing Present
Glucose and lactose present
Glucose present

Operon On

Lactose Present, no glucose
Lactose present

Lac L: Regulatory Gene

Operator

Positive Regulation
No Activator
Activator bound

Transcription

Negative Regulation
No repressor
Repressor bound

No transcription

Operon

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DNA Replication

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

Models of DNA Replication
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Conservative Replication

Two parental strands reassociate after functioning as templates for new strands

Restore the parental double helix

Dispersive Replication

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

Initiation of DNA Replication
Enzymes separate the two strands

Helicase unwinds and separates parental DNA strands

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

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

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

DNA Polymerases

Two DNA polymerases needed in bacterial replication

DNA Polymerase III

DNA Polymerase I

Need sliding clamp

Converts DNA pol III from being distributive to processive

Need RNA primer to add nucleotides to

Nucleotides added to 3' end of primer

Polymerization occurs in 5' to 3' direction

Add complementary base to daughter strand

Primase synthesizes RNA primers and uses parental DNA as a template

Single-strand binding proteins stabilize unwound parental strands

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

Relieves the strain caused by unwinding

DNA Expression

Translation

Translation is the synthesis of a protein from an mRNA template.


Enzymes and Factors


Elongation factors

mRNA Processing
Splicing
Poly A tail
5' cap
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).


Experiments

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.

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.

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

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.

RNA Splicing

Introns (Removed)

Exons (Expressed)

Termination
Elongation
Transcription factors
RNA Polymerase
Chromatin Modifications
Remodeling
Histone Acetylation
Gene Activation
Regulatory Elements

Silencers

Promoter

DNA Regulation

Prokaryotes
Eukaryotes
Control Elements

Distal

Bind to specific transcription factors (activators/repressors)

Enhancers

Proximal

Bind to general transcription factors

10nm fiber

Nucleosomes

30nm fiber

300nm fiber

Metaphase Chromosome

Transcription Factors

Specific

Repressors

If there is a high level of transcription, reduces levels

Activators

Increases levels of transcription

General

(Basal/background) low levels of transcription

DNA Structure

Enables a cell molecule to copy itself during cell division
Double Helix
Discovered by James Watson and Francis Crick
The strands run antiparallel

3' -> 5'

5' -> 3'

Made up of Phosphate groups
Made up of Deoxyribose

Attached to the sugars are the four Nitrogenous bases:

Thymine (T)

Guanine (G)

Cytosine (C)

Adenine (A)

Connected by chemical bonds