Categories: All - replication - dna - translation - enzymes

by shirley nguyen 14 days ago

166

Concept Map 1

The process of DNA replication involves several key steps and enzymes working together to ensure accurate copying of genetic material. The initial phase begins with helicase unwinding the double-stranded DNA, while single-strand binding proteins stabilize the unwound strands to prevent them from re-annealing.

Concept Map 1

Photosynthesis

6CO2 + 6 H2O + Energy --> C6H12O6 + 6O2


GOAL= Make sugar for energy

Calcin Cycle

Reduction
Regeneration
Carbon Fixation

Parts

Chlorophyll
Stromata
Chloroplast

Photorespiration Adaptations

C4 Plants

DIFFERENT CELLS

CAM Plants

DIFFERENT TIME OF DAY

Light Reactions

Cyclic Electron Flow
Linear Electron Flow

Glycoprotein

Tags bind to cytosol receptors

Protein ready for secretion
Proteins transport back to Rough ER
Protein transports back to Golgi Apparatus
Protein transports back to Lysosome

Ribosome (rRNA)

Composed of proteins and RNA. Ribosomes (prokaryotic 70S and eukaryotic 80S) have two subunits: large (50S prokaryotic and 60S eukaryotic) and small (30S prokaryotic and 40S eukaryotic) that's about 52 proteins, if prokaryotic, or about 78 proteins, if eukaryotic, attached to mRNA for translation.

Small Subunit

Large Subunit

E site
tRNA exits ribosome

Release factor

Release factor dissociates the ribosome and mRNA is released

Free polypeptide

Polypeptide chain forms to form the protein signaled

Newly formed protein is transferred to the rough ER to refine protein for pathway

Rough ER

Protein Sorting

Plasma Membrane

Extracellular Matrix (Eukaryotes Only)

Secretion

Back to ER

Lysosomes

Membrane Protein

Types of Secreted Proteins

Serum Proteins (Albumin)

Digestive Enzymes (Amylase)

Milk Proteins (Casein)

Extracellular Matrix Proteins (Collagen)

Peptide Hormones (Insulin)

P site
A site
Peptidyl Transferase

Polypeptide chain formed

Concept Map 3

pre-mRNA
poly-A tail

About 50 to 250 adenine nucleotides are added to the 3' end

5' cap

A modified guanine with three phosphate groups is attached to the 5' end of pre-mRNA.

Introns and Exons

Introns are non-coding sequence regions that are removed in RNA splicing.

Exons are genetic coding regions that are combined into one large region for mRNA after RNA splicing.

Alternative RNA Splicing

Sometimes mRNA doesn't need all the exons in the sequence, so introns can be used to extract parts of exons in the sequence to code for different proteins. For example, if there are 7 exons in the chromosomal DNA sequence, but only exons 1, 3, 4, 5, 7 are needed for protein A, then spliceosomes will reduce the mRNA sequence to code for protein A after translation is complete.

RNA Splicing

Spliceosomes can be used to make cuts in pre-mRNA to extract introns to combine exons.

mRNA

Translation

Anti-Codons
tRNA with Amino Acid
Codons

DNA Structure

Single Strand
Nitrogenous Bases
Sugar-Phosphate backbone from 5' to 3'
Double Stranded DNA

Semi-conservative replication

Messleson and Stahl Experiment

The experiment was to use bacterial cells and extract DNA from those cells to predict band distribution. The cells were grown in Nitrogen-15 (high density) combined with CsCl and were spun in a centrifuge for 20 minutes for the first round of replication. The bacteria was then transferred and grown in Nitrogen-14 (normal density) with CsCl and were spun in a centrifuge for 20 minutes for the second round of replication. The experiment concluded that DNA replication was semi-conservative.

Double Helix Structure

Adenine, Cytosine, Guanine, and Thymine

(T and C)

Uracil is also a pyrimidine, but only in RNA.

(A and G)

DNA Mutations

Mutation Sequence & Consequences
Most Dangerous

Frameshift and Nonsense Mutations are generally the most harmful because they severely disrupt the protein’s structure and function.

Missense Mutations can also be dangerous if they affect a critical region of the protein, such as an active site.





Ironically, I originally wanted to study more into the consequences of Missense mutations and their effects on PrP gene. Prions are an interesting disease that effects proteins and their structure.


This basically causes a protein version of cancer. There is no cure for prion diseases. Commonly this will happen in the brain and the misfolded protein will cause other proteins to fold too

How it Occurs

Spontaneous: Errors during DNA replication not caught by proofreading mechanisms.

Induced: Exposure to mutagens (e.g., UV radiation, chemicals, or carcinogens) damages DNA. Dont smoke cigarettes! This is one of the most common carcinogens!

Types of Mutations
Frameshift

Definition: Insertion or deletion of nucleotides (not in multiples of three), shifting the reading frame of the genetic code.

Consequence: Alters all downstream codons, usually leading to nonfunctional proteins.

Missense


Example in RNA Transcription


CAU -> His


Missense mutation that would change it to


CAG -> Gln

Nonsense



Silent



DNA Replication

Process Overview

Process Overview

  1. Helicase unwinds the DNA, and SSBs stabilize the unwound strands.
  2. Topoisomerase relieves tension.
  3. Primase lays down primers.
  4. DNA polymerase III synthesizes the leading strand continuously and the lagging strand in fragments (Okazaki fragments).
  5. DNA polymerase I removes primers and fills with DNA
  6. Ligase seals any remaining nicks to finalize the strand.


Initiation: Helicase unwinds the DNA, primase lays down RNA primers.

Elongation: DNA polymerase synthesizes new strands (leading and lagging).


Enzymes
Exonuclease

Function: Removes incorrect nucleotides during replication to ensure fidelity.

Interaction: Built into DNA polymerase as a proofreading mechanism.



DNA Ligase



DNA Polymerase III



Primase

Function: Synthesizes a short RNA primer to provide a starting point for DNA polymerase.

Interaction: Adds RNA primers for polymerase to extend.

Topoisomerase

Function: Relieves supercoiling and torsional strain ahead of the replication fork. Basically Untangles the DNA upstream

Interaction: Works upstream of helicase to ensure smooth unwinding.

SSB Proteins

Function: Stabilize the unwound DNA strands, preventing them from reannealing or being degraded.

Interaction: Coat the strands to keep them separated.

Helicase

Function: Unwinds the double helix by breaking hydrogen bonds between base pairs, creating the replication fork.

Interaction: Opens the DNA so other enzymes can access the strands.

Gene Regulation

Regulation
Negative
Positive
Lac I

Repressor Protein

Lac Operon

GOAL = Break down Lactose --> Glucose

Lactose & Glucose Present

OPERON OFF

Lactose Present

OPERON ON - POSITIVE REGULATION

CAP

No Lactose

OPERON OFF - NEGATIVE REGULATION

Operon

Operator

Structural Genes

Lac Z

Beta-Galactosidase

Lac A

Transacetylase

Lac Y

Permease

PCE

Proximal Control Element

General Factors

Promoter
DCE

Distal Control Elements/ENHANCERS

Specific Factors

Activators


Repressors

Transcription

Eukaryotes
RNA Processing

Spliceosome

Alternative Splicing

Transcription

Termination

3' Poly A Tail

5' Cap

Elongation

Initiation

TATA Box

RNA Polymerase II

Transcription Factors

Prokaryotes
RNA Polymerase


Types of Receptors

Extracellular

Membrane-bound

Intracellular

Concept Map 2

Membrane - Basics

Membrane Fluidity

Membrane Fluidity


Membrane Permeability

Low Permeability

Large, uncharged molecules such as glucose cannot cross on its on


As well as ions like Na+ and K+

Diffusion

Solvent moving from low solute concentration to higher solute concentration. Desire to create an equilibrium.

Facilitated Diffusion

Facilitated Diffusion is passive transport aided by channel proteins. However, no ATP is required for this type of transport

Plant Tonicity

Animal Tonicity

High Permeability

High permeability


Selective Permeability

Selective permeability of Plasma Membrane




Transport proteins allow the passage of hydrophilic substances across the membrane

Active Transport

Sodium- Potassium Pump

The Sodium-Potassium Pump: A specific case of Active Transport






Voltage Difference

Due to these pumps, a voltage difference is made


Ion Channels

Voltage-gated

Open and clsoe in response to changes in membrane potential

Ligand-gated

Open and close when a neurotransmitter binds to channel

Stretch-gated

Also known as sense stretched, open when membrane is mechanically deformed

Ungated

Always Open

Carrier Protein Pump

Carrier Protein Pump: Carries from protein from inside to outside the cell, uses ATP energy to change shapes within the molecule

Proton Pump



Protons want to go back in so they go down the concentration gradient using facilitated diffusion in a Sucrose cotransporter



Electrogenic Pump

Plasma Membrane - Outer Layer of the Cell
Membrane Proteins

Membranes have a variety of proteins



Some Functions of Membranes Proteins Include:


Metabolism/Enzymes

Enzymes
Competitive Inhibior

Competitive Inhibitors bind to the active site of a enzyme prevent substrates from binding to the enzyme and lower overall efficiency of reactions.

Noncompetitive Inhibitor

Binds to another part of the enzyme but affects the shape so that original substrates cannot bind to the new active site

Made of Specialized Proteins with An Active Site

Enzymes are also pH and Temperature Sensitive.

Most Enzymes have an ideal pH or Temperature that they work at most efficiently, and when these fall outside the parameters the enzyme not might work as well or overall completely denature back to a polypeptide chain.

Overall Goal: Speed up Chemical Reactions

Lower Activation Energy of Reactions to Take Place

The Metabolic Pathway Maintain Homeostasis
Conservation of Energy

Thermodynamics


Laws of Thermodynamics

Free Energy & Free Energy Change

Free Energy is Cellular Work


Entropy = Gibs Free Energy + T(Enthalpy)


G = H -TS


Measuring change in each at constant of T


Free-Energy Change (ΔG)

Ideally in life, we want most reactions to be ΔG<0

Types Include: Cellular Respiration via Glucose is oxidized.

Additional: Anabolic Pathways such as Polymerization and Photosynthesis

Eukaryotic Cells

DEFINED BY:


EXTERNAL MEMBRANE:

INTERNAL MEMBRANE:

Animals ONLY
Junctions

Gap Junctions

Desmosomes

Tight Junctions

ECM

Fibronectin

Collagen Fibers

Integrins

Proteoglycan

Specialized Cells
T Lymphocytes
Macrophage
Lymphocytes
Both Plants and Animals
Nucleus

Nuclear Pores

Nucleolus

Nuclear Lamina (TEM)

Cytoskeleton

Intermediate Filaments

Microfilaments

Cytoplasmic Streaming

Amoeboid Movement

Muscle Contraction

Microtubules

Mitochondria


Ribosomes

Free Ribosomes

Bound Ribosomes

Endomembrane System

Nuclear Envelope

Lysosome


Autophagy

RECYCLE

Phagocytosis

EAT

Vacuoles

Contractile Vacuole

Central Vacuole

Food Vacuole

Golgi Apparatus

Endoplasmic Reticulum

Plants ONLY
Cell Wall
Plasmodesmata
Chloroplast

Cell Signaling

Notes

Long-Distance Signaling
Hormonal Signaling

Steroid Hormone Receptors

The steroid hormone, aldosterone, passes through the plasma membrane. Aldosterone binds to an intracellular receptor protein in the cytoplasm, activating it. The hormone-receptor complex enters the nucleus and binds to specific genes. The bound protein acts as a transcription factor, stimulating the transcription of the gene into mRNA. The mRNA is translated into a specific protein.

Epinephrine

One steroid hormone can have multiple effects on cells. If can have the same receptor but different intracellular proteins to activate, or it can have different receptors.

Local Signaling
Paracrine Signaling

Local regulators (or signals or ligands) diffuse through the extracellular fluid to get to the target cell.

Signaling Molecule

Intracellular Receptors

Membrane Receptors

Ion Channel Receptor

Ion channel receptors often have ligand-gated receptors in which the channel will remain closed until a ligand binds to the receptor. When the ligand binds to the receptor and the channel opens, specific ions can flow through the channel and rapidly change the concentration of that particular ion inside the cell. This change may directly affect the activity of the cell in some way. When the ligand dissociates from this receptor, the channel closes and ions no longer enter the cell.

Ligand binds to receptor

Channel opens allowing ions to flow down the concentration gradient

Ions enter the cytoplasm and trigger a cellular response

Ligand dissociates and channel closes

G-Protein-Linked Receptor

Phosphorylation Cascade

Here, we'll look at an example of the amplification effect caused by binding epinephrine to the receptor and causing millions of molecules to be made.

Epinephrine binds to G-Protein-Linked Receptor

Inactive G-Protein is activated and slides across the membrane to bind and activate Adenylyl Cyclase

The ligand can stay on the receptor and continue the amplification effect or dissociate from the receptor and end the effect

After the G-Protein activates Adenylyl Cyclase, it can continue to activate the enzyme or deactivate by delinking a phosphate group from GTP and making GDP and shift back to it's origin

ATP is used to activate Adenylyl Cyclase

Activated Adenylyl Cyclase converts ATP to Cyclic AMP (cAMP) as a secondary messenger

cAMP activates a series of Protein Kinases

Protein Phosphatase (PP) removes a phosphate group to deactivate the proteins

Phosphodiesterase (PDE) deactivates cyclic AMP (cAMP) and converts it to AMP

Cellular Response (millions of molecules)

Synaptic Signaling

Electrical signals along nerve cells trigger a release of neurotransmitters that diffuse across the synapse to reach the target cells so that they can become stimulated and get the signal.

Fermentation

Lactic Acid
Alcohol

Cellular Respiration

Citric Acid Cycle
Oxidative Phosphorylation
Chemiosmosis
Electron Transport Chain
  1. Electrons from NADH travel through Complexes I, Q, III, C, and IV down ELECTRON TRANSPORT CHAIN
  2. Complexes I, III, and IV pump out H+ into the intermembrane space
  3. Energy from electrons transferring down ETC is used to pump H+ AGAINST concentration gradient
  4. Once electrons reach Oxygen, water is formed
Pyruvate Oxidation
Glycolysis
Output
Step 3
Step 1

Plant Cells Only

Prokaryotic - The Basics

Archaea - Basics

Archea is rumored to be one of the first-ever cells of life. They are extremely basic, yet this simple structure provides the basis for a stable organism and some unique properties.


Archaea Metabolism

Some Archaea are Methanogens, which live in swaps and marshes. These produce Methane a waste product of their metabolism. This provides those environments with a "rotten" smell.

Bacteria - Basics

Bacteria are small simple cells that consist of a fundamental Cell Structure.


These usually consist of


Certain Bacteria also contain:


Other minor organells:

Bacterial Metabolism

There are four major nutritional modes of Prokaryotes


Autotrophic Method


Heterotrophic


Roles of Oxygen in Metabolism

Differences Between Kingdoms

While the Kingdoms might be similar, there are a few major differences, like their organelles:


Andrew

Lipids

Function

Lipids are one of the most important molecules for cells to have function:


Structure

Lipids are made from building blocks of sugar:


These saccharides link through the Glycolic Cvalend bond - meaning water performs a hydrolysis reaction that breaks this bond. Fructose and Glucose come in contact and allow water to use hydrogen bonds.



Types of Polysaccharides


Glycerol fatty acids can have multiple chains formed through ester bonds. Tails that contain only a single bonded chain are called saturated fats. Tails that contain double bonds are called unsaturated fats


Trans geometric structures cases have the hydrogens on both sides of the double bond


Cis geometric structures cases have the hydrogen on the same side of the double bond; this results in a large bend on the hydrocarbon tail.

Eukaryotic - The Basics

To not go too much into structure, this is just the basics of Eukaryotic cells. Eukaryotic cells are very complex cells that have different organelles across different cell types.



Common Organelles:


These are pretty common organelles but multiple Eukaryotes have cell-exclusive organelles:


Differences Between Eukaryotic & Prokaryotic Cells & Endosymbiotic Theory

Prokaryotic - Basic small cells with a limited number of organelles

Eukaryotic - Complex larger cells with the presence of membrane-bound organelles



Endosymbiotic Theory


Prokaryotes were the first cells with Eukaryotes coming after. The proposed theory states that a protoeukaryotic cell absorbs a prokaryotic cell to make Mitochondria, and an autotrophic prokaryotic cell makes Chloroplasts.


Evidence for the Endosymbiotic Theory

Joey

Nucleic Acids

RNA
DNA

Bonds

Intramolecular
Colavent

Polar


Nonpolar


Ionic
Intermolecular

BETWEEN MOLECULES


Ion Dipole



Hydrophobic
Van der Waals
Hydrogen

Carbohydrates

Carbohydrates are organic molecules that serve as energy fuel for short-term storage. Carbohydrates are one of the biomolecules that contain monomers and polymers. The monomers of carbohydrates are called monosaccharides while the polymers of carbohydrates are polysaccharides.

Carbohydrate skeletons can be drawn in four structures: linear, double bond position, branching, and rings.


Monosaccharides

Monosaccharides are monomers that are simple structures like glucose, fructose, and galactose.

Polysaccharides

Polymers are synthesized through dehydration/condensation. Polymers are broken down via hydrolysis and enzyme catalysts.

There are different types of polysaccharides: storage and structure.

Structure Polysaccharides
Storage Polysaccharides

Storage polysaccharides

Glucose

The difference between all the types of polysaccharides is the type of linkages they have and whether or not they are alpha glucose or beta glucose.

Amylopectin

Amylopectin uses alpha 1-6 glycosidic linkage to form branched helix chains. Amylopectin is soluble in water and does produce a gel when hot water is present.

Amylose

Amylose uses alpha 1-4 glycosidic linkage to form helix chains. Amylose is not soluble in water and doesn't produce a gel when hot water is present.

Cellulose

Cellulose is a beta glucose molecule and to make the structure of cellulose found in the cell membrane, it uses beta 1-4 glycosidic linkage. Enzymes cannot be used to break down the linkages, so it is not digestible. Another type of structure polysaccharide is chitin, which is also found in plant cells.

Glycogen

What we would think of when we think glucose. Glycogen is a large, formed polysaccharide that is used by the body as fuel. It uses alpha 1-6 glycosidic linkage to branch out the glucose to store energy to use for fuel.

Concept Map 1

Proteins

Functions
Amino Acid Monomer



Main Chain
R Groups


Glycine is NOT an Enantiomer because there are not 4 unique groups around central Carbon

Denuturation
Protein Folding

Water

High Heat of Vaporization
High Specific Heat
Cohesion
Universal Solvent
States of Water

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