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Prokaryotic elongation has a similar process to eukaryotes for synthesizing lagging and leading strands. however, Prokaryotic elongation also includes the process of removing RNA primers and linking fragments.
Both Eukaryotic and Prokaryotic termination come from replication forks fusing. However, Eukaryotic replication forks fuse from 2 different replication bubbles, whereas Prokaryotic replicaiton forks that fuse come from the same replication bubble.
Nitrogenous Bases
Purines are molecules consisting of 2 connected carbon rings. Purines include either Adenine (A) or Guanine (G) in both RNA and DNA.
Pyrimidines consist of a single carbon ring structure.
Thymine (T) and Cytosine (C)
Uracil (U) and Cytosine (C)
Sugar
Consists of pentose sugar called deoxyribose sugar which is missing a hydroxyl group on the 2' carbon.
Consists of pentose sugar called ribose sugar which includes the hydroxyl group on the 2' carbon.
Phosphate Group
Negatively charged phosphate groups link either deoxyribose sugar in DNA or ribose sugar in RNA through the formation of phosphodiester bonds.
Anti-parallel structure means that the two sugar-phosphate backbones run in opposite 5'-3' orientations.
DNA polymerase I and III
Initiation begins with a specific nucleotide sequence contained within the only ORI within the prokaryotic chromosome. A helicase binds to either template strand and begins expanding the replication bubble.
SSBPs will hydrogen bond to expoosed nitrogenous bases to prevent the dsDNA from reforming into a double helix.
Finally, Primase will lay down primers for DNA polymerase to expand into newly synthesized daughter strands of DNA.
As the replication bubble expands, the replication forks slowly move further away from the ORI. Synthesis of the lagging strand begins at an RNA primer near the replication fork on the 3' end of the template strand.
Elongation of the Okazaki fragment continues until the DNA polymerase encounters the RNA primer for the leading strand or the RNA primer for a previously synthesized okazaki fragment.
Elongation for the leading strand starts at RNA primers laid down at the ORI and is continuously synthesized from 5' to 3' in either direction towards the replication fork.
Elongation ends when DNA polymerase III runs into an already replicated portion of DNA.
The formation of 2 circular chromosomes, each of which consist of one parent strand and one newly synthesized daughter strand that are discontinuous and still connected.
At this point, the two daughter molecules are made continuous by nuclease first cleaving the phosphodiester bonds keeping the RNA primer in place. DNA polymerase I then adds DNA nucleotides where the Primer used to be, leaving a small gap until between it and the next strand.
DNA ligase removes the gaps by forming phosphodiester bonds between discontinuous daughter strands.
With the 2 new daughter molecules still attached, termination is the process by which the replication forks fuse thanks to recognizing certain termination sequences.
2 continuous circular chromosomes that are genetically equivalent and no longer connected.
2 helicase enzymes recognizes a specific nucleotide sequence called the origin of replication (ORI) and separates the double-stranded DNA (dsDNA) on either side of the replication bubble, forming 2 replication forks.
Topoisomerase helps relieve tension from the unwinding double helical structure of DNA as helicase widens the replication bubble.
As helicase moves in either direction away from the ORI, SSBPs hydrogen bond to the exposed nucleotides and prevent the dsDNA from reforming.
The enzyme primase will create an RNA primer which is elongated to allow DNA polymerase to bind and begin elongation.
The stage at which DNA polymerase extends the RNA primer or series of RNA primers with DNA nucleotides.
This strand starts at the ORI and is synthesized continuously towards the 5' end of the template strand or from the ORI towards the replication fork.
Starting at the RNA primer at the ORI, DNA polymerase III begins synthesis of the new daughter DNA strand continuously from the 3' end of the primer.
DNA and RNA can only be synthesized from 5' to 3', meaning the template strand is read from 3' to 5'.
Consists of a series of RNA primers going towards the 5' end of the template strand, but are synthesized from the replication fork towards the ORI in a series of Okazaki fragments. DNA polymerase then detaches before running into previous RNA primer.
As the replication bubble expands, Primase lays down an RNA primer near the replication fork at the 3' end of the template strand. As the primer is elongated by DNA polymerase III, the replication bubble continues to expand and a new RNA primer is laid down, which when elongated from 5' to the 3' will eventually end just before the RNA primer of the previous Okazaki fragment.
A series of short Okazaki fragments consisting of an RNA primer and an extended sequence of DNA nucleotides that aren't connected along the sugar-phosphate backbone.
Elongation ends when DNA polymerase III encounters sections of DNA that have already been replicated, leading it to disconnect from the DNA.
Another enzyme, nuclease, moves through the DNA and cleaves RNA primers. DNA polymerase then adds DNA nucleotides onto the daughter strand, leaving a small gap beetween where the RNA primer was and the next strand.
Termination ends with the final enzyme, DNA ligase, moving along the daughter strand and connecting the gaps between where RNA primers used to be by forming phosphodiester bonds.
Untwists the double helix structure of DNA at the replication forks. Helps expose DNA to replicating machinery.
Topoisomerase
Enzyme responsible for relieving strain from unwinding the double helix.
Single-Strand Binding Proteins (SSBPs)
SSBPs help DNA replication by binding to the unwound parent DNA strands to prevent the hydrogen bonds from reforming.
Primase
Since DNA Polymerase can only add nucleotides onto an existing chain, primase creates a short RNA primer which then can be used by DNA polymerase to create a copy of the parent strand.
DNA Polymerase I and III
Adds nucleotides to the 3' end of RNA primer, detaching if/when it reaches the next primer.
Removes the RNA primer and replaces with DNA nucleotides.
DNA Ligase
Nuclease
Aids in DNA replication and repair by replacing certain damaged or incorrect sequences by cleaving the phosphodiester bond.
Helps join the final nucleotide between Okazaki fragments to make a continuous daughter strand through the formation of phosphodiester bonds in the sugar-phosphate backbone.
Prokaryotes only makes cells that they need , for that reason most are almost immediatly used
Proteins leave the free ribosomes and goes to the ER
In the ER a carbohydrate group is added to the protein
The protein then travels from the ER to the Golgi
From the Golgi the proteins can move to other organelles/ locations with the help of secreting enzymes
Mitochondria, Chloroplast, Nucleus, Peroxisomes, cytoplasm
SRP (signal recognition particle)
First the SRP binds to the signal peptide in the free ribosomes, then SRP binds to a receptor protein located in the ER
RNA Processing
Regulates by removing nucleotides that are not needed
The process of certain parts of the mRNA strand being removed to create the RNA strand that will be translated.
Enzyme: Spliceosome
Exons: nucleotides that stay in RNA to be used in translation to make a certain protein
because they exit the nucleus and go to the cytoplasm for translation
Intros: nucleotides that are not needed to make a certain protein
Stages of Transcription
Regulates by being specific with the nucleotides being added
occurs when the termination site is reached
A Poly-A Tail is added to the end of the mRNA strand
RNA nucleotides are added to the 3' end to create a chain of nucleotides
at some time during the process a 5' CAP is added to the mRNA strand
mRNA strand
Initiation
RNA Polyerase II binds to the promoter region to start transcription
A DNA strand is being used to make mRNA
the nucleus
Operons
Lac Operon
Lactose is present
The cell uses lactose to eventually make glucose and galactose for energy and carbon
The repressor will bind to lactose, preventing it from binding to the operator. This allows RNA polymerase to bind to the promoter to start transcription.
Lac A
Transacetylase
Adds acetyl group to lactose
Lac Y
Permease
Allows lactose to enter cell
Lac Z
Beta- Galactosidase
Breaks glycosidic linkages to form glucose and galactose
Glucose is Present
Lactose gene expression is off because the cell will rather use glucose for energy and for carbon.
Genes that can turn a function on or off
Operator
located next to the promoter
A protein will bind to the operator and either turn on or off gene trancription
Repressor
Turns off gene expression
Negative Regulation
Activator
Turns on gene expression
Positive Regulation
Scans along the mRNA until AUG sequnec is found,AKA starts codon
A tRNA with an anticodon of 3' UACS'
A tRNA molecule consist of a single RNA moluclue with about 80 nucletides
In three dimension tRNA hasn anticodones on its ends
Large ribosome now joins the complex
Has three active sites
P Site
Growing Polypeptide
E Site
Exist Site
A Site
Amino Acids
A translation initiation complex is formed
Elongation
The next tRNA carrying the corrcet amino acid comes to site A
A peptide is formed between the two amino acids formed by the enzyme Peptidyl transferase
tRNA is now empty in the P site and moves to the E site to be released while the tRNA from A site moves to the P site and a new tRNA comes to the A site
mRNA is read from 5' to 3' direction while teh amino acids are added from N to C direction
Termination
Once a stop codon is reached in the A site no tRNA corresponds to a stop codon
A release factor sits in the A site
Dissociation of the ribosome complex causing translation to stop; This is a GTP driven process
Proteins called initiation factors
Hydrolysis of GTP provides energy for the assembly
The initiator tRNA is in the P site; the A site is available to the tRNA bearing the next amino acid.
through hydrogen bonds
Amino acid,Met
RNA Polymerase ll
Moves along the template DNA adding ribonucleotides to the 3' end of the following RNA Strand
pre-mRNA
RNA Processing takes place
Splicesomes
Removes introns and splice together exons
mRNA
Prokaryotic cells do have mRNA without the slicing
3' end with a polyA tail
Enzyme called polyA polymerase
A 5' cap made of modified guanine AKA cap or G-P-P-P
Stability
Translation
DNA sequences that define where transcription of a gene by RNA polymerase begins
can remove a phosphate group= contains phosphatase function
Activated G protein activates enzyme and removes phosphate from GTP, converting to GDP
Adenylyl Cyclase: An enzyme located on the membrane that produces ATP by synthesizing ADP.
Target cell to have something to receive the signal molecule
Receptor
Intracellular Receptors
Intercellular Signaling
In cytoplasm, In nucleus
Nonpolar or hydrophobic
Steroid and Thyroid hormones of animals and nitrite in plants and animals
Membrane Receptors
Signal molecule is hydrophilic and can't pass the membranes phospholipid bilayer; needs transmembrane recptores
Happens when signal molecule is in the membrane;second messanger
Response
Signal triggers a certain response
Transduction
Reception protein changes. Multistep pathway to amplify a signal
cAMP
Acts as second messanger in a G Protien Signaling Pathway.
Activated adenylyl cyclase converts ATP to cAMP
Binds to and activates another protein, kinase, which goes to activate another Kinase, leading to a cellular response
Reception
Chemical signal binds to receptor protien
Types of membrane receptors
Tyrosine kinase receptor
Two pollypeptides that dimerize
Have the ability to function as a kinase
An enzyme that catalyze the transfer of phosphate groups from ATP to proteins
After phosphate group is added to the polypeptide after taken from ATP, the tyrosine is referred to as tyrosine kinase receptor
The activated receptor now interacts with other protiens to bring about cellular response
Ion Channel Recptor
Proton Pump
uses energy to transport protons from the matrix of the mitochondrion to the inter-membrane space
Its a proton generates a proton concentration gradient across the inner mitochondrial membrane because there are more protons outside the matrix than inside.
Sodium-Potassium Pump
Moves Na+ ions out of the cell and moves K+ ions into the cell. For every 3 Na+ ions pumped only 1 K+ is pumped.
Depolarization: Occurs when too may positive ions are pumped into the cell making the inside of the cell more positive than the outside.
Once Depolarization reaches a peak, repolarization occurs. It is the negative slope after the peak.
Repolarization: When the membrane potential is being changed back to a negative state.
Hyperpolarization: Occurs when too many positive ions are pumped out of the cell making the inside of the cell negative
Present in a target call that recovers the signal molecule
Molecules released by a cell to be recived by another cell
Long-distance
Hormonal Signaling
Local Signaling
Paracrine Signaling
Synaptic Signaling
Synapses are a chemical process that carries information from the presynptic
The arrival of action potential causes Ca2+ channels to open causing influx of Ca2+; the depolarization opens the voltage gates
Vesicles that were carrying neurotransmitters fuse with the presynaptic membrane and release them into the synaptic cleft
The neurotransmitter binds to lingand-gated the ion channels in postsynaptic membrane.
G Protein linked receptor
Glucose is converted into pyruvate through glycolysis, but instead of being oxidized, is reduced to regenerate NAD+ for use in the energy payoff phase of glycolysis to continually synthesize ATP through substrate-level phosphorylation.
Lactic Acid Fermentation
Alcohol Fermentation
C6H12O6 + 2 NAD+ + 2 ADP + 2 P(i) --> 2 pyruvate (3-carbon) + 2 NADH + 2 H+ + 2 ATP
Refers to the process by which Pyruvate is transported to the mitochondrial matrix in eukaryotic cells, and oxidized into Acetyl CoA.
2 Pyruvate + 2 NAD+ --> 2 Acetyl CoA + 2 CO2 + 2 NADH + 2 H+
2 Pyruvate, 2 NAD+ + 2 H+
2 Acetyl CoA, 2 NADH, and 2 CO2
Citric Acid Cycle
The Citric Acid Cycle refers to the sequential series of 8 steps that fix Acetyl CoA onto oxaloacetate, where the repeated oxidation of this molecule produces intermediary molecules and the energy is captured by NAD+ or FAD+. This process is aided by enzymes at each step.
This phase, primarily characterized by the carbon fixation of Acetyl CoA onto oxaloacetate, involves steps 1 and 2. More specifically, this carbon fixation allows oxaloacetate to enter a higher energy state, then being oxidized.
This phase, including steps 3 and 4, involves the oxidation of isocitrate and the other intermediary molecules in order to reduce NAD+ into NADH, along with using substrate-level phosphorylation to produce ATP.
This phase, referencing step 5, includes the use of substrate-level phosphorylation in order to synthesize ATP.
This phase, including steps 6-8 involve the regeneration of oxaloacetate by oxidizing succinate and other intermediary molecules to reduce either NAD+ or FAD+.
Regenerated oxaloacetate, 2 NADH, and 2 FADH2.
2 ATP (one per Acetyl CoA)
you
2 Acetyl CoA
2 Isocitrate
2 Acetyl CoA + 6 NAD+ + 2 FAD+ + ADP + GTP --> 2 CO2 + 6 NADH + 6 H+ + 2 FADH2 + ATP + GDP
Oxidative Phosphorylation
Regenerates NAD+ and FAD+ in addition to producing 26-28 ATP molecules
Oxidative Phosphorylation is the final step in cellular respiration in which the chemical energy captured from food in NADH and FADH2 is moved through the electron transport chain to fuel the movement of protons out of the mitochondrial matrix and into the intermembrane space to drive the synthesis of ATP.
Electron Transport Chain/Respiratory Chain
Proton Gradient
Electrochemical Gradient
Chemical Gradient
The movement of molecules resulting from the uneven concentration of a solute in two different areas results in the passive diffusion of particles down the concentration gradient.
Electrical Gradient
The difference in membrane potential that results from the unequal concentration of ions on either side of a semi-permeable membrane. Drive ions away from areas of similar electric charge.
Energy-Coupling
Energy-coupling is the concept of coupling 2 biological reactions. This more specifically refers to the pairing of 2 biological reactions where one releases energy, and the other uses that energy to drive the second reaction.
The proton gradient is a biological "battery" that serves to store the potential chemical energy that was gathered from food and stored in NADH and FADH2.
Hydrogen exists in higher concentrations in the intermembrane space than in the matrix, meaning that region is also lower pH.
Protein Complexes 1, 3, and 4
Serve both as areas for redox reactions to take place for the Electron transport chain,
Protein Complex 1
NADH enters in the first protein complex because it has relatively higher potential energy than FADH2
Protein Complex 2
Cytochromes
Cytochromes are a group of proteins with heme bound that make up the majority of proteins in the ETC that donate and accept electrons.
FADH2 enters in the second protein complex because it has less potential energy than NADH, and thus enters at a lower energy level.
Chemiosmosis
ATP Synthase
ATP Synthase is the enzyme is chemiosmosis that is responsible for the facilitated diffusion of protons down their concentration gradient, which uses the energy from proton movement to synthesize ATP from ADP and inorganic phosphate.
Higher saturation of the hydrocarbon tails in phospholipids will decrease membrane fluidity.
Higher temperature means greater membrane fluidity.
In between the size of microtubules and microfilaments, these structures are composed of several different types of proteins that are wound into tight coils.
helps maintain cell shape and anchor nucleus and other organelles.
Helps with maintenance and changes in cell shape, muscle contractions, cell motility, and cell division.
Thus, these early cells eventually consumed a oxygen using, energy-producing prokaryote to lead to the endosymbiont theory (see free ribosomes).
Ribozymes are a type of RNA with enzymatic function, helping jump start cellular life.
Nucleus
Nucleolus
Membrane-less structure primarily responsible for the synthesis of ribosome subunits and ribosomal RNA (rRNA)
Chromosome
Chromatin
Made up of proteins and nucleic acids.
Primary protein components are known as Histones.
Form into tightly wound coils to form chromosomes during cell division.
Discrete units of DNA within the nucleus that serve primarily to carry genetic information.
Nuclear Envelope
Double membrane each consisting of a phospholipid bilayer with embedded proteins.
Separates the nucleoplasm and cytoplasm, assisting in separating gene transcription from gene translation.
Runs continuous with Endoplasmic Reticulum and allow passage of molecules through protein structures in nuclear envelope known as nuclear pores.
Nuclear Lamina
Represents the inner face of the Nuclear Envelope and are involved in both gene expression (through chromatin organization) and helping to maintain structure of the nucleus.
Serves as the control center of the cell, housing most of the cell's DNA, made up of chromosomes, which guide gene expression and protein synthesis.
Nucleoplasm
Thick liquid that suspends contents of Nucleus.
External Cell Structures
Cellular Connections
Tight Junctions
Desmosomes
Gap Junctions
Consist of membrane proteins that sit in the membrane to allow passage of ions, sugars, amino acids, and other small molecules between cells.
Necessary for communication between cells in addition to the transport of molecules between cells.
Intermediate filaments made of keratin that anchor it into the cytoplasm and are responsible for connecting muscle cells in a muscle.
Helps fasten layers of cells together into a strong sheet.
Connect adjacent cells to allow the passage of some molecules (hence, "leaky" junction)
Consists of a network of proteins that interact to form connections from which no molecules can pass through.
Stops leakage of molecules within an environment into the outside environment or vice versa, allowing the body to compartmentalize more easily.
Tightly connects adjacent cells.
Flagella
Specialized arrangement of microtubules sheathed in the plasma membrane that project from some cells.
Primary function of the flagella is to help with the locomotion of the cell.
Extracellular Matrix
Composed of glycoproteins and other carb containing molecules.
The most abundant glycoprotein in animal cells, Collagen, is embedded in a network of proteoglycans. Here, fibronectin reacts with integrin in the ECM to bind cells to the surface.
Helps support the structural integrity and motility of the cell for functions such as amoeboid movement.
Provide Tracks for which transport proteins can transport molecules throughout the cell.
Cytoplasm
Thick, gel-like fluid that makes up all of the cell contained within the cell membrane.
Cytosol
Represents the intra-cellular fluid inside cells from which organelles are suspended.
Free Organelles
Free Ribosomes
Vacuole
Peroxisomes
Mitochondria
Centrosome
In certain animal cells, the centrosome resides near the nucleus and organize microtubules for the cytoskeleton and during cell division.
Centriole
A ring composed of microtubules arranged in nine sets of triplets.
A pair of centrioles oriented perpendicularly to each other compose a Centrosome
Consists of 2 phospholipid bilayers each with a unique set of membrane proteins.
The main site of cellular respiration in the cell, or the metabolic process that uses oxygen to metabolize macromolecules and convert that energy into ATP.
Outer membrane is smooth.
Separates the intermembrane space, or space between the inner and outer membrane, from the cytosol of the cell.
The inner membrane is convoluted with cristae, or folds in the inner membrane that help increase the surface area for sites of cellular respiration. Membrane proteins as enzymes help catalyze cellular respiration.
Separates intermembrane space from mitochondrial matrix, the compartment contained by the inner membrane.
The widely accepted endosymbiont theory states that early ancestors to eukaryotes engulfed oxygen-using, non-photosynthetic prokaryotic cells, forming a relationship between the prokaryote and the host.
This eventually led to the host cell and the endosymbiont merging into a single organism, a eukaryotic cell containing mitochondrion.
Specialized metabolic compartments bound by a single membrane with enzymes that remove hydrogen from certain molecules and transfer them to oxygen to make hydrogen peroxide (H2O2).
Detoxify harmful compounds such as alcohol by removing a hydrogen and making hydrogen peroxide.
Contain and dispose of toxic hydrogen peroxide.
Single membrane bound organelle that resembles a vesicle except for its larger size and longevity.
To help transport water, nutrients, and waste in and out of the cell.
Complexes made of ribosomal RNA and protein.
Sites where RNA and other cellular components come together to carry out protein synthesis.
Endomembrane System
Group of membranes and organelles that work together to metabolize, package, and transport lipids and proteins throughout the cell.
Lysosomes
Single membrane bound organelle containing a diverse set of enzymes.
Primarily responsible for the break down of macromolecules, worn-out cell parts, and pathogenic invaders for use by the cell.
Golgi Apparatus
Consists of Cisternae that separate each individual cisterna and the internal space from the cytosol.
Consists of Cis face ("receiving" side) and Trans face ("shipping" side)
Location in the cell where molecules are received, sorted, altered, or manufactured to be shipped out to other parts of the cell.
Vesicles
Compartment made of at least one lipid bilayer
Used to transport molecules in processes such as digestion and secretion.
Endoplasmic Reticulum
Consists of phospholipid bilayer with embedded proteins
Made of Cisternae, or interconnected, stacked, fluid-filled sacs, allowing the ER to run continuous through ER Lumen.
Rough Endoplasmic Retiuclum
Primarily involved in the steps of protein synthesis, including protein folding and protein sorting.
Contains Bounded Ribosomes
Ribosomes bound in the membrane of the Rough ER help with secretive protein and membrane-bound protein synthesis.
Smooth Endoplasmic Reticulum
Lacks Bounded Ribosomes.
Plays a key role in the synthesis of important lipids such as phospholipids and cholesterol.
Help breakdown drugs and other metabolic wastes
responsible for the production and secretion of some steroid hormones
When some archaea are able to live in extreme conditions
Extreme Halophiles
Live in highly saline environments
Extreme Thermophiles
Thrive in very hot environments
Some branched hydrocarbons
They allow for the membrane to remain sturdy to counter any harsh environmental conditions
Area where DNA is located because bacteria does NOT have a nucleus.
Ribosomes
Capsule
Protects against dehydration
Polysaccharide layer
Carbohydrate
Sugars
Polysaccharides:
Structure Polysaccharide
Chitin
Cellulose
Plant Call Walls
Storage Polysaccharide
Dextran
Starch
Plants
Glycogen
Animals
Disaccharides
Glycosidic Bond/Linkage
Monosaccharides
Glyceraldehyde
Dihydroxyacetone
Ribulose
Ribose
Galactose
Fructose
Glucose
To provide energy
Cell Wall
It gives support, protects the cell, and maintains the cells shape.
Peptidoglycan
A polymer of modified sugars cross-linked with short peptides
Gram Positive
Gram Negative
Fimbriae
Flagellum
Used to stick to the substrate or to another bacteria cell
Pili
Used for bacterial mating
Projections used to attach to surfaces
