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Gene regulation in eukaryotic cells involves multiple processes to regulate and control the transcription of genes. This regulation is essential for conserving energy and resources within the cell.
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Once the signal attaches to GPCR then it gets activated and the GDP attaches.
An operon is a transcription unit of genes whose products are required under identical circumstances. it facilitates the coordinated expression of multiple genes.
The DNA sequence of an operon comprises three different components.
The three genes can be transcribed together as polygenic mRNA.
Protein is essential to lactose metabolism.
Protein is essential to lactose metabolism.
Permease forms pores in the bacterial cell membrane
Protein is essential to lactose metabolism.
This enzyme breaks down lactose to simple sugar residues that can then be used
The operator is a part of the DNA where a repressor can bind to, controlling access to the promoter
If a repressor is bound to the operator, blocks RNA polymerase and no mRNA can be made.
In the absence of lactose, a repressor protein is bound to the lac operator. This binding prevents transcription of the downstream lac genes.
Lac I
The repressor protein is encoded by the regulatory gene Lac I. Lac I is located upstream.
Repressor bound to operator
Operon is OFF (Basil expression)
When lactose is present, lactose binds in the form of allolactose to the permanently expressed repressor protein. This binding inactivates the repressor, unblocking the operator. Now the RNA polymerase can bind to the promoter and read the genes.
Repressor Bound to Lactose
Glucose Present?
Glucose Present
In the presence of glucose, lactose degradation is possible but not essential for survival
Glucose presence inhibits cAMP production, reducing CAP binding and transcription.
Adenylyl Cyclase Inactive
cAMP levels Low
CAP inactive
Operon is OFF
Lac repressor protein binds tightly to the operator and prevents transcription of the lac genes by blocking RNA polymerase from binding to the promoter
Glucose Absent
Cell will use lactose as energy source, makes allolactose, binds to and inhibits to the repressor and triggers the expression of the lac gene.
Adenylyl Cyclase Active
cAMP levels High
cAMP then binds to CAP
CAP Active
cAMP and CAP complex forms a dimer that binds to the DNA close to the lac promoter and increases RNA polymerase activity
Operon is ON
a promoter is a sequence of DNA where RNA polymerase can bind to initiate transcription
many adenines at the 3' end of the mRNA that serve to help with transportation of the mRNA
guanine at the 5' end of an mRNA serving to let the mRNA out of the nucleus and attach to a ribosome
Eukaryotic Gene Regulation tries to prevent the formation in transcription phase as it is attempting to conserve energy and save its resources
Transcription factors attach to the TATA box, they assist RNA polymerase 2 to initiate transcription. There are two typed, General and Specific.
Specific
Change the level of transcription.
Distal control elements
Enhancers
Activators/ Repressors bind specific transcription factors
Upstream or Downstream of the Gene
Activation of enhancers
Activator proteins
Bind to the distal control elements grouped as enhancers in DNA contains 3 binding sites
DNA bending protein
DNA bending protein bends the activator close to the promoter
Then General transcription factors, mediators and RNA polymerase are attracted.
Transcription Initiation complex
The activators bind to the mediator protein and general transcription factors and RNA synthesis occurs.
Repressors
If high levels of transcription, then they reduce levels.
Activators
increase levels of transcription.
General
Bring about Low levels of transcription
(Background/Basal)
Proximal control element
Sequences in DNA close to the promoter
Bind general transcription factors.
Transport to cytoplasm
Translation
Protein processing
Transport to cellular Respiration
differences include lack of post-transcription modification and the things it brings with it (splicing, g-cap, poly-a tail), coupling of transcription and translation, and the setting of the process (cytoplasm for prokaryotes)
Eukaryotic transcription uses DNA polymerase 2
it occurs in the nucleus and it has the addition of the 5 guanine cap and the Poly A tail. Its first product is also pre-mRNA.
the process of DNA making an mRNA strand; takes place in the nucleus of a eukaryotic cell and the cytoplasm of a prokaryotic cell
a DNA sequence that calls for the end of transcription and the separation of the DNA and RNA Polymerase II
the final product of transcription for eukaryotes
pieces of the pre-mRNA that are kept and are actually used for translation in the specific cell
pieces of the pre-mRNA that are removed if not used, depending on what gene needs to be translated
only happens in eukaryotes; the process after transcription that modifies the pre-mRNA
a complex serving to remove introns from pre-mRNA
the final product of prokaryote transcription and post-transcription modification in eukaryotes; serves to code for a protein using a ribosome
DNA sequence that dictates where RNA polymerase will bind and start transcription
an enzyme that transcribes DNA and forms an mRNA by adding ribonucleotides to the 3' end of its strand
proteins that regulate the rate of transcription by binding to DNA
eukaryotes are multicellular and are more complex organisms
Fibronectin, peptiglycan and collagen
provide structure for animal cells.
Actin
maintains cell shape, cell motility and cell division
Vesicles walking on microtubes
Proteins in the kreatin family
maintains cell shape , anchorage of the nucleus formation of lamina
FunFunctionsFunFunctions: maintain cell shape, anchorage of nucleus and certain other
organelles, and formation of nuclear lamina
Functions: maintain cell shape, anchorage of nucleus and certain other
organelles, and formation of nuclear lamina
ctions: maintain cell shape, anchorage of nucleus and certain other
organelles, and formation of nuclear lamina
alpha and beta Tubulin
Cell shape, cell motility, chromosome movements in cell division
some things can pass between cell
everything can pass between cell
Nothing can pass between cell
This doubble membrane structure is the site where cellular respiration occurs
Utilizes hydrogen peroxide as a biproduct
to break down molecules and creates water
All DNA is organized in this structure. Site of transcription
A double membrane structure
regulates transport
When a protein enters the endomembrane system, polypeptide synthesis resumes, with the polypeptide being inserted into the ER lumen.
Has bound ribosomes. site of synthesis fro glycoproteins.
attached in the nucleus
synthesizes lipids
metabolizes carbs
and is used in detoxifying drugs/ poison
Large membrane-bound organelles are used for storage of food, water, and ions.
packed with enzymes needed to break covalent bonds
has low PH
breaks down molecules to smaller parts
Proteins that are destined to go to the lysosomes are tagged with specific tags, they then function
The cis face of this structure takes in molecules from the ER to further fold and change molecules to the intended final structure that leaves from the trans face.
Cite of storage
Found in plant cells.
Allows water nad nutrients to travel from one cell to another.
The double membrane structure holds the site of photosynthesis (thylakoid membrane)
attactchmnet to surfaces and bacteria mating
Does not require energy and goes down its concentration gradient.
Open and close in response to membrane potential
Open and close when a neurotransmitter binds to a channel
Open when membrane is mechanically deforemed
Aided by proteins helps non polar or large molecules
carrier proteins binds molecules and carries them out
Can easily flow through always open
Requires energy, goes against its concentration gradient
Signal transmission
Both gates of Na close but the activation gates on some K+ channels are still open. Then returns to resting membrane potential
The inactivation gates on most Na+ channels close blocking the Na+ influx. The activation gates on most K+ channels opens permitting K+ efflux which again makes inside of the cell negative.
Depolarization opens the activation gates on most Na+ channels while the K+ channel's activation gates remain closed. Na + influx makes the inside of the membrane positive concerning the outside
A stimulus Opens the activation gates on some Na+ channels Na+. Na+ influx through those channels depolarizes the membrane. If it reaches the threshold. it triggers action potential.
The activation gates on the Na+ and K+ channels are closed and the membrane resting potential is maintained.
when two forces are balanced
uses ATP to power the transport
When the membrane is under hot temperatures, it becomes more fluid, this occurs with unsaturated fats.
Low permeability is when molecules have a difficult time passing through the membrane.
LARGE AND POLAR CANNOT PASS MEMBRANE
High permeability is when they can easily pass through the plasma membrane.
This is when molecules are small and non polar
This energy is primarily produced through cellular respiration, where glucose and oxygen are converted into ATP, the main energy currency of the cell.
Potential energy is the stored energy in a system.
Chemical energy refers to the energy stored in the bonds of molecules, such as glucose, which can be released during cellular processes like respiration.
Kinetic energy is the energy of motion, which in biological systems is seen in processes like the movement of muscles or the flow of molecules across cell membranes.
Fermentation is a metabolic process in which cells convert sugars into energy in the absence of oxygen
Consumers are organisms that obtain energy by eating producers or other consumers
Producers are organisms that can produce their own energy
Decomposers are organisms that breakdown dead organic matter
Thermodynamics refers to the study of energy flow and transformations within living systems
Metabolism refers to the life sustaining chemical reactions in organisms that convert food into energy and build or breakdown molecules for growth, repair, and maintenance.
Photosynthesis harnesses light energy. There are two stages of photosynthesis. Stage one involves Light reactions and stage 2 involves the Calvin cycle. Photosynthesis is summarized as electrons are extracted from water and transferred to CO2. H2O is oxidized and CO2 is reduced.
photosynthesis is important to life on earth because it provides energy to plants that gives energy to those who eat them
The calvin cycle is stage 2 of photosynthesis and occurs in the stroma of the chloroplast.
The Calvin cycle produces sugar from CO2 with the help of the NADPH and ATP produced by the light reactions.
Inputs of the calvin cycle are CO2, 6 NADPH, and 6 ATP
Outputs of the calvin cycle are 9 ADP, 6 NADP+, and 1 G3P
Carbon Fixation is the first step of the calvin cycle.
It involves the addition of CO2 from atmosphere to Ribulose Bisphosphate (carbon acceptor) using the enzyme Rubisco (adds carbon from atmosphere.
This forms a 6 carbon unstable intermediate.
Immediately splits to form 2 molecules of 3 carbon ( also called 3 phosphoglycerate).
To form 1 molecule of glucose (6C) we need 6 CO2 to be fixed. 12 NADPH and 19 ATP.
G3P
The product of the calvin cycle is G3P (a sugar)
Light reactions occur in the thylakoid membrane in chloroplast.
Light reactions convert solar energy into chemical energy. H2O is split to provide electrons and protons.
Light energy excites the electrons to a higher energy level in Photosystem II which are then transferred to Photosystem I and in the process reduce NADP+ to NADPH for the Calvin cycle.
In the process of the noncyclic flow of electrons in the photosystems, ATP is made from the ETC.
Inputs of the light reaction cycle: H2O, ADP, NADP+ and Light
Outputs of the light reaction cycle: O2, ATP, and NADPH
Reaction center chlorophyll a absorbs at 680nm hence called p680
Splits H2O, releasing O2 and generates some ATP
Photosystem I
reaction center chlorophyll a absorbs at 700nm hence called P700
reduces NADP+ to NADPH
NADPH
Cells that releases signals are near the cells that receive the signals.
Uses a target Cell and usually flows through blood vessels
Signal travels through bloodstream.
Present in a target cell that receives the signal molecule.
A non-polar signal can diffuse directly across the lipid bilayer.
Through the steroid hormone aldosterone passes through the plasma membrane
Hormone receptor complex
Aldosterone binds to a receptor protein in the cytoplasm activating it.
Enters the nucleus
The hormone receptor complex enters the nucleus and binds to specific genes.
Transcription Factor
The bound protein acts as a transcription factor, stimulating the transcription of the gene into mRNA
translated
the mRNA is translated into a specific protein.
The signal molecule is hydrophilic, a receptor in the membrane.
Response
Once the last kinase is activated in the cascade it enters the nucleus.
transcription factor
Then the transcription factor gets activated
DNA
Active transcription factor then binds the DNA and it stimulates transcription of a specific gene.
Transduction
Once the GDP attaches to the GPCR it then turns into GTP.
Activated Adenynly cyclase
The GTP then binds adenylyl cyclase and then it is activated. Then it releases a cellular response.
Second messengers
Adenenly cyclase turn AMP to Cyclic AMP which then bind to the first Kinase.
Phosphodiesterase turns Cyclic AMP to AMP
Phosphorylation Casade
The cyclic AMP activates the first kinase then it starts the casade, where each kinase activates a new one using the enzyme Kinases which transfers phosphate groups to activate. Then it gets unactivated when it removes a phosphate group with the enzyme phosphatase.
Reception
During reception, there is a signal molecule that attaches to the GPCR.
Electrons are transferred from NADH and FAD2 to oxygen, forming water.
Cellular respiration relies on the breakdown of glucose.
The last step of cellular respiration
the overall products of oxidative phosphorylation
makes ATP from the energy of incoming protons
Movement of protons across a selectively permeable membrane, down the electrochemical gradient. This utilizes the proton gradient created by the ETC to drive synthesis of ATP to ADP and phosphate. The protons flow back across the membrane through ATP synthase, providing the energy needed to make ADP into ATP.
Chemiosmosis in photosynthesis, the proton gradient across the thylakoid membrane generates a proton force so that the protons flow back into the stroma through ATP synthase, synthesizing ATP from ADP and phosphate.
Essential for ATP production.
the input of ATP synthase
ATP
the output of ATP synthase
In photosynthesis and more specifically the light reaction cycle, ATP is generated by adding a phosphate group to ADP in a process called photophosphorylation.
an electron carrier and proton pump that serves to make NAD+ through NADH
the input of complex one
NAD+
the output of complex one
an electron carrier and make FAD
the input of complex two
FAD
the output of complex two
an electron carrier as well as a proton pump and makes water from oxygen
oxygen; the input of complex four
In photosynthesis and in the light reaction cycle o2 is released as a waste product.
H2O
water; the output of complex four
In photosynthesis, specifically the light reaction cycle H2O is split to ptovide electrons and Protons.
pumps protons out of the matrix into the intermembranespace
an electron carrier
The ETC generates a proton gradient across a membrane by pumping H+ from one side of the membrane to the other. Transport of electrons through reactions.
Essential for ATP production.
Inner Mitochondrial Membrane
The location of the Electron Transport Chain in cellular reparation is in the inner mitochondrial membrane.
Thylakoid Membrane
The location of the Electron Transport chain in Photosynthesis is in the thylakoid membrane of chloroplasts.
the third step of cellular respiration
the overall products of the CAC
acetyl coenzyme A; input for step one of the Citric Acid Cycle (CAC)
Output: Citrate
the product of acetyl CoA
the input of the third step of the CAC
Output: alpha-ketoglutarate
the output from isocitrate
The second step of cellular respiration
the inputs
the outputs
The first step of cellular respiration
When there is no oxygen present, some cells go through fermentation where the only cellular respiration process done is glycolysis producing very few ATP
the overall products of glycolysis
made by phosphoglucose isomerase
fructose 1,6 biphosphate
made from the enzyme phosphofructo kinase
a carbohydrate
Glucose 6-phosphate
the product of the enzyme Hexokinase
lacks an OH group making it more stable
deoxyribonucleic acid
Chargaff's rule states that DNA is paired with one purine and one pyrimidine. He also states that the number of A=T and G=C
both strand are opposite one is 3'-5' while the other is 5'-3'
This is separate from transcription and translation and requires the assistance of multiple enzymes to accomplish.
Eukaryotes have multiple origins of replication
Prokaryotes have one origin of replication
Hershey and Chase discovered that DNA was the genetic material and not protein in their experiment with bacteriophage where they found that the DNA was entering the cell nd making copies of more bacteriophage.
Messelson and Stahl discovered that DNA was replicated in a semiconservative manner after his experiment showed intermediate after the first replication and intermidiete and light in his second round of replication.
Discovered that there was a genetic material but did not know what it was. This was found in his experiment with the rats where the heat killed s transformed the R to kill the rat.
This theory suggested a mixture of both parent and daughter strands. this was later disproved.
The theory suggests that DNA replicates with the assistance of a parent strand and then the parent strand reforms. This theory was later disproved.
The Meselson and Stahl experiment Proved that DNA uses a parent strand to form the newly synthesized daughter strands. This was proven right after the experiment showed intermediate and light in their replication rounds.
Enzymes/Proteins
Primase
adds the RNA Primer, this is necessary so that DNA polymerase 3 knows where to go.
Ligase
Ligase glues the Okazaki fragments made in the lagging strand so that it makes a continuous strand.
Lagging strand
The lagging strand synthesizes away from the replication fork.
Okazaki fragments
since the lagging strand is going away from the replication fork it is made through Okazaki fragments, which are small segments of dna polymerase that are glued with ligase.
Leading strand
The leading strand synthesizes towards the replication for and it is continuous
DNA Polymerase 1
removes the RNA primer
DNA polymerase 3
DNA polymerase is responsible for adding DNA it needs The Rna primer and can only go from a 5 to 3 direction
Topoisomerase
Topoisomerase is responsible for relieving the tension from the coiled DNA strand.
SSB
The SSB is the protein that stabilizes the DNA so that it would wind again.
Helicase
Helicase is the first step it unzips the two strands of DNA it breaks the hydrogen bonds.
Origin of Replication
The origin of Replication is formed with the helicase making a bubble. The ORI then makes two replication for that are bidiretional.
Replication fork
The replication fork is bidirectional
There are hydrogen bonds in between the two strands of DNA
has an OH group making it less stable
ribonucleic acid
Connected by phosphodiester linkage
Links nucleotides together with phosphodiester bonds
has base paring A-T and G-C
The base paring for DNA is T, A, C, G
The base paring for RNA is U, A, C, G
double ring structure
A G
single ring structure
C U T
present in RNA replaces T with U
forms the sugar-phosphate backbone of DNA and RNA
protein synthesis
In the end of the making the protein, the rest of the completed polypeptide leaves the ribosome.
Polypeptide synthesis begins on a free ribosome in the cytosol. The cytosol is the fluid part of the cytoplasm, found inside the cell but outside the organelles. It fills the space between the cell membrane and the organelles.
The function of the SRP is that it recognizes and binds to the signal sequence of a newly synthesized protein emerging from the ribosome. The SRP halts translation temporarily to stop the protein from being synthesized completely in the cytosol. The SRP guides the ribosome-protein complex to the ER membrane by binding the SRP receptor protein to the ER. Then the SRP leaves once at the ER.
when it is solid it will float thus insulating the water underneath, this is crucial to maintain life.
Since water is polar it dissolves other polar and ionic compounds. It can also form a hydration shell around molecules such as NA and Cl. Water however cannot dissolve non polar molevcules.
The amount of heat required to change liquid water to vapor. Water has a high heat of vaporization.
When water freezes it expands as molecules are held together by a rigid state
High specific heta can help moderate temperature
Cohesion allows for water transport in plants and it can create high surface tension
Ester linkages connect the phospholipid by connecting the phosphate head with the two fatty acids. Triglyceride has ester links with glycerol and three fatty acids.
To identify a saturated fat from an unsaturated fat, look at the fatty acid chain where all the carbon bonds are single bonds (no double bonds present) which makes the carbon chain saturated with H atoms. Results in a straight, tightly packed, solid structure at room temperature.
Solid at room temperature.
To determine if a fatty acid is unsaturated, look for a chain with at least one double bond between carbon atoms. Double bonds indicate an unsaturated fatty acid.
Trans= opposite
Margarine
Cis=Same Side
Oil
some archea live in extrem enviorments
extremophiles
live in high saline enviorments
Thrive in very hot enviorments
Translation is the process by which ribosomes use mRNA as a template to synthesize proteins. During translation tRNA molecules bring amino acids to the ribosome where they are linked together in the sequence specified by the mRNA codons forming a polypeptide chain that folds into a functional protein
Translation occurs in the cytoplasm. The ribosomes directly bind to the mRNA aligning the start codon (AUG) for protein synthesis. Prokaryotic translation doesn’t involve mRNA processing or nuclear compartmentalization
Prokaryotes contain Formal MET
When a stop codon is reached, the ribosome releases the completed polypeptide, and the translation process ends.
The ribosome moves along the mRNA, and tRNA bring amino acid to the ribosome. The ribosome links the amino acids together to form growing polypeptide chain.
The ribosome assembles around the mRNA, and the first tRNA, carrying the starting amino acid, binds to the start codon on the mRNA.
For Eukaryotes the tRNA binds the 5 guanine cap and searches for the start codon
Ribosomes are cellular structures composed of RNA and proteins and they act as a side of protein synthesis
Prokaryotes have 60s ribosomes
Eukaryotes have a 70s Ribosome
TNA is a type of RNA that helps translate genetic information from mRNA into the correct sequence of amino acids protein synthesis
mRNA is a type of RNA that carries a genetic instructions from DNA in the cell nucleus to the ribosomes in the cytoplasm where it serves as a template for protein synthesis
Translation is separated from transcription by the nuclear membrane, and mRNA undergoes modifications (capping, splicing, polyadenylation) before being translated in the cytoplasm or on the rough ER. Eukaryotic translation also involves larger ribosomes and more complex initiation mechanisms.
Exons are left
Only contains exons
Intron are removed
Formed by Dehydration synthesis
Consists of more than one polypeptide chain, multiple chains come together to form a larger protein structure.
Tertiary structure is the shape of the polypeptide chain and it includes secondary structures.
-Hydrophobic interactions occur between non-polar side chains
-When acidic and basic it is Ionic bonds
-Disulfide with S-S and S-H bonds (the only covalent bond)
Hydrogen bonds in between the backbones stabilize the alpha and beta sheets and helps with folding .
There are covalent bonds present in the primary structure
can be a linear sequence.
Prokaryotes are single cell organisms
helps with movement
gives bacteria shape and protection from lysisin dilute solutions
peptodiglycan
Resistance to phagocytosis adherance to surfaces
Survival under harsh enviormental conditions
Bouyancy for floating in aquatic enviorment
selective permiable barrier
mechanical boundry of cell
nutrient and waste transport
Nucleic acids are polymers made up of small units called nucleotides.
There are two types of nucleic acids
A nucleoside is a structural component of DNA and RNA comprising a 5 carbon sugar and nitrogenous base. Lacks a phosphate group
Can be digested quickly.
Saccharides
Polysaccharide
An entire polysaccharide is a polymer.
Cellulose
Glycogen
Starches
Amylopectin
A branched polysaccharide. Alpha (1,4) and alpha (1,6) linked.
Amylose
A linear polysaccharide linked by alpha (1,4).
Proteins are made of one or more polypeptide chains.
Proteins are made when the signal peptide is cleaved by signal peptidase in the receptor protein complex and the protein is now inside the ER lumen and folds into its final conformation.
Proteins are then directed to their final destination based on their sorting signals.
Proteins that need to be secreted are packaged into secretory vesicles. The vesicles merge with the plasma membrane, releasing the protein outside the cell.
A glycoprotein is a type of protein that has carbohydrate groups attached to the polypeptide chain. Glycoproteins help maintain structural integrity by stabilizing the cell membranes and supporting the ECM.
Amino Acids are linked by peptide bonds. There are 20 amino acids that humans use.
Hydrogen
Amino Group
Side Chain
The classification of an amino acid is determined by its R group which is the side chain. Certain aspects can classify an amino acid as basic, acidic, polar, or non-polar.
When the R groups are OH or NH they will be polar and hydrophilic.
Nonpolar
When the R groups end with CH or H they will be non-polar and are hydrophobic
Ionic
When the R groups are either + (Basic) or - (acidic) they will form Ionic bonds
Carboxyl Group
Cholesterol is found embedded within the cell membrane.
It also helps with membrane stability and fluidity.
Low Density Cholesterol
High Density Cholesterol
4 fused rings
Lipid bilayers form the structure of the membrane. made of hydrophilic head and hydrophobic tail
The phosphate group is hydrophilic
held together by ester linkages
Proteins that need to go to the plasma membrane are embedded into the vesicle membrane. The vesicle merges with the plasma membrane, integrating the protein into the cell surface.
Amphipathic
The membrane contains both hydrophilic and hydrophobic characteristics
Cell membrane engulfs matrials
Takes in fluids
takes in food
takes in specific proteins
releases materials and they leave the plasma membrane
equal sharing of electrons
Examples: C-H Cl-Cl
These molecules tend to separate from water such as oil
Unequal sharing of electrons
Interacts with water.
These bonds occur in between two molecules.
Uneven distribution of electron clouds
Hydrogen bonding occurs when an H molecule binds with F< O or N. They are typically strong.
Examples: H2O and NH3
Interactions of electrons of non-polar substances.
These bonds occur within the molecule.
Transfer of electrons, this is usually seen with salts.
NaCl
Sharing of electrons some examples are C-H,N-H, S-H.
