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CO2 is incorporated into an organic molecule
NADPH provides electrons to reduce CO2
ATP provides energy
ATP is generated by adding a phosphate group to ADP
O2 is released
H2O is split for protons
2 Lactate
2 Pyruvate
2 Ethanol
gains electrons
loses electrons
ATP synthase
ATP synthesis
powered by the flow of H+ back across the membrane
creates H+ gradient across the membrane
NADH and FADH2 carry electrons
Proton Pumps
Transfer of electrons and release of energy at each step rather than all at once
2 Cycles
2 ATP 6 NADH 2 FADH2
1 Cycle
1 ATP 3 NADH 1 FADH2
8 Steps
1 Acetyl CoA per pyruvate
2 Pyruvate + 2H2O 2 ATP 2 NADH + 2H+
Energy Payoff
2 NAD+ +4 electrons +4 H+-> 2 NADH +2H+ & 2 Pyruvate + 2 H2O
4 ADP +4Pi
Energy Investment
2 ATP -> 2 ADP +2 Pi
Bulk Transport - The use of vesicles to move large molecules such as polysaccharides and proteins in bulk cross the membrane .
Endocytosis - Contents collect onto the plasma membrane, and they fuse into a transport vesicle where the contents travel within the cell.
Pinocytosis - When a cell takes in extracellular fluid from outside in vesicles. This allows the cell to take in any dissolved molecules.
Receptor-Mediated Endocytosis - A very specialized form of pinocytosis that allows the cell to acquire bulk quantities of a specific substance. This can occur due to the presence of receptors on the plasma membrane which allow for the binding of specific solutes.
Phagocytosis - When a cell engulfs large food particles by extending part of its membrane out. The ingested particle is now in a food vacuole where it will fuse with lysosomes and be digested.
Exocytosis - Transport vesicles migrate to the membrane, fuse with it, and release their contents.
Electrogenic Pump - A transport protein that helps create a voltage difference across membranes.
Proton (H+) Pump - A pump that transports H+ against its concentration gradient. As positive charge leaves the cell, we see a slight negative charge develop inside the cell and a slight positive charge develop outside the cell.
Cotransport - When active transport of a solute indirectly drives transport of other substances. (Ex: H+/Sucrose Cotransporter)
Sodium-Potassium Pump - Typically, the outside of the cell has an abundance of Na+ and the inside of the cell has an abundance of K+, so if the cell needs to take out more Na+ or bring in more K+ it needs to do it against the concentration gradient. For every 3 Na+ transported outside the cell, 2 K+ ions are transported inside. (Requires ATP)
Facilitated Diffusion - Membrane transport that does not require energy but does utilize a transport protein and a concentration gradient to exchange large, uncharged molecules across the membrane. (With Concentration Gradient)
Carrier Proteins - Proteins that undergo a subtle change in shape, alternating between two shapes. The shape change may be triggered by the binding and release of the transported molecule.
Channel Proteins - Proteins that provide corridors or channels that allow a specific molecule or ion to cross the membrane
Aquaporin - A channel protein that is present in the membrane that helps facilitate water through the membrane by use of aqua pores.
Diffusion - The tendency for molecules of any substance to spread out evenly into the available space because of thermal motion, moving from an area of high concentration to an area of low concentration.
Osmosis - The diffusion of free water across a selectively permeable membrane, going from an area of higher solute concentration to an area of lower solute concentration.
Tonicity - The ability of a surrounding solution to cause a cell to gain or lose water.
Plant Cells - Cell walls in plant cells help maintain water balance.
Hypotonic Solution - Solute concentration is less than that inside the cell; cell gains water. (Turgid)
Isotonic Solution - Solute concentration is the same as the inside of the cell, no net water movement. (Flaccid)
Hypertonic Solution - Solute concentration is greater than that inside the cell; cell loses water. (Plasmolyzed)
Animal Cells - Due to no cell wall, animal cells fare best in isotonic environments unless they have special adaptations.
Hypotonic Solution - Solute concentration is less than that inside the cell; cell gains water. (Lysed)
Isotonic Solution - Solute concentration is the same as the inside of the cell, no net water movement. (Normal)
Hypertonic Solution - Solute concentration is greater than that inside the cell; cell loses water. (Shriveled)
Integral Proteins - Proteins that are partially or fully inserted into the membrane.
Transmembrane Proteins - Proteins spanning the entire membrane. N-terminus on extracellular side and C-terminus on intracellular side.
Peripheral Proteins - Proteins that are anchored to the membrane.
Membrane Fluidity
Hydrocarbon Tails - The type of hydrocarbon tails affects membrane fluidity. Unsaturated fatty acids allow the membrane to more freely and saturated fatty acids pack tightly so the membrane cannot move as much.
Cholesterol - Cholesterol also affects membrane fluidity. Its presence between phospholipids reduces movement at moderate temperatures and prevents phospholipids from packing tightly at low temperatures.
Temperature - Temperature affects membrane fluidity. Above specific phase transition temperature, the lipid is in a liquid crystalline phase and below the lipid is in a gel phase.
Centrosomes - "Microtubule organizing center" that helps with cell division. (Composed of 9 sets of triplet microtubules)
Cilia - Mobility structure that occurs in large numbers on cell surface. (Cell motility, composed of microtubules (9 doublets surrounding 2 microtubules))
Flagella - Mobility structure that is limited to one or few per cell. (Cell motility, composed of microtubules (9 doublets surrounding 2 microtubules))
Stroma - Internal fluid
Granum - Stack of thylakoids
Thylakoid - Membranous sac
Matrix - Space inside the inner membrane where DNA is
Intermembrane Space - Space between inner and outer membranes
Cristae - Folds within the mitochondria
Cis Face - Receives cargo shipped out by ER
Trans Face - Releases cargo after making changes
Smooth ER - Synthesizes lipids, metabolizes carbohydrates, detoxifies drugs and poisons, and stores calcium ions
Rough ER - Secretes glycoproteins, distributes transport vesicles, and is considered the membrane factory of the cell
Central Vacuoles - Found in plant cells and serves as a repository for inorganic ions and water
Contractile Vacuoles - Pump excess water out of cells
Food Vacuoles - Formed when cells engulf food or other particles
Autophagy - A process that uses hydrolysis enzymes to recycle cell's own organic material
Phagocytosis - Extending a cell's membrane to engulf a foreign cell or food particle
Lamina - Protein filament meshwork that lines the inner surface of nuclear envelope and keeps its structure
Nuclear Pores - Small openings lined with porin proteins that assist in transport
Chromatin - Material consisting of DNA and histone proteins
bond between a glycerol and fatty acid
Between the phosphate group and sugar of 2 nucleotides
Sugar phosphate backbone
Between the amino and carboxyl group
Primary structure of protein
Non-charged
Slight/ partial charges
Monosaccharides to form polysaccharides
Alpha glycosidic linkages
Starch, Dextran, Glycogen, Amylose, and Amylopectin
Beta glycosidic linkages
Cellulose
Tertiary structure of proteins: Cysteine (R-group)
Hydrogen Bonds (H to O, N, or F)
Secondary structure of proteins
forms the alpha helix and beta sheets of the one protein and occurs in the main chain only.
Water molecules
Water properties
Complementary base pairing
The genes are grouped in operons. Several sequences of DNA are operators that can turn on or off the gene expression.
Only at transcription level
operons (genes), operators (sequences of DNA), activators/repressors, promoters, mRNA, and proteins
Negative regulation repressors while positive regulation is associated with activators
Examples seen through the Lac Operon
increases gene expression level
Lactose present: The lac repressor from LacI (which is constitutively expressed, meaning continuously expressed) will bind to the lactose instead of the operator. RNAP is activated by cAP (which is activated by cAMP, a product of adenylyl cyclase) and binds to the promoter to increase the level of transcription for proteins that will break down lactose to a high level. The operon is on.
decreases gene expression to a basal level
Lac operon with glucose present, regardless if there is lactose: Glucose blocks the function of adenylyl cyclase, meaning no cAMP can be generated. Due to this, CAP is not activated to then also activate RNAP. If RNAP is not activated, it cannot bind to the promoter to bring about the high level of transcription. This means the operon is off as it cannot transcribe its structural genes (lacZ, lacY, and lacA).
Lac operon with no lactose present: Repressor is bound to the operator thus lacZ, lacY, and lacA are not transcribed for Beta-glactosidase, permease, and transacetylase. Operon is off as the activated repressor blocks the binding of the RNA polymerase to the promoter.
Eukaryotes
Regulation can also occur at RNA processing, translation, and protein activity or modifications.
Transcription
Transcription Factors
General
Proximal control elements
Bring transcription levels to background or basal (meaning lower)
Specific
Distal control elements
Combinatorial control of gene expression
Liver and cell cells expressing different levels of the albumin and crystallin genes.
upstream or downstream of DNA
proximity to the gene they regulate can vary
Enhancers
If repressors were to bind to an enhancer: The main goal of a repressor is to block or decrease the probability the RNA polymerase II can bind to the promoter. By decreasing the effectiveness, it decreases levels of transcription of the pre-mRNA
If activator was to bind to enhancers: The activator proteins are brought to be near the promoter by a DNA-bending protein. With this the activators then can also bind to more (mediator) proteins that form an initiation complex. Through these interactions and the development of the complex, it assists RNA polymerase II to bind to the promoter in order to increase the level of transcription.
Changes level of transcription by increasing or decreasing
Activator
Repressor
DNA material present in the nucleus
DNA wraps around histones to form nucleosomes and further coil into the chromatids of chromosomes.
RNA Splicing
Exons - Coding sequences of mRNA that are used to encode proteins.
Introns - Non-coding sequences that are removed during RNA splicing.
Alternative Splicing - Due to the presence of introns, different combinations of exons can be generated through the removal of different introns to form different mRNAs.
Spliceosomes - Complexes of RNA and proteins that bind junctions of the introns and makes cuts to release introns from the DNA. The exons are then joined together.
pre-mRNA Processing
Poly A Tail - A tail of 100-200 A's that is added to the 3' end of pre-mRNA, near the AAUAAA sequence. This poly A tail helps with the stability of the mRNA.
Poly A Polymerase - The enzyme that adds the poly A tail to the pre-mRNA. (Requires ATP)
5' Cap - A modified guanine (G) nucleotide added to the 5' end of the pre-mRNA that will be used for translation.
Termination - This step occurs in eukaryotes differently as an AAUAAA sequence signals the cell to make a cut in the newly formed pre mRNA and release it from the DNA.
Ribonuclease - The enzyme that makes the cleavage to form the pre-mRNA.
Elongation - This step follows initiation as the transcription initiation complex moves downstream, unwinding the DNA and elongating the RNA transcript in the direction of 5' to 3'. (Uses condensation/ dehydration reactions)
Initiation - The beginning of transcription that occurs when the enzyme RNA polymerase binds to the promoter. (RNA Polymerase II)
TATA Box - A eukaryotic promoter commonly includes a TATA box, which is a nucleotide sequence containing TATA that is about 25 nucleotides upstream from the transcription start point.
Transcription Factors - In eukaryotes, the addition of these proteins is required in order for RNA polymerase II to bind to the promoter. One recognizes the TATA box and binds to the promoter.
RNA Polymerase II - The RNA polymerase seen in eukaryotes which is used to produce pre mRNA, snRNA, and micro RNA. (Makes new strand of mRNA in 5' to 3' direction)
Transcription Initiation Complex - Additional transcription factors bind to the DNA along with RNA polymerase II, forming this complex. RNA synthesis can now begin at the start point on the template strand.
Occurs in the Nucleus (Not coupled with Translation, translation occurs in the cytoplasm.)
Template Strand - The DNA strand that is used to form the new RNA strand. (Template strand is in the 3' to 5' direction because transcription occurs in the 5' to 3' direction.)
Transcription Start Point - The nucleotide in DNA where transcription starts.
Downstream - To the right of the transcription start site, nucleotides are numbered by positive numbers.
Upstream - To the left of the transcription start site, nucleotides are numbered by negative numbers.
Promoter - Region on the DNA upstream of the start site where RNA polymerases bind to.
Stages of Transcription
Termination -This step occurs when the RNA transcript is released, and the polymerase detaches from the DNA. This happens once the RNA polymerase reaches the termination site on the DNA.
Elongation - This step follows initiation as RNA polymerase moves downstream, unwinding the DNA and elongating the RNA transcript in the direction of 5' to 3'. (Uses condensation/ dehydration reactions)
Initiation - The beginning of transcription that occurs when the enzyme RNA polymerase binds to the promoter. (RNA Polymerase)
RNA Polymerase - The RNA polymerase seen in prokaryotes. (Makes new strand of mRNA in 5' to 3' direction)
Occurs in the Cytoplasm (Coupled with Translation, mRNA is made and immediately translated)
Replication process
Occurs in one direction
5' to 3'
Enzymes
DNA Ligase
Joins DNA together
DNA Polymerase I
Removes RNA nucleotides and replaces them with DNA nucleotides
DNA Polymerase III
Synthesizes new DNA 5' to 3' by using the parental DNA as a template
Nucleotides connect through phosphodiester bonds using dehydration reaction
Primase
Makes RNA primers at 5' end of leading strands and each Okazaki fragment
Topoisomerase
Relieves overwinding strain ahead of replication forks by rejoining DNA strands
Single Strand Binding (SSB)
Binds and stabilizes single stranded DNA and prevents it from rebinding
Helicase
Unwinds parental double helix at replication forks
Needs origin of replication (ORI)
3 Models of DNA Replication
Dispersive
Each strand of both daughter molecules contains a mixture of old and new synthesized DNA
4 helices
2 helices
Contain pieces of parental strand and pieces of new DNA
Semiconservative
Two parent strands separate and each functions as a template for a new complementary strand
2 helices
Contain one parental strand and one new strand
2 new complementary helices
Two helix
Each helix contains one parent strand and one new strand
Conservative
Two parent strands reassociate after acting as template strands and restore the parental double helix
Second Replication
One parent helix
3 daughter helices
First Replication
One new helix
One parent helix
Double Stranded Helix
Complementary base pairing
Purine+Pyrimidine
Guanine(G)+Cytosine(C)
Adenine(A)+Thymine(T)
Nuceotide
Bond connecting each nucleotide= phosphodiester bond
Nitrogenous base
Phosphate Group
Nitrogenous bases
Adenine (A)
Cytosine (C)
Guanine (G)
Thymine (T)
Sugar phosphate backbone
Sugar
Phosphate group
Chargaff's Rule
A+G= T+C
Guanine= Cytosine
Adenine= Thymine
Messleson & Stahl
Found from density bands that DNA replicates semiconservatively
Bacteria in 14N
"Light"
Bacteria in 15N
"Heavy"
Hershey & Chase
Asked what was the component that was injected by bacteriophages inside bacterial cells, DNA or Protein?
Determined DNA carried genes
Determined DNA was injected
One tube of Radioactive Sulfur (35S)
Labeled Proteins
Mixed
Centrifuged
One tube of Radioactive Phosphorus (32P)
Labeled DNA
Mixed
Shook tube to release bacteriophages from bacterial surface
Centrifuged
Recovered radioactivity inside bacterial cells
Griffith
Experiment
Heat-killed S & Living R
S. components entered live R. and changed the genetic makeup of R to S
Heat-killed S
Living R
Mouse healthy
R. strain found to be nonpathogenic
Living S
Mouse dies
S. strain found to be pathogenic
Injected mice with
R. pneumoniae
Nonpathogenic
"rough" no capsule
S. pneumoniae
Pathogenic
"smooth" presence of capsule
Bacteria
Archea
Extremophiles
Methanogens
Produce methane as a waste product
Swamps
Extreme Thermophiles
Extreme Temperaters
Extreme Halophiles
Highly Saline Environments
Internal Cell Structures
Periplasmic Space
Contains hydrolytic enzymes and binding proteins
nutrient processing and uptake
Ribosomes
protein synthesis
Nucleiod
contains DNA
Cell Surface Structures
Plasma membrane
Functions
Nutrient Transport
Waste Transport
Protection from environment
Permeable Barrier
Capsule & Slime layers
Adherence
Resistance
Phagocytosis
Flagella
Archaeal Flagella
Powered by ATP
Bacterial Flagella
Powered by H+ Flow
3 Main Parts
Filament
Hook
Motor
Movement
Fimbriae & Pili
Bacterial Mating
Attachment to surfaces
Cell Wall
Peptidoglycan
Gram Negative
Thin Layer of peptidoglycan
Gram Positive
Thick Layer of Peptidoglycan
Cell
Shape
Shape
Spirilla
Spiral Shape
Basillus
Rod Shape
Coccus
Spherical Shape
G-protein linked receptor
Signaling molecules that use GPCR: epinephrine, hormones, and neurotransmitters
Reception: Ligand binds to the G protein-coupled receptor. This in turn causes a change of shape of the GPCR for the G-protein to bind to it. Now, GDP converts to GTP to bind to G-protein and activate G-protein.
Transduction: In turn causes a change of shape of the GPCR for the G-protein to bind to it. Now, GDP converts to GTP to bind to G-protein and activate G-protein. , the G-protein detaches from the GPCR and binds to Adenylyl Cyclase. The Adenylyl Cyclase then turns ATP to cAMP (the second messenger).
G-protein switch: Phosphodiesterase converts cAMP to AMP. Due to the conversation of cAMP to AMP, there is no secondary messenger to continue in the signaling pathway.
Transduction (amplifying): cAMP activates Protein Kinase A to transfer ATP to activate another kinases
phosphorylation cascade: kinases that phosphorylate and activate each other.
Dephosphorylation: The use of phosphates to inactivate kinases, by removing phosphate groups.
Cellular response : Will different due to the different GPCR and the cells.
Tyrosine kinase receptor
dimerize once ligand binds to each of the tyrosine polypeptides
autophosphorylation - activation of the kinase function to transfer phosphate from ATP to the other tyrosine polypeptide
creates the tyrosine-kinase receptor
activated tyrosine-kinase receptor creates a cellular response
Used for cell division
Ion channel receptor
Ligand binds to a ligand-gated channel receptor
Ligand-gated channel receptor will open and specific ions will flow through the channel
The ligand will unbind from receptor which then closes the ligand-gated ion channel
The ions flowing in will change the ion concentration within the cell.
Pertaining to the nervous system: action potential due to the change of voltage across the cellular membrane.
Ligand (First Messenger): Hydrophilic
Location: Cell membrane
Second messenger
Location: inside the cell
Ligand: Hydrophobic or nonpolar molecule
Thyroid and steroid hormones
Ligand will pass through the membrane
Ligand will bond to a receptor protein in the cytoplasm
Hormone-receptor complex will enter the nucleus and binds to specific genes
Bound protein is a transcription factor (controls gene expression) and regulates the transcription of mRNA
mRNA is translated
Communications through gap or plasmodesmata junctions. Physical contact communication can also occur through surface protein and binding of the surface proteins.
Seen in paracrine and synaptic signaling
Seen in hormonal signaling
