Chemical Bonds-Daniel

Transfer of electrons between oppositely charged ironsCan lead to ion-dipole interactions in water

Two atoms share one or more pairs of electrons to achieve stability.

stores genetic information 

gel like substance that fills the cell and and keeps the organelles in place

selectively permeable barrier, mechanical boundary of cell, nutrient and waste transport, location of many metabolic processes (respiration and photosynthesis), detection of environmental cues for chemotaxis

buoyancy for floating in aquatic environments

protein synthesis

storage of carbon, phosphate, and other substances 

localization of genetic material (DNA)

contains hydrolytic enzymes and binding proteins to nutrient processing and uptake

Gives bacteria shape and protection from lysis in dilute solutions

resistance to phagocytosis

adherence to surfaces 

 attachment to surfaces

bacterial mating 

movement

survival under harsh environmental conditions  

found in the ECM, proteoglycan are  proteins with sugars attached, involved in organizing extracellular matrix

located outside the membrane, this  structure has many parts: fibronectin, proteoglycan (animal cell ECM), and collagen. Changes in this structure can trigger processes inside the cell

 structure connects cells together that are semi-sealed. Desmosomes use proteins and are programed to selectively allow materials

secure cells very tightly, keeps stuff from freely moving around 

structures that connect cells, things can pass through very easily

 located outside the cell membrane, made of cellulose, and helps maintain cell shape

double membrane organelle that has its own DNA and performs photosynthesis

stores water, nutrients, and waste  

channels  found in plant cells that allow for the movement of water and other materials to move between cells

 store food and make pigment 

double membrane enclosing the nucleus; performed by pores; continuous with ER, also known as the nuclear lamina 

non membranous structure involved in production of ribosomes; a nucleus has one or more nucleoli 

 material consisting of DNA and protein; visible in a dividing cell as individual condensed chromosomes 

 membrane enclosing the cell

complexes that make proteins; free in cytosol or bound to rough ER or nuclear envelope 

organelle active in synthesis, modification, sorting, and secretion/transportation of cell products

digestive organelle where biomolecules are broken down, hydrolysis reaction 

 organelle where cellular respiration occurs and most ATP is generated 

organelle with various specialized metabolic functions; produces hydrogen peroxide as a by product and then converts it to water  

projections that increase the cells surface area 

reinforces cell shape; functions in cell movement; components are made of protein, includes…

made of actin, helps maintain cell shape but also aid with movement 

in the middle, anchor organelles to the cell and help maintain a cell’s shape, composed of keratin proteins.

made of tubulin, this hollow shape maintains the shape of the cell. very structural and moves organelles 

composed of ribosomes that perform protein synthesis

attached to nucleus synthesizes lipids (can also help detoxify) 

Vehicle of the cell,  the golgi apparatus packages things into vesicles where vesicles can then transport cellular materials.

gel like substance that fills the cell and and keeps the organelles in place

Sharing of electrons between two atoms with an EN difference of less than 0.5

Sharing of electrons between two atoms with an EN difference of 0.5 or greater

Unlike DNA, RNA has oxygen

DNA provides directions for its own replicationDNA directs the synthesis of messenger RNA (mRNA), and through mRNA, DNA can control protein synthesis, this process is known as gene expressionDNA is double helix polymerDeoxyribose (DNA)--> no oxygen

Nucleic acids are polymers made of monomers-- called nucleotides

NOTE: LIPIDS ARE NOT POLYMERS!A process of dehydration occurs to make a fat molecule.Heating can change the chemical composition of an oil/fat. Repeated heating and cooling cycles can denature and change the composition of double bonds. However, only a fraction of fats are effected though.

Carbohydrates serve as fuel and building materials

Cellular respirations purpose if to make ATP Glucose is oxidized Oxygen is reduced Three total processes: glycolysis, pyruvate oxidation and critic acid cycle, and oxidative phosphorylation

Occurs in the cytoplasm. Total output- 4 ATP, 2 NADH, 2 pyruvate Net output- 2 ATP, 2 NADH, 2 pyruvate

First five steps- require energy to prepare molecule for breakdown -2 ADP are formed

Starting molecule: glucoseEnzyme: hexokinaseProduct: glucose 6-phosphate

Starting molecule: fructose 6-phosphate Enzyme: phosphofructokinaseProduct: fructose 1,6-biphosphate

Last five steps- generate net gain by producing ATP that was invested -2 pyruvate, 2 NADH, and 4 ATP are formed

-Pyruvate, from glycolysis, is oxidized to form Acetyl CoA-Oxygen is required

Formed: ATP= 1NADH= 3FADH2= 1

Starting molecule: Acetyl CoAEnzyme: OxaloacetateProduct: Citrate

Starting molecule: IsocitrateEnzyme: looses electrons --> NAD to NADH Product: ketoglutarate

Components: -Complex I, II, III, IV-Q-CytEnergy is released at each step-NADH --> complex I --> Q --> complex III- ->Cyt c--> complex IVProtons are getting pumped into inner membrane C6H12O6 is oxidized CO2 is reduced

Protons go back through the ATP synthase, moving from a high concentration to low concentrationThe energy from the ATP synthase gives ADP energy to make ATP

The goal of photosynthesis is to produce glucose (sugar) H2O is oxidized and CO2 is reduced

Occurs in the stroma Produces sugar from CO2 with the help of NADPH and ATP produced by the light reactions -CO2 is initially incorporated into an organic molecule through a process called carbon fixation -ATP provides the necessary chemical energy, and NADPH provides electrons needed to reduce CO2 Input: -ATP+Pi-NADPH-CO2Output: -ADP+Pi-NADP+-CH2O

-CO2 is taken in through the stomata and added to Ribulose biphosphate to form Rubisco- an organic molecule -From Rubisco, 6 carbon intermediate are formed

Photosynthetic adaption to arid conditions -CAM plants opened their stomata's at night and incorporate CO2 into organic acids -Stomata's close during the day and CO2 is released to form organic acids and used int he Calvin Cycle

Occurs in different cells

Same Cells

Located in the thylakoid membrane Convert solar energy into chemical energy -H2O is split to provide electrons and protons (H+) -O2 is released as a waste product -The electron acceptor NADP+ is reduced to NADPH -ATP is generated by adding a phosphate group to ADP in a process called photophosphorylationInput:-Light -H2O -NADP+-ADP+PiOutput: -ATP -NADPH -Oxygen -H+

Only PS1 is used! Formed: -ATP Electrons are recycled back through Photosystem 1, where ATP is the only thing generated

H2O is oxidized Forms: -Oxygen -NADPH -ATP -Electrons move down a path-Water is first oxidized in photosytem II (PS II)-Electrons move down a transport chain to photosytem (PS I)-ATP is generated-NADP+ is reduced to NADPH

Enhance CO2 uptake and reduces photorespiration to adapt to hot, arid climates

If the cell receiving the signal is far from the cell, and it has the receptor that receives the signal, then it is long distance signaling. One example is hormonal signaling.

If cells release the ligands or signal molecules in close proximity to cells that have the receptor to receive the signals, then it is local signaling.

Send secretary vesicles to target cells

Send neurotransmitters

Present in a target cell that receives a signal

Transmembrane protein with alpha helix domain. Once it is bound by signaling molecule, its shape is changed which allows it to bind to G protein.

When it is bound to GPCR, it changes shape and makes the bound GDP to be replaced with GTP. G protein with GTP bound is activated.

Active G protein can then activate Nearby enzyme, such as adenylyl cyclase.

Activate adelylyl cyclase converts ATP to cAMP, which is a second messenger. Once cAMP started to activate the signal transduction cascade, it is converted to AMP by phosphodiesterase.

cAMP binds and activates protein kinase A, which goes on to activate another kinase and so on.

An example of cellular response occurs in the nucleus. Signaling pathways finally activate a transcription factor which binds DNA and turns on or off genes in the nucleus.

Acts as a gate for ions. When a signal molecule binds a receptor, the receptor changes shape, allowing specific ions to go through.

Present in cytoplasm in nucleus.

Molecules released by a cell which is received by another cell

Aldosterone is a steroid hormone that is secreted by cells of the adrenal gland and enters cells all over the body. The hormone passes through the plasma membrane, binds the receptor protein in the cytoplasm, and activates it. The active receptor enters the nucleus and binds to specific genes, promoting transcription of genes.

Biological Membrane: Cell membranes are selectively permeable barriers

Cell membranes are composed of a phospholipid bilayer. This phospholipid bilayer comprises an outer hydrophilic head and an inner hydrophobic tail.

Helps phospholipid bilayer to maintain ideal consistency, rigid enough to have structure but fluid enough to move materials through the membrane.

Transmembrane protiens are imbeded in the phospholipid bilayer with an extracellular facing side and a cytoplasmic facing side.Some functions of membrane proteins include:transportationenzymatic activitysignal transductioncell-cell recognitionintercellular joiningattachment to the cytoskeleton and ECM (extracellular matrix)

The type of hydrocarbon tails present in the phospholipid (ie. saturated, unsaturated) affects the plasma membranes fluidity. Unsaturated hydrocarbons tails with kins leas to a fluid consistencySaturated hydrocarbon tails lead to a viscous stateEvery phospholipid has a specific phase transition temperature. When above ideal temperature the lipid becomes fluid in a liquid crystalline phase.When below this temperature the lipid is rigid and in a gel phase.

Highly permeable molecules (meaning molecules that are able to easily pass through the phospholipid bilayer) include small, nonpolar molecules. Large, uncharged, polar molecules have lower permeability and charged ions have the lowest permeability.Molecules that have low permeability typically need assistance from transport proteins to pass through the membrane.

Passive transport is the diffusion of a substance across a membrane, going with the concentration gradient. In passive transport it's important to note that there is no energy investment.

Diffusion is the movement of molecules across a cell membrane from an area of high concentration to an area of low concentration. This method of transportation requires no energy input from the cell.

Osmosis is the movement of water across a semi-permeable membrane from a region of low solute concentration (high water concentration) to a region of high solute concentration (low water concentration), which is done without the use of energy.Key terms related to Osmosis:Tonicity is the ability of a surrounding solution to cause a cell to gain or lose waterIsotonic solution: Solute concentration is the same as inside the cell; no net water movement across the plasma membraneHypertonic solution: Solute concentration is greater than that inside the cell; cell loses waterHypotonic solution: Solute concentration is less than that inside the cell; cell gains waterWater balance in plant cells:Hypotinic solution-- Turgid (normal)Isotonic solution-- FlaccidHypertonic solution-- Plasmolyzed

Facilitated diffusion is a type of passive transport where molecules move across a cell membrane with the help of transmembrane proteins (channel or carrier proteins), down their concentration gradient, without the use of cellular energy.

Active Transport is the movement of substances from a low to high concentration. The most important element of active transport that separates it from passive transport is the use of cellular energy (ATP).Electrogenic pumps: a transport protein that generates voltage across a membrane, this is known as the membrane potentialCan also help store energy that can be used for cellular work

Cotransport is the coupled transport by a membrane protein. This occurs when active transport of a solute indirectly drives the transport of other substances.

There are two main types of ion channels:UNGATEDAlways openGATED: Open and close in response to stimuliStretch-gated – sense stretch – open when membrane is mechanically deformedLigand-gated – open and close when a neurotransmitter binds to channelVoltage-gated – open and close in response to changes in membranepotential

Two strands of the parental DNA separate, and each functions as a template for synthesis of a new complementary strand.

Three models were proposed: conservative, semi-conservative, and dispersive models. In the experiment, Messleson and Stahl grow bacteria in a growth medium that contains the heavy isotope of N15, and transferred the bacteria to medium containing N14. After the bacteria were grown for one round, DNA were extracted and centrifuge in CsCl gradients, there is only one intermediate density band showing. After bacterial were grown for two rounds of replication, there appeared two bands: one intermediate density, and one light density. The results supported the semi-conservative model.

ORI is the origin of DNA replication. DNA get separated here and form a bubble, which is called a replication bubble and there are two forks at each end of the bubble

Prokaryotic DNA is circular and there is only one ORI.

Long DNA molecules have multiple ORI and replication bubbles.

Unwids parental double helix at replication forks

Binds and stabilizes single-stranded DNA

Relieves the strain caused by DNA unwinding

Synthesizes RNA primers using parental DNA as a template

Using parental DNA as a template, adds nucleotides only to the 3' end of DNA strand

Removes RNA nucleotides of primer from 5'end and replaces them with DNA nucleotides

Joins 3' end of DNA of leading strand and joins Okazaki fragments of lagging strand

ORI is in the middle of the replication bubble. The two forks at each end of the bubble move in opposite direction, so DNA replication is bidirectional.

Nucleotides are added continuously in the direction of the fork

Nucleotides are added in short segments called Okazaki fragments, in the opposite direction of the fork

Fredrick Griffith studies Streptococcus pneumoniae. He used two strains of the bacteria, the pathogenic S strain and the nonpathogenic R strain. He found that the living S cells kill mouse, while injecting living R cells or heat-killed S cells, mouse are healthy. However, when combining heat-killed S cells and living R cells, he found that the R cells are converted into S cells and kill the mouse. This experiment shows that some genetic traits can be transferred from S to R strain.

Bacteriophage is only made of two components: DNA and proteins. Hershey and Chase labeled the DNA with P32, and proteins of bacteriophage with S35. The bacteriophage and bacteria were mixed in a tube, and centrifuged the mixture. The bacteria cells form a pellet at bottom and free phages (lighter) remain at the supernatant. They found that only P32 is detected in pellet , indicating that it was the DNA injected inside bacteria and not protein. DNA is the genetic material.

The amount of Adenine equals the amount of Thymine. The amount of Guanine equals the amount of Cytosine.

A is paired with T, G is paired with C

One way to control gene expression is to keep the chromosomes compacted so the genes are not accessible to enzymes and proteins for transcription.

2 copies of histone proteins each: H2A, H2B, H3, H4.

Activator proteins bind to enhancers in DNA. A DNA-bending protein brings the bound activators closer to the promoter, further recruiting general TFs and mediator protein to form transcription initiation complex on the promoter.

Bring low level of transcription (background)

Increase (activators) or decrease (repressors) level of transcription

LacZ: encode for beta-galactosidaseLacY: encode for beta-galactosidase permeaseLacA: encode for beta-galactosidase transacetylase

LacI: encode repressor protein

Adenylyl cyclase converts ATP to cAMP, which binds CAP and activate it. Activated CAP helps RNAP to bind promoter to start transcription.

When lactose is present, lacI binds to lactose, so it no longer bind to the operator sequence, so RNAP can now bind promoter. In addition, when glucose level is low, adenylyl cyclase level is high, which converts ATP to cAMP. cAMP binds CAP and activated CAP helps RNAP to bind promoter to start transcription.

Two scenarios: When lactose is not present, lacI bind to operator and prevent expression of lac operon genes.When glucose is present, it inhibits adenylyl cyclase, which results in no cAMP. so CAP is not activated, and cannot help RNAP bind promoter.

A cluster of genes that are involved in the same pathway and regulated together

DNA switches, positioned near/within the promoter

Mutations are any types of changes in DNAMutations occur in the coding sequence

Change in DNA= No change in amino acid

Change in DNA= Amino acid changed

Change in DNA= stop codon

Change in DNA= Reading frame changed causing a change in amino acids Only see frameshift when one or two nucleotides are added/deleted! Anything more isn't a frameshift

**Note: before initiation occurs, DNA is packed into nucleosomes by histones that make DNA accessibleTranscription factors bind to the promoter region (e.g., TATA box).TATA box tells RNA polymerase II to "start here."RNA polymerase II is recruited to the promoter (written as +1), forming the pre-initiation complex.The DNA strands are separated, exposing the template strand.

RNA polymerase II begins synthesizing RNA using the DNA template strand.The enzyme moves along the gene, building the pre-mRNA strand in the 5′→3′ direction.Elongation factors help the polymerase move through nucleosomes.

RNA polymerase II transcribes beyond the end of the gene.The pre-mRNA is cleaved, and a poly-A tail is added.RNA polymerase II detaches from the DNA.

The newly made pre-mRNA is capped at the 5′ end.Introns are removed (splicing), and exons are joined.A poly-A tail is added at the 3′ end.The mature mRNA is exported from the nucleus to the cytoplasm for translation.

In prokaryotes, transcription occurs in the cytoplasm and is coupled with translation.

RNA polymerase attaches to a specific spot on the DNA called the promoter.The DNA unwinds so the enzyme can read one strand.

RNA polymerase moves along the DNA, building an RNA strand by matching RNA bases to the DNA template.The new RNA strand grows longer as the enzyme moves.

When RNA polymerase reaches a special sequence called a terminator, it stops.The RNA strand is released.

**Nearly identical to translation in eukaryotes,note that translation is coupled with transcription in prokaryotes. Both processes occur simultaneously in the cytoplasm, unlike in eukaryotes.

The small ribosome subunit binds to a specific sequence on the mRNA called the Shine-Dalgarno sequence (just before the start codon).The initiator tRNA (fMet) pairs with the start codon (AUG).The large ribosome subunit joins to form a complete ribosome.

The ribosome reads the next codon on the mRNA.A matching tRNA brings in the correct amino acid.The ribosome links the new amino acid to the growing protein chain.The ribosome moves to the next codon, and the process repeats, adding more amino acids.

When the ribosome reaches a stop codon (UAA, UAG, or UGA), no tRNA matches.A release factor binds, causing the ribosome to release the finished protein.The ribosome subunits separate and can be used again.

TerminationWhen the ribosome reaches a stop codon (UAA, UAG, or UGA), no tRNA matches.A release factor binds, causing the ribosome to release the finished protein.The ribosome subunits separate and can be reused.

Key steps to initiation in translation:The small ribosome subunit binds to the 5' cap of the mRNA.It scans along the mRNA to find the start codon (AUG).The initiator tRNA (carrying methionine) pairs with the start codon.The large ribosome subunit joins, forming a complete ribosome.from here a a polypeptide/ amino acid chain can begin to form

Key step to Elongation in translation:Now that the ribosome is completed, and the first t-RNA has bound to the start codon in the P slot, more t-RNAs can bind their anti-codons to codons along the mRNA A codon matching tRNA brings in the correct amino acid with it.The ribosome links the new amino acid to the growing protein chain.The ribosome moves to the next codon, and the process repeats, adding more amino acids.Ribosomal slotsThe initiator tRNA enters the middle P slot to begin protein synthesisThis is where the chain will begin to formThe ribosome will move across the mRNA, reading 5' to 3' with a new amino acid carrying tRNA entering the A slotAs amino acids are attached going down the mRNA, the tRNA detaches and exits from the E slot in the ribosome

Key parts of Termination in translationWhen the ribosome reaches a stop codon (UAA, UAG, or UGA), no amino acid-carrying tRNA matches.Instead, a release factor binds, causing the ribosome to release the finished protein.The two ribosomal subunits separate from each other and can then be reused.

Depending on a protein's function, sometimes there are additional steps before a protein can be useful to a cell.In the secretory pathway, a signal sequence binds to the ribosome, that's creating a polypeptide, to the SRP on the Endoplasmic Reticulum. In the ER, a process called glycolysis occurs, where carbohydrates are bound, creating a more complex protein. After carbohydrates are added, signal peptidase removes the signal sequence, and the protein can be sent to the Golgi apparatus. Here, proteins are packaged and sent to work for lysosomes or the plasma membrane.

Glycosylation is the process by which a carbohydrate is covalently attached to a target macromolecule, such as proteins and lipids.