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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.
Key parts of Termination in translation
Key step to Elongation in translation:
Ribosomal slots
Key steps to initiation in translation:
**Nearly identical to translation in eukaryotes,
In prokaryotes, transcription occurs in the cytoplasm and is coupled with translation.
**Note: before initiation occurs, DNA is packed into nucleosomes by histones that make DNA accessible
Mutations are any types of changes in DNA
Mutations occur in the coding sequence
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
Change in DNA= stop codon
Change in DNA= Amino acid changed
Change in DNA= No change in amino acid
DNA switches, positioned near/within the promoter
A cluster of genes that are involved in the same pathway and regulated together
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.
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.
Adenylyl cyclase converts ATP to cAMP, which binds CAP and activate it. Activated CAP helps RNAP to bind promoter to start transcription.
LacI: encode repressor protein
LacZ: encode for beta-galactosidase
LacY: encode for beta-galactosidase permease
LacA: encode for beta-galactosidase transacetylase
Increase (activators) or decrease (repressors) level of transcription
Bring low level of transcription (background)
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.
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.
A is paired with T, G is paired with C
The amount of Adenine equals the amount of Thymine. The amount of Guanine equals the amount of Cytosine.
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.
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.
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 in short segments called Okazaki fragments, in the opposite direction of the fork
Nucleotides are added continuously in the direction of the fork
Joins 3' end of DNA of leading strand and joins Okazaki fragments of lagging strand
Removes RNA nucleotides of primer from 5'end and replaces them with DNA nucleotides
Using parental DNA as a template, adds nucleotides only to the 3' end of DNA strand
Synthesizes RNA primers using parental DNA as a template
Relieves the strain caused by DNA unwinding
Binds and stabilizes single-stranded DNA
Unwids parental double helix at replication forks
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
Long DNA molecules have multiple ORI and replication bubbles.
Prokaryotic DNA is circular and there is only one ORI.
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.
Biological Membrane: Cell membranes are selectively permeable barriers
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.
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:
There are two main types of ion channels:
Cotransport is the coupled transport by a membrane protein. This occurs when active transport of a solute indirectly drives the transport of other substances.
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.
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.
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:
Water balance in plant cells:
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.
Transmembrane protiens are imbeded in the phospholipid bilayer with an extracellular facing side and a cytoplasmic facing side.
Some functions of membrane proteins include:
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.
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.
Molecules released by a cell which is received by another cell
Present in a target cell that receives a signal
Present in cytoplasm in nucleus.
Acts as a gate for ions. When a signal molecule binds a receptor, the receptor changes shape, allowing specific ions to go through.
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.
Cellular responses
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.
Protein Kinase A
cAMP binds and activates protein kinase A, which goes on to activate another kinase and so on.
ATP to CAMP
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.
Adenylyl Cyclase
Active G protein can then activate Nearby enzyme, such as adenylyl cyclase.
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.
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 neurotransmitters
Send secretary vesicles to target cells
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.
The goal of photosynthesis is to produce glucose (sugar)
H2O is oxidized and CO2 is reduced
Enhance CO2 uptake and reduces photorespiration to adapt to hot, arid climates
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 photophosphorylation
Input:
-Light
-H2O
-NADP+
-ADP+Pi
Output:
-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
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
Same Cells
Occurs in different cells
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
-CO2
Output:
-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
Cellular respirations purpose if to make ATP
Protons go back through the ATP synthase, moving from a high concentration to low concentration
The energy from the ATP synthase gives ADP energy to make ATP
Components:
-Complex I, II, III, IV
-Q
-Cyt
Energy is released at each step
-NADH --> complex I --> Q --> complex III- ->Cyt c--> complex IV
Protons are getting pumped into inner membrane
C6H12O6 is oxidized
CO2 is reduced
Formed:
ATP= 1
NADH= 3
FADH2= 1
Starting molecule: Isocitrate
Enzyme: looses electrons --> NAD to NADH
Product: ketoglutarate
Starting molecule: Acetyl CoA
Enzyme: Oxaloacetate
Product: Citrate
-Pyruvate, from glycolysis, is oxidized to form Acetyl CoA
-Oxygen is required
Occurs in the cytoplasm.
Total output- 4 ATP, 2 NADH, 2 pyruvate
Net output- 2 ATP, 2 NADH, 2 pyruvate
Last five steps- generate net gain by producing ATP that was invested
-2 pyruvate, 2 NADH, and 4 ATP are formed
First five steps- require energy to prepare molecule for breakdown
-2 ADP are formed
Starting molecule: fructose 6-phosphate
Enzyme: phosphofructokinase
Product: fructose 1,6-biphosphate
Starting molecule: glucose
Enzyme: hexokinase
Product: glucose 6-phosphate
Beta pleated sheets
Alpha Helices
Basic
Acidic
Non-polar
Carbohydrates serve as fuel and building materials
starch
glycogen
cellulose
NOTE: LIPIDS ARE NOT POLYMERS!
Nucleic acids are polymers made of monomers-- called nucleotides
Phosphodiester link connects phosphites and sugars
H-bonding through complitary base pairing forms DNA double helix
Unlike DNA, RNA has oxygen
Sharing of electrons between two atoms with an EN difference of 0.5 or greater
Sharing of electrons between two atoms with an EN difference of less than 0.5
Vehicle of the cell, the golgi apparatus packages things into vesicles where vesicles can then transport cellular materials.
attached to nucleus synthesizes lipids (can also help detoxify)
composed of ribosomes that perform protein synthesis
reinforces cell shape; functions in cell movement; components are made of protein, includes…
Microtubules
made of tubulin, this hollow shape maintains the shape of the cell. very structural and moves organelles
Intermediate filament
in the middle, anchor organelles to the cell and help maintain a cell’s shape, composed of keratin proteins.
Microfilaments
made of actin, helps maintain cell shape but also aid with movement
projections that increase the cells surface area
organelle with various specialized metabolic functions; produces hydrogen peroxide as a by product and then converts it to water
organelle where cellular respiration occurs and most ATP is generated
digestive organelle where biomolecules are broken down, hydrolysis reaction
organelle active in synthesis, modification, sorting, and secretion/transportation of cell products
complexes that make proteins; free in cytosol or bound to rough ER or nuclear envelope
membrane enclosing the cell
material consisting of DNA and protein; visible in a dividing cell as individual condensed chromosomes
non membranous structure involved in production of ribosomes; a nucleus has one or more nucleoli
double membrane enclosing the nucleus; performed by pores; continuous with ER, also known as the nuclear lamina
store food and make pigment
channels found in plant cells that allow for the movement of water and other materials to move between cells
stores water, nutrients, and waste
double membrane organelle that has its own DNA and performs photosynthesis
located outside the cell membrane, made of cellulose, and helps maintain cell shape
structures that connect cells, things can pass through very easily
secure cells very tightly, keeps stuff from freely moving around
structure connects cells together that are semi-sealed. Desmosomes use proteins and are programed to selectively allow materials
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
found in the ECM, proteoglycan are proteins with sugars attached, involved in organizing extracellular matrix
survival under harsh environmental conditions
movement
bacterial mating
attachment to surfaces
adherence to surfaces
resistance to phagocytosis
Gives bacteria shape and protection from lysis in dilute solutions
contains hydrolytic enzymes and binding proteins to nutrient processing and uptake
localization of genetic material (DNA)
storage of carbon, phosphate, and other substances
protein synthesis
buoyancy for floating in aquatic environments
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
gel like substance that fills the cell and and keeps the organelles in place
stores genetic information
Two atoms share one or more pairs of electrons to achieve stability.
Transfer of electrons between oppositely charged irons
Can lead to ion-dipole interactions in water
