por Sara Lim hace 1 año
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Final Concept Map
por Sara Lim hace 1 año
210
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Cell
V
Biomolecules
Proteins
Primary
Primary: Primary is the first level of protein fold which mean it is just a long string of amino acids bonded together at the main chain by peptide bonds.
Secondary
Secondary: This is the secondary level folding. Here there will be two types of structure:
Alpha Helices
Alpha Helices: this can be a single chain polypeptide. Alpha helice occurs when the polypeptide winds up and forms a spring-like structure. The structure is held together through hydrogen bonds. It is most used secondary structure and is used in the protein-DNA interface interaction. It also determines the global structure of proteins and their functions.
Beta Pleated Sheets
Beta Pleated Sheets: this cannot be a single polypeptide because it needs one or more strands. It is crucial for lipid metabolism and the structure of proteins that binds with fatty acids. They also bond together through hydrogen bonds but instead of forming spirals, they are parallel to each other.
Quaternary
Quaternary: This level occurs with tertiary structures interact with each other through their R chains. The way they interact also depends on if they are non-polar, polar, or charged. At this level, it would allow proteins to have multiple functions in gene expression, macromolecular transport, and chemical reaction regulation. However, not all protein have quaternary structures.
Tertiary
Tertiary: the third level of protein level. In tertiary level, R chains are involved in bondings. Non-polar would interact through hydrophobic interactions. Polar would interact with dipole-dipole, disulfide, covalent, hydrogen bonds, or hydrophilic interactions. Charged groups will interact with ionic interactions. Tertiary structure also determines how hormone regulates receptor activations. In this phase, polypeptide chains become functional. It becomes three-dimensional and allows it to interact with other molecules.
Charged
Charged: The R group contains charges either an acidic (negative) or basic (positive). They would react with opposite charges through ionic bonds.
Polar
Polar: The end of the R group is a polar component like OH, SH, and NH2. They would usually be found on the outside when reacting with water because they are hydrophilic. They would interact with each other through dipole-dipole, covalent, or hydrogen bonds.
Non-Polar
Non-polar: The end of the R group is a non-polar component like H, CH, or a hexagon ring. If proteins are made up of non-polar R groups, it would mostly be found tucked in when reacting with water because of being hydrophobic reaction.
Nucleic Acid
DNA (Deoxyribonucleic Acid)
Deoxyribonucleic Acid (DNA): DNA is made up of two strands that wrap or wind up around each other, which is also called a double helix. These two strands are connected together with hydrogen bonds. It also replicates and store genetic informations. The reason people use DNA more than RNA when it comes to genetics is because DNA is more stable which makes it safer when it comes to keeping genetic information.
(RNA) Ribonucleic Acid
Ribonucleic Acid (RNA): RNA is made up of one strand or single helix. Its main function is to create proteins and carry genetic information that is translated by ribosomes. Because it is a single helix, it is less stable making it not as reliable compared to DNA whenever it comes to the stability in genetics. There are three main types of RNA: mRNA, rRNA, and tRNA.
Lipids
Unsaturated Fats
Cis Fat
Cis Fat: Hydrogens around the double bond will be on the same side which means the acid would be more bent, making it less solid and packed. This makes it liquid at room temperature and easier to digest. Making it the healthier option to consume.
Trans Fat
Trans Fat: Around the double bond of carbon in the fatty acid, there will be two hydrogens on the opposite sides. This makes it straighter than cis fats. Since it is straighter, it will be more solid than cis fats which means it can also become solid at room temperature. Trans fat is usually a result of trying to transform a liquid oil to solid. This makes it harder to digest and break down and can cause a increase level in LDL (low-density lipoprotein) or bad cholesterol.
Unsaturated Fats: The fatty acids in unsaturated fats have some double bonds between carbon and hydrogen which means the acids aren’t as packed and more spread out compared to saturated fats. In room temperature, foods with unsaturated fats will stay in liquid form.
Saturated Fats
Saturated Fats: Consist of a glycerol and three fatty acids, or is called a triglyceride. The fatty acids in saturated fats are all single bonds between carbon and hydrogen. This makes the structure straight and packed. Which means in real life, food with more saturated fat in room temperature will become solid.
Carbohydrates
Monosaccharides
Galactose
Galactose: Another isomer of glucose, which means same formula but different structure. The main difference is the hydroxyl arrangement at carbon four. Compared to glucose, galactose is not as sweet as glucose and less soluble in water.
Fructose
Fructose: It has the same chemical formula as glucose just different structure. It is found in fruits, vegetable, honey, and more. Fructose helps provide energy when glucose is not sufficient. Compared to glucose, Fructose is a five-membered ring.
Beta Glucose
Beta glucose: Hydroxyl group is facing above the main structure. Cellulose is made up of beta glucose.
Alpha Glucose
Alpha glucose: Hydroxyl group is facing down from the main structure. This makes it more reactive to enzymes and less stable. Glycogen and starch are made up of alpha glucose.
Polysaccharids
Glycogen
Glycogen: A long polymer chains of glucose that are bonded with an alpha acetal linkage (1-4). It has branching at after every 4-8 residues and is bonded by a 1-6 glycosidic bond. Glycogen is used as a storage that allows fast energy release when it is needed. The branchings makes it possible for rapid hydrolysis which allows more respiration during exercises.
Cellulose
Cellulose: It is an unbranched polysaccharide that is used for structure in plants. Being unbranched makes it able to form a long and straight chain which allows rigidity in the plant cell and maintain its shape.
Starch
Amylose
Amylose: Amylose is a unbranched polysaccharide chain. It helps plant store energy and break up starch molecules in maltose and maltotriose.
Amylopectin
Amylopectin: A branched polysaccharide that is stored in starch, it stores glucose for later use for energy source. The branching helps glucose units to be synthesized and stored.
Cell Regulation
Negative regulation
Activator is not bonded to operator
transcription
Activator is Bonded to operator
Eikaryotic ONLY
Transcription factors bind before RNA Polymerase II
RNA Polymerase II binds
Additional Transcription factors bind along with RNA polymerase II
Transcription/DNA unwinds
cant bind so no transcription
Positive Regulation
Active repressor doesn't bind to operator
Operon "on"
Operon "on"/ transcription
Operon ON
Operon OFF
Active repressor binds
No transcription
Cell Membrane are Selectively permeable barriers
Simple Diffusion
Electron transport chain
Diffusion of a substance across a membrane with no energy investment. Since non-polar doesn't have a charge, it can easily go through the membrane without a transport protein nor extra energy will be required
Osmosis
the diffusion of free water across a selectively permeable membrane. Water diffuses across a membrane from the region of lower solute concentration to the region of higher solute concentration until the solute concentration is equal on both sides
Transport Protein
Proteins that help molecules move across a membrane within a cell. These are usually polar and ion molecules that can't go through the membrane alone like non-polar molecules
Against or along concentration
Active Transport
It is energy-driven and helps move molecules across cells against their concentration gradient, which is from low to high concentration
Sodium Potassium Pump
Facilitated Transport
Channels
Non-gated Channels
Allows molecules to pass by under any circumstances
Provide corridors or channels that allow a specific molecule or ion to cross the membrane
Gated Channels
Stretch-Gated
Ligand-Gated
Voltage-Gated
A type of diffusion which means that movement of molecules is from high to low concentration or down concentration gradient. It speeds transport of a solute by providing efficient passage through the membrane but does not alter the direction of transport
Carrier Protein
It undergo a subtle change I shape that translocate the solute binding site across the membrane
Co transport
SUmport
Antiport
steps
Glycolysis
Glucose
Glucose 6-phosphate
Fructose 6-phosphate
Fructose 1,6-biphosphate
Dihydroxyacetone phosphate
Glyceraldehyde 3-phosphate
1,3-bisphosphoglycerate
3-phosphoglycerate
2-phosphoglycerate
phosphoenolpyruvate
Pyruvate
Pyruvate Oxidation
Citric Acid Cycle / Kreb's Cycle
Oxidative Phosphorylation
Citrate
5-carbon molecule
4-carbon molecule
GDP, Pi to GTP
FAD to FADH2
NADH to NAD+
Oxaloacetate
Acetyl CoA
PROKARYOTES
Complexes that synthesize protein. Made up of two RNA complexes.
Fimbriae and Pili
Some bacteria contain on their surface short hair like projections called fimbriae. Some bacteria also contain long projections called pili which are involved in forming a channel between two bacterial cells to transfer DNA from one cell to another.
Flagellum
Flagella of bacteria , archaea and eukarya differ in their composition and mechanics of movement. Flagellum contains a hook and basal body. It rotates 360 degrees to propel the cell.
Capsules and Slime Layer
The cell wall of many bacteria is surrounded by a sticky layer made of polysaccharide or protein. The capsule is dense and well defined or a slime layer if diffuse. Both of these outer layers help bacteria to stick (adhere) to a substance or other individuals in a colony. These layers also protect against dehydration and some capsules protect bacteria from attacks by host's immune system.
This is the structure present outside of the plasma membrane. Functions include: provides bacteria with support, protects the cell, and maintains shape.
Plasma Membrane and Nucleoid
Bacterial chromosome, nucleoid, is in the cytoplasm because there is no nucleus. The presence of DNA that is separate from the main bacterial chromosome is plasmid (made of proteins and phospholipids).
outer layer that maintains cell’s shape and protects cell from mechanical damage; made of cellulose, other polysaccharides, and protein
organelle with various specialized metabolic functions; produces hydrogen peroxide as a by-product and then converts it to water
photosynthetic organelle; converts energy of sunlight to chemical energy stored in sugar molecules
network of membranous sacs and tubes; active in membrane synthesis and other synthetic and metabolic processes; has rough (ribosome-studded) and smooth regions
Smooth ER
Rough ER
complexes that make proteins; free in cytosol or bound to rough ER or nuclear envelope Microfilaments Intermediate filaments Microtubules
reinforces cell's shape; functions in cell movement
Microvilli: projections that increase the cell’s surface area
Microtubes
Intermediate filaments
Microfilaments
Organelle active in synthesis, modification, sorting, and secretion of cell products
Cell's Signaling
Receptor
Present in target cell that receives the signal molecule
Membrane receptors : hydrophilic- first messenger & requires a second messenger
Ion channel receptors
tyrosine kinase receptor
G-protein linked receptor
when the signaling molecule binds to the extracellular side of the receptor, the receptor is activated and changes shape. Its cytoplasmic side then binds and activates a G protein. The activated G protein carries a GTP molecule.
The activated G protein leaves the receptor, diffuses along the membrane, and binds to an enzyme, altering the enzyme's shape and activity. Once activated the enzyme can trigger the next step leading to a cellular response. Binding of signaling molecules is reversible. The activating change in the GPCR, as well as the changes in the G-protein and enzyme, are only temporary; these molecules soon become available for reuse.
Intracellular receptors: In cytoplasm & nucleus
Local signaling
Realeases a signal ( requires the target cell to have sometging to receive signal
Synaptic signaling
Paracrine signaling
physical contact
interacts with receptor on the membrane of adjacent cell
the signaling molecule is not free, it is bound to the membrane cell
occurs in neighboring cells that are in physical contact.
long distance signaling
membrane enclosing the cell
digestive organelle where macromolecules are hydrolyzed
Autophagy
2. Hydrolytic enzymes digest organelle components
1. Lysosomes fuses with vesile contaning damaged organelles
Phagocytosis
3. Hydrolytic enzymes digest food particles
2. Lysosomes fuses with food vacuole
1.Lysosome contains active hydrolytic enzymes
organelle where cellular respiration occurs and most ATP is generated
DNA Replication
Watson and Crick noted that the specific base pairing suggested a possible copying mechanism for genetic material where each strand serves as a parent strand with information to make the other strand. Based on this as it retains the parent and uses this information to form a new (daughter) strand this was coined as the semi conservative model. This model – semiconservative replication was proposed, But is this the correct model? There were competing models proposed as well.
There is a sequence of nucleotides in DNA called ORI for origin of replication. The goal is to separate the two strands of DNA at ORI sequences and form a bubble as shown here. This is called a replication bubble and there are two forks at each end of the bubble. Now each separated strand here has to be used as the parent strand to form complementary daughter strand starting at the ORI sequence, as suggested by the semiconservative model.
For the long DNA molecules in eukaryotes, multiple replication bubbles form and eventually fuse, speeding up the copying of DNA, while as Prokaryotic DNA is circular there is only one ORI sequence.
An enzyme Helicase separates the two strands to form the replication bubble. SSB or single stranded proteins keep the DNA single stranded. Another enzyme Topoisomerase helps relieve any strain caused by unwinding of the DNA.
Primase – makes RNA primers complementary to the DNA parent strand sequence. Now the DNA polymerase III will add nucleotides only to the 3’ end. Note the arrow.
So to form a strand we have to connect nucleotides through phosphodiester bonds using dehydration/condensation reactions! Yay for chapter 3! We need enzymes for this. The enzyme here is a DNA polymerase. In bacteria it is DNA polymerase III. But for a DNA polymerase to add nucleotides it has two constraints: It adds nucleotides ONLY to the 3’ end of an existing nucleotide. Which means it adds nucleotides in 5’ to 3’ directions and needs something to add nucleotides to – we call this a primer. Typically in cells the primer for replication is a short sequence of RNA and the enzyme that makes an RNA primer is called a Primase.
Along one template strand of DNA, the DNA polymerase synthesizes a leading strand continuously, moving toward the replication fork. Only one primer is required to synthesize the leading strand. Again keep in mind the strand is made in one direction 5’ to 3’
In forming the lagging strand, multiple RNA primers have to be laid down and then extended by DNA polymerase III to form short Okazaki fragments. So how are these RNA primers removed? Another enzyme, DNA polymerase I removes the RNA and replaces it with DNA nucleotides. Another enzyme called ligase seals any gaps by connecting nucleotides by phosphodiester linkages.
. Each fork moves in the opposite direction hence replication is called bidirectional. Blue strands of DNA are the daughter strands. So what are the red lines? That’s the RNA primer. The arrows on the light blue strands tell us the direction in which new nucleotides are added. So in this case when the nucleotides are added continuously in the direction of the fork that strand is called the leading strand. Now as DNA is antiparallel, the opposite strand will be made in the opposite direction, right? Yes, but the opposite strand is formed in short segments called Okazaki fragments, and is called the lagging strand. In bacteria, DNA polymerase III forms these new strands through condensation synthesis.
DNA polymerase III. This enzyme will add nucleotides only to the 3’ end.
DNA polymerase III is the enzyme that makes daughter DNA strands, but first it needs a short (20 nucleotides or so) strand to add new nucleotides to. This is called a primer. In replication this is an RNA primer. The DNA polymerases adds new nucleotides complementary to parent DNA, to the primer in ONE direction only – 5’ to 3’, so always adding nucleotides to the 3’end of a previous nucleotide. Another protein called Sliding Clamp works with DNA polymerase III. It helps keep DNA pol III on the parent strand so it doesn’t fall off during replication.
DNA Structure
Subtopic
Central Dogma of Molecular Biology
DNA, RNA, PROTEIN
DNA
Processes: Replication
Function: stores genetic information
Transcription
Initiation
Transcription factors: proteins that assist in the binding of RNA polymerase to the promoter
Promoter Region: specific DNA sequence signaling the start of transcription
Elongation
Complementary base pairing: A-U, G-C in RNA synthesis
Template strand: the DNA strand used as a template for RNA synthesis
Termination
Release of RNA: RNA polymerase and the newly formed RNA molecule detach from the DNA template
RNA produced
rRNA: major component of ribosomes
tRNA: transfer amino acids to the ribosome during translation
Translation
Site: ribosomes, involves tRNA bringing amino acids to the ribosome
tRNA binding: initiator tRNA carrying methionine binds to the start codon
ribosome binding: small ribosomal subunit binds to mRNA at the start codon
Translocation: ribosome moves along mRNA, reading codons and synthesizing the growing polypeptide chain
Peptide bond formation: Ribosome catalyzes the formation of peptide bonds between amino acids
Amino acid addition: tRNA molecules bring amino acids to the ribosome
Codon Recognition
disassembly: ribosome dissociates into its subunits
release factor: binds to the stop codon, causing the release of the polypeptide chain
Protein Synthesis
Genetic code: the correspondence between codons and specific amino acids
codons: three-nucleotide sequences on mRNA
Stop codon signals the end of translation
Start codon: AUG on mRNA signals the beginning of translation
mRNA: carries the genetic information from DNA to the ribosome
Terminator sequence: DNA sequence signaling the end of transcription
RNA Synthesis: RNA polymerase reads the DNA template and synthesizes complementary RNA
RNA Polymerase: enzyme that initiates transcription
Structure: Double-stranded helix
The amount of Guanine equals the amount of Cytosine. The amount of Adenine equals the amount of Thymine.
Based on Chargaff’s data, X ray diffraction pattern of DNA by Rosalind Franklin, Watson and Crick came up with the double helix model of DNA. Remember this from chapter 3 – note base complementarity. The way this structure would satisfy the X ray image was if the two strands were antiparallel.
Structures of purines and pyrimidines were connected by hydrogen bonds.
Experiments
Watson and Crick’s semiconservative model of replication predicts that when a double helix replicates, each daughter molecule will have one old strand (derived or “conserved” from the parent molecule) and one newly made strand. Competing models were the conservative model (the two parent strands rejoin) and the dispersive model (each strand is a mix of old and new)
Bacterial cultures grown in regular 14N or 15N are the controls. After several rounds of growing bacteria in 15N, they were transferred to medium containing 14N. After they were grown for about 20 min (one round of replication), bacteria were removed, DNA extracted from these bacteria and subjected to centrifugation with CsCl. They combined the DNA with CsCl – and spun at high speeds in an ultracentrifuge. This resulted in forming a gradient of CsCl concentrations. The density of CsCl was highest at the bottom of the tube and lowest at the top. DNA in this solution formed a band at the point in the tube where the density of CsCl corresponded with its density.
So three bands distribution are possible – high density (bottom of tube), intermediate density (middle of the tube), low density (top of the tube). After the first round of replication they noted the distribution of bands. Based on what they observed after one round of replication (one band with intermediate density) they could eliminate conservative model of replication, as you would expect a high density band as well for this model. After the second round of replication they were able to eliminate the dispersive model. So the correct model of replication is semiconservative!
The next experiment done was by Hershey and Chase to determine what was that component that was injected by the bacteriophage inside bacterial cells. As the bacteriophage is only made of two components – DNA and proteins – they labeled DNA of one tube of bacteriophages with radioactive phosphorus (32P) and the proteins of bacteriophages in another tube with radioactive sulfur (35S). They infected bacteria with 35S labeled bacteriophages (shown here as pink) and another set of bacteria cells with bacteriophages with 32P labeled DNA (shown here as blue). The bacteria and the bacteriophages were mixed in a tube, after some time they shook the tube to release the bacteriophages from bacterial surface of course first giving the bacteriophage enough time to inject their genes in the bacteria. Then they centrifuged the bacterial cells and looked for the presence of radioactivity – in supernatant and in the pellet. What did they find? The found that they could recover radioactivity inside bacterial cells only when they used 32P labeled bacteriophages. This indicated that it was the DNA that was injected inside bacteria and not protein! Yay! Definitely check out the animation for this experiment.
In 1928, Fredrick Griffith, a British medical officer, was trying to develop a vaccine against pneumonia. He was studying Streptococcus pneumoniae, a bacterium that causes pneumonia in mammals. He had two strains of the bacteria – one pathogenic (disease causing, S strain) and the other nonpathogenic (R strain). The S strain had a smooth surface due to presence of a capsule outside the cell wall, the R strain lacked the capsule. So the presence of capsule made the bacteria pathogenic. So when he injected the S strain into mouse the mouse died, while when he injected it with R strain it lived – as expected. When he injected the mouse with heat killed S strain the mouse lived. But if he added a live R strain with heat killed S components the mouse died. On further analysis, he found that the R strain had changed to S killing the mouse. So something from the S components had entered live R changing the genetic makeup of R to S! What was this component? Are these genes to make capsule present in DNA, RNA, protein or some other molecule? Nobody knew that time…the favored candidate though was protein!
Prokaryotic cells do not have a nucleus
DNA is in the nucleus, and it is bounded by a double membrane.
Chromatin: material consisting of DNA and proteins; visible in a dividing cell as individual condensed chromosomes
This segment of a chromosome from a nondividing cell shows two states of coiling of the DNA (blue) and histone protein (purple) complex. The thicker form is sometimes also organized into long loops.
Nucleolus: nonmembranous structure involved in production of ribosomes; a nucleus has one or more nucleoli
Nuclear envelope: double membrane enclosing the nucleus; perforated by pores; continuous with ER
