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storage of water, toxins, oils and carbohydrates
What is the atomic number? Mass number?
Atomic Number: number of protons in an atom (this never varies)Mass Number: number of protons + number of neutrons (this can vary- isotopes)
What are valence electrons? How are they contribute to a atom’s reactivity?
Valence electrons=unpaired electrons; atoms become stable once there are no longer outer orbitals that only contain single electrons.
What are covalent bonds – polar and non-polar?
Could be non-polar or polar, it depends:
1) If the two atoms share the electrons equally=non-polar.2) If one atom is more electronegative it will pull the electrons closer to its nucleus=polar.
An ionic bond consists of: one atom loses an unpaired electron and another element gains an electron to fill its orbital.
A cation is a positively charged ion; an anion is a negatively charged ion.
EX: NaCl Na has a +1 charge Cl has a -1 charge Na would be the cation; Cl the anion.
A hydrogen bond involves the bonding between H and one of three different elements- N,O, or F (Nitrogen, Oxygen, or Fluorine). These bonds are fairly weak and are easily broken.
1) It has polarity
2) Hydrogen bonding
a) gives water structure: cohesion
b) high specific heat (amount of heat to raise T 1ºC)
c) High heat of vaporization
3) It is a good solvent for ionic, polar molecules4) Nonpolar molecules do not dissolve in water
Define hydrophobic and hydrophilic.
Potential Energy- the amount of energy stored in the reacting moleculesEntropy- the amount of disorder in the reacting molecules
What determines if a particular reaction is spontaneous?
If ▵G is (-), then spontaneous; if ▵G (+), then nonspontaneous.
For ▵G to be (-) (regardless of T), ▵H needs to be (-) and ▵S would need to be (+).
What is the formula for Gibb’s free energy of a reaction? Define the variables.
▵G= ▵H - (T ▵S)
▵G- total free energy change in a reaction ▵H- change in potential energyT- temperature ▵S- change in entropy
Define endergonic, exergonic, endothermic, exothermic reactions. Which are spontaneous?
Endergonic- energy must be absorbed into system; this would be nonspontaneous (also anabolic)
Exergonic- energy is released; this would be spontaneous (also catabolic)
Endothermic- energy, in the form of heat, being absorbed; this would be nonspontaneous
Exothermic- energy, in the form of heat, being released; this would be spontaneous
Side groups determine properties of particular amino acids. Side groups could be any one of the following: polar, acidic, basic, or nonpolar. The sequence of the amino acids (and therefore the side groups) determine how these side groups will interact with each other and will affect what shape the overall protein takes.
structure made up of multiple polypeptide chains together (there would need to be more than one protein involved to make this structure)
1) Catalysts reactions (speeds up reaction)
2) Defense (antibodies in immune system)
3) Movement (actin and myosin)
4) Signaling (insulin receptors)
5) Cell Structure (keratin in hair)
also...6) Transport (Na+K+ exchangers across membranes)
How do enzymes catalyze biological reactions?
By reducing the activation energy required for spontaneous reactions
How do enzymes affect the transition state & activation energy?
It lowers both of them
Do enzymes change the overall free energy change of a reaction?
Coenzymes- small inorganic molecules often within active siteBoth of these help increase levels of reaction within enzymes
The competitive inhibitor will bind to the active site. It can do this because it often has a similar shape to the substrate. It “competes” with the substrate to bind to the active site.
The allosteric activator or deactivator will bind to someplace on the enzyme other than the active site. Depending on how and where it binds, the molecule could change the shape of the enzyme to make it better able to bind with substrates (allosteric activation) or it could change its shape so that substrate have a hard time to bind (allosteric deactivation).
pH levels and temperature can denature enzymes
one 5-carbon sugar, a phosphate group, and a nitrogenous base
Three of the nitrogenous bases are the same for both RNA and DNA: guanine, adenine, and cytosine. Thymine, the fourth base pair found in DNA, is replaced by uracil in RNA.
DNA has deoxyribose sugar while RNA has ribose sugar. The deoxyribose sugar has one less oxygen atom than the ribose sugar.
The bases thymine and cytosine present in DNA are pyrimidines. Purines are the bases adenine and guanine present in DNA and RNA.
DNA is two strands, and RNA is one strand
One end runs three prime to five prime, the other runs 5 prime to three prime.
RNA because it can act as a catalyst to itself, ribsomal RNA (rRNA)
Carbon, Hydrogen, and Oxygen
What is the bond between sugars in oligo- and polysaccharides?
Phospholipids are a class of lipids that make up the main component in cell membranes
Small nonpolar= highly permeable. Small uncharged polar= moderately permeable. Large uncharged polar= moderately permeable. Charged ions= impermeable.
1) Saturation of fatty acid tail- lowers permeability; more saturated=less fluid membrane
2) More cholesterol=less fluid membrane
3) Temperature- lower fluidity with lower temperature due to closer packing of fatty acid tails
Diffusion- molecules going from high to low concentrations
Osmosis- water diffusing from high to low concentration
hypertonic- there is too much water outside the cell and not enough inside the cell causing the cell to shrivel up.
hypotonic- too much water in cell and not enough outside cell, causes cell to swell and bursts. isotonic- water moves throughout cell evenly the difference between channel and carrier proteins. ***All of these are involved in osmosis.***
Diffusion is a passive process. Facilitated diffusion is an active process.
Carrier proteins= carry large/uncharged molecules across a membrane(very selective). Channel= carry ions across a membrane(slightly selective).
Endo= into the cell (engulf). Exo= out of the cell (excrete).
A gradient of electrochemical potential, for an ion that passes through a membrane. (electrical potential and chemical concentration).
Nucleus=must have a nuclear localization signal. ER= must have an ER signal sequence.
NLS interacts with importin -> which interacts with the pore complex. Exportin= brings molecules out of the nucleus. SRP binds to signal sequence which then a ribosome docks to the signal sequence.
SRP binds to ER signal sequence-> ribosome docks with ER-> Protein is deposited into lumen of ER-> (Rough ER)= proteins in the lumen get folded into tertiary shape-> (Smooth ER)= proteins get glycosylated (sugar tag added)-> proteins enter transport vesicles.
The golgi assigns additional sugar tags to the proteins and then they get shipped to their specific destination that matches their sugar tag.
Movement in muscle cells.
Move transport vesicles along microtubules. Kinesin= motor protein associated with this.102
provides tight seal between adjacent cells (tight junctions), a removable anchor between cells ( anchoring junctions) and allow for nutrients, etc., between cells ( gap junctions).
Desmosomes= cell-cell attachments (most common anchoring junction). Cadherin= proteins link cells.
Gap junctions in plants where the ER extends between cells.
What is the overall purpose of cellular respiration?
6H12O6 + 6 O2->
6 CO2 + 6 H2O
Mitochondria (makes ATP). Glycolysis= cytosol. Pyruvate processing and Krebs Cycle= in mitochondrial matrix. Electron transport, chemiosmosis & oxidative phosphorylation= in inner mitochondrial membrane.
ATP is used to fuel all of the other cycles/processes but the more ATP is out into the cycle, the more ATP is yielded. Exergonic= ATP is released. Endergonic= ATP is absorbed. Coupled reactions= ATP is both lost and gained.
A reaction in which there is a transfer of electrons. One is reduced and another is oxidized.
OIL RIG = Oxidation is losing electrons; Reduction is gaining electrons
What is being oxidized and what is being reduced in the equation in C6H12O6 + 6O2=6CO2+6H20
Oxygen is being oxidized; Glucose is being reduced
Pyruvate processing, krebs cycle, ETC- mitochondria.
For glycolysis, pyruvate processing and Kreb’s cycle, list (1) reactants and products; (2) ATP formation? ; (3) CO2 released?; (4) electron carrier reduced?; (5) overall purpose.
Electron carriers bring electrons into mitochondrial inner membrane.
Energy is being released.
Proton accumulation inside cristae builds up a proton gradient.
Protons try to force back into the matrix along the concentration gradient (proton motive force). Basically, builds up energy.
Chemiosmosis & Oxidative Phosphorylation.
Because the cycle needs to be broken down into those steps in order for the most ATP to be made.
What is the final electron acceptor in lactic acid fermentation? What is the product of this process?
What is the final electron acceptor in alcohol fermentation? What it the product of this process?
acetylaldehydeProduct- 2 ethanol
CO2 + H2O+ light energy-> sugars + O2.
Inside thylakoid membranes. Absorb light. Chlorophylls= green. Carotenoids= orange/yellow. Blue & red are absorbed & green is reflected.
Photosystems I & II are pigment clusters on the membrane. Reaction center receives light energy.
electrons go to electron transport proteins and is then released as energy.
The electron is given to the electron transport chain.
The electron lost from PSI is replaced by an electron transferred from PSII via another electron transport chain. PSII replaces its electrons by extracting electrons from water molecules, releasing O2 as a byproduct.
Water separates into O2, H+ ions, and electrons.
What occurs in the reduction phase of the light independent reactions? Regeneration phase?
G3P, 1 of 6 will make sugars.
Oxygen is a competitive inhibitor of the Rubisco enzyme. Photorespiration=a light-dependent process in some plants resulting in the oxidation of glycolic acid and release of carbon dioxide that under some environmental conditions (as high temperature) tends to inhibit photosynthesis.
After S phase, chromosomes are replicated and the sister chromatids connect at the centromere.
Prophase= replicated chromosomes condense. mitotic spindle forms, sister chromatids are visible. Nuclear envelope starts to breakdown.
Prometaphase= nuclear envelope breaks down, spindle fibers reach chromosomes and contact kinetochores.
Metaphase= Chromosomes line up at the middle.
Anaphase= spindle fibers shorten, sister chromatids separate and chromosomes are pulled to opposite poles.
Telophase= spindle disappears, nuclear envelope reforms and chromosomes begin to unwind.
The splitting of the cell membrane to form two new cells.
Chromosomes that code for the same traits are said to be ________ chromosomes.
Cells that contain a complete set of chromosomes from Q151 are said to be ______ whereas cells that only contain one set of chromosomes are said to be ________.
Homologous chromosomes come together (synapsis) and from a tetrad. Crossing over occurs at chiasmata -homologous chromosomes exchange segments.
Do homologous chromosomes separate in meiosis I or II?
Mitosis produces __ daughter cells that are ______ and genetically ________ whereas meiois produces ___ daughter cells that are _______ and genetically ________.
Nondisjunction is the failure of one or more pairs of homologous chromosomes to separate normally during nuclear division, usually resulting in an abnormal product of meiosis
It leads to genetic variation because you get 23 chromosomes from your Mother and Father each. So there is some variation. That way, people are not the same as their family members.
DNA polymerase III builds new strands of DNA. It builds in a 5’→3’ direction.
When two strands become four strands after replication, then each double helix has one new strand and one old strand. This means that the newly formed double helix is half new and half old.
What must first be placed so that DNA polymerase 3 can build a new DNA strand? What enzyme catalyzes this?
What is the leading strand? Lagging strand?
Leading strand: In DNA replication, the strand of new DNA that is synthesized in one continuous piece, with nucleotides added to the 3’ end of the growing molecule (continuous strand.) Lagging strand: In DNA replication, the strand of new DNA that is synthesized discontinuously in a series of short pieces that are later joined together (discontinuous strand.)
Short fragments of DNA synthesized on the lagging strand during DNA replication
DNA is arranged in a circular shape and there is only one replication origin when replication starts. Eukaryotic chromosomes have multiple origins of replication.
Chemicals in tobacco, cell divides when not ready, high levels of proto-oncogenes or mitogens, defective cyclins and cdk.
What molecule brings information on how to construct a protein from the nucleus to ribosomes in the cytoplasm?
Central Dogma summarizes the flow of information in cells. It states that DNA codes for RNA, which codes for proteins. Information in cells flows in one direction. *DNA (info storage) →RNA (info carrier) →Proteins (active cell machinery). Exceptions: 1) many genes code for RNA molecules that do not function as mRNA, they are not translated into proteins. 2) In some cases, information flows in reverse, RNA back to DNA.
Because there several different codons for only a few proteins. 1 protein can code for multiple things. ratio= 61 codons:20 amino acids.
Silent= does not affect final protein (often in 3rd base of codon).
Missense= changes sequence of amino acid (replacement).
Nonsense= results in a STOP codon (shortened-truncated protein).
Frameshift= insertion or deletion of a base shifts the reading frame of the codons which changes the sequence of amino acids.
Gene= region of DNA that carries hereditary info.
Promoter= starts transcription.Terminator= causes everything to disassociate and translation stops.
It is recognized and bound by a subunit of RNA polymerase during initiation of transcription. This region of the DNA is also the first place where base pairs separate during prokaryotic transcription to allow access to the template strand.
5’ caps and 3’ poly A tails in order to keep enzymes from chewing it up.
transfer RNA. Bring amino acids to ribosomes.
61 codons: 40 tRNAs. wobbling occurs at the 3rd position of the codon.
What are the roles of the E, P and A sites within the large ribosomal subunit?
E= holds a tRNA that will exit. P= holds the tRNA with growing polypeptide attached. A= holds an aminoacyl tRNA.
Describe what occurs during translation in (1) initiation; (2) elongation and (3) termination.
Initiation= mRNA binds to small subunit, tRNA binds to AUG codon, large subunit binds to complete assemble.
Elongation= 2nd tRNA binds to A site, peptide bond forms between 1st and 2nd amino acids, ribosome moves in 3’ direction, tRNA that was in P site no9 longer has an attached amino acid and enters E site, new tRNA moves into A site, peptide bond forms between amino acid in A site and the growing chain in the P site, chain is transferred by the formation of bond to the A site, ribosome moves in the 3’ direction, tRNA in E site exits and empty tRNA in P site is transferred to E site.
Termination= ribosome reaches a stop codon, protein is released, ribosomal subunits separate and mRNA is released.
Benign is not cancerous, malignant is. Malignant tumors have differences in cell differentiation and have uncontrolled cell division.
To make sure that the damaged DNA does not replicate.
What class of proteins promote the cell cycle? Sets breaks to the cell cycle?
genes that when mutated or expressed at high levels helps turn a normal cell into a tumor cell
Made of cyclin B and cyclin-dependent kinase (cdk). MPF promotes the entrance into mitosis (the M phase) from the G2 phase by phosphorylating multiple proteins needed during mitosis. MPF is activated at the end of G2 by a phosphatase, which removes an inhibitory phosphate group added earlier. The MPF is also called the M phase kinase because of its ability to phosphorylate target proteins at a specific point in the cell cycle and thus control their ability to function.
When CDKs and cyclin form a complex and activate CDK, it is called an MPF or maturation-promoting factor. The presence of enough MPFs will cause the cell to move from the G phase into the mitotic or M phase.Towards the end of mitosis, the MPF deactivates itself by promoting the degradation of cyclin. The CDKs remain for later use but are now inactive because of the lack of cyclin.
MPF-induces mitosis in all eukaryotes. MPF is a dimer consisting of a cyclin and a cyclin-dependent kinase (Cdk). Cdk catalyzes phosphorylation of other proteins to start mitosis.
breast-ovarian- tumor suppressors that help in DNA repair
colo-rectal-mutations in genes for mismatch repair system.
Pattern- All material is made of cells
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