Midterm II Slide Notes Flashcards
What is metabolism?
The totality of an organism’s chemical reactions; the transformation of energy from one form to another.
What does metabolism include?
Catabolic and Anabolic Reactions
What do enzymes do with the presence of substrates?
They convert substrates to products.
Metabolism is a series of linked _____ reactions.
Enzymatic
What are anabolic reactions?
The building of complicated molecules from simple building blocks; energy is consumed linked in a bio synthetic pathway.
What are catabolic reactions?
The breaking down of complicated molecules to simpler ones; energy is RELEASED.
Define Bioenergetics
The study of how energy flows through living organisms.
Define Kinetic Energy
Energy associated with motion.
Define Thermal Energy
The KE associated with the random movement of atoms and molecules.
_____ is thermal energy in transfer between objects.
Heat
Define Potential Energy
The energy that matter possesses because of its location or structure.
Define Chemical enERGY
The potential energy available for release in a reaction.
Metabolism is based on the laws of _____.
Thermodynamics
Define Thermodynamics
The study of energy transformations.
An isolated system, such as that approximated by liquid in thermos, is _____ to exchange energy or matter with its _____.
Unable-Surroundings
Organism are an example of what type of system?
Open System; energy and matter can be transferred between the system and its surroundings.
What is the first law of thermodynamics? What is another name for it?
The energy of the universe is constant; energy can be transferred and transformed, but it cannot be created or destroyed. It’s also called the principle of conservation of energy.
What does energy transfer increase in the universe?
Increases the entropy (disorder) of the universe.
What is the second law of thermodynamics?
During every energy transfer or transformation, some energy is usable and some is often lost as heat; energy transformations and transfers increases the entropy of the universe.
Define Entropy
The measure of molecular disorder, or randomness.
What happens to some of the energy that is transferred in cellular reactions?
Some of it is lost as heat.
Define Spontaneous Process
Processes that can occur without an input of energy; they can happen slowly or quickly. They INCREASE the entropy of the universe.
Define Non-Spontaneous Process
Processes that decrease the entropy of the universe; no energy input is required.
Do all biological activities accompany a release of heat which increases entropy?
YES
What is the equation for Gibbs Free Energy?
Delta G= Delta H- TDELTAS ; Delta G can also be written as G products - G Reactants
What does Delta G mean?
The change in free energy; energy available to do work when the temperature and pressure are uniform as in living cells.
What are the two types of reactions when it comes to Gibbs free energy?
Exergonic and Endergonic
What happens in exergonic reactions and how can they be regarded?
The reactants have more energy than products; energy is released; they can be regarded as SPONTANEOUS.
What happens in endergonic reactions? How can they be regarded?
Reactants have less energy than the products; energy is required; it can be regarded as NONSPONTANEOUS.
If DELTA G is negative, what can we say?
That the reaction is spontaneous and that it is EXERGONIC.
Do living systems ever reach equilibrium?
No, not until they die.
What are the three types of main work that the cell does?
Chemical-Transport-Mechanical
Define Chemical Work
Pushing endergonic reactions.
What is an example of transport work done in cells?
Pumping substances against the direction of spontaneous movement.
What is an example of mechanical work?
Contraction of muscle cells.
How does ATP power cellular work?
By coupling endergonic and exergonic reactions; energy coupling.
What is ATP consisted of?
Ribose (Sugar), adenine (a nitrogenous base), and three phosphate groups.
What does phosphorylation mean?
Addition of a phosphate group to a substance.
Define Activation Energy
The energy that is needed to start a chemical reaction. It is often supplied in the form of thermal energy that the reactant molecules absorb from its surroundings.
How do enzymes speed up metabolic reactions?
By lowering the activation energy.
Define Catalyst
A chemical agent that speeds up a reaction without being consumed by the reaction.
An _____ is a catalytic protein.
Enzyme
Define Substrate
A reactant that an enzyme acts on.
How is an enzyme-substrate complex formed?
The enzyme binds to its substrate/
Define Active Site
The region on the enzyme where the substrate binds.
Define Induced Fit
Induced fit of a substance brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction.
How are substrates held in the active site?
By weak interactions, such as hydrophobic or ionic bonds.
Do the enzymes lower the time required to turn reactants into products?
Yes
What does it mean for enzymes to have optimal conditions?
This means that the enzyme can perform at certain temperatures and pHs.
Define Cofactors
Non-protein enzyme helpers. Can be organic or inorganic
What are organic cofactors called?
Coenzymes; they include vitamins.
Define Allosteric Site
Any site outside of the active site is called the allosteric site.
What do competitive inhibitors do?
They bind to the active site of an enzyme, competing with the substance.
What do non-competitive inhibitors do?
They bind to another part of the enzyme, causing the enzyme to change shape and making the active site less effective. In other words, non-competitive inhibitors bind to an allosteric site.
What are some examples of inhibitors?
Toxins and Antibiotics.
How does feedback inhibition work?
When a substrate binds to the allosteric site, the protein changes shape and the active site is no longer available.
The membrane of a cell is _____.
Hydrophobic
What are redox reactions?
Reactions that involve the oxidation and reduction of a substance.
What happens when something is oxidized?
It loses an electron. OL
What happens when something is reduced?
It gains an electron. RG
An oxidizing agent gets _____.
Reduced
O2 becoming H2O in the product side is an example of it getting _____.
Reduced
Define Reducing Agent?
The electron DONOR is called the reducing agent. RAD
An oxidizing agent _____ electrons.
Accepts
When electrons get transferred from a less electronegative substance to a more electronegative substance, is it endergonic or Exergonic?
EXERGONIC
In the reaction of breakdown of glucose, is glucose oxidized or reduced?
Oxidized. GO
What is NAD+?
The most versatile electron ACCEPTOR in cellular respiration.
What are some important things to note about NAD+?
A coenzyme key in many biological oxidation reactions; electrons from organic compounds are usually first transferred to NAD+.
As an electron acceptor, NAD+ functions as an OXIDIZING agent during cellular respiration.
Each NADH (reduced form of NAD+) represents stored energy that is tapped to synthesize ATP.
Why is NAD+ such as good electron carrier?
Because it can cycle easily between its oxidized form and its reduced form (NADH).
What are the stages of cellular respiration?
Glycolysis (breaking down of glucose to two pyruvate molecules)- The Krebs Cycle (completion of the breakdown of glucose)- Oxidative Phosphorylation (accounts for the majority of ATP Synthesis)
Glycolysis happens in the _____; citric acid cycle and oxidative phosphorylation happen in the _____.
Cytosol-Mitochondria
What happens in substrate based ATP synthesis?
Kinase converts ADP to ATP.
What is the net return from Glycolysis?
2 ATP- 2NADH- 2 Pyruvate
What is aerobic respiration?
A chemical process in which oxygen is used to Kate ATP
What is included in Anaerobic Respiration?
Fermentation which includes alcohol and lactate production.
What are some important things to note about anaerobic respiration?
The final electron acceptor of the ETC uses (SO4)2-; the sulfate accepts electrons and gets reduced to SH2.
What essentially happens in fermentation?
The main objective is to recycle “waste material” (pyruvate and NADH) to get NAD+ to make more glucose; NADH gets oxidized to NAD+
Where does the Krebs Cycle occur?
In the mitochondrial matrix.
What is the net return from the Krebs Cycle?
6 NADH, 2ATP, 2FADH2
How many CO2 are released during the Krebs cycle?
2
What is the role of coenzyme A in the Krebs cycle?
Brings up the potential energy; goes inside the mitochondria.
What are multiprotein complexes?
Proteins that interact with each other in the same vicinity.
What essentially happens in the ETC?
Electrons are passed to progressive more electronegative complexes until they are accepted by oxygen to make water.
Can NADH or FADH2 create more spontaneous reactions?
NADH
What is the general equation for what happens in the ETC?
2e- + 2H+ 1/2 O2 —-> H2O
Is substrate based phosphorylation slower or oxidative phosphorylation?
Substrate Based
For the transfer of every _____ electrons, a _____ is released during the ETC.
2- Proton
What happens in oxidative phosphorylation?
As we go form one electron acceptor to the next in the ETC, H+ is being pumped out. The concentration of H+ in the inter membrane space builds up, creating an electrochemical gradient. The H+ goes down its concentration gradient (high concentration to low concentration), allowing for the turning of ATP Synthase. ATP synthase turning jams a phosphate group to ADP, producing ATP.
What is photosynthesis consisted of?
Light Dependent Reactions and Calvin Cycle.
What happens in Light Dependent Reactions?
Light energy plus water and carbon dioxide leads to the production of ATP, NADPH, and O2. They happen in the thylakoid membrane of the chloroplasts.
Define Wavelength
The distance between crests of the electromagnetic waves.
What is the range for visible light in the spectrum?
380 nm to 750 nm.
In the light dependent reactions, what regions have what concentration of H+?
There is a higher concentration of H+ in the thylakoid lumen (interior) compared to the stroma.
What happens in the Calvin Cycle
CO2 from the atmosphere and NADPH and ATP are used to produce Phoshoglyceraldehyde; ribulose biphosphate (a 5 carbon structure w/ 2 phosphates) combines with CO2 (an endergonic reaction). The energy comes from the oxidation of ATP and NADPH. From there, PGAL gets produced and the majority of it is used to reproduce RuBP. The Calvin Cycle happens in the stroma.
What are the three types of communications that cells undergo?
Direct Contact Signaling (cell-cell contact and cell-junctions)
Local Signaling (Autocrine, Paracrine, and Synaptic).
Long Distance Signaling (hormonal)
What are gap junctions?
Localized sets of channels.
Which ER contains ions?
Smooth ER
How can neurons communicate by gap junctions?
Through the body of the cell.
What happens in contact trough gap junctions?
Cells extremely close together in the vicinity interact with each other through gap junctions, allowing for the exchange of material.
How do cells communicate through cell-cell recognition?
The protein of one cell binds to the receptor of another cell, allowing for the distribution and exchange of material.
What happens in autocrine signaling?
A cell influences itself; signals bind to the receptor on the same cell.
How do cells communicate in paracrine signaling?
Cells relatively close together in the vicinity interact with each other through a secretory vesicle in the main cell excreting material and influencing the other target cells.
How do cells communicate in synaptic signaling?
Neurotransmitters from one neuron get diffused across the synapse (the small space in between neurons) and influence the other neuron.
Endocrine signaling is _____ distance and has to be _____.
Long Distance-Precise
Define Ligand
A molecule that binds to another (usually larger) molecule.
Define Signal Transduction
The series of steps in which a cell converts a signal into a response.
What are some examples of ligands?
Growth Factors, Hormones, and Neurotransmitters. GHN
Growth factors are associated with the _____ of cells.
Growth
What are G proteins?
Specialized proteins which have the ability to bind GTP and GDP.
What generally happen in the functioning of a G-protein linked receptor?
GDP is bound to an inactive protein; when the ligand binds to the GPCR, GTP binds to the G protein and GDP is released. The protein with the GTP binds to the inactive enzyme, making it active. After the process is done, GDP is bound to the inactive protein and inorganic phosphate is released.
The G-Proteins function like a _____. They are either _____ or _____.
Switch-On-Off
What type of molecule is cAMP?
Second Messenger
What are second messengers and what are some examples?
Small molecules or ions that relay signals received by cell-surface receptors to effector proteins. Examples are cAMP, IP3, Ca2+, Na+
What happens in tyrosine kinase receptors?
They exist as monomers in the cell with an extra cellular singla receiving portion and an intracellular portion containing tyrosines. Once the signaling molecule binds to the extra cellular side, dimerization occurs. Dimerization activates the tyrosine kinase region of each monomer, adding a phosphate group from an ATP to the other monomer. Once the receptor is fully activated, it is recognized by relay proteins. Relay proteins bind to a specific phosphorylated tyrosine, changing shape and leading to a transduction pathway and a cellular response.
How do ligand-gated ion channel receptors function ?
Without the binding of a ligand, the gate remains closed. Once the ligand binds to the receptor, the gate is open and allows for the passage of ions into the membrane.
How do intracellular receptors function?
A hormone, (testosterone for example), binds to the intracellular receptor protein. The hormone receptor complex then goes inside the nucleus, into the DNA, and alters gene expression.
What is a key factor for distinguishing living and non-living things?
The ability to reproduce.
How does cell division occur in prokaryotes?
They do not have a nucleus so they divide by binary fission (separation in the middle). The chromosome is consisted of a circular DNA molecule and is divided.
How do unicellular eukaryotes divide?
Through longitudinal division.
A typical human cell has _____ of DNA; this is _____ times bigger than the diameter of the cell. The human has about _____ genes.
2 meters- 25,000- 40,000
Define Genome
The entire collection of genes characteristic of a particular species.
Define Haploid
A cell containing only 1 set of chromosomes. (1n)
Define Diploid
A cell containing 2 sets of chromosomes (2n); one set from each parent.
Define Polyploid
A cell containing more than 2 sets of chromosomes.
How do humans start off as?
As one cell (a fertilized egg); the fusion between an ovum and a sperm.
Which cells in our body are haploid?
Gametes (1n); sex cells.
Which cells in our body are diploid?
Somatic Cells (2n).
What are examples of when normal controlled cell division occurs?
Reproduction-Replacement of Aged Cells-Healing of Wounds
What is an example of abnormal cell division?
Cancer and Keloids
Define Mitosis
A multi step complex process that passes along the genome from one cell to its daughter cells. The daughter cells are identical to each other and the parental cell.
What are the key steps in cell division and what is each step consisted of?
Interphase (G1, S Phase, G2); Mitosis (Prophase-Prometaphase-Metaphase-Anaphase-Telophase)-Cytokinesis
When cells are not dividing, what are they doing?
They are in the G0 phase (working).
In which step does the cell spend most of its time in? Shortest time?
Interphase is the longest; Mitotic phase (mitosis and cytokinesis) the shortest.
Define Chromosome
A large piece of DNA alongside its associated proteins.
Define Centromere
A condensed region of DNA; the region of the condensed chromosomes where the 2 sister chromatids join.
Why are chromosomes most visible during mitosis and meiosis?
Because the DNA is folded and coiled onto itself.
When are condensed chromosomes present?
From prophase to anaphase.
In which phase do the sister chromatids separate?
They separate in Anaphase; each chromatid becomes its own chromosome.
Define Chromatin
The complex of DNA and proteins (histones) that make up each chromosome.
Define Euchromatin
The less condensed form of chromatin that is available for transcription.
Define Heterochromatin
The very highly condensed form of chromatin
What is going on in the G2 Phase?
Centrosome with centriole pairs, nuclear envelope, nucleolus, and plasma membrane are all present.
What goes on in Prophase?
The mitotic spindle (a structure made of micro tubules responsible for organizing chromosomes) begins to form- The chromosomes start to condense- The nucleolus (part of the nucleus where ribosomes are made) disappears.
What goes on in Prometaphase?
Chromosomes become even more compact- Nuclear Envelope breaks down- Further growth of the mitotic spindle.
What goes on in Metaphase?
All the chromosomes align at the metaphase plate- Kinetochore Microtubules from opposite centrosomes are connected.
What goes on in Anaphase?
The microtubules push poles apart, resulting in the separation of chromosomes and formation of sister chromatids (each now its own chromosome)
What goes on in telophase?
The chromosomes start to decondense-Spindle begins to disappear- Nuclear membrane and nucleolus form. Basically, it is the opposite of prophase.
What goes on in cytokinesis?
The cytoplasm divides to form two new cells.
Define Kinesin
A motor protein that transports the chromosomes on microtubules.
Cytokinesis is accomplished through the utilization of _____.
Microfilaments.
Generally speaking, what is the main purpose of meiosis I and what is the main purpose of meiosis II?
Meiosis I: separation of homologous chromosomes
Meiosis II: separation of sister chromatids.
Define Homologous Chromosomes
Chromosome that are similar in structure and size, have the same genes, you get one from each parent. They can have different alleles. One from father and one from mother.
Define Sister Chromatids
Replicated forms of a chromosome joined together by the centromere.
Define Synapsis
The pairing of replicated homologous chromosomes during prophase I of meiosis I.
Define Crossing-Over
The exchange of genetic material between non-sister chromatids during synapsis in meiosis I.
Define Chiasma
The region of the non-sister chromatids where exchange of the genetic material takes place during Meiosis I.
What is the outcome obtained from meiosis?
4 haploid daughter cells that are different from the parental cells.
What happens in prophase I?
The homologous chromosomes pair and exchange genetic information. This happens at the chiasma.
What happens in metaphase I?
The tetrads line up at the metaphase plate.
What happens in anaphase I?
Homologous chromosomes separate, 2 chromosomes are left in each cell.
What are some key differences between meiosis and mitosis?
Mitosis results in two daughter cells with 2n and meiosis results in 4 daughter cells with 1n.
Meiosis has 2 divisions whereas mitosis only has 1 set of divisions.
Synapsis (the pairing of homologous chromosomes in prophase I) is unique to meiosis and does not occur in mitosis.
What are contributors to genetic variation in species that reproduce sexually?
Independent Assortment of homologous chromosomes at the metaphase plate in meiosis I- Crossing Over- Random Fertilization
What does independent assortment entail?
The homologous chromosomes can line up in a myriad of ways in the metaphase plate at the end of metaphase in meiosis I.
Each gamete has a _____ chance of having paternal or maternal chromosomes or of having both.
50:50
The number of possible combinations for the gametes is _____ where n is the number of chromosomes in the genome.
2^n
How does the production of no ATP affect replication?
If no ATP is produced, replication cannot happen.
What are the cell cycle control proteins?
Kinases and Cyclins
Define Kinases
Enzymes that activate or de-activate other proteins by phosphorylating them.
What are cyclins and what are types of cyclins?
Cyclins get their name because they cycle in concentration throughout the cell cycle. The two types of cyclin are cdk2 and cyclin B
How is MPF (M-Phase promoting factor) formed?
Through the combination of cdk2 and cyclin B
Which of the cyclins are always present in high amounts?
Cdk2
What are some affects of MPF being activated?
Stimulates the condensation of chromosomes- Early formation of the spindle- Breakdown of the nuclear envelope.
How is MPF inactivated?
When cyclin is degraded.
When is MPF activated?
At the G2 checkpoint (G2-Prophase)
When is MPF active? When is MPF inactive?
From prophase to the end of anaphase.
At the beginning of telophase, the MPF is inactivated.
How do the sister chromatids separate during anaphase?
Cohesions, Securin, and Separase
What is the function of separase?
It degrades cohesins, allowing for the sister chromatid separation during anaphase.
What does the APC (Anaphase Promoting Complex) do?
It stimulates the degradation of a protein called securin in the proteosome; it also tags cyclin so it can be degraded in the proteosome, leading to the loss of MPF function.
What is a karyotype?
The display of chromosome pairs of a cell arranged by size, shape, and staining patterns.
How do you prepare a karyotype?
You obtain sample cells from an individual, plate them on a Petri dish, stop their division in metaphase, stain them, and examine them.
What does aneuploidy mean?
A chromosomal alteration in which certain chromosomes are present in extra copies or deficient in #.
What does non-disjunction mean?
The improper separation of homologous chromosomes in meiosis I or the improper separation of sister chromatids in meiosis II.
Define DNA Replication
The process by which a DNA molecule is replicated.
_____ is the genetic material.
DNA
Define Transformation
A change in genotype and phenotype due to the assimilation of external DNA by a cell.
Define Bacteriophage
A virus that infects bacteria; also called a phage.
Define Virus
An infectious particle inacabable of replicating outside of a cell, consisting of RNA or DNA genome surrounded by a protein coat,
In Hershey’s experiment, what was the DNA tagged with?
The protein was tagged with a radioactive isotope of sulfur and the DNA was tagged with a isotope of phosphorus.
The two sugar phosphates were observed by Watson to be anti-parallel. What does this mean?
Means that the subunits ran in opposite directions.
Adenine can form _____ hydrogen bonds with thymine and guanine can form _____ hydrogen bonds with cytosine.
2-3
Define the Origin of Replication
Sites where the replication of a DNA molecule begins, consisting of specific sequence of nucleotides.
Define Replication Fork
A Y-shaped region on a replicating DNA molecule where the parental strands are being unwound and the new strands are being synthesized.
Define Helicase
An enzyme that untwists the double helix of DNA at the replication forks, separating the two strands and making them available as template strands.
Define Single-Strand Binding proteins
A protein that binds to the unpaired DNA strands during replication, stabilizing them and holding them apart while they serve as templates for the synthesis of complementary strands.
Explain everything about Griffith’s experiment.
Isolated 2 strains for bacteria that caused pneumonia in mice; S bacteria caused death; r bacteria led to no death. The S bacteria had a capsule that prevented them from being recognized by the immune system. The R bacteria lacked that capsule.
Through heating the S-bacteria, he killed them. After mixing it with the living R cells, the mice still died. Living S cells were somehow found in the sample of blood from the mice and bacterial transformations were discovered.
Explain Bacterial Transformation
The change in phenotype and genotype of a bacteria by acquisition of genetic material.
Explain everything about Avery’s Experiment.
They wanted to know if the transformation factor was consisted of protein, RNA, or DNA. He removed the carbs and lipids, thus isolating the protein, RNA, and DNA. He then mixed it with the R-bacteria and injected it into the mice. He found that with the elimination of DNA, the mice survived.
Explain everything about Chargaff’s Experiment.
Found that DNA is composed of deoxyribose-phosphate- and 4 nitrogenous bases. He then analyzed DNA from many different eukaryotic cells and found that the % and order of the nitrogenous bases varied within the species. A and T were always together and C and G were always bonded together.
Explain everything about Hershey and Chase’s Experiment.
The DNA of the virus was injected into the bacteria during infection, leaving the protein outed (coated with radioactive sulfur).
The injected DNA provides genetic information that makes the bacteria produce new viral DNA and protein which assemble into new viruses (DNA coated with radioactive phosphorus).
What is PET?
An imaging technique that reveals how tissues and organs are functioning; the tracer collects in areas of the body where chemical activity is high, which often correspond to the areas of diseases.
What is RNA composed of?
Ribose-Phosphate-Adenine-Uracil-Cytosine-Guanine
What is the difference between ribose and deoxyribose?
Deoxyribose has one LESS hydroxyl group.
How many rings do purines have and what nitrogenous bases fall under it?
2-A-G
How many rings do pyrimidines have and what nitrogenous bases fall under it?
1-C-T-U
Phosphate groups are linked to the _____ carbon of the sugar.
5’
What bonds are present in the sugar phosphate backbone?
Phosphodiester Bonds
What did Watson and Crick infer from Franklin’s data?
DNA was a double helix; 2nm space in the diameter..
The bases in the DNA were separated by 0.34nm. The helix makes one full turn every 3.4nm. There were the base pairs per turn. Inferred that the sugar phosphate backbone faced the outside of the helix.
For the measurements to be appropriate, there had to be a combination of _____ and _____.
1 Purine and 1 Pyrimidine
Is the double helix polar?
Yes
Watson and Crick proposed a _____ model when it came to the structure of the DNA.
Semi-Conservative; this means that each chain that separated would serve as a template for the formation of a new chain.
What were the proposed models for DNA Replication?
Conservative- Semi Conservative- Dispersive
What is meant by semi-conservative replication?
The two strands of the original helix separate, and each strand functions as the temperature for the synthesis of a new complementary strand; half is conserved.
What is meant by conservative replication?
The original double helix get back together replication, therefore the new one lacks any of the old one; full conservation of one helix.
What is meant by dispersive replication?
The two strands of the original double helix separate, and each strand of both daughter molecules contains a mixture of old and newly synthesized parts; old and new mixture.
What did Meselson and Stahl use for their experiment?
14 N and 15N.
Meselson and Stahl analyzed the DNA extracted from the bacteria in terms of _____.
Weight
One round of bacterial takes _____.
20 minss
What are the mechanisms of DNA replication?
Unwinding of the DNA strands- Initiation of Replication- Elongation of the DNA Strands being replicated- Termination of Replication.
Origins of replication are associated with a _____.
Bubble
Each replication bubble has ______ replication forks.
2
Which order of strands are continuous?
From the origin of replication, 3’ to 5’ strands are continuous.
Define Helicases
Enzymes that untwist the double helix at the replication forks, separating the 2 strands and making them available as templates.
Which enzyme is responsible for releasing the tension in DNA strands?
Topoisomerase
Define Topoisomerase
An enzymes that breaks, swivels, and rejoins the DNA strands. During the replication of DNA, this enzyme helps relieve the strain in the double helix ahead of the replication fork.
Define Single Strand Binding Proteins
Proteins that bind to the unpaired DNA strands during replication, stabilizing them and holding them apart while they serve as templates for the synthesis of complementary DNA strands.
Define Primase
An RNA Polymerase that joins RNA nucleotides to make the primer using parental DNA strands as a template.
Define DNA Polymerase III
A complex of enzymes that catalyzes the elongation of new DNA by adding nucleotides to the 3’ end of an existing chain. It elongates in the 5’ to 3’ direction and READS in the 3’ to 5’ direction.
What is an important thing to note about DNA Polymerase III?
It can only add nucleotides to the 3’ end of a sequence and CANNOT do it by itself. It needs the Primase enzyme to add a sequence of nucleotides.
The _____ end has to en free to allow for further binding.
3’
What is the bond formed between the carbon ends and the phosphate groups of another nucleotide?
Phosphodiester Bond
What happens to the phosphate group when DNA Polymerase allows for the binding of nucleotides?
2 inorganic phosphates get released in the cytoplasm and the nuclear matrix.
_____ must be removed; this is done by _____.
Primers- DNA Polymerase I
Define DNA Polymerase I
An enzyme that removes and replaces the RNA primer.
Define Ligase
An enzyme that ligates the ends of DNA molecules.
What is the main difference between leading DNA strands and lagging strands?
The main difference is that the leading strand is continuous and the lagging strand is in Okazaki FRAGMENTS.
Define Okazaki Fragments
Short sections of DNA. Formed at the time of discontinuous synthesis of the lagging strand during replication of DNA.
What is meant by the proofreading activity of DNA Polymerase?
Polymerase has the ability to check each nucleotide against the template soon after it is added to the growing strand. In real life, we find 1 in 10 million mistakes.
How do mismatched nucleotide evade DNA Polymerase proofreading?
They evade proofreading or occur after DNA replication because of the exposure of cells to things such as chemical carinogens and UV light.
How is the mismatched nucleotide problem fixed?
Thymine dimer distorts the DNA molecule.
A nuclease enzyme cuts the damaged DNA strand at two points.
DNA polymerase fills the gap.
DNA ligase seals the remaining nick.
How many enzymes aid in the fixing of nucleotide mismatching? What is a defect in these enzymes associated with?
We have about 130 enzymes. Defects of one of these enzymes is associated with colon cancer.
What happens in the process of chromatin packing?
Proteins called histones allow for the wrapping of strands to make nucleosome beads. The beads pack together. The domains further loop and get more and more condensed.
Which histones are available to us? Which histones do the nucleosome contain?
H1,H2A,H2B,H3,H4 are available to us.
H2A,H2B,H3,H4 are contained in the nucleosome (2 of each)
Which histone is not present in the octamer? Where is it located?
H1; it is attached near the nucleosome.
What are histone modifications?
Methylation of Histones leads to the condensation of DNA and PREVENTS transcription of genes.
Acetylation of HIstones leads to the decondensation of DNA and ALLOWS for the transcription of genes.
What is the basic idea of the Central Dogma?
DNA to mRNA is transcription and mRNA to proteins is translation.
Why do we need mRNA between DNA and protein?
Because one mRNA molecule can make many proteins thereby amplifying the process. Few mRNAs can translate many proteins.
What is the Beadle and Tatum gene theory?
They believed that genes would only code for enzymes. It was later discovered that many proteins are not enzymes. So, this theory became the one gene one protein theory. THE RIGHT VERSION IS ONE GENE ONE POLYPEPTIDE.
What does it mean that transcription and translation are coupled?
Transcribed mRNA begins to translate into a polypeptide while still being transcribed.
Which key enzyme is involved in transcription?
RNA Polymerase II
What are polyribosomes?
Multiple ribosomes
Where does transcription occur in prokaryotes and where does it occur in eukaryotes?
In prokaryotes, transcription happens inside of the cell itself and in eukaryotes, transcription happens inside of the cytosol.
What is the initial transcript of DNA called?
Heterogenous Nuclear RNA (hnRNA) or pre-mRNA or primary transcript.
What does the primary transcript of DNA contain?
Introns and exons; introns are then spliced in the spliceosome.
What is a transcription unit?
A transcription unit is a portion of the gene which consists of a start sequence and a termination sequence.
How many genes does one transcript unit have in eukaryotes and prokaryotes?
1 in eukaryotes and many in prokaryotes.
What are the present stages in transcription?
Binding of RNA Polymerase II- Unwinding of the DNA- Initiation- Elongation- Termination
Define Promoter
Promoter is the binding region for RNA Polymerase II; once the Polymerase binds to the promoter, transcription begins.
Which strand is called the template strand in transcription?
The strand that contains RNA Polymerase II is called the template strand.
In what direction is DNA read in transcription?
3’ to 5’.
Does RNA Polymerase II have proofreading activity?
No, it does not.
What are the detailed steps that occur in transcription? (In prokaryotic cells)
RNA polymerase II elongates the DNA much like DNA polymerase III but uses RIBONUCLEOTIDES instead of deoxyribonucleotides. Only one strand is transcribed at a time. The RNA polymerase II untwists one turn of the double helix DNA at the time and the terminator sequence in prokaryotes signal the end of transcription.
In eukaryotic cells, RNA polymerase II needs the help of other proteins called _____ to find the promoter region.
Transcription Factors
Define Transcription Factors
Proteins that recognize the sequence of nucleotides next to the promoter sequence.
What happens in transcription ind teal for eukaryotic cells?
The promoter region extends significantly upstream of the TATA box and contains a number of sequences that bind proteins called transcription factors and activator proteins.
Is hnRNA larger than mRNA??
Yes, it is; it contains both introns and exons.
What are the modifications done to pre-mRNA?
The 5’ guanine cap is added and the 3’ poly A tail is added in the nucleus.
