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Cells & Genes (DNA)
Central Dogma
65
Biology
Undergraduate 2
04/10/2012

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Cards

Term
mRNA Splicing
Definition

This is a modification of RNA after transcription, in which introns are removed and exons are joined. This is needed for the typical eukaryotic messenger RNA before it can be used to produce a correct protein through translation.

Term

Which scientists are responsible for determining DNA was the genetic material? Make sure you understand each experiment discussed in class and the significance of the results. 

Definition

Hershey and Chase

Term

Which scientists are responsible for determining the 3D structure of DNA? 

Definition

Watson and Crick

Term

What is the structure of DNA?  

Definition

A right-handed double helix, with 10 nucleotides pair per helical turn. Each spiral strand, composed of a sugar phosphate backbone and attached based, is connected to a complementary strand by hydrogen bonding between base pairs A, T, C, G.

Term

What type of bonding is important to maintain the 3D structure?

Definition

Hydrogen bonding is important to maintain the 3D structure of DNA. Also, Van der Waals forces plays an important role for holding the molecules together; only occur in molecules that are close together.

Term

What are the nucleotides in DNA and what is their structure? 

Definition

The nucleotides found in DNA are sugar, phosphate and bases,

 

 

 

Term
prymidines
Definition
a heterocyclic aromatic organic compound containing two N atoms at the positons 1,3 
Term

What do the designations 3' and 5' mean?

 

Definition
this actually refers to the number of carbon atoms that the nucleotides are bound to; the ribose backbone. the ringed sugars have carbon atoms that are numbered 3 at the bottom of the ring anf 5 on the top.
Term

what does antiparallel means?

 

Definition
DNA is  made of antiparallel strands, meaning that while one strands runs from 3' to 5' its complementary strand runs from 5' to 3'. The two strands are parallel, but running in opposite directions.
Term

DNA replication is semi-conservative -- can you diagram this type of replication? 

Definition
Term
Steps involved in DNA Replication
Definition

DNA Helicases: helps to unwound the DNA strand

DNA binding proteins: attached to unwound the DNA and prevents them from winding back together

DNA polymerase: used to catalyze the elongation of the leading strand and lagging strands

DNA Primase: helps to build the primes

Okazaki Fragments: attached to the completed portion of the lagging strand 

DNA Ligase: used to catalyze the reaction

Term

introns

Definition
non-coding sequences of base pairs 
Term
exons
Definition
coding sequence
Term
Chemiosmotic Theory
Definition
an experiment describing the ATP Synthase by a way of proton electrochemical coupling
Term
transcription
Definition
DNA acts as a template for the synthesis of RNA. Only one part of the DNA is transcribed to produce nuclear RNA
Term
RNA Splicing
Definition
exons and introns
Term
Protein Synthesis 
Definition

Two parts:

(1) Transcription 

(2) Translation

Term
codon
Definition
a sequence of three adjacent nucleotides constituting the genetic code that determines the insertion of a specific amino acid in a polypeptide chain during protein synthesis
Term
Start Codon
Definition
AUG
Term
Anticodon
Definition
three bases that are complementary to a codon in the mRNA. during translation these bases form base pairs with bases of the codon by forming hydrogen bonds
Term
Chemiosmotic Hypothesis
Definition
movement of protons; relaxation of protond, e- at high energy coming from NADH or FADH2, composed of series of components that will pump protons, proton gradient forms an electrochemical gradient
Term
Reduction potential
Definition
the tendency for a chemical species to be reduced, and is measured in volts at standard conditions. The more positive the potential is the more likely it will be reduced
Term
Photosynthesis
Definition
the process by which plants, algae, and photosynthetic bacteria use ligh energy to drive the synthesis of organic compounds.
Term
Photosynthesis
Definition
provides the energy and reduced carbon required for the survival of virtually all life
Term
Light Energy
Definition
consists of electron and proton transfer reactions. occur in a  complex membrane system that is made up of protein complexes, electrons carriers, and lipid molecules. converts energy into several forms 
Term
Dark Energy 
Definition
consists of the biosynthesis of carbohydrate from CO2.
Term
Steps involved in Light Reaction
Definition
conversion of a photon to an excited electron state, excited electron is then transferred over the antenna molecule
Term
Reaction Centers
Definition

Photosystem I

Photosystem II

Term
Photosystem I
Definition
composed of multiprotein complex. uses light energy to mediate the flow of electron in the chloroplast thylakoid membrane of plants. in linear flow, PSII is coupled w/ PSI and produces a pH gradient and in the cyclic flow PSI generates a pH gradient and ATP
Term
Chloroplasts
Definition
provides energy and reduced carbon needed for plant growth and development, while the plant provides it w/ CO2, H2O, Nitrogen. located in specialized leaf cells; defined by an inner and outer envelope membrane
Term
Inside the chloroplast
Definition
known as the photosynthetic membrane that contains most of the proteins required for the light reactions. the proteins required for the fixation and reduction of CO2 are located outside the photosynthetic membrane in the surrounding aqeuous space
Term
Photosystems I & II
Definition
PSII uses light energy to drive two chemical reactions-the oxidation of H2O and the reduction of plastoquinone; PSI catalyzes the oxidation of plastocyanin and the reduction of ferrodoxin. it is composed of a heterodimer of proteins that act as ligands for most of the electron  carriers
Term
Electron Transport 
Definition
transported between large protein complexes by small mobile molecules; creates the proton electrochemical potential of the photosynthetic membrane by the two types of reactions-release of proton during the oxidation process and the translation of protons from the outer aqueous phase to the inner aqueous phase by the coupled reactions
Term
ATP Synthase
Definition
the conversion of proton electrochemical energy into chemical free energy is accomplished by a single protein complex. this enzyme is a phosphorylation reaction, which is the formation of ATP
Term

Chemiosmotic Experiment

(Peter Mitchell)

Definition

Evidence:

mitochondria generated a H+ gradient (pH)

destroyed H+ gradient-> no ATP

therefore gradient is connected to ATP synthesis

Term
electron tower
Definition
epxlains the utilization order of electron acceptor for respiration
Term
reaction center
Definition
host of protein complexes built to harnest light energy 
Term
cyclic photophosphorylation
Definition
electrons are recycled; excited electrons are received by the primary electron acceptor and then transferred
Term
non-cyclic photophosphorylation
Definition
refers to thw ATP generated by protons moved across the Thylakoid membrane during z-scheme
Term
Carbon Fixation
Definition
refers to the process through which gaseous carbon dioxide is converted into a solid compound. 
Term
phosphodiester bond
Definition
a group of strong covalent bonds between a phosphate group and two 5-carbon rig carbohydrates over two esters.
Term
Griffith's Experiment
Definition
shows that bacteria can get DNA through a process called transformation--used two strains of pneumoccus; smooth and rough strains.
Term
S-Strain
Definition
covers itself with polysaccharide capsule that protects it from the host's immune system
Term
R-strain
Definition
does not have a protective shield around it and is likely killed by the host's immune system
Term
Hershey & Chase's Experiment
Definition
bacterial viruses, called phage were used to demonstrate that DNA is the genetic material. when phage infect bacteria they attach to the surface of the bacterium and inject the DNA into the cell
Term
Semi-conservative
Definition
describes the mechanism by which DNA is replicated in all known cells. Produces two copies that each contains one of the original strands and one new
Term
Dispersive
Definition
produces two copies of the DNA, both containing distinct regions of DNA composed of either both original strands and both new strands.
Term
Conservative
Definition
leaves the two original DNA template strands together in a double helix and would produce a copy composed of two new strands. 
Term
How do we know chemiosmotic coupling drives ATP synthesis?
Definition
if uncoupler prevents ATP synthesis, then an artificial gradient should promote ATP synthesis
Term
Difference between RNA polymerase and DNA polymerase
Definition
RNA: catalyzes the linkage of ribonucleotide; not deoxiribonucleotides; can start the RNA chain w/o a primer; transcription need not to be accurate; not the permanent storage for genetic info. in cells; polymerase makes about 1 mistake for every 10^4 nucleotides and for DNA 1 for every 10^7.
Term
Gene Expression
Definition

refers to the process by which the info. encoded in DNA sequence is translated into a product that has some effect on a cell or organism.

the final product of a protein tells that gene expression included both transcription and translation

Term
Differences in Transcription of DNA and RNA
Definition
RNA: does not remain H-bond to the DNA template strand; chains are displaced and teh DNA helic reform; molecules are single-stranded; molecules are shorter; polymerase carries out RNA transcription; polymerase catalyzes the formation of the phosphodiester bonds; polymerase moves stepwise along the DNA
Term
Leading Strand
Definition
the DNA strand that synthesize in the 5' to 3' direction towards the replication fork
Term
Lagging Strand
Definition
the DNA strand that is discontinuously synthesized against the overall direction of the replication fork; produce Okazaki fragments in the 3' to 5' direction
Term
Primer
Definition
short RNA segments that is necessary to begin DN replication; only one is necessary for the replication of the leading strand, but many for the lagging
Term

Why do electrons flow in one direction

(redox potential graph)

Definition
electrons are negatively charged. electricity is similar to osmosis; the movement of electrons from an area of high concentration (neg. charged) to an area of low concentration (pos. charged).
Term
Comparison of Mitochondria and Chloroplasts
Definition

Mitochondria: cristae, inner membrane space, outer membrane space, intermembrane space, matrix, DNA, ribosomes

Chloroplast: inner, outer, intermembrane space, stroma, thylakoid space, ribosomes, thylakoid membrane

Term
Building blocks of DNA
Definition
sugar phosphate + base = nucleotide
Term
Steps of Replication
Definition

(1) initiator protein binds

(2) helicase attaches 

(3) primase binds to first priming sequence

(4) DNA polymerase use primer to initiate 

(5) RNA primer made for lagging strand

(6) RNA primer removed 

(7) DNA ligase links Okazaki fragments 

Term
The Calvin Cycle
Definition
begins w/ the initial cooperation of Carbon (carbon fixation); reduces fixed carbon to carbohydrate by the addition of electrons by NADPH+ATP; called the light independent dark reaction; occurs in the stroma; light reactions convert solar energy to chemical energy of ATP and NADPH
Term
Messelson and Stahl's Experiment
Definition
supported the hypothesis that DNA replication was semiconservative. The double helix separates so that each old strand serves as a template for a new strand. 
Term
Steps involved in translation
Definition

(1) Initiation-small units of ribosome binds

(2) Elognation-tRNA base pair w/ next codon

(3) Termination- when the ribosome reaches one or more stops.

Term
Sigma Factor
Definition
an intiator protein needed in the synthesis of RNA 
Term
Photosynthesis
Definition
C6H12O6--> 6CO2 + NADH + FADH + 2ATP + 2GTP
Term
Proteins involved in DNA replicatino
Definition

helicase--separate DNA

Single Stranded Binder--keeps DNA single-stranded

DNA gyrase-relaxes the coil 

primase-puts down RNA primer

polymerase-polymerizes DNA

 

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