Central Dogma Part 1 Flashcards
Ability to coordinate a wide variety of
chemical reactions that makes a cell “a cell”
Metabolic Regulation
Metabolic Regulation Key Feature:
flow and control of information
Similar to computers
Information storage, processing and transmission
Information flow and Control
Molecular Biology
Important Region
DNA , RNA and Protein
Synthesis of mRNA in the _________
nucleus
Movement of mRNA into cytoplasm via _________
nuclear pore
Language of the Cellular
DNA
Consist only of four letters:
A,G,T,C
These letters make 3-letter _________ in a variety of combinations
“words”
These words when __________ represent a particular amino acid
“expressed”
Or a _______ or stop synthesis
“period”
Words put into sequence:
sentence
Sentence:
gene
Numerous sentences:
book
___________________ for each of the 3 steps
Macromolecular template
level language preservation and expression
Genetic
___________________: strands are complementary
Double helix structure is important in preservation
Information is in the arrangement of the _____
four letters
Initiation:___________
predetermined site; origin of replication
___________ breaks hydrogen bonds between DNA strands at origin
Initiator proteins/ enzymes
________ strands separate
DNA
The ___________ is formed
replication fork
___________ added at initiation site to start DNA synthesis
RNA “primer”
________ is a small piece of RNA that is complementary to a specific section of DNA and will bind to that section of DNA
“primer”
DNA synthesized by enzyme ___________
DNA polymerase
Nucleotides of DNA always added to __________
terminal 3’ group
______________ synthesized continuously
“Leading” strand
DNA polymerase must jump ahead and work backward on ____________
“lagging” strand
DNA fragments on lagging strand are called ____________
Okazaki fragments
Fragments joined by an enzyme called __________
DNA ligase
Transcription, Primary Substances Involved:
m-RNA
t-RNA
r-RNA
RNA synthesis is mediated by the
enzyme RNA polymerase
RNA polymerase always reads in
the 3’ to 5’ direction
Necessary parts of DNA become unbound
Transcription: RNA Synthesis
One strand is the template for each gene.
Transcription: RNA Synthesis
A gene will encode for one protein
Transcription: RNA Synthesis
RNA polymerase _________ DNA and synthesizes mRNA
‘reads’
RNA polymerase consists two parts:______________
core and sigma subunit
Three transcription substeps:_________
Initiation, elongation, termination.
_________ (in procaryotes) consists of a promoter, genes, and a terminator
An operon
__________ begins with binding of sigma factor to promoter region of DNA
Initiation
________ vary in binding affinity for the sigma factor
Promoters
When the sigma factor is released, ______
elongation begins
m-RNA synthesis stops when RNA polymerase encounters a ________ (specific sequence of bases) (can vary in strength also)
terminator
______ can be polygenic (multiple controlled by one promoter) genes
Procaryotic transcription
__________ do not do polygenic messages
Eukaryotic
transcription and translation occur simultaneously.
In procaryotes
mRNA in eucaryotes can have nonsense segments, called _______
introns
__________ in eucaryotes undergo further processing
mRNA
_________ splicing
mRNA
__________ make it more difficult to transfer eukaryotic genes to procaryotes
Introns
Do not occur in _________
procaryotes
______________ is modified by the addition of a guanine nucleotide with a methyl grp attached.
RNA capping- 5’ end
A string of adenine nucleotides are added to the 3’ end.
Polyadenylation
These processes are thought to increase ___________ and facilitate transport across the nuclear membrane
m- RNA stability
Three translation substeps:
Initiation, elongation, termination
In prokaryotes, initiation is the formation of a _________ initiation complex.
30s and 50s rRNA
______ means ribosomal RNA, 30s and 50s are the sizes of two parts of the ribosome,
rRNA
Aside from those 3 proteins called initiation factors, and the _________ should also be present
phosphate bond energy from GTP
m-RNA must first bind to the ribosomes Other mRNA processing steps
In eukaryotes
All protein synthesis begins with the _________
AUG initiation codon
Initial AUG encodes for N formylmethionine (special amino acid); ___________
middle AUG encodes regular methionine
____________; ten nucleotides upstream the initial AUG
Shine-Dalgarno box
____________ uses tRNA with attached amino acids as decoders
Elongation
__________ on tRNA match the codons on mRNA
“anti-codons”
Three letter ___________ of four possible letters (U,C,A,G) form ________ on mRNA (64 possible, many redundant)
“words”, “codons”
Three codons ____________ do not code for amino acids and are “stop” codons. Translation stop, or translation termination sequence.
(UAA, UAG, and UGA)
Translation start codon is _____
AUG
Two sites on the ribosome for the tRNA-called ___________
P and A
When a ___________ is reached, protein is released from the ribosome with a release factor (RF)
nonsense codon
A single m-RNA can be read simultaneously by ______________
10 to 20 ribosomes at once
___________ from ribosome undergoes further processing before becoming truly useful
Polypeptide
Sometimes several proteins must associate to form enzyme or ___________
structural protein
Folding: __________that assist in folding.
chaperones (proteins)
____________: signal sequence = a sequence of 20-25 amino acids on the front of a protein that directs the protein to be secreted out of the cell.
Secretion
The signal sequence is _______ during secretion.
clipped off
___________ addition of sugars to the protein structure.
Glycosylation:
__________: secretion through the cytoplasmic membrane.
Procaryotes
___________: transport vesicles - bud around the proteins and transport to the membranes.
Eurcaryotes
Three main mechanisms by which membrane-bounded organelles import proteins.
- Transport through nuclear pores
- Transport across membranes
- Transport by vesicles
The protein remains folded during the transport steps in mechanisms 1 and 3 but usually has to be unfolded in mechanism 2. ________
All of these processes require energy.
______________ is only accomplished in organisms.
N-linked glycosylation
____________ pattern is a target for the body to clear (remove) proteins. Non- native glycosylation patterns will be removed. Critical implications for producing therapeutic proteins for human injection.
Glycosylation
the processes by which cells synthesize biomolecules and generate energy.
Metabolism
the process of breaking down larger molecules to extract energy and create reaction substrates.
Catabolism:
the process of synthesizing large molecules for maintenance and new cell generation.
Anabolism:
Cells require energy for ____________
synthesis, transport, motility, signaling
Energy in cells is transferred largely through ___________
ATP (adenosine triphosphate).
NAD(P)+
Nicotinamide adenine dinucleotide (phosphate)
Different from NAD+
NAD(P)+
_________: reduced form
NAD(P)H
Electron donor/receptor for oxidation- reduction reactions
NAD(P)+
Provides reducing power (hydrogen atoms) for biosynthetic process
NAD(P)+
Provides electrons for ATP formation in respiration
NAD(P)+
The process by which ATP is formed as a result of the transfer of electrons from NADH or FADH2 to O₂ by a series of electron carriers.
Oxidative Phosphorylation
Occurs via the electron transport chain (proton gradient).
Oxidative Phosphorylation
The major source of ATP for aerobic organisms.
Oxidative Phosphorylation
Composed of two coupled functions
Electron Transport Chain
Transfer of electrons from NADH or FADH2
Electron Transport Chain
Use of protons to phosphorylate ADP to ATP
Electron Transport Chain
Glycolysis/EMP
Glucose - Pyruvate
TCA Cycle/Krebs/Citric Acid
pyruvate - CO2 + NADH
Three major pathways:
hexose monophosphate (HMP, also called pentose phosphate), Entner-Doudoroff: (ED), and Embden-Meyerhof-Parnas (EMP, also called glycolysis)
Primary pathway is _______, an anaerobic pathway that terminates with the production of pyruvate
EMP
Net Reaction
For each glucose molecule, two molecules of ATP are regenerated and 2 molecules of pyruvate are produced.
pyruvate enters the TCA cycle producing CO2 and NADH.
Aerobic-
pyruvate is converted to ethanol, lactic acid, acetone, butanol and/or acetic acid (original definition of fermentation)
Anaerobic-
Called the tricarboxylic acid (TCA) cycle, Krebs cycle, or citric acid cycle
TCA Cycle
Pyruvate undergoes oxidative decarboxylation with coenzyme A (CoA) to form acetyl-CoA, the immediate precursor for the TCA cycle
TCA Cycle
______ carbon atoms enter cycle
Two
__________ of hydrogen atoms leave the cycle in four oxidative reactions
Four pairs
______ high energy phosphate bond is formed (GTP)
One
________ water molecules are consumed
Two
___________ formed is used as reducing power to generate ATP in electron transport chain
NADH
These intermediates are replaced by anaplerotic reactions (Greek “to fill up”)
Replenishing Intermediates
Cells can also _______ CO₂ to replace intermediates (heterotropic CO2 fixation).
“fix”
Growth rate can actually be ____________
limited by CO2 availability.
____________ can occur by using nitrate as a terminal electron acceptor in the electron transport chain
Anaerobic respiration
Many cell can also generate energy without the electron transport chain, but with a lower efficiency.
Anaerobic Alternatives
No net oxidation or reduction since electron transport chain is not available to produce NAD+ required TCA cycle
Alcohol and Lactate Formation
Generates NADPH (reducing power for biosynthesis) and 5 carbon sugars (makes up ATP, RNA, DNA, others)
Pentose Phosphate Pathway
