chapter 6-molecular genetics Flashcards
Central Dogma
the transmission of information through DNA, RNA, and proteins
DNA’s full name
deoxyribonucleic acid
what is the basic unit of DNA
nucleotide
what is a nucleotide made of
of deoxyribose ( a sugar) bonded to both a phosphate group and a nitrogenous base
compare purine and pyrimidines
1) Purines: adenine, guanine
- larger bc 2 ring bases
2) Pyrimidines: cytosine, thymine, uracil
describe the structure of DNA
- double-stranded helices of complementary strands with the sugar-phosphate chains on the outside of the helix and the nitrogenous bases on the inside
- These strands are held together by H bonds between the bases oriented towards the centre
- Purines bind with pyrimidines linking the polynuclotide chains
- One strand of DNA has its 5’ end points up and the other has its 3’ end pointing up = antiparallel arrangement
what holds the 2 strands of DNA together
H bonds
what does DNA helicase do
breaks the H bonds between the N bases separating the 2 strands
what is a replication fork
opening in the DNA mc created by DNA helicase
what does topoisomerase do
removes the torsional strain caused by the twisting of DNA as the replication fork travels upstream of the DNA mc
- it cuts, twists and rejoins the strands
what is a replication bubble
area where the replication fork has passed a portion of DNA and the 2 strands are separated
what is semiconservative replication
a new daughter helix contains an intact strand from the parent helix and a newly synthesized strand
how are the daughter strands formed during DNA replication ( which enzyme)
DNA polymerase
what does DNA polymerase do
reads the parent strand and creates a complementary antiparallel daughter strands
which way does DNA polymerase read the parent strand? what end does it add nucleotides to?
Reads in the 3’-5’ creating a new daughter strand in a 5’-3’ direction only adding nucleotides to the 3’ end
what is the leading strand
it has its 3’ end facing towards from the replication fork allowing DNA polymerase, DNA synthesis and replication to travel in the same direction and is continuously synthesized
what is the lagging strand
has its 3’ end facing away from the replication fork
- synthesis and replication fork move in opposite direction
Okazaki fragments
short fragments synthesized due to the discontinuous synthesis
what is a gene
a unit of DNA that encodes a specific RNA mc through the process of transcription and through translation that gene ca be expressed as a protein
what is transcription
process in which genetic information is passed from DNA to RNA
what direction is mRNA transcribed
5’-3’ direction and is complementary and antiparallel to the DNA template strand
what is translation
the process in which genetic information is passed from mRNA to protein
- converts the N base message of mRNA to the amino acid language of proteins
what direction is the mRNA translated and protein synthesized
ribosome translates the mRNA in the 5’-3’ direction and the protein is synthesized from the amino terminus (N terminus) to the carboxyl terminus (C terminus)
what is RNA
ribonucleic acid- a polynucleotide
structure of RNA is different than DNA how
1) the sugar constituent is ribosome (instead of deoxyribose)
2) uracil is used in place of thiamine
3) most RNA is single-stranded
where is RNA found
nucleus and the cytoplasm
function of mRNA
carries the complement of a DNA sequence then transports this information from the nucleus to the ribosome for protein synthesis
monocistronic
one mRNA strand is coded for one polypeptide
what is tRNA
small RNA mc found in the cytoplasm
function of tRNA
assists in the translation of mRNA nucleotide code into a sequence of amino acids by brining the amino acids coded for in the mRNA sequence to the ribosomes during proteins synthesis
how is an aminoacyl-tRNA complex formed
each a.a has its own aminoacyl-tRNA which has an active site that binds to both the amino acid and its its corresponding tRNA and it catalyzes their attachment to form the complex
what is a charged tRNA
when a tRNA is complexed with the appropriate amino acid
how many tRNA’s are there
~40
how many tRNA are there for each a.a
at least 1
what RNA type is most abundant
rRNA
where is rRNA synthesized in Euk and Prok.
in the nucleolus ( Euk) and cytoplasm ( prok)
function of rRNA
-Important part of the ribosomal machinery used during protein assembly in the cytoplasm
the most common promoter region in Euk and Prok during transcription
TATA box ( TATAAT) - ~30bp upstream AND Pribnow box ( TTGAGA) - ~10bp upstream
steps of transcription
1) RNA polymerase binds to the DNA template strand at a promoter region ( short DNA sequence) found upstream from the site where transcription of a specific RNA is going to take place
2) RNA polymerase surrounds the DNA mc after it has been opened by the actions of DNA helicase and topoisomerase ( all so RNA polymerase can bind to the promotor site)
3) Once RNA polymerase is bound to the template DNA strand it recruits and add complementary RNA nucleotides = transcribing a new RNA strand
- Reads DNA in 3’ end and creates a new daughter strand in the 5’-3’ end
4) RNA sequence is complementary to the original DNA sequence except A binds to U
how does RNA leave the nucleus after post-transcriptional modification
through nuclear pores
what are introns
extra nucleotides not necessary to create the corresponding protein and are spliced out by splicosomes
what are exons
nucleotides necessary to make the protein and are kept during the post transcriptional processing
what must the spliced RNA receive before leaving the nucleus and why
a 5’ guanine cap and a 3’poly A tail to protect against RNA degrading enzymes in the cytosol
what is hetero-nuclear RNA or pre-RNA
RNA that has not been processed and contains extra nucleotides not necessary to create the corresponding protein
what is a codon
: 3 nucleotide sequences on the mRNA that correspond to a specific amino acid
how many possible nucleotides are there for each of the 3 positions in a codon?
3
how many possible codons are there
64
genetic code
used to decipher the message of genetic material into amino acid sequence and is universal
what direction are codons written
5’-3’
what are the stop codons
UAA, UGA, UAG
can the mRNA sequence cannot be regenerated from the amino acid sequence
No, bc the code is degenerate
wobble position
the third a.a does not effect which amino acid the codon corresponds to
where does translation occur and what does it involve
occur in the cytoplasm and involves ribosomes (rRNA), tRNA, mRNA, a.a, enzymes and other proteins
what are the 4 stages of translation
initiation, elongation, translocation and termination
what occurs during initiation ( translation)
1) When the small ribosomal subunit binds to the mRNA near the 5’ end after it scans the mRNA until it binds to a start codon
2) The initiator aminoacyl-tRNA complex, methionine tRNA, ( with the anticodon 3’- UAC-5’) base pair with the start codon
3) When mRNA, small ribosomal subunit and aminoacyl-tRNA complex are bound the large ribosomal subunit binds forming the completed intiation complex
what is the start codon and what does it code for
( AUG) which codes for methionine
what is the start codon and what does it code for
(AUG) which codes for methionine
What is elongation
- is a 3 step cycle that is repeated for each a.a added to the protein after the initiator methionine
- The ribosome moves in the 5’ to 3’ direction along the mRNA synthesizing the protein from its amino ( N-) to carboxyl ( C-) terminus
what are the 3 important binding sites of the ribosome in elongation
a) A site: holds the incoming aminoacyl-tRNA complex which will be the next a.a added to the growing chain
- the incoming aminoacyl-tRNA complex is determined by the mRNA codon
b) P site: holds the tRNA that carries the growing polypeptide chain and where the initiation complex formed (methionine)
- a peptide bond is formed as the polypeptide is passed from the tRNA in the P side to the tRNA in the A site
this action requires energy and is completed by the ribosome
c) E site: the now uncharged tRNA briefly pauses before it is expelled from the ribosome to be recharged
describe translocation of translation
1) the ribosome advances 3 nucleotides along the mRNA in the 5’ to 3’ direction
2) When the ribosome advances, the tRNA position on the ribosome shift
3) The charged tRNA ( bound to the polypeptide) is transferred from the A site to the P site
4) The uncharged tRNA is transferred from the P side to the E site where it is expelled
4) End result is an empty A site ready for the entry of aminoacyl-tRNA corresponding to the next codon
5) This cycle continues until a stop codon is encountered triggering termination
what is cleavage during post translation modification
certain amino acid sequences are removed from the chain or addition where biomolecules are added to the peptide
Common addition processes during post translation modification are
- Phosphorylation: addition of a phosphate group
- Carboxylation: addition of carboxylic acid group
- Glycosylation: addition of oligosaccharides (sugars), completed in the gogi body
- Prenylation: addition of lipid groups, allowing for incorporation of the protein into membranes
Difference between eukaryotic and prokaryotic during transcription
1) in Euk transcription occurs in the nucleus but bc Prok don’t have membrane bound organelles transcription occurs in the cytoplasm
2) no nucleus for Prok so post-translational modification do not occur and have polycistronic mRNA transcripts and Euk have monocistronic mRNA transcripts
3) the ribosomes have major differences
4) translation and transcription occur in the same spot and concurrently in Prokaryotes
what does monocistronic mean?
one transcript translates to one protein
what does polycistronic mean?
one transcript translates to multiple proteins often due to multiple start codon
what is the primary structure of a protein
- the sequence of a.a determined by its mRNA strand
- Lists a.a from the N terminus to C terminus
- Peptide bonds, the bonds linking linear a.a together are central to a proteins primary structure
what is the secondary structure of a protein
the 3D structure of neighboring amino acids which is determined by the primary protein structure of the protein
what results in the stability of the secondary structure
H bond formation between a.a side chains
what is the tertiary structure of proteins
the folding of a polypeptide forming the 3D structure of the entire protein itself
-Folding process is often assisted chaperones (cellular proteins that stabilize transition states in the folding process.
what kind of interactions does the tertiary structure rely on
hydrophobic and hydrophilic interactions of amino acid side groups as well as disulphide bonds
what is the quaternary structure of proteins
: describes the combing of polypeptides to form a complete protein complex
what kind of interactions does quaternary structure rely on
- The stability relies on both hydrophobic and hydrophilic interactions and disulfide bonds
non-enzymatic proteins can either which 2 types of proteins
structural or binding proteins
what is the function of structural proteins
have the primary functions to fix cellular components in place or to move cellular components to their needed locations
what is the function of binding proteins
serve to transport, attach or sequester mc by directly adhering to the mc
what are enzymes
proteins that have catalytic functions, often called organic catalysts
what are catalysts
any substance that affects the rate of a chemical rxn while remaining unchanged or being regenerated as a product
how does a catalyst increase the rxn rate of a rxn
reduction of the activation energy of the rxn
how can you increase enzymes variability
conjugation
what are conjugated proteins
are proteins covalently bond to other groups like lipids, sugar, cation that often serve as coenzymes or cofactors
what is the substrate
the mc the enzyme acts on
are most enzyme-catalyzed reaction reversible?
Yes, the product synthesized by an enzyme can be decomposed by the same enzyme
what are the 4 characteristics of all enzymes
1) Enzymes do NOT alter the eqm constant
2) Enzymes are OT consumed in the rxn meaning they will appear in both R and P
3) Enzymes lower the activation energy of a rxn thereby speeding up the rxn
4) Enzymes are pH and temperature sensitive with optimal activity at specific pH ranges and temperatures
describe the Lock and Key theory
- Spatial structure of an enzymes active site is exactly complementary to the spatial structure of its substrate
- The 2 fit together like a lock and key
describe the induced fit theory
- The active site has flexibility of shape
- When the appropriate substrate comes in contact with the active site the confirmation of the active site changes to fit the substrate which results in the beginning of the enzymatic process
what type of environmental factors effect the enzymes action and the rxn rate depends?
emperature, pH, the concentration of enzymes
how does temperature effect the rate of enzyme action
increase temperature the rate of enzyme action increases until an optimum temperature is reached (~37C) after this heat alters the shape of active site of the enzyme mc and deactivates it leading to a rapid drop in rate of action
how does pH effect the rate of enzyme action
+ what is the optimal pH for most of human bodily fluid + pepsin + pancreatic enzymes
above or below the optimal pH the enzymatic activity declines
- For humans optimal pH is ~7.2 of most bodily fluids except pepsin in the stomach works in highly acidic conditions ( pH=2) and pancreatic enzymes which works in small intestines is best at alkaline conditions (pH= 8.5)
- The optimal pH matches the conditions under which the enzyme operates
how does substrate [ ] effect enzyme action
increasing the [ ] will increase the reaction rate until all the active site is occupied but after that the reaction rate will to change no matter how much substrate you have added = maximal velocity is reached
how to change Vmax
add more enzyme
what is Vmax
the reaction ate as substrate concentration goes to infinity
What is Michaelis constant (km)
- The substrate concentration needed to fill half of the enzymes active sites so the substrate concentration needed to reach ½ Vmax
- Used to asses an enzymes affinity for a substrate
how is affinity and km inversely related
Higher km requires a higher [ ] of substrate to reach ½ Max so lower the enzymes affinity for the substrate
what are 2 ways biological systems require tight control over biochemical reactions
- increasing the rate of reaction and enzyme inhibition
what are the 2 types of enzyme inhibition
competitive and noncompetitive
what is competitive inhibition
- if a similar mc is present in a concentration comparable to the concentration of the substrate it will compete with the substrate for binding sites on the enzyme and interfere with enzyme activity
- The enzyme is inhibited by the inactive substrate or competitor
can Vmax be reached with the presence of a competitive inhibitor
yes, If sufficient quantities of the substrate are introduced the substrate can outcompete the competitor and will still be able to reach Vmax
what is non-competitive inhibition
- substrate that binds to an enzyme at an allosteric site
- Change in structure of the enzyme results in a non-functional active site
can Vmax still be reached with a non-competitive inhibition
No
what is an allosteric site
substrate that binds to an enzyme at a site other than the active site
what are the 6 categories enzymes are classified under
- Ligase
- Isomerase
- Lyase
- Hydrolase
- Oxidoreducatse
- Transferases
what is a ligase enzyme
- catalyze the cleavage of single mc into 2 products
- Don’t require water as a susntrate and don’t acts as oxidoreductases
- Can also go backwards ( reverse ) so 2 products into 1 –>Often called synthases
what is a hydrolase enzyme + ex
catalyzes the breaking of a compound into 2 mc using the addition of water
ex. Phosphatase cleaves a phosphate group from proteins, nucleic acids and lipids respectively
what is a oxidoreductase enzyme
- catalyze oxidation reduction rxn (transfer of e between biological mc)
- Often have a cofactor that acts as an e carrier ex NAD+ or NADP+
- Electron donor is the reductant and electron acceptor is the oxidant
- Enzymes with dehydrogenase or reductase in their names are usually oxidoreductases
- Enzymes where O is the final e acceptor often includes oxidase their name
what are transferase enzymes + 2 examples
- catalyse the movement of a functional group from one mc to another
- Ex. Protein metabolism an aminotransferase can convert aspartate and alpha-ketoglutarate
- Ex kinases are also part of this class they catalyze the transfer of a phosphate group generally from ATP to another mc
