Molecular Genetics Flashcards
What is the central dogma of molecular biology?
DNA->RNA->protein
What provides the basis for evolution?
- DNA is mutable
- changes in DNA are passed down from generation to generation
nucleotide
- the basic unit of DNA
- deoxyribose sugar bound to a phosphate group and a nitrogenous base
purines
- adenine and guanine
- 2 rings
pyrimidines
- cytosine and thymine
- 1 ring
antiparallel arrangement
one strand is 5’ to 3’ and the other strand is 3’ to 5’
DNA helicase
breaks the hydrogen bonds between the nitrogenous bases on each strand
replication fork
the opening in the DNA made by DNA helicase
topoisomerase
relieves torsional strain due to DNA twisting by cutting, twisting, and rejoining the DNA strands
semiconservative replication
each new daughter helix has one strand from the parent and one new strand
DNA polymerase
- reads the parent DNA strand and creates a complementary, antiparallel daughter strand
- reads in the 3’ to 5’ direction and creates a new daughter strand in the 5’ to 3’ direction (can only add to the 3’ end)
leading strand
- 3’ end faces toward the replication fork
- DNA polymerase and replication fork travel in the same direction
- continuously synthesized
lagging strand
- 3’ end faces away from the replication fork
- synthesis of lagging strand and movement of DNA polymerase are in opposite directions
- synthesized in fragments called Okazaki fragments
DNA ligase
joins Okazaki fragments on the lagging strand
gene
- a unit of DNA that encodes a specific RNA molecule
- through the process of transcription and translation can be expressed as a protein
transcription
DNA->mRNA
template strand
DNA strand that is complementary and antiparallel to mRNA strand
coding strand
DNA strand that is identical to mRNA strand(except thymine is exchanged for uracil)
translation
mRNA->protein
What direction is DNA transcribed?
5’->3’
What direction is mRNA translated?
5’->3’ (protein is synthesized from N terminus to C terminus)
structure of RNA
- sugar is ribose instead of deoxyribose
- uracil instead of thymine
- mostly single stranded
mRNA
- messenger RNA
- carries the complement of a DNA sequence
- transports information to the nucleus to the ribosomes for protein synthesis
- in eukaryotes, mRNA is monocistronic (one mRNA strand codes for one polypeptide)
tRNA
- transfer RNA
- found in the cytoplasm
- assists in the translation of mRNA
- brings amino acids coded for in the mRNA sequence to the ribosomes during protein synthesis
- recognizes mRNA codon and corresponding amino acid
- 3D structure with anticodon on one end and site of amino acid attachment on the other end
- at least one type for each amino acid
anticodon
3 nucleotide sequence that is complementary to an mRNA codon
aminoacyl-tRNA synthetase
- forms the aminoacyl-tRNA complex (charged tRNA)
- active site binds to amino acid and corresponding tRNA
rRNA
- ribosomal RNA
- synthesized in the nucleus of eukaryotes and the cytoplasm of prokaryotes
- integral part of ribosomal machinery used during protein assembly in the cytoplasm
- most abundant type of RNA in the cell
steps of transcription
- RNA polymerase binds to the DNA template strand at a promoter region (ex: TATA box) with the assistance of transcription factors
- RNA polymerase surrounds the DNA molecule after it has been opened by the actions of DNA helicase and topoisomerase
- RNA polymerase recruits and adds complementary RNA nucleotides to transcribe a new RNA strand in the 5’ to 3’ direction
- Final result is an RNA strand complementary to the template DNA strand except A binds with U instead of T
post-transcriptional processing
- introns are spliced out (stay in the nucleus) and exons are kept (exit the nucleus as part of mRNA)
- 5’ guanine cap and 3’ poly-A tail are added to protect from RNA-degrading enzymes in the cytosol
hnRNA
- hetero-nuclear RNA or pre-RNA
- RNA that has not been processed
spliceosome
removes introns
codon
- three nucleotide sequence on mRNA that corresponds to a specific amino acid
- 64 possible
- each codon codes for only one amino acid
stop codons
- instruct the ribosome to stop translation
- UAA, UGA, UAG
Why is the genetic code degenerate?
- multiple codons code for the same amino acid
- mRNA sequence can not be regenerated from the amino acid sequence
wobble position
- 3rd position
- aminoacyl tRNA can still bind to the mRNA despite having non-complementary base pairs for the third nucleotide
4 stages of translation
- initiation
- elongation
- translocation
- termination
initiation
- Begins when the small ribosomal subunit binds to the mRNA near its 5’ end
- Ribosome scans the mRNA until it binds to a start codon (AUG, Met)
- Aminoacyl tRNA for methionine base pairs with the start codon
- Large ribosomal subunit binds to form the completed initiation complex
elongation
- 3 step cycle repeated for each amino acid added to the protein after methionine
- ribosome moves in 5’ to 3’ direction along the mRNA to synthesize the protein from N terminus to C terminus
- ribosome contains A site, P site and E site
A site
holds incoming aminoacyl-tRNA complex which will be the next amino acid in the growing chain
P site
- holds the tRNA that carries the growing polypeptide chain
- where the initiation complex is formed
- peptide bond (requires energy) is formed as the polypeptide is passed from the tRNA in the P site to the tRNA in the A site
E site
uncharged tRNA briefly pauses before it is expelled from the ribosome to be recharged
translocation
- ribosome advances 3 nucleotides along the mRNA in the 5’ to 3’ direction
- charged tRNA (bound to the polypeptide) is transferred from the A site to the P site
- uncharged tRNA is transferred from the P site to the E site where it is expelled
- A site is empty and ready for the aminoacyl-tRNA that corresponds with the next codon
termination
- end of translation
- signaled by a stop codon (UAA, UGA, UAG)
post-translational modifications
- cleavage
- addition:
- -phosphorylation
- -carboxylation
- -glycosylation
- -prenylation
cleavage
removal of certain amino acid sequences
addition
biomolecules are added to the peptide
phosphorylation
addition of a phosphate group
carboxylation
addition of carboxylic acid groups
glycosylation
addition of oligosaccharides (sugars), completed in the Golgi body
prenylation
addition of lipid groups, allowing for the incorporation of the protein into membranes
Where does transcription occur in eukaryotes?
the nucleus
Where does transcription occur in prokaryotes?
the cytoplasm
differences between prokaryotic and eukaryotic processes
- in eukaryotes, transcription occurs in the nucleus
- in prokaryotes, transcription occurs in the cytoplasm
- posttranscriptional modifications do not occur in prokaryotes
- prokaryotes have polycistronic mRNA (one transcript translates to multiple proteins due to multiple start codons)
- eukaryotes have monocistronic mRNA
- transcription and translation occur concurrently in prokaryotes because they happen in the same location
protein levels of organization
- primary
- secondary
- tertiary
- quaternary
primary structure
- sequence of amino acids from N terminus to C terminus determined by the mRNA strand
- amino acids are linked by peptide bonds
secondary structure
- local 3D structure of neighboring amino acids determined by the primary structure
- stability relies on hydrogen bond formation between amino acid side chains
- ex: alpha helices, beta sheets
tertiary structure
- the folding of a polypeptide forming the 3D structure of the protein
- folding process is assisted by chaperones
- relies on hydrophobic and hydrophilic interactions of the side chains as well as disulfide bonds
quaternary structure
- combining of polypeptides to form a complete protein complex
- relies on hydrophobic and hydrophilic interactions and disulfide bonds
- only some proteins have quaternary structure
non-enzymatic protein function
- structural proteins
- binding proteins
structural proteins
- cytoskeleton components
- motor proteins
- fix cellular components in place or move cellular components to their needed location
binding proteins
- transport, attach, or sequester molecules by directly adhering to the molecule
- ex: hemoglobin, cell adhesion molecules, immunoglobulins
enzymes
- proteins that have a catalytic function (organic catalysts)
- crucial to all living things
conjugated proteins
enzymes covalently bonded to other groups (lipids, sugars, cations, etc) that serve as coenzymes or cofactors
substrate
- the molecule the enzyme acts on
- binds to the active site of the enzyme
Do enzymes alter the equilibrium constant?
No
Are enzymes consumed in the reaction?
No (appear in reactants and products)
How do enzymes speed up a reaction?
by lowering the activation energy
lock and key theory
- spatial structure of an enzyme’s active site is exactly complementary to the spatial structure of its substrate (fit like a lock and key)
- largely discounted
induced fit theory
- when the appropriate substrate comes in contact with the active site, the conformation of the active site changes to fit the substrate
- this change in shape begins the enzymatic processes
- more widely accepted
How are enzymes affected by temperature?
- as temperature increases, the rate of enzyme action increases until an optimum temperature is reached (usually around 37 degrees C)
- beyond optimum temperature, heat alters the shape of the active site and deactivates/denatures the enzyme
How are enzymes affected by pH?
- each enzyme has an optimum pH
- above and below the optimum pH, activity declines
- maximal activity of many human enzymes occurs at a pH of 7.2
- pepsin, which works in the stomach has an optimum pH of 2
- pancreatic enzymes in the small intestine have an optimum pH of 8.5
- optimum pH matches the pH of the environment that the enzyme operates in
Vmax
- maximum velocity of reaction
- the reaction rate as the substrate concentration goes to infinity
- adding more enzyme changes the Vmax
Km
- Michaelis constant
- the substrate concentration needed to fill half the enzyme’s active sites
- substrate concentration at 1/2 Vmax
- high Km means lower affinity for substrate
- low Km means higher affinity for substrate
competitive inhibition
- a molecule similar to the substrate binds to the active site of the enzyme
- if the concentration of the substrate is increased, the substrate can outcompete the competitor and can still reach Vmax
noncompetitive inhibition
- substance binds to the enzyme at a site other than the active site (allosteric site)
- this changes the structure of the enzyme, resulting in a nonfunctional active site
- cannot be overcome by adding more substrate
- Vmax decreases
- a type of allosteric inhibition
ligases
- catalyze addition or synthesis reactions, generally between large, similar molecules
- often require ATP
- most likely to be encountered in nucleic acid synthesis and repair
isomerases
- catalyze the rearrangement of bonds within a molecule (reactions between stereoisomers and constitutional isomers)
- some also can be classified as oxidoreducatases, transferases, or lyases
lyases
- catalyze the cleavage of a single molecule into two products
- do not require water as a substrate
- do not act as oxidoreductases
- can also synthesize two molecules into a single molecule (then referred to as synthases)
hydrolases
- catalyze the breakdown of a compound into two molecules using the addition of water
- usually named for their substrate
- ex: phosphatase (cleaves phosphate group), peptidases, nucleases, lipases
oxidoreductases
- catalyze redox reactions (transfer of electrons)
- often have a cofactor such as NAD+ or NADP+
- electron donor is the reductant
- electron acceptor is the oxidant
- enzymes with dehydrogenase or reductase in their name are in this category
- if oxygen is the final electron acceptor, then oxidase will be in the name
transferases
- catalyze the movement of a functional group from one molecule to the other
- ex: aminotransferase can convert aspartate to alpha-ketogluterate, kinases catalyze the transfer of a phosphate group
