Biology Molecular Genetics Flashcards
The transmission of information through DNA, RNA, and proteins is called the ___ dogma of molecular biology
central
___ is the basis for heredity
DNA
DNA is ___ and can be altered under certain conditions
mutable
DNA is transcribed (__) into RNA which is then translated (translation) into proteins
transcription
CUT the PYe: C, U, and __ are pyrimidines
Thymine
PURe As ___
Gold
Pyrimidines have one ring in their ___
structure
Purines have two rings in their ___
structure
___: basic unit of DNA
nucleotide
___ uses Uracil instead of Thymine
RNA
If the 5’ carbon is at the end of the DNA strand, then that end is referred to as the 5’ ___
end
DNA is most commonly found in nature as a double-stranded helices of complementary strands with the sugar-phosphate chains on the outside of the helix and the nitrogenous basis on the ___
inside
The strands of DNA are held together by hydrogen bonds between the bases oriented toward the ___
center
Adenine forms two hydrogen bonds with ___
Thymine
Guanine forms three hydrogen bonds with ___
Cytosine
DNA replication involves the breaking of hydrogen bonds between nitrogenous bases from each ___
strand
The opening of the DNA molecule created by DNA helicase is known as the ___ fork
replication
As DNA is replicated, the replication fork continues to travel up the DNA molecule which could cause a buildup of ___ strain (due to twisting of the DNA molecule) upstream of the replication fork
torsional
___ removes torsional strain involved in DNA replication by cutting, twisting, and then rejoining the strands of DNA
Topoisomerase
The area that takes place after the replication fork has passed a portion of DNA is known as the ___bubble
replication
Each single strand of DNA can act as a template for complementary base pairing and allows for the ___ of two new daughter strands
synthesis
Each new daughter helix contains an intact strand from the parent helix and a newly ___ strand; this type of replication is called semiconservative
synthesized
The daughter strands of DNA formed from the parent strands are ___ to the parent strands
identical
Creation of daughter strands is the result of DNA ___
polymerase
With the exception of DNA polymerase’s reading direction (a few untested ___), everything in molecular biology is 5’ to 3’
endonucleases
DNA polymerase reads 3’ to 5’, but the following processes occur 5’ to 3’: DNA syntheses, DNA repair, RNA ___, RNA translation (reading of codons)
transcription
DNA polymerase can only add nucleotides to 3’ ends of DNA ___
strands
The leading strand has its 3’ end facing towards the replication fork, thereby allowing DNA polymerase/DNA synthesis and the replication fork to travel in the same ___
direction
Since the leading strand has its 3’ end facing toward the replication fork the result is the leading ___being continually synthesized
strand
The lagging strand has its 3’ end facing away from the replication ___
fork
In order to replicate the entire lagging strand, additional DNA polymerase proteins must reattach to the parent strand near the continually moving ___ fork
replication
___ fragments: Discontinuous synthesis results in short fragments of synthesized DNA
Okazaki
During DNA polymerase’s sequence, these ___ are joined together by DNA ligase
fragments
Transcription is the process in which ___ information is passed from DNA to RNA
genetic
Messenger RNA, is transcribed in 5’ to 3’ direction and is complementary and ___ to the DNA template strand
antiparallel
The coding __ of DNA is identical to the mRNA strand (with the exception that all thymine bases are exchanged for uracil)
strand
___ is the process in which genetic information is passed from mRNA to protein
translation
The ribosome translates the mRNA in the 5’ to 3’ direction and the protein is synthesized from the amino terminus (N-terminus) to the ___ terminus (C-terminus)
carboxyl
For RNA, the ___ constituent is ribose (instead of deoxyribose)
sugar
Most RNA is ___ stranded
single
RNA can be found in both the ___ and the cytoplasm of the cell
nucleus
Three major types of RNA include: mRNA, tRNA and ___
rRNA
___ RNA carries the complement of a DNA sequence. It then transports this information from the nucleus to the ribosomes for protein synthesis
Messenger
mRNA is made from ___ complementary to the template strand of DNA
ribonucleotides
Eukaryotic mRNA is ___, meaning that one mRNA strand codes for one polypeptide
monocistronic
___ RNA is a small RNA molecule found in the cytoplasm
tRNA
tRNA assists in the translation of mRNA’s ___ code into a sequence of amino acids coded for in the mRNA sequence to the ribosomes during protein synthesis
nucleotide
tRNA recognizes both the mRNA ___ and its corresponding amino acid
codon
tRNA has a dual ___ and this is reflected in its three dimensional structure
function
One end of tRNA contains a three-nucleotide sequence, the ___, which is complementary to one of the mRNA codons
anticodon
rRNA (ribosomal RNA) is synthesized in the nucleolus of eukaryotes and in the ___ of prokaryotes
cytoplasm
Transcription is the process through which information coded in the sequence of DNA is used to direct the ___ of a strand of RNA
synthesis
After ___ modification, the RNA leaves the nucleus through nuclear pores
post-transcriptional
The first step of transcription occurs when RNA polymerase binds to the DNA ___ strand at a promoter region, a short DNA sequence found upstream from the site where transcription of a specific RNA is going to take place
template
In a process very similar to DNA replication, the RNA polymerase surrounds the DNA molecule after it has been opened by the actions of DNA ___ and topoisomerase
helicase
Once RNA polymerase has bound to the template DNA strand, it recruits and adds complementary RNA ___, thereby transcribing a new RNA strand
nucleotides
RNA that has not yet been processed is known as hetero-nuclear RNA (hnRNA), or pre-RNA and contains extra nucleotides that are not ___ to create the corresponding protein
necessary
Extra sequences on hnRNA are called ___ and are subsequently spliced out (removed) by the spliceosome
introns
___ are the nucleotides necessary to make the protein and are kept during the post-transcriptional processing
exons
The function of the terminal structures RNA receives before leaving the nucleus is to provide protection from RNA-degrading ___ within the cytosol
enzymes
Once these three modifications are made to the RNA molecule, it is termed messenger RNA (mRNA) and can ___ the nucleus
leave
Stop codons are UAA, UGA and ___
UAG
The redundancy in amino acid sequence codons accomodates a ___ position which is a third nucleotide in a given sequence having a corresponding amino acid in common with other sequences
wobble
___ is the process through which mRNA codons are translated into a sequence of amino acids
translation
translation occurs in the ___
cytoplasm
initiation begins when the small ribosomal subunit binds to the ___ near its 5’ end
mRNA
Initiation occurs when the ribosome scans the mRNA until it binds to a start ___, which codes for methionine
codon
Once the mRNA, small ribosomal subunit, and the aminoacyl-tRNA complex is bound, the large ribosomal subunit binds, forming the ___ initiation complex
completed
Elongation is a ___ step cycle that is repeated for each amino acid added to the protein after the initiator methionine
three
During elongation, the ribosome moves in the 5’ to 3’ direction along the mRNA, synthesizing the protein from its amino (N-) to ___ (C-) terminus
carboxyl
The ___ contains three important binding sites
ribosome
The A site holds the incoming aminoacyl-tRNA complex, which will be the next amino acid added to the ___ chain
growing
The incoming aminoacyl-tRNA complex is determined by ___ codons
mRNA
The P site holds the tRNA that carries the growing polypeptide chain where the initiation ___ formed (methionine)
complex
A ___ bond is formed as the polypeptide is passed from the tRNA in the P site to the tRNA in the A site
peptide
On the P site, the peptide bond requires ___ and is completed by the ribosome
energy
The E site is where the now uncharged tRNA briefly pauses before it is expelled from the ___, to be recharged
ribosome
Elongation is completed by translocation, in which the ribosome advances three ___ along the mRNA in the 5’ to 3’ direction
nucleotides
When the ribosome advances during translocation, the tRNA’s ___ on the ribosome shifts
position
During ___, the charged tRNA (bound to the polypeptide) is transferred from the A site to the P site
translocation
During translocation, the uncharged ___ is transferred from the P site to the E site, where it is expelled
tRNA
After translocation, the result is an ___ A site ready for the entry of the aminoacyl-tRNA corresponding to the next codon
empty
When a stop codon is reached, ___ is triggered
termination
Modification of a newly translated polypeptide chain can include ___, where certain amino acid sequences are removed from the chin, or addition, where biomolecules are added to the peptide
cleavage
___: addition of a phosphate group
phosphorylation
___: addition of a carboxylic acid groups
carboxylation
___: addition of oligosaccharides (sugars), completed in the Golgi body
glycosylation
___: addition of lipid groups, allowing for incorporation of the protein into membranes
prenylation
In eukaryotes, transcription occurs in the nucleus while in prokaryotes, this occurs in the ___(due to a lack of membrane-bound organelles)
cytoplasm
Since prokaryotes do not have a ___, posttranscriptional modification does not occur
nucleus
prokaryotes have polycistronic mRNA transcripts while eukaryotes have ___ mRNA transcripts
monocistronic
Monocistronic means one transcript ___ to one protein
translates
polycistronic means one transcript translates to multiple ___, often due to multiple start codons
proteins
In addition, due to the lack of membrane-bound organelles in prokeryotes, transcrption and translation can occur at the same ___ in the cell. This results in transcrption and translation occuring concurrently in prokaryotes
location
The primary structure (1 degree) of a protein is the sequence of amino acids determined by its ___ strand
mRNA
Primary structure lists amino acids from the ___ to the C-terminus
N-terminus
Peptide bonds are central to a protein’s ___ structure
primary
The local 3D structure of neighboring amino acids of a protein which is determined by the primary structure is the ___ structure
secondary
The most common secondary structures are alpha-helices and ___-sheets
beta
Secondary structure stability relies on ___ bond formation between amino acid side chains
hydrogen
The ___ structure of a protein refers to the folding of a polypeptide forming the 3D structure of the entire protein itself
tertiary
The folding which occurs in a tertiary structure of a protein is often assisted by chaperones, cellular proteins that stabilize transition states in the ___ process
folding
Tertiary structure relies on the ___ and hydrophilic interactions of amino acid side groups as well as disulfide bonds
hydrophobic
The ___ structure of a protein describes the combining of polypeptides to form a complete ___ complex
protein
Quaternary structure relies on both hydrophobic and hydrophilic interactions as well as ___ bonds
disulfide
Not all proteins have ___ structure
quaternary
Two major types of proteins are non-enzymatic and ___
enzymatic
Non-enzymatic functions are wide-reaching but generally fall into two major categories: structural and ___
binding
Structural proteins, including cytoskeleton components and motor proteins, have the primary functions to fix cellular components in place or to move ___ components to their needed location
cellular
Binding proteins serve to transport, attach, or sequester molecules by directly ___ to the molecule
adhering
A catalyst is any substance that affects the rate of a chemical reaction while remaining ___ or being regenerated as a product
unchanged
Typically, catalysts, and therefore enzymes, increase the reaction rate through reduction of the activation ___ of the reaction
energy
Conjugated protein covalently bond to other groups (lipids, sugars, cations, etc.) that often serve as ___ or cofactors
coenzymes
The molecule the enzyme acts on is called the ___
substrate
There is an area on each enzyme to which the substrate binds, called the ___ site
active
Most ___ reactions are reversible
enzyme-catalyzed
The product synthesized by an enzyme can be decomposed by the ___ enzyme
same
Enzymes do NOT ___ the equilibrium constant
alter
Enzymes are NOT ___ in the reaction
consumed
Enzymes will appear in both the ___ and the products of a given reaction
reactants
Enzymes lower the activation energy of a ___, thereby speeding up the reaction
reaction
Enzymes are pH-and temperature-sensitive, with optimal activity at specific pH ___ and temperatures
ranges
The Lock and Key Theory holds that the spatial structure of an enzyme’s active site is exactly ___ to the spatial structure of its substrate
complementary
When the appropriate substrate comes in contact with the active site, the conformation of the active site ___ to fit the substrate (Induced Fit Theory)
changes
Enzyme action and the reaction rate depend on several environmental factors including ___, pH, and the concentration of enzyme and substrate
temperature
Beyond optimal temperature, heat alters the shape of the active site of the enzyme molecule and deactivates it, ___ to a rapid drop in rate of action
leading
Vmax is the reaction rate as substrate ___ goes to infinity
concentration
In order to change Vmax, more ___ must be added
enzyme
Km represents the substrate concentration needed to fill half of the enzyme’s ___ sites
active
Km can be used to assess an enzyme’s ___ for a substrate
affinity
A higher Km requires a higher ___ of substrate to reach 1/2Vmax
concentration
Affinity and Km are ___ related
inversely
If sufficient quantities of the substrate are introduced (competitive inhibition), however, the substrate can outcompete the competitor and will still be able to reach the Vmax; however, this will require much higher concentrations of ___ than would be necessary without the competitor
substrate
A noncompetitive inhibitor is a substance that binds to an ___ at a site other than the active site
enzyme
The interaction of the noncompetitive inhibitor at an ___ site (allosteric means “other site” or “other structure”) changes the structure of the enzyme, resulting in a nonfunctional active site
enzyme
Noncompetitive inhibition is considered to be a type of ___ inhibition
allosteric
___ catalyze addition or synthesis reactions, generally between large, similar molecules, and often require ATP
Ligases
___ catalyze the rearrangement of bonds within a molecule
Isomerases
Some isomerases can also be classified as oxidoreductases, transferases, or lyases, depending on the ___ of the enzyme
mechanism
Isomerases ___ reactions between stereoisomers as well as constitutional isomers
catalyze
___ catalyze the cleavage of a single molecule into two products
Lyases
Lyases do not require ___ as a substrate and do not act as oxidoreductases
water
When a Lyase catalyzes the synthesis of two small molecules into a single molecule, it is common for them to be ___ to as synthases
referred
___ catalyze the breaking of a compound into two molecules using the addition of water
Hydrolases
LIL’HOT
Ligase, Isomerase, Lyase, Hydrolase,Oxidoreductase, Transferase
___ catalyze oxidation-reduction reactions, that is, the transfer of electrons between ___ molecules
Oxidoreductases
In reactions catalyzed by oxidoreductases, the electron donor is known as the ___, and the electron acceptor is known as the oxidant
reductant
___ catalyze the movement of a functional group from one molecule to another
Transferases
Kinases are also a member of the ___ class
Transferase
___ catalyze the transfer of a phosphate group, generally from ATP to another molecule
Kinase
