Ch.17 APBIO (The Central Dogma - From Gene to Protein) Flashcards

DNA
Terms Definitions
Human Genome Project
An international effort to map the complete human genetic code. This effort was essentially completed in 2001, though analysis is ongoing.
Keratin
a fibrous scleroprotein that occurs in the outer layer of the skin(epidermis) and in horny tissues such as hair feathers nails and hooves, lead to the revison of the one gene- one enzyme hypothesis.
Neurospora crassa
studied by Beadle and Tatum using X-Ray , a common bread mold that grows on a very simple medium containing sugar and simple inorganic salts
Gene Expression
the process by which DNA directs the synthesis of proteins, Has two stages transcription and translation.
Transcription
the synthesis of RNA on a DNA template, the information is copied from one molecule to another, resulting in a faithful copy the gene's protein coding genes(mRNA), occurs in the NUCLEUS.
Translation
the process whereby genetic information coded in messenger RNA directs the formation of a specific polypeptide at a ribosome in the CYTOPLASM
Archibald Garrod
The first to suggest that genes dictate phenotypes through enzymes that catalyze specific chemical reactions in the cell., Reported Alkaptonuria as the first human example of what is now known as Mendelian inheritance.
Gibberellins
A growth hormone that causes a wide variety of effects. One role is to stimulate growth of stems by promoting cell division. Farmers use it to make fruit grow larger.
Alkaptonuria
Defect in homogentisate oxidase, resulting in accumulation of homogentisic acid (Alkapton) which results in black urine, and Polymerized forms results in damage to joints, calfications in CV and UT, red skin
George Beadle
Man who hypothesis that each of the various mutations affecting eye color in Drosophila blocks pigment synthesis at a specific step by preventing production of the enzyme that catalyzes that step
Along with Tatum he mutated bread mold (Neurospora Crassa) using x-rays and observed difference in food requirements by providing different enzymes at differnt steps in the catabolic pathway and discovered that each class was blocked at different steps in the pathway because mutations in the class lacked the enzyme that catalyzes the blocked step this lead to the one gne one enzyme hypothesis - which then lead to the one gene one polypedptide hypothesis
One gene One polypeptide hypothesis
The hypothesis that every gene directs the synthesis of a particular polypeptide chain; originally called the one geneone enzyme hypothesis.
Minimal medium
a defined medium that contains the minimal ingredients needed by genetically normal (wild type) strains of a particular species.
Complete Growth Medium
This is a minimal medium that is supplemented with all 20 amino acids and a few other nutrients, usually required by the mutated species.
RNA
A type of nucleic acid consisting of nucleotide monomers with a ribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and uracil (U); usually single-stranded; functions in protein synthesis and as the genome of some viruses.
Polypeptide
A polymer (chain) of many amino acids linked together by peptide bonds.
Messenger RNA
RNA that copies the coded message from DNA in the nucleus and carries to the protein synthesizing machinery of a cell into the cytoplasm
Ribosomes
A cell organelle constructed in the nucleolus and functioning as the site of protein synthesis in the cytoplasm; consists of rRNA and protein molecules, which make up two subunits, act as the sites of translation, and facilitate the orderly linking of amino acids into polypeptides.
Nuclei
Because bacteria lack _____, their DNA is not segregrated from ribosomes and the other protein synthesizing equipment.
pre- mRNA
Precursor mRNA; the first strand of mRNA produced by the gene transcription that contains both introns and exons
RNA processing
Modification of RNA transcripts(pre mRNA), including splicing out of introns, joining together of exons, and alteration of the 5' and 3' ends
Primary Transcript
in eukaryotes, the initial RNA product containing introns and exons produced by transcription of DNA; must be processed to form proteins
The Central Dogma
1. DNA is the genetic material, containing the genes that are responsible for the physical traits (phenotye) observed in all living organisms
2. DNA is replicated from existing DNA to produce new genomes
3. RNA is produced by reading DNA in a process called transcription
4. this RNA serves as the message used to decode and transmit the genetic information and synthesize proteins according to the encoded information. This process of protein synthesis is called translation.
64
The amount of possible base code words( 4 ^3), enough to code for the 20 amino acids known. 61 code for things while 3 are either start or stop codons.
Triplet Code
A set of three-nucleotide-long words that specify the amino acids for polypeptide chains.
Template Strand
the DNA strand that provides the pattern, or template, for ordering the sequence of nucleotides in an RNA transcript using DNA Polymerase.
Complementary Strand
A newly synthesized strand of RNA or DNA that has a base sequence complementary to that of the template strand
Codons
A three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code. Written in 5` to 3` direction.
Marshall Nirenberg
made poly-U mRNA (UUUUU); when mixed with amino acids, ribosomes, & proper enzymes, a polypeptide containing only one amino acid (phenylalanine)(AAA) was produced
AUG
Start codon for protein synthesis(METHIONINE)
Redundancy
Repetition of messages to reduce the probability of errors in transmission, found in mRNA base sequences
Reading Frame
the way in which a cell's mRNA-translating machinery groups the mRNA nucleotides into codons.
RNA Polymerase
Enzyme similar to DNA polymerase that binds to DNA and separates the DNA strands during transcription, can only assemble in 5` to 3` ends.
Promoter
a nucleotide sequence on a DNA molecule to which an RNA polymerase molecule binds, which initiates the transcription of a specific gene, upstream from the terminator, determines which DNA strand is used as the template.
Terminator
A special sequence of nucleotides in DNA that marks the end of a gene. It signals RNA polymerase to release the newly made RNA molecule, which then departs from the gene
Transcription Unit
unit, a region of a DNA molecule that is transcribed into an RNA molecule
RNA Pol 2
In Eukaryotes it is the RNA polymerase that transcribes DNA template strand when signaled by promoter
Initiation
the first phase of transcription; RNA polymerase binds to DNA @ the promoter, and unwinds the double helix
Elongation
2nd stage where amino acids brought by tRNAs are joined together by the ribosome in the order determined by the mRNA
Termination
The last stage of trranscription, stop of mRNA synthesis (i.e., transcription) at the terminator site, in Eukaryotes it involves the use of a polyadenton sequence.
Transcription Factors
to initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called _________ _________, which usually contains a TATA box
TATA Box
A DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex
Transcription Initiation Complex
the completed assembly of transcription factors and RNA polymerase bound to the promoter
Polyadenylation
last step of splicing, adds poly-a to the tail with the AUAAA code with poly-A-polymerase, then 10 to 35 nucletides the pre-mRNA is released
The 5` Cap
Contains a modified inverted nucleotide (7-methyl guanosine) which confers stability against nucleases and provides a mechanism to be recognized by the translation machinery. elps protect the pre mRNA from hydrolytic enzymes, and facilitate the export of mature mRNA from the nucleus.
Poly A Tail
The modified end of the 3' end of an mRNA molecule consisting of the addition of some 50 to 250 adenine nucleotides. Helps protect the pre mRNA from hydrolytic enzymes, and facilitate the export of mature mRNA from the nucleus.
UTR
Untranslated regions at the 5 and 3 primed ends; are part of the mRNA that will not be translated into protein but promote ribosome binding
RNA Splicing
the removal of introns and joining of exons in eukaryotic RNA, forming an mRNA molecule with a continuous coding sequence; occurs before mRNA leaves the nucleus.
Introns
a non-coding, intervening sequence within a eukaryotic gene removed during RNA splicing
Exons
A coding region of a eukaryotic gene. Exons, which are expressed except for the UTR, are separated from each other by introns.
Small Nuclear Ribonucleoproteins
(snRNPs) recognize splice sites; are composed of RNA, protein molecules at the end of introns, they are located in the cell nucleus, the RNA within it is called a (snRNA) or small nuclear RNA, forms part of spliceosomes
snRNA
short for small nuclear RNA and found within snRNPs. It can remove introns during the process: RNA splicing
Spliceosomes
A spliceosome is a complex of specialized RNA (snRNPs) and protein subunits that removes introns from a transcribed pre-mRNA (segment. This process is generally referred to as splicing.
Ribozymes
An RNA molecule that functions as an enzyme, catalyzing reactions during RNA splicing
Tetrahymena
A type of protists called ciliates; small, unicellular organisms that can be found in pond water, and object of self splicing rRNA
Alternative RNA splicing
a type of eukaryotic gene regulation at the RNA-processing level in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns, also explains why humans can get along with a relatively small amount of genes.
Domains
discrete structural and functional regions of proteins
Exon shuffling
the presence of introns in a gene may facilitate the evolution of new and potentially useful proteins as a result of a process known as _______ _________, by increasing the probability of a crossover (like recombinant DNA by increasing distances between exons)
Transfer RNA
Short-chain RNA molecules (L Shaped) present in the cell (in at least 20 varieties, each variety capable of combining with a specific amino acid) that attach the correct amino acid to the protein chain that is being synthesized at the ribosome of the cell, at 3` end it has amino acid.
Anticodon
A sequence of three bases of a tRNA molecule that pairs with the complementary three-nucleotide codon of an mRNA molecule during protein synthesis.
aminoacyl- tRNA synthetase
Enzyme which joins amino acids to the correct tRNA
Aminoacyl tRNA
A tRNA with an amino acid attached. This is made by an animoacyl-tRNA synthetase specific to the amino acid being attache.d
Wobble
A violation of the base-pairing rules in that the third nucleotide (5' end) of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position (3' end) of a codon.
Ribosomal RNA
The MOST abundant type of RNA, which together with proteins, forms the structure of ribosomes. Ribosomes coordinate the sequential coupling of tRNA molecules to mRNA codons. Made in the nucleolus
Nucleolus
The organelle where ribosomes are made, synthesized and partially assembled, located in the nucleus
Streptomycin
An antibiotic produced by the actinomycete Streptomyces griseus and used to treat tuberculosis, works because of the differential sizes of rRNA in bacteria and humans.
Tetracycline
an antibiotic (trade name Achromycin) derived from microorganisms of the genus Streptomyces and used broadly to treat infections,orks because of the differential sizes of rRNA in bacteria and humans.
P Site
one of a ribosome's three binding sites for tRNA during translation. It holds the tRNA carrying the growing polypeptide chain.
A Site
One of a ribosome's three binding sites for tRNA during translation. This site in the ribosome holds the tRNA carrying the next amino acid to be added to the polypeptide chain.
E Site
One of a ribosome's three binding sites for tRNA during translation. This site is the place where discharged tRNAs leave the ribosome.
GTP
A nucleotide composed of guanine, ribose, and three linked phosphate groups. It is incorporated into the growing RNA chain during synthesis of RNA and used as a source of energy during synthesis of proteins
N Terminus
The amino end of the methionine(START) in an RNA. The amino end
C Terminus
The end of a polypeptide chain that contains the last amino acid to be incorporated during mRNA translation; usually retains a free carboxyl group
Initiation Factors
proteins that bind to ribosomal subunits and mRNA that bring components together in the correct positions to start translation
Elongation Factors
One of a group of nonribosomal proteins required for continued translation of mRNA (protein synthesis) following initiation
GTP
Two molecules of _______ are required for Codon recognition, and it also increases the accuracy and efficency, one more _____ is hydrolyzed to provide energy fro the translocation step.
Release Factor
A cytoplasmic protein that binds to a stop codon where it appears in the A-site of the ribosome. modify the peptidyl transferase activity of the ribosome, so that a water molecule is added to the end of the completed protein. This releases the finished protein from the final tRNA, and allows the ribosome subunits and mRNA to disassociate.
Polyribosomes
Found in eukaryotic and prokaryotic cells, enable a cell to make many copies of a polypeptide very quickly during translation; multiple ribosomes attached to an MRNA strand
Post Translation Modification
occurs mainly in Golgi
includes addition of sugars, lipids, etc. to complete polypeptide
also have polypeptides that are cleaved or several different polypeptides that come together to form final protein
(ex.- hemoglobin)
Primary Structure
The first level of protein structure; the specific sequence of amino acids making up a polypeptide chain.
Secondary Structure
The localized, repetitive coiling or folding of the polypeptide backbone of a protein due to hydrogen bond formation between constituents of the backbone.Alpha helices and beta pleated sheets describe this
Quaternary Structure
The fourth level of protein structure; the complex shape resulting from the association and aggregation of two or more polypeptide subunits.
Tertiary Structure
Irregular contortions of a protein molecule due to interactions of side chains involved in hydrophobic interactions, ionic bonds, hydrogen bonds, and disulfide bridges. (Making Up the 3-D Structure)
Free Ribosomes
ribosomes that float in the cytosol to make the proteins that are used there
Bound Ribosomes
ribosomes that are attached to the endoplasmic reticulum to make proteins to be exported, to be embedded in membranes, and to be shipped elsewhere within the cell
Carboxyl Group
A functional group present in organic acids and consisting of a single carbon atom double-bonded to an oxygen atom and also bonded to a hydroxyl group.
Carbonyl Group
an organic molecule, a functional group consisting of a carbon atom linked to a double bond to an oxygen atom, C=O
Amino Group
A functional group that consists of a nitrogen atom bonded to two hydrogen atoms; can act as a base in solution, accepting a hydrogen ion and acquiring a charge of +1., -NH2
Thiol Group
SH
Phosphate Group
A chemical group consisting of a phosphorus atom covalently bonded to four oxygen atoms; important in energy transfer., , -OPO3^-2; contributes neg charge to molecule of which it is a part ; has potential to react with water releasing NRG
Hydroxyl Group
A functional group consisting of a hydrogen atom joined to an oxygen atom by a polar covalent bond. Molecules possessing this group are soluble in water and are called alcohols.
Signal Peptide
A sequence of about 20 amino acids at or near the leading (amino) end of a polypeptide that targets it to the endoplasmic reticulum or other organelles in a eukaryotic cell.
Signal Recognition Particle
(SRP), a protein-RNA complex that recognizes a signal peptide as it emerges from a ribosome and helps direct the ribosome to the endoplasmic reticulum (ER) by binding to a receptor protein on the ER
Translocation
During protein synthesis, the third stage in the elongation cycle when the RNA carrying the growing polypeptide moves from the A site to the P site on the ribosome
snoRNA
small nucleolar RNA that form snoRNPs that modify rRNA and other snRNAs
siRNA
class of double-stranded RNAs about 23 nucleotides in length that silence gene expression; act by either promoting the degradation of mRNAs with precisely complementary sequences or by inhibiting the transcription of genes containing precisely complementary sequences, also called small interfering RNA
miRNA
(microRNA) about 20 nucleotides long, a small, single-stranded RNA molecule, generated from a hairpin structure on a precursor RNA transcribed from a particular gene, it associates with one or more proteins in a complex that can degrade or prevent translation of an mRNA with a complementary sequence, up to 1/3 of all human genes may be regulated by ______
Mutations
Random errors in gene replication that lead to a change in the sequence of nucleotides; the source of all genetic diversity
Point Mutation
mutation that affects a single nucleotide, usually by substituting one nucleotide for another
Base Pair Substitution
A type of point mutation; the replacement of one nucleotide and its partner in the complementary DNA strand by another pair of nucleotides. Some are called silent mutations
Missense Mutation
A point mutation in which a codon that specifies an amino acid is mutated into a codon that specifies a different amino acid.
Nonsense Mutation
A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.
Insertions
A mutation involving the addition of one or more nucleotide pairs to a gene.
Deletions
a nucleotide is deleted, which changes the amino acid sequence.
Frameshift Mutation
A mutation occurring when the number of nucleotides inserted or deleted is not a multiple of three, resulting in the improper grouping of the following nucleotides into codons.
Mutagens
agents, such as chemicals or radiation, that damage or alter genetic material in cells
p53
This tumor suppressor gene causes cell cycle arrest in G1, providing time for DNA repair. If repair is successful, cells re-enter the cycle. If unsuccessful, apoptosis
proto oncogenes
normal cellular genes that are important regulators of normal cellular processes, they promote growth. alterations in the expression of these cells resulr in oncogenes
Silent Mutation
A point mutation in which a codon that specifies an amino acid is mutated into a new codon that specifies the same amion acid.
Spontaneous Mutations
Natural changes in the DNA caused by unidentified environmental factors
Hermann Muller
Scientist(s) who demonstrated that mutations and hereditary changes can be caused via radiation.
Oncogenes
research on tumor viruses led to the discovery of cancer-causing genes called ___________ in certain retroviruses
Retroviruses
An RNA virus that reproduces by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancer-causing viruses.
Gene
A _______ is a region of DNA whose final product is either a polypeptide or an RNA molecule.
Sickle Cell Disease
A human genetic disease caused by a recessive allele that results in the substitution of a single amino acid in the hemoglobin protein; characterized by deformed red blood cells that can lead to numerous symptoms.
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