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108 Cards in this Set

  • Front
  • Back
What violates Mendel's first law of segregation?
What violates Mendel's second law of independent assortment?
Human leukocyte antigen is an example of which concept?
multiple alleles
partial (or incomplete) dominance
the condition resulting when one allele is not completely dominant to another allele so that the heterozygote has a phenotype between that shown in individuals homozygous for either individual allele involved
the situation in which the heterozygote exhibits the phenotypes of both homozygotes
the degree to which a particular genotype is expressed in the phenotype (i.e. polydactylism in cats)
the frequency with which a dominant or homozygous recessive gene manifests itself in the phenotype of an individual (i.e. hemochromatosis)
multiple phenotypic effects resulting from a single mutant gene (i.e. cystic fibrosis)
polygenic traits
traits encoded by many loci
one gene “masks” or alters the expression of another
recessive epistasis
conceptually, one enzyme’s function leads to the formation of another enzyme’s substrate (i.e. flower color, 9:3:4)
duplicate recessive epistasis
homozygous recessives at either of two genes produce the same phenotype as the homozygous recessive for both genes (i.e. flower color in sweet peas, 9:7)
duplicate dominant epistasis
both genes need to be mutant for recessive phenotype (i.e. ovoid or triangular leaf shape, 15:1)
dominant epistasis
the dominant allele at one trait is sufficient to produce the dominant phenotype (i.e. color in squash, 12:3:1)
lethal allele
an allele that results in the death of an organism (i.e. yellow gene in mice, 2:1)
conditional mutant
a mutant organism that is normal under one set of conditions but becomes seriously impaired or dies under other conditions (i.e. neurotransmitter gene in flies and colors in Himalayan rabbits)
central dogma of molecular biology
DNA replicates and is transcribed into RNA, which is translated into protein
a region of DNA that is necessary to encode an RNA molecule and is passed from parent to offspring and is capable of change (mutation- recombination)
the transfer of information from a double-stranded DNA molecule to a single-stranded RNA molecule
a specific regulatory nucleotide sequence in the DNA to which RNA polymerase binds for the initiation of transcription
What are the two sites in bacterial transcription initiation promoter?
-35 and -10
-35 consensus sequence
-10 Pribnow box consensus sequence
What is the RNA holoenzyme made up of?
RNA polymerase (two a, a b and a b’ subunits) + sigma factor
Which species of eukaryotic RNA do these polymerases transcribe?
RNA polymerase I
RNA polymerase II
RNA polymerase III
RNA polymerase I- rRNA
RNA polymerase II- mRNA and snRNA
RNA polymerase III- tRNA
Which box is located in the eukaryotic promoter region at approximately -25?
TATA box (TATAAA consensus sequence)
Which eukaryotic promoter consensus sequence is located at about -75?
CAAT box
Which eukaryotic promoter consensus sequence is located at about -90?
GC box (consensus sequence GGGCGG)
What are three structural motifs of transcription factors?
basic helix loop helix (BHLH), leucine zipper, zinc finger
What are the events that occur during the initiation of transcription in eukaryotes?
TBP binds to TATA box. TAF binds to TBP to become TFIID. Dimer of TFIIA and TFIIB binds. RNA polymerase can then bind. TFIIF, TFIIE, TFIIH, and probably many others stabilize this.
RNA polymerase “reads” the template strand and puts in the corresponding rNTP
prokaryotic rho dependent termination
rho is a protein that unwinds the DNA-RNA heteroduplex; it finally catches up to the polymerase and when it does, it destabilizes the RNA polymerase holoenzyme
prokaryotic rho independent termination
usually a secondary structure called a hairpin in the RNA destabilizes the RNA polymerase binding
What is a 5' cap?
When eukaryotic pre-mRNA is 20 to 30 nucleotides long, a capping enzyme adds 7-methyl guanosine to the 5' end, forming a 5'-5' linkage.
What is the purpose of the 5' cap and 3' polyadenylation?
They are recognition factors for nuclear export, and they increase the longevity of the molecule by protecting against RNAses.
How is eukaryotic pre-mRNA trascription terminated?
Elongation continues thousands of base pairs past a polyadenylation site, which is a consensus sequence of AAUAAA. CPSF (cleavage and polyadenylation specificity factor) binds to AAUAAA sequence. CstF binds to a GU/U region as well as to CPSF, forming loop in pre-mRNA. CFI and CFII bind to and cleave RNA. Once RNA is cut, PAP (poly A polymerase) puts in a variable length of adenine.
What is the consensus sequence that defines a splice site?
5' GU......YNCURAY......AG 3'
(Y=pyrimidine, R=purine, N=any nucleotide)
What is a snRNP?
small nuclear ribonucleoprotein
What are the events involved in splicing?
U1 binds to 5' splice site. U2 binds to A in branch point sequence. U4/U6 binds to U5, which binds to U1 and U2, forming a loop. U4 leaves. This is an active spliceosome and splicing occurs. Intron released in lariet shape with snRNPs.
What's the purpose of splicing?
Different forms of the same/similar protein can be formed with the same gene. Specific biochemical properties of proteins can be regulated.
What is the benefit of RNA editing?
It is a mechanism to increase the number of different proteins available without the need to increase the number of genes in the genome. It may protect the genome against some viruses. It also may allow for intramolecular base pairing to form double-stranded RNA.
How many different amino acids are there?
What is the basic structure of an amino acid?
An amino group, an R group, and a carboxyl group.
an ion that has both a positive and negative charge
What kind of bonds to amino acids form to each other?
peptide bonds
What are the four levels of structural arrangments in proteins?
primary- amino acid sequence
secondary- regular folding and twisting of single polypeptide chain like a-helices and b-pleated sheets
tertiary- three-dimensional structure caused by folding
quaternary- complex of polypeptide chains in a multisubunit protein
molecular chaperones
proteins which function to keep other proteins in the correct conformation/structure
Where are ribosomes located?
in the cytoplasm or associated with the endoplasmic reticulum
aminoacyl-tRNA synthetase
charges amino acid with tRNA
How many different aminoacyl-tRNA synthetases are there?
What are the events of protein synthethis in prokaryotes?
Initiation factors bind to 30S ribosomal subunit. 30S binds to Shine-Dalgarno sequence and AUG initiation codon. Initiator tRNA binds to start codon. Initiation factors dissociate, and GTP is hydrolyzed. 50S subunit is attached.
elongation in translation
addition of amino acids to the growing polypeptide chain
p site
peptidyl site of the ribosome where start codon-anticodon is bound
elongation factor Tu with GTP binds to next aminoacyl-tRNA molecule in the A (aminoacyl) site of the ribosome
peptidyl transferase
forms peptide bond between between freed peptide from P site and amino acid in A site
dissocation of Ef-Tu and GTP ratchets the ribosome forward, making the A site the P site
What are the events of translation termination?
Release factors and unspecified tRNAs recognize stop codon. Polypeptide is released from tRNA at P site, tRNA is released from ribosome, and ribosome dissociates.
wobble hypothesis
a theory proposed by Francis Crick which proposes that the base at the 5' end of the anticodon (3' end of the codon) is not as constrained as the other two bases; this feature allows for less exact base pairing so that the 5' end of the anticodon can potentially pair with one of three different bases at the 3' end of the codon
somatic mutation
mutation in a somatic cell that can harm the individual
germline mutation
mutation that occurs in a germ cell, which won't really harm the individual but will be passed on to offspring
point mutations
a mutation caused by a substitution of one base pair for another
transition mutation
a specific type of base-pair substitution mutation that involves a change in the DNA from one purine-pyrimidine base pair to the other purine-pyrimidine base pair at a particular site (i.e. AT to GC)
transversion mutation
a specific type of base-pair substitution mutation that involves a change in the DNA from a purine-pyrimidine base pair to a pyrimidine-purine base pair at the same site (i.e. AT to TA or GC to TA)
silent mutation
substitution mutation that does not change the amino acid the codon is coding
missense mutation
changes the identity of a single amino acid; may or may not impact the function of the protein (conservative amino acid changes versus non-conservative amino acid changes)
nonsense mutation
changes an amino acid specifying codon into a stop codon; leads to premature termination of the protein
addition or deletion of bases can alter the “reading” frame of the mRNA
forward mutation
a mutational change from a wild-type allele to a mutant allele
reverse mutation
a mutational change from a mutant allele back to a wild-type allele
suppressor mutation
diminishes effects of first mutation by acting at another site
intragenic suppressor
second mutation occurs within the same gene, could restore proper reading frame
intergenic suppressor
second mutation within another gene (i.e. Tyr-tRNA mutant reads stop codon in E. coli)
spontaneous mutations
mutations that occur without the use of chemical or physical mutagenic agents
mutation rate
probability of a specific type of mutation as a function of time
mutation frequency
number of occurrences of a mutation as a proportion of cells/individuals in a population
tautomeric shift
changing from base to tautomer of base allows for abnormal base pairing; tautomers will revert to original form unless bout of replication occurs
strand slippage
occurs at highly repetitive sequences of DNA, polymerase “slips” and either repeats or deletes bases, usually accompanied by intramolecular base pairing
removal of an amino group off a base (if C is methylated and then deaminated, it is converted to T)
bond between the purine and deoxyribose breaks; if not repaired prior to replication, no base is specified and a random base is inserted
induced mutation
mutation that results from treatment with mutagens
ultraviolet radiation
induces pyrimidine dimers, mostly TT, which are unable to base pair correctly
base analogs
compounds that are similar in structure to the normal complement of nitrogenous bases and so can be incorporated into the double helix; although they do not behave the same (i.e. 5-bromouracil acting like T)
base modifying agent
changes the chemistry/behavior of existing bases (i.e. nitrous acid as deaminating agent and EMS and DMS as alkylating agents)
intercalatating agent
compounds that insert themselves between adjacent nucleotides on the double helix, typically cause frameshifts
mutator mutations
mutations which increase the overall number of mutations within an organism, affect various DNA repair mechanisms (i.e. mutD affecting DNA Polymerase III, loss of exonuclease activity)
one way by which thymine dimers can be repaired; the dimers are reverted directly to the original form by photolyase and exposure to visible light in the wavelength range 320–370 nm
excision repair
enzymes recognize distortion of helix, endonucleases excises 10-12 bases of helix surrounding distortion, glycosylases remove damaged bases leaving a hole, AP endonucleases cleave phosphodiester bond around missing base, DNA polymerase fills in the missing sequences, ligase reattaches adjacent bases
mismatch repair
mutS binds to mismatch, recognizing newly synthesized DNA; mutL and mutH excise new strand; DNA polymerase III fixes
SOS response
severe DNA damage induces this response in E. coli; if there's no damage, lexA represses transcription of about 17 gene involved in DNA repair; damage activates recA protein which cleaves lexA protein; DNA repair genes are transcribed
Why isn't SOS response left on all the time?
response itself is mutagenic; CG-TA transitions are most common with CC dimers
unequal crossing over
mechanism that leads to the addition or loss of chromosomal material
abnormal condition in which one or more whole chromosomes of a normal set of chromosomes either are missing or are present in more than the usual number of copies
What are the consequences of this loss/addition of genetic material?
most homozygous deletions lead to lethality, heterozygotes "uncover" the other allele, can be used in deletion gene mapping
cri-du-chat syndrome
results from observable deletion of part of the short arm of chromosome 5
Prader-Willi syndrome
results from deletion of part of long arm of chromosome 15; infants weak because sucking reflex is poor, by 5 or 6 they become compulsive eaters and can eat themselves to death
What can happen if two breaks occur on the same chromosome?
inversions or small deletions
a change in the order of genes along a chromosome
How does inversion affect alignment in meiosis?
leads to the formation of a loop in the inverted chromosome
paracentric inversion
does not include centromere, forms inviable dicentric and acentric chromosomes
pericentric inversion
forms monocentric chromosomes, some inviable deletion/duplication products
exchange of genetic material between non-homologous chromosomes
Robertsonian translocation
not reciprocal, involves the fusion of two non-homologous acentric chromosomes
mutational hotspots
repetitive sequences, AT rich, C methylation, palindromic sequences, transcriptional active spots
conditional mutation
a mutation which changes a phenotype only under certain environmental conditions
How can environmental conditions affect gene expression?
Environmental conditions can affect what genes are expressed as well as the amount of expression.
Where is the point of major gene expression control?
transcriptional regulation- what genes, how many transcripts, where and when
cis acting element
"same," these are DNA sequences
trans acting element
"across," proteins encoded by different genes