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107 Cards in this Set

  • Front
  • Back
Primary structure of proteien
sequence of AA
secondary structure of protien
alpha helix and beta pleated sheets, interactive folding
tertiary structure of protein
further interactions cause more folding
quaternary structure of protein
2 or more polypeptides
degenerate code
aa specify more than one codon
iso-accepting tRNA
tRNAs that accept more than one aa
4 stages of translation
1. bind aa to tRNA
2. initation (assemply at ribosome)
3. elongation
4. termination
step 1 of translation
all tRNAs have CCA at 3'end

COO- attaches to OH of adenine
specficity is due to aminoacyl-tRNA synthetases

requires ATP
step 2 of translation
components needed: rRNA, ribosome, initation factor proteins, initiator fMet-tRNA, GTP
1) mRNA binds to small ribosomal subunit
2) initiator tRNA binds to mRNA (base pairing of anticodon and codon)
3) large subuint joins complex
Initation Factors
IF-3 pairs with SSU preventing LSU from binding
IF-1 enhances dissoaction

Shine Delgarno sequence within ribosomal binding site

IF-2 needed to attach iniation codon and GTP
translation in eukaryotes
no shine delgarno, recognizes 5' cap instead

SSU moves until it finds AUG
translation: elongation
need: 70S complex, charged tRNA, elongation factors, GTP

3 sites on ribosome can be occupied:
Aminoacyl (A site)
peptidyl (P site)
Exit (E site)

initiator tRNA (fMET) is the only one that can bind to the P site, all others bind to the A site
3 steps to Elongation in translation
1) charged tRNA + EF-Tu and EF-Ts + GFP complex enter A site
2) GTP cleaved and EF-TU-GDP complex release
3) peptide bond forms between A and P site
releases AA at Psite from tRNA
4) Translocation: ribosome moves down the mRNA
Translation Termination
no tRNA for stop codon

release factor RF1-3, they bind to the stop code and release polypeptide chain from ribosome
translation in pro vs eu
initation: shine delgarno for pro and 5' cap for eu

in seperate locations in cell for eu
1/2 life of mRNA is longer
post-translational modification
1) precursor enzymes cleave and trim it
2) carbohydrates added
3) molecular chaperon proteins needed for folding
4) methyl, phosphate or carboxyl groups may be added
translation in eukaryotes
no shine delgarno, recognizes 5' cap instead

SSU moves until it finds AUG
translation: elongation
need: 70S complex, charged tRNA, elongation factors, GTP

3 sites on ribosome can be occupied:
Aminoacyl (A site)
peptidyl (P site)
Exit (E site)

initiator tRNA (fMET) is the only one that can bind to the P site, all others bind to the A site
3 steps to Elongation in translation
1) charged tRNA + EF-Tu and EF-Ts + GFP complex enter A site
2) GTP cleaved and EF-TU-GDP complex release
3) peptide bond forms between A and P site
releases AA at Psite from tRNA
4) Translocation: ribosome moves down the mRNA
Translation Termination
no tRNA for stop codon

release factor RF1-3, they bind to the stop code and release polypeptide chain from ribosome
translation in pro vs eu
initation: shine delgarno for pro and 5' cap for eu

in seperate locations in cell for eu
1/2 life of mRNA is longer
post-translational modification
1) precursor enzymes cleave and trim it
2) carbohydrates added
3) molecular chaperon proteins needed for folding
4) methyl, phosphate or carboxyl groups may be added
3 principle elements in mRNA sequences in bacterial cells
5' UTR shine delgarno, protein encoding region, 3' UTR
what is the 5' cap?
it is an extra guanine nucleotide thta is methylated.

it occurs by removing a phsophate group from the 5' end and bonding the guanine and then methylating it. increases stability and ribosome binds to it
what is the poly-A tail how is it added
poly A tail is the processing of the 3' end. the consensus sequence is AAUAAA and is 11-30 upstream cleavge site

protiens find cleavae site and reomve 3' end. after cleavage is complete, adenine nucleotides are added to the new 3' end, creating poly-A tail
splicesome
consits of 5 snRNPs. splicing of pre-mRNA nuclear introns takes place within the splicesome
explain splicing
pre-mRNA is cut at 5' splice site, freeing exon 1 from the intron and the 5' end of intron attaches to the branch point; intron folds back on itself froming lariat

second step of RNA splicing, a cut is made at the 3'splice site and the 3'end of exon 1 becomes covalently attached to the 5'end of exon 2

intron is released as a lariat
2 types of alternative processing pathways
alternative splice sites and multiple 3' cleavage sites
RNA editing and guide RNAs
alters sequence of an RNA molecule after transcription by the insertion,d leetion or modification fo nucleotides

the guide RNAs provide templates for the lateration of nucleotides in RNA molecules undergoing editing

the gRNAs base pair to the pre-edited RNA molecule. the binding determines the location of the alteration of nucleotides
pre-mRNA processing
5' cap
cleavage of 3' end + poly(A)
splicing of introns
3 basic stages of transcription
iniation: transcription apparatus assembles on promoter and begins synthesis of RNA

elongation: RNA pol moves down DNA and adds rNTPs to growing 3'end

termination: RNA molecule separates from DNA temp
similarities btwn DNA and RNA pol
sim: both use DNA templates, read in 3-5 direction, complementary strand is synthesized in 5-3 direction, antiparallel to the template, both us triphosphates as substrates, actions enhanced by accesory protiens

differencts: RNA pol uses rNTPS, DNA pol requires primer, RNA pol sytnesize a copy of one one of the DNA strands, DNA pol copies both strands
3 ways in which archaea are similar to eukaryotes
TATA box, TFIIB proteins, TBP
3 things needed for transcription
a) DNA template
b) raw materials
c) transcription apparatus to catalzye reaction
translation in bacteria
1) At the initiation of translation the first step is when the mRNA binds to the small subunits of the ribosome (30S and 50S subunits). The IF-3 (initiation factor 3) binds to the small subunit preventing the 50S from binding to the 30S. This allows for the mRNA to bind to the 30S unit.

2) At this time a tRNA forms a complex with IF-2 and GTP and this complex binds with the initiation codon (shine dalgarno sequence)

3) while IF-1 binds to the 30S subunit. All IF factors and complexs dissosate and the 50S can now bind to the 30S with the mRNA creating the 70S complex.

4) Elongation is first started by the binding of the fMet-tRNA to the P site of the ribosome.

5) After the EF-Tu (elongation factor Tu) binds to GTP and tRNA to form a complex in which enters the A site of the ribosome.

6) GTP is cleaved and GDP is formed and the EF-Tu along with GDP is released to combine with another charged tRNA. A peptide bond is formed between the P and A sites.

7) Translocation begins as the ribosome moves down the mRNA molecule in the 5 to 3 direction. This process reguires EF-G and GTP.

8) The complex is now at the E site and releases tRNA which moves to the cytoplasm.

9) Termination begins as the translocation hits a stop codon. When this occurs RF-1 (release factor 1) attaches to the A site of the complex.

10) RF 3 forms a bond with GTP and the ribosome. The peptide that was translated is released from the complex.

11) GTP associates with RF 3 and the complex releases itself from one another.
siRNA vs miRNA
siRNA
miRNA
Origin- can be mRNA, a transposon, or virus
Origin-transcribed from a different gene
forms long hairpins from RNA duplex or ssRNA
Forms short hairpins from ssRNA
Triggers degradation of mRNA
Some trigger mRNA degradation other inhibit translation
Target genes from which they were transcribed
Target genes other than those from which they were transcribed
crucial point in eukaryotic translation
The DNA must be made available for transcription, which is difficult because eukaryotic DNA is complexed with histone proteins. Acetyltransferases add acetyl groups to the amino acids at the end of histones to destabilize the nucleosome.
attenuation
During attenuation in the trp Operon of E. coli, transcription is terminated when the secondary structure hairpin forms by the base pairing of regions 3 and 4 of the 5’ UTR. This hairpin is followed by a string of uracil NTs and only occurs when tryptophan levels are high.
anti-sense RNA
Anti-sense RNA is a form of gene regulation. It is complementary to mRNA; it binds and inhibits translation. Is found in both prokaryotic and eukaryotic cells.
splicin process
In a pre-mRNA an intron lies between an upstream exon and a downstream exon. First the pre-mRNA is cut in the 5’ splice site. The 5’ end of the intron attaches to the branch point. A cut is made at the 3’ splice site. Then, the intron is release as a lariat and the two exons are spliced together. The bond holding the lariat is broken, and the linear intron is degraded. Finally, the spliced mRNA is exported to the cytoplasm and translated.
stop codons
UAA, UAG, and UGA.
why is DNA more stable than rna
The presence of the free 2'OH in the ribose sugar makes RNA more susceptible to degradation under alkaline conditions. DNA molecules contain the sugar deoxyribose and lack the 2'OH found in ribose sugars, so DNA is more stable.
4 types of introns
1) Group I introns are found in rRNA genes and some bacteriophage genes.
(2) Group II introns are found in protein-encoding genes of mitochondria, chloroplasts,
and a few eubacteria.
(3) Nuclear pre-mRNA introns are found in the protein-encoding genes of the nucleus.
(4) Transfer RNA introns are found in tRNA gene
types of RNA Pol
RNA polymerase I transcribes rRNA.
(2) RNA polymerase II transcribes pre-mRNA and some snRNAs.
(3) RNA polymerase III transcribes small RNA molecules such as 5S rRNA, tRNAs,and some small nuclear RNAs.
2 types of transcriptional control
pos/neg
bacterial transcription summary
Transcription in bacteria, begins with (1) initiation, in which the transcription apparatus assembles on the promoter and begins the synthesis of RNA; (2) elongation, in which DNA is threaded through RNA polymerase, while it unwinds the DNA and add new nucleotides to the 3' end of the RNA strand; and (3) termination, where the recognition of the ending trascription unit takes place causing the separation of the RNA molecule from the DNA template.
Pribnow box
A Pribnow box is a consensus sequence found in bacteria. It is also called the -10 consensus sequence.

35 consensus sequence, TTGACA
why we think RNA preceeded DNA
1. Self splicing introns I, II in mitochondrial DNA.
2. The structure and function of Spliceosomes.
and ribozymes
alloploidy
polyploids that arise through hybridization between species
autoploidy
polyploids that arise from a single parental form
3 parts to a chromosome
1. Centromere = attachment site for spindle –
Spindle microtubules = move chromosomes during cell
division – Complexes with kinetochore proteins & spindle
microtubules attach

2. Telomeres = tips; stabilize ends.

Origin of replication = sites where DNA synthesis begins
sister chromatids
Copies of a chromosome • Held together at the centromere
4 major types of chromosomes
1. Metacentric- centromere is located in the middle and both arms of chromosomes are of equal length
2. submetacentric- centromere is moved toward one end creating a long arm and short arm.
3. Acrocentric- Centromere is near one end producing a long arm and a knob at the other end.
4. Telocentric- centromere is moved to or at the complete end of the chromosome.
2 major phases of mitosis
Interphase and M phase
Interphase
Stage G1: – Several hours long (10 hrs in mammals)
• Stage G0 (optional): – Before G1/S checkpoint, stable state, constant size, extended period of
time; regulatory signal
• Stage S-phase: – DNA synthesis; DNA duplicated (9 hrs) – BEFORE S phase = 1 chromatid – AFTER S phase = 2 sister chromatids but same # of chromosomes
(held together by centromere) • Stage G2: Prep for M phase (4 hrs)
M phase
Five stages of M phase
– Prophase: chromosomes condense – Prometaphase: nuclear membrane disintegrates;
attachment of spindle to kinetochore – Metaphase: move to metaphase plate – Anaphase: Separation of sister chromatids – Telophase: chromosomes at spindle poles; nuclear
membrane forms
when does DNA material double?

when does chromosome double?
DNA doubles post S phase

chrosome # doubles after the separation of sis tids in anaphase
cancer and cell cycle
So, CANCER cells differ from normal cells in that they mostly rely on the G2 checkpoint phase which follows G1 and precedes cell division.
• If you could silence the G2 checkpoint, you would push CANCER cells into cell division without repair to the damage
– They would divide with a mess of broken chromosomes and DIE.

knocking out G2 checkpoint would not be bad bc cells have G1
work of p53
p53 PROTEIN binds DNA & stimulates another gene to produce p21 protein that interacts with a cell division-stimulating protein (cdk2).
• When p21 is complexed with cdk2 the cell CANNOT pass through to the next stage of cell division.
theta replication
Begins at origin, dsDNA unwinds, replication bubble forms, replication fork, ssDNA, bidirectional replication in both directions
requirments of DNA rep
template
dNTPs
enzymes, ex: pol, topio, etc
rolling circle replication
initiated by a break in one of he nucleotide strands, producing a ds-stranded circular dna MOLECULE AND A SINGLE STRANDED LINEAR dna MOLECULE, THE ATTER OF WHICH MAY CIRCULARIZE AND SERVE AS A TEMPATE FOR the synthesize of a compliementary strand
aneuploidy
Aneuploidy is the change in number of individual chromosome. Human: Down’s syndrome, Trisomy 21 (caused by non-disjuction during meiosis) Animal: Mule (cross between a mare and a jackass) (monosomy)

Anueploidy is the change in the number of individual chromosomes.

Polyploidy is the change in the number of chromosome sets.
genetics
a. Molecular genetics: one gene or part of a gene
b. Transmission genetics: from individuals from one generation to the next generations
c. Population genetics: multiple group, genomes and populations.
d. Evolutionary genetics: over time
transolcation vs crossing over
Crossing over in meiosis occurs when homologous chromosomes exchange a portion of their DNA. In translocation, the same process occurs but with nonhomologous chromosomes or within the same chromosome.
prokaryotic and eukaryiotic differences
Eukaryotes
-have a nucleus
-posses membrane bound organelles
-Large
-Posses a linear DNA

Prokaryote
-Do not have a nucleus
-Are relatively small
-Lack cytoskeleton
-Have a circular DNA
-Have more than one chromosome, but they are not homologous.
pangenisis concept and the germ-plasm theory
pangenesis, particles called gemmules carried genetic material from each part of the body to the reproductive organs where they entered the embryo at conception. In the currently held germ-plasm theory, cells in the reproductive system already have complete genetic information for the whole body, which is then passed on to the sperm and egg.
crossing over
Crossing over is the exchange of genes between nonsister homologous chromatids during late prophase 1 of meiosis 1, creating more genetic variation.
checkpoints
The G1/S checkpoint ensures that the cell has all enzymes necessary for DNA replication. The G2/M checkpoint ensures the DNA is undamaged.

The spindle assembly checkpoint ensures that each chromosome is aligned on the metaphase plate and attached to spindle fibers from opposite poles.
purines and prymidines
Each purine consists of a six-headed ring attached to a five-sided ring, some examples of purines are adenine and guanine. Each pyrimidine consist of a 6-headed ring, some examples of pyrimidines are cytosine, thymine and uracil.
gene vs trait
he main difference between genes and traits is that while genes are inherited directly, traits are not. Genes determine the expression of traits due to external factors such as changes in the environment. Therefore, the genetic information that an individual organism possesses is its genotype and the trait is its phenotype.
what does DNA and RNA consist of
A DNA nucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base. RNA nucleotide consists of a ribose sugar, a phosphate group, and a nitrogenous base.
performationism vs blending inheirtanc
Performatationism occurs when all of a person's gentic code is inherited from one individual while blending inheritance occurs when both parents contribue to the person's traits.
replication in prokaryotes
1) initator proteins bind to the orgin of rep and open it up slightly so helicase can come in

2) helicase entes and uniwnds the dna creating a bubble called replication fork. single strand binding protiens assure the DNA does not fold up. DNA gyrase (topioisomerase) relieves supercoiling strain farther down in the DNA

3) RNA primase enters and lays down RNA based nucleotdies called primers. it is able to do this bc it does not require a bond to OH

4) DNA pol III begins to add dNTPS to the leading strand in the 5-3 direction. for the lagging strand, RNA pol has deposited primers throughout the strand so that DNA pol III can add in the 5-3 direction. this creates a series of gramgents called Okazaki gragents

termination: sequence or merging of rep forks

DNA pol I replaces the primers with DNA based nucleotides and DNA ligase seals the fragments
semi conservative rep
semiconserv rep entails the parent DNA strand to pen and serve as a temp; new complimentary bases are added, yielding a final product of one parent strand and one new strand
Multiple allele
Pattern of inheritance where there are more than two alleles present in population but only two are still present in an individual.
chromatids/chromosomes
Prophase: 12 chromosomes, 24 chromatids
Metaphase: 12 chromosomes, 24 chromatids
Anaphase I: 12 chromosomes, 24 chromatids
Telophase I: 6 chromosomes, 12 chromatids
Prophase II: 6 chromosomes, 12 chromatids
Metaphase II: 6 chromosomes, 12 chromatids
Anaphase II: 12 chromosomes, 12 chromatids
Telophase II: 6 chromosomes, 6 chromatids
penetrance
Percentage of individuals having a particular genotype that express the expected phenotype
epistatic
The gene that hides the effect of the other at different locus
What is the difference between sex-limited trait and sex-influenced trait?
sex-limited trait: a trait determined by an autosomal gene that is expressed in only one sex

sex-influenced trait: a trait determined by an autosomal gene that is more easily expressed in only one sex
the gene whose effect is hidden in epistasis
hypostatic
test cross
test cross is performed by crossing the individual with the unknown genotype with an individual possessing a homozygous recessive genotype for the trait.
chi-squared test
The goodness-of-fit chi-square test is a statistical test that determines whether the differences between observed values and expected values are statistically significant or whether they are due to chance alone.
genomic imprinting
differential expression of gene based off which parent it came from --> does not follow mendel's principle of inheritance
species accounts for 2 phenomena
distincitveness of a local species and connection that exist among diff pop of same species
repro barriers
geographical
mechanical
temporal
behavioral
ecological
gametic fusion
post zygotic
speciation
transformation of one species or the splitting of one ancestoral species into 2 descendant species
sympatric speciation
the differenitation of a population within a local area
species that occur together are:
- distinctive entitties
- behave separately
- phenotypically different
- utilize differnet parts of habittat
ecological isolation
utilize diff parts of habitat such that they never meet ex: tigers and lions, or anything living on the tree tops and something on earths floor
random divergence
may affect traits responsible for reproductive isolation --> speciation may occur
instantenous speciation
polyploidy (plants) : individual is reproductively isolated from all other members of the species
alloloploidy and speciation
hybridization of 2 parents, offspring has one set of chromosomes from each species

is infertile

can reproduce asexually

can become fertile if chromosomes spontaneously doubled (polyploidy)
- that would be like the donkey + horse = mule, which gave the odd number of chrom. if those doubled, the mule would = new species
adapative radiation
closely related species that have recently evolved from a common ancestor by adapting to different parts of the environment
• Occurs – in an environment with few other
species and many resources
– Hawaiian and Galápagos Islands
– Catastrophic event leading to extinction of other species
sympatric avoidance
(blue footed boobie)– Visual signals – Sound production – Chemical signals: pheromones – Electrical signals: electroreception
post zygotic development
prevents normal development into reproducing adults
hybridization
mating between two different species with a zygote being formed
• Hybrids often: – Do not develop into adults – Do not develop into fertile adults
Example: mule
evolution
changes w/in populations over time2 step process: (1) genetic variation occurs (mutation, changes); (2) increase/decrease of allelic frequencies
anagenesis
evolution within a single group ( lineage) over time
cladogenesis
evolution that causes the splitting of a group over time, evolve independently from each other
cell time line
1. 4 bya : single cells invade other cells = compartmentalization (cyanobacteria in alagae etc)

1 bya: single cell organisms of plants and animals diverge

600-900mya: primitive multicellular organisms

570: explosion of mulitcellular organisms, plant and animal
point of phylogenetic trees
Phylogenictreesconstructedtoinferchangesin character states originating with a common ancestor
humans vs chimpanzees
Divergence may be due to a few thousand isolated genetic changes not yet identified
Probably in regulatory sequences
molecular markers
Genetic/protein data: easy to interpret
• Can be used with all organisms
• Can assess evolutionary history between distantly related organisms
• Can be quantified • Can provide information about the
processes of evolution • Databases are HUGE and growing!!
Can use DNA sequence variations
– Restriction enzymes (molecular scissors) to find sequence differences
– Microsatellite variation w/in populations – DNA sequence gene of interest
genome evolution
Exon Shuffling = exchange, mosaics of genes created
• Duplication creates multi-gene families that are similar but encode different products
• Whole genome duplication (two copies of every gene--will acquire new function; yeast S. cerevisiae)
• Horizontal gene transfer (bacteria)
gradualism
small changes over great amount of time
puncuated equilibrium
long periods of stasis followed by rapid change
--> Stabilizing and oscillating selection is responsible for stasis
humans + future + evolution
Changing patterns of natural selection
• Globalclimatechange: majorchallenge for many species
• Decreased population sizes will increase the likelihood of genetic drift
• Geographic isolation will remove homogenizing effect of gene flow
• Chemicals and radiation could increase mutation rate