Bio exam 3
Diploid cells
A cell containing two sets of chromosomes (2n), one set inherited from each parent.
The ras gene
A proto-oncogene Ras normally relays signals from outside the cell that tell the cell to divide
The p53 gene
A tumor suppressor gene P53 is a transcription factor which normally responds to abnormalities in cell division by pausing or stopping the process
After transcription the 5' end receives ____ and the 3' end gets _______ . what does these changes do?
- 5' end gets a modified nucleotide 5' cap - 3' ends get a poly-A-tail (AAA...) - these changes help ribosomes attach to the 5' end - protect mRNA from hydrolytic enzymes
Bacteria (prokaryotic)
- Circular genome - Single DNA molecule - 1 origin of replication
elongation
- DNA polymerase III (deals with the leading strand and get match up the other nucleotides that the RNA primer has already started - DNA polymerase I (deals with the lagging strand where it takes out RNA and replaces it with DNA) - Ligase then goes over what the poly I did and fuses any gaps from Okazaki fragments together
What are the two steps that translation requires?
- First: a correct match between a tRNA and an amino acid, done by the enzyme aminoacyl-tRNA synthetase - Second: a correct match between the tRNA anticodon and an mRNA codon
Bread Mold Experiment
- Healthy mold ○ Grows on minimal medium Minimal medium = fewest nutrients that allow growth ○ mutant mold (x-ray damage to DNA) § Will not grow on minimal medium § Identify specific enzymes (steps in the metabolic pathway) are non functional Damage to DNA = enzymes are non functional
Initiation
- Helicase unwinds DNA - SSB stabilizes ssDNA - Primase adds an RNA primer which will be the basis for elongation
Humans (eukaryotic)
- Linear genome - Multiple linear chromosomes - Multiple origins of replication on each chromosome
What are Chargaff's rules?
- The base composition of DNA varies between species - In any species the number of A and T bases are equal and the number of G and C bases are equal
RNA Polymerase
- catalyzed by RNA synthesis - it pries the DNA strands apart and hooks together the RNA nucleotides
DNA polymerases
- catalyzes the elongation of new DNA at a replication fork - adds nucleotides only to the free 3' end of a growing strand; therefore a new DNA strand can only elongate only in the 5' to 3' direction
polyribosome (polysome)
- forms because a number of ribosomes that can translate a single mRNA simultaneously - enables a cell to make many copies of a polypeptide very quickly
prokaryotes
- translation can begin before transcription has finished - no processing of RNA before translation
Eukaryotes
- translation is completely separate from transcription - RNA is processes in the nucleus
in transcription, how many DNA bases are used and how many RNA bases are produced?
1 DNA base; 1 RNA base
What are the three steps in DNA replication? And why do does DNA replication happen?
1. initiation 2. elongation 3. termination - cell division for reproduction
Part of a gene contains the sequence 3'CAT5' on the template strand of DNA. What is the sequence of the anti-codon on a tRNA molecule that will eventually bind to the mRNA made from this sequence?
3'-CAU-5' because 3' CAT 5' leads to: mRNA --> 5' GAU 3' (codon) then that leads to: tRNA --> 3' CAU 5' (anti-codon)
in translation, how many RNA bases are used and how many amino acids are produced?
4 RNA bases; 20 amino acids
If a double-stranded DNA sample were composed of 10% thymine, what would be the percentage of guanine?
40%
Consider the DNA molecule below. Which of the following would be the sequence of the mRNA molecule produced if this DNA sequence was transcribed? 5' ATGCCAGTC 3' 3' TACGGTCAG 5'
5' AUGCCAGUC 3'
If one strand of a DNA molecule has the sequence of bases 5'ATTGCA3', the other complementary, antiparallel strand of DNA would have the sequence:
5'TGCAAT3'.
How many distinct 3-letter codons can be formed by an RNA molecule?
64 - because Lock: 3 digits long - You could have digits 000-999 = 1000 combos - 10^3 = 1,000 So - 4 nucleotides 4^3 = 64
The mechanism that RNA polymerase uses to unwind the DNA double helix makes which of these proteins obsolete for transcription? A. Helicase B. Single Strand Binding protein C. Topoisomerase D. A and B E. A, B, and C
A,B, and C
At what rate does transcription progress?
At a rate of 40 nucleotides per second in eukaryotes
Single Strand Binding Protein (SSB)
Binds to and stabilizes single-stranded DNA until it can be used as a template
_______ are the material inherited from one generation to the next.
Chromosomes (which is made up of protein and DNA)
what is the substance of inheritance?
DNA
what replaces RNA primers?
DNA
How was the fundamental relationship between genes and proteins discovered?
DNA --> RNA --> Protein
what is chromatin composed?
DNA and Histone proteins
exonuclease
DNA pol III is able to correct mistakes in replication
lagging strands
During DNA replication, a DNA strand made as a series of small Okazaki fragments that are eventually connected to each other to form a continuous strand.
When wobble occurs at the third base of a codon, why are the bases A and G usually grouped together and the bases C and U grouped together?
Each grouping is of bases of a similar size
Topoismerase
Fixes supercoiling (works ahead of the replication fork) by breaking covalent bonds along the backbone then later reattach it
alternative RNA splicing
Genes giving rise to two or more different polypeptides depending upon which segments are treated as exons during splicing
What type of bond connects nitrogenous bases?
Hydrogen bonds
terminator
In bacteria, the sequence signaling the end of transciption
We describe DNA as the hereditary material of an organism. What does it mean for something to be hereditary?
It must be passed from one generation to the next
Recruitment of RNA Polymerase to a specific promoter requires:
Multiple transcription factors binding near that promoter
deletions
Mutation involving the removal of one or more nucleotide pairs from a gene
Without the activity of the primase enzyme what would happen during DNA replication?
Neither strand would form because new DNA cannot be synthesized without a primer
tRNA
Non-coding RNA - is not translated into protein Links mRNA to specific amino acids - two binding sites on the tRNA molecule -- anti-codon, which base pairs with a codon forming hydrogen bonds -- 3' ed binds to a specific amino acid
introns
Noncoding segments of nucleic acid that lie between coding sequences.
Why does the addition of a phosphate group to histone proteins lead to a loosening of chromatin structure?
Phosphate groups contain a negative charge that disrupts interactions between histones and DNA
RNA splicing
Process by which the introns are removed from RNA transcripts and the remaining exons are joined together. - creates an mRNA molecule with a continuous coding sequence
why are prokaryotes capable of performing transcription and translation at the same time with the same RNA transcript while eukaryotes are not?
Prokaryotes lack a true nucleus - ribosomes can be directly adjacent to DNA
Primase
Provides an RNA primer to start new DNA strand synthesis
RNA synthesis is catalyed by _______, which pries the DNA strands apart and hooks together the RNA nucleotides
RNA polymerase
_______ is carried out by spliceosomes
RNA splicing
Who discovered the double helix?
Rosalind Franklin
Origins of Replication
Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides.
If I wanted to radioactively label proteins (but not DNA, RNA, sugars, or lipids) which of the following radioactive isotopes would I use? Phosphorus 32 (P^32) Tritium (H^3) Iodine 125 (I^125) Sulfur 35 (S^35)
Sulfur 35 (S^35)
Who found chromosomes on DNA?
T.H. Morgan
A promoter called _______ is crucial in forming the initiation complex in eukaryotes
TATA box
a promoter called a ________ is crucial in forming the initiation complex eukaryotes
TATA box
RNA
The bridge between genes and the proteins for which they code
epigenetic inheritance
The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence
How do the leading and the lagging strands differ?
The leading strand is synthesized towards the replication fork, while the lagging strand is synthesized away from the replication fork.
If DNA pol I was non-functional, how would that affect the leading strand during DNA synthesis in a eukaryotic cell?
The leading strand would not be able to connect to the lagging strand approaching it from the next origin of replication
transcription unit
The stretch of DNA that is transcribed
Eukaryotic cells have multiple origins of replication on their chromosomes. Why do you think that prokaryotic cells have only one origin of replication on their chromosomes?
They have less total DNA to copy
DNA --> RNA What is this process called?
Transcription
The completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a _______.
Transcription initiation complex
The stretch of DNA that is transcribed is called a ______.
Transcription unit
RNA --> protein
Translation
Who created a model for the double helix?
Watson and Crick
semiconservative replication
When a double helix consists of one old chain and one new chain
chromatin
a complex of DNA and protein, is found in the nucleus of eukaryotic cells
Which of the following types of mutation, resulting in an error in the mRNA just after the AUG start of translation, is likely to have the most serious effect on the polypeptide product?
a deletion of two nucleotides
wobble
a flexible pairing at the third base of a codon that allows some tRNAs to bind to more than one codon
codon
a set of three RNA nucleotide which code for a specific amino acid
histone acetylation
acetyl groups are attached to positively charged lysines in histone tails - loosens chromatin structures so it promotes the initiation of transcription
DNA polymerase III
assembles new DNA stran in the 5' to 3' direction
Point mutations in the proto-oncogene or its control elements
cause an increase in gene expression
type of point mutations: missense mutations
change a codon so that a different amino acid is inserted at the position in the protein
type of point mutations: nonsense mutations
change a codon to a stop codon so that the growing polypeptide is cut short - nearly always leads to a nonfunctional protein
how is cancer often caused?
changes in expression of genes that regulate cell growth and division
mutations
changes in the genetic material of a cell or virus
point mutations
chemical changes in just one base pair of a gene ex/ normal red blood cell shape to a sickle-cell
CUG
codes for the amino acid Leucine
AUG
codes for the amino acid Methionine
spliceosomes
consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites
heterochromatin
densely packed chromatin
Addition of a polymer is...
endergonic
telomerase
expressed in germ cells to maintain telomeraes at their original length
exons
expressed sequence of DNA; codes for a protein; usually translated into amino acid sequences
telomeres
fixes chromosome shortening
Which of the following would not typically cause a proto-oncogene to become an oncogene? A. gene suppression B. increased transcription C. amplification D. point mutation E. retroviral activation
gene suppression
tumor suppressor genes
gene that regulate cell division - helps prevent uncontrolled cell growth
oncogenes
genes that normally promote divsiion, normally heavily regulated - cancer causing genes
proteasomes
giant protein complexes that bind protein molecules and degrade them
type of point mutations: silent mutations
have no effect on the amino acid sequence of the protein produced because of redundancy in the genetic code
P site
holds the tRNA that carries the growing polypeptide chain
A site
holds the tRNA that carries the next amino acid to be added to the chain
When can a RNA sequence not be translated into amino acid sequence?
in a 1:1 ratio
Amplification of a proto-oncogene
increases the number of copes of the gene
What does the enzyme aminoacyl-tRNA synthetase do?
it correctly matches a tRNA and an amino acid
Ligase
joins two DNA stands together at their ends
euchromatin
loosely packed chromatin
Transcription produces ________ .
messenger RNA (mRNA)
frameshift mutation
mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide
RNA primer
prepares the piece for replication so enzymes can recognize it
The DNA sequence where RNA polymerase attaches is called the ________ .
promoter
Primase
provides an RNA primer to start new DNA strand synthesis
DNA polymerase I
removes RNA nucleotides and fill in the gap with DNA nucelotides
Helicase
separates DNA strands, breaking hydrogen bonds
Promoters signal the transcriptional _______ and usually extend several dozen nucleotide pairs upstream of the start point
start point
leading strands
synthesized continuously in the 5' to 3' direction
In bacteria, the sequence signaling the end of transcription is called the _______.
terminator
promoter
the DNA sequence where RNA polymerase attaches
DNA Methylation
the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some species - causes long-term inactivation of genes in cellular differentiation
transcription initiation complex
the completed assembly of transcription factors and RNA polymerase II bound to a promoter
E site
the exit site, where discharged tRNAs leave the ribosome
differential gene expression
the expression of different genes by cells with the same genome
What does RNA polymerase II transcribe?
the polyadenylation signal sequence (AAUAAA)
Ribosomes
the sites of translation
Transcription
the synthesis of RNA using information in DNA
Translation
the synthesis of a polypeptide, using information in the mRNA
Which property of RNA molecules like tRNA and snRNA is most responsible for their ability to bind to specific sequences on other nucleic acids?
they are single-stranded
________ mediate that binding of RNA polymerase and the initiation of transcription
transcription fctors
What would you use to separate mRNA molecules from other types of RNA?
use a string of T nucleotides
Bacteriophage
virus which infects bacteria cells; made of protein and DNA - phages make more of itself
insertions
when a nitrogenous base is inserted into the DNA sequence
nucleoid
where the DNA is "supercoiled" in a bacteria cell
what are the two ribosomal subunits?
○ Small subunit § Responsible for scanning the 5' end of the mRNA to find the START Codon ○ Large Subunit § Recruited only after the small subunit has located the START codon § Responsible for elongation of the new protein