Chp. 16, 17 & 20 : Gene Expression & Regulation Flashcards
When did Fred Griffith conduct his experiment?
1920s
What did Fred Griffth study?
Pneumococcus bacteria
What is the S- strain of Pneumococcus bacteria?
pathogenic due to the presence of polysaccharide capsule
What is the R-strain of Pneumococcus bacteria?
nonpathogenic lacks capsule
What was the general protocol/results of Fred Griffith’s experiment?
Injected live S bacteria= dead mouse
Injected live R bacteria= live mouse
Heat killed S bacteria= live mouse
Injected heat killed Sbacteria & live R bacteria= dead mouse
What was the conclusions of Fred Griffith’s experiment?
If the pathogen is dead then how did the mouse die?
Determined that a transforming principle led to the genetic material from S bacteria to transfer in to the live R bacteria
When did Avery, McCarthy and MacLeod’s experiment occur?
1940s
What was the purpose of Avery, McCarthy and MacLeod’s experiment?
Was trying to find what the transforming principle was
What was the general protocol for Avery, McCarthy, and MacLeod’s experiment?
isolate the effects of components in S bacteria
he used enzymes to block proteins, lipids, carbohydrates, DNA and RNA
What were the findings/ results of Avery, McCarty, and MacLeod’s experiment?
Found that when DNA was blocked, transformation of R to S did not occur, however with other macromolecules it did occur
this led to him believing that DNA is the transforming material→ disputed amongst many scientists.
When did the Hershey-Chase experiment occur?
1950
What was the purpose of the Hershey-Chase experiment?
confirm DNA is genetic material
What are bacterophages>
viruses that attack bacteria-
phages cause transformation is bacteria; must be injecting bacteria with genetic material
What was the general protocol of the Hershey-Chase experiment?
labeled phage with radioactive isotopes of P32 and S35
P32- DNA
S35- proteins
What were the findings/ conclusions of the Hershey-Chase experiment?
radioactivity found in bacteria infected with P32 labeled phage
Only DNA got inside bacteria
DNA is responsible for transformation of bacteria
DNA is genetic macterial
DNA not protein is the genetic material
When did Watson and Crick’s experiment/ discovery occur?
1953
When did Meselson and Stahl’s experiment occur?
in 1957
What was the purpose of Meselson and Stahl’s experiment?
determine the type of replication: dispersive replication, conservative replication, semi-conservative replication
What was the general protocol for Meselson and Stahl’s experiment?
used two nonradioactive isotopes of nitrogen and would ananlyze the arrangement of them after replications and hypothesize how each replication would look like with each type of replication
conclusions of Meselson and Stahl’s experiment
got a result of G3 that 75% of DNA is 14N14N and 25% of DNA is 15N14N
shows that this is semi-conservative replication
What is the Chargaff rule?
Equal percentage of A and T; C and G in a given species
What were the contributions of Rosalind Franklin and Maurice Wilkins?
Rosalind Franklin found DNA picture in Wilkins lab
What were the contributions for Watson and Crick?
formulate an accurate description of the structure of DNA- double helix
What is DNAs structure?
double stranded; contains nitrogenous bases and sugar phosphate backbone
strands run in antiparallel direction
5’🡪 3’ runs antiparallel to 3’🡪5’
What are the 4 nitrogenous bases of DNA?
Adenine, Guanine, Cytosine, and Thymine
What is the sugar phosphate backbone held together by?
held together by covalent phosphodiester bonds
What type of sugar does DNA have?
deoxyribose- one less oxygen than ribose
What are the pyrimidines and its structure?
Cytosine, Thymine and Uracil
single ring
What are the purines and the structure of it?
Adenine and Guanine; double ring
How many hydrogen bonds are between A-T
double hydrogen bonds
How many hydrogen bonds are there between G-C?
Triple Hydrogen Bonds
What is the 5” end?
where phosphate is attached to carbon 5
What is the 3” end?
where carboxyl group is attached to carbon 3
Where does DNA replication occur in eukaryotes?
in the nucleus
Define replication fork
the strands get separated as helicase moves down the fork grows bigger
Define DNA helicase
breaks hydrogen bonds between nitrogenous bases
Define single stranded binding protein
prevents the two strands that are separated from joining again
Define DNA polymerase
bonds new nucleotides with A, T, C and G
Define Topoisomerase
prevents super coiling of a DNA molecule; releases Tension
Define RNA primer
short stretch of nucleic acid complementary to the template- necessary for DNA polymerase to work
Define DNA Primase
creates RNA primer
Define DNA Ligase
binds Okazaki fragments tighter
Define leading strand
strand of DNA that is continuously synthesized
Define the lagging strand
synthesize strand in Okazaki fragments
Define Okazaki Fragments
fragments of synthesized DNA on lagging strand
In what direction are nucleotides added?
3’ end of existing strands (both leading and lagging), but the new forming strands elongate in a 5’—> 3’ direction
what is the central dogma of biology?
DNA🡪mRNA🡪 Protein
What is the exception to the central dogma of biology and define it?
Retroviruses: these are RNA viruses that convert RNA->DNA
Describe the sequence of integration of retroviral DNA into host cell and expression of viral proteins
Retroviral RNA🡪 DNA🡪 DNA replication🡪 DNA integration into host chromosome
use host cell machinery to transcribe and translate Retroviral DNA to
express retroviral genes and synthesize retroviral proteins
Where does transcription occur?
in the nucleus
What are the 3 steps of Transcription?
Initiation
Elongation
Termination
What occurs during initiation in transcription?
the template strand is used to code for the new strand; transcribed for DNA
What is the promoter region?
where RNA polymerase begins transcription & template strand is determined
What allows the promoter sequence to be recognized?
TATA box sequence
What is the enzyme that synthesizes mRNA?
RNA polymerase
In prokaryotes where does the RNA polymerase stop?
At the terminator sequence
What occurs during Elongation in Transcription>
nucleotides are added to 3’ end of growing RNA molecule; RNA polymerase elongates 5’———3’ and the DNA template strand is read 3’———5’
What occurs during termination during transcription?
stop signal; Terminator region
Where does translation take place in eukaryotes?
in the cytoplasm
What are 3 steps of translation?
initiation
elongation
termination
What occurs during initiation during translation?
rRNA interacts with mRNA at first codon
What occurs during Elongation in translation?
tRNA brings new amino acids and rRNA adds them
What occurs during termination during translation?
stops when STOP codon is reached
Where does mRNA processing occur in eukaryotes?
in the nucleus for eukayotes
What is the difference between replication in eukaryotes and prokaryotes?
eukaryotes have multiple origins of replication while prokaryotes have 1
What DNA is strand is used to code for the new strand?
the template strand
What are some other names for the template strand?
antisense, noncoding, and minus strand
What are some names for the no template strand?
sense, coding, plus strand
What are the steps for a Pre-mRNA to become a mature RNA?
Occurs after transcription
- Will go through eukaryotic mRNA processing
- RNA splicing
What occurs during the eukaryotic mRNA processing?
involves the addition of poly-A tail to 3’ end, and a guanine cap is added to 5’ end;
What occurs during RNA splicing?
introns removed; exons remain; role of spliceosomes
What are ribozymes?
RNA molecules that act as enzymes and splice their own introns (self- splicing
What did the discovery of ribozymes lead to?
a conclusion that not all enzymes are proteins
Define alternative splicing
produces a variety of mRNA transcripts, leading to a variety of polypeptide chains
What are SnRNPs?
splice out introns; recognize splice sequences to cut
What are SnRNPS made of?
small nuclear RNA, protein
What is a sliceosome?
a group of SnRNP
what are transcription factors?
bind to promoter and enhances affinitiy to start transcription occurs during initiation
What is a UTR?
untranslated region with the exons, but does translate to amino acids, poly-A tail after
what does AUG codon code for?
start sequence
what is the purpose of the modified guanine added as a 5’ cap?
has phosphate that help protect the beginning of mRNA & help attach to ribosome
What is teh purpose of the poly-A tail?
extends life of mRNA–> enzymes cuts off DNA in cytoplasm
Define origin of replication
the area in the gene where the DNA replication starts
Prokaryotes cell traits
circular chromosomes
smaller
has plasmids in cytosol
Eukaryotes cell traits
multiple linear chromosomes
bigger
contains plasmids in nucleus
define plasmids
small, extra-chromosomes, double stranded, circular DNA molecule
Define replication bubble
where the two strands of DNA open up
Describe the steps of DNA replication
- Helicase separates the DNA, so the DNA opens up into two
2.RNA primer is placed which is made by DNA primase
3.One strand (runs from 5’ to 3’) is continuously synthesized through DNA polymerase. The other strand runs from 3’ to 5’ and it is not continuously synthesized because it runs in a different direction. It is synthesized by DNA polymerase in Okazaki fragments.
4.DNA Ligase connects the Okazaki fragments
what does upstream of the DNA mean?
above the promoter sequence
What can happen to amino acid chain after translation?
Binding of 2 or more polypeptide chains
Cleave the chain
Name some post translation additions
Glycosylation, Phosphorylation, Ubiquitylation, Methylation and Acetylation
Define glycosylation
adding sugar resides to proteins→ glycoproteins; cell surface receptors
Define phosphorylation
activating proteins in signal transduction pathways
Define ubiquitylation
death tag- protein should be degraded- sent to proteasome- proteins get broken down
define methylation
shut down gene expression- silences the gene
Define Acetylation
enhances gene expression
Why is a codon made up of 3 bases?
smallest unit of uniform length that can code for all amino acids–> there can be 64 possible code forms
define mRNA codon
three nucleotides that instructs what amino acid to get
define tRNA anticodon
complementary base nucleotides to mRNA codon; attached to mRNA codon
How is there redundancy in genetic code?
an amino acid can be coded for by more than one codon
How do you read a codon chart>
Remember to look at codons (not anticodons) when determining the sequence of amino acids
How many codons are there and amino acids?
64 codons (including 1 start= Methionine; 3 stop=no amino acids) but only 20 amino acids).
What are ribosomes made out of?
small subunits made of rRNA and proteins
How do ribosomes interact with mRNA?
mRNA is between the large unit and small unit
What are EPA sites?
three sites for tRNA binding, designated the P (peptidyl), A (aminoacyl), and E (exit) sites.
Difference between prokaryotic ribosome subunits and eukaryotes?
smaller than eukaryotes
How do bases bond in tRNA?
hydrogen bonds
How do tRNA and amino acids bond?
through covalent bonds
What is a wobble codon
allows the anticodon of a single form of tRNA to pair with more than one triplet of the codon, 3rd nucleotide in the codon making it looser
Define point mutation
1 2, or 3 base affected
What are the two results of a point mutation?
substitution and frame shift mutations
define substitution & what can it lead to
substitute a base
missense, nonsense, and silent mutations
Missense mutations
substitution changes amino acids
define nonsense mutations
substitution leads to STOP codon
define silent mutation
substituting base doesn’t do anything
define frame shift mutations
changes everything downstream, making more problematic - addition or deletion of a base pair which can result in missense or nonsense mutations
-more likely to cause problems in resulting protein than base substitutions
define multiple base pair mutations
substitution, insertion, or deletion of more than one base pair.
What are the 4 types of chromosome mutations?
translocations, duplication, inversions and deletions
define translocations
: breaking off a piece and adding to non-homologous
define duplication
copies of specific DNA segments are made on the chromosome
define inversions
order of genes are inverted
define deletions
removal of 1 or more bases from the chromsome
what is the mutation is base excision repair?
fixes mutations with chemical changes resulting in messed up bases
Deamination: removal of nitrogen atoms
Methylation
Alkylation
Define glycosylase
makes a snip between sugar- base excision repair
Define endonucleases
makes a snip in the phosphate backbone
define DNA polymerase role in base exicion repair
acts as an endonuclease
What are the mutation in nucleotide excision repair
Thymine Dimers- UV damage
Bulky Lesions- affects shape
What are the are the cutting enzymes in nucleotide excision repair
UVr repair enzymes
what is the mutation in mismatch repair
Wrong letter was inserted
what are the cutting enzymes in mismatch repair
exonucleases
What is the nucleotide insertion enzyme for all repair mechanisms
DNA polymerase
What is the DNA sealing enzyme for all repair mechanisms>
DNA ligase
Define transformation
uptake of naked DNA- DNA not protected by proteins or other molecules, comes from external sources
define transduction
transmission of foreign DNA into a cell when a viral genome integrates with a host genome
Define conjugation
cell to cell transfer fo DNA
allows small segments of DNA to move from one cell to another
connects cells and allows transfer
define transposition
movement of DNA segments within and between DNA molecules
lytic cycle
- bacteriophage injects its DNA into the bacteria
- bacteria- host DNA falls apart by the viral DNA
- Viral proteins produce more viruses which breaks open the bacterial cell
lysogenic cycle
- virus injects DNA into bacteria cell
2, viral DNA integrates itself into the host DNA - Cell will start to divide and will have the small piece of viral DNA
- phage induction: puce of viral DNA pops out and will have to do the lytic cycle
define generalized transduction
a segment of DNA is transferred b/w bacterial cells by a bacteriophage
generalized transduction steps
- phage injects DNA. phage enzyme breaks down the host DNA into smaller fragments
- phage DNA is replicated and proteins are produced
- phage heads may surround bacterial DNA instead of phage DNA
when the DNA is integrated- integrated into host cells’ DNA, transferring genes now multiplies and carries new genetic material
define homologous recombination
A+ and A-
occurs during transduction
define specialized transduction
transfer of specific genes between bacterial cells through a phage
specialized transduction steps
- injects phage DNA & integrates onto a specific site of the host chromosome
- sometimes bacterial DNA is attached to phage and phage DNA is left behind - can still affect other cells
define transposons
moving sections fo DNA that can move within and between genomes
define conjugation pilus
binds other bacteria
define competer
bacteria able to bind to large amounts of DNA- increased cell wall and cell permeability
