Gene expression Flashcards
Cell specificity___________ is determined by gene expression
Phenotype
Nucleotides that made DNA
Adenine
Thymine
Cytosine
Guanine
Each nucleotide is made up of?
Base ( nitrogenous)
Sugar ( 5 carbons)
Phosphate group
Contains genetic information
DNA
Nucleotides that made RNA
Cytosine
Uracil
Guanine
Adenine
3 types of RNA
mRNA
tRNA
rRNA
Largest RNA
mRNA
Numerous RNA
rRNA
Smallest RNA
tRNA
Only portions of the DNA are transcribed
RNA
Proteins are made up of amino acids, and each amino acids has?
Amino group
Carboxylic acid group
Structure of DNA
Double stranded
Negatively charged
Long sequence
Structure of RNA
Single stranded
Short sequence
Location of DNA
Nucleus or nucleoid body
Location of RNA
Nucleus
Cytoplasm
Location of proteins
Ribosome
Golgi apparatus
Process of DNA
Replication
Process of RNA
Transcription
Translation
Expression of a gene is increased by a factor activator
Positive regulation
Expression of a gene is decreased by a factor repressor
Negative regulation
Increased gene expression dependent upon the continued presence of the inducing signal
Type A response
Either activator or repressor
Effector
Increased gene expression that is transient despite the continued presence of the inducing signal
Type B response
Increased gene expression that persist and is irreversible even after the termination of the signal
Type C response
Commonly observed in prokaryotes in response to sudden changes in the intracellular concentration of the nutrients
Type A response
Characterizes the action of many drugs.
Commonly occurs during the developmant of the organism
Type B response
Typically occurs during the development of differentiated function in tissue or organ
Type C response
No nucleus, no post transcriptional modifications
Prokaryotes
Maybe polcistronic or multiple genes
Prokaryotes
Model for study of gene expression in humans.
Control of trnscription
On and off switching is usually seen
Prokaryotic gene expression
Example of prokaryotic gene expression
Lac OPeron
Bacteriphage Lambda
No lactose or with lactose but with high glucose
Repressed state
With high lactose and no glucose
Activated state
Lac operon composed of
Promoter site Operator lac1 lacZ lacY lacA
In lac operon, what is the inducer?
Lactose
Cannot transcribe operator and dsital genes if there is low lactose and higher glucose
RNA polymerase
Produce repressor sub unit
lac1
Repressor sub unit is
Protein
Inactivate the repressors that lead to RNA polymerase to transcribed
Inducers
Break down glucose
Beta galactosidase protein
Allows the enter of lactose
Permease protein
Lac Operon found in the genes of the?
Intestinal E. coli
Negative regulator
Lac1,
Repressing by increased lactose or inducer
Positive regulator
CAP-cAMP
Activator of promoter region that leads to decrease of glucose
When the reppressor gene is on
Cro gene is off
Reppressor gene is both
Positive regulator ( activate itself) Negative regulator ( inhibits cro gene)
Cro promoter
Or1 and Or2
Responsible fr dormacy of virus
If the repressor protein concentration becomes too high, it will attach to OR3 and diminish transcription of repressor gene until repressor protein concentration drops
When Cro gene is activated
Lytic pathway is irreversible
Repressor promoter
Or3 and Or2
Give way to RNA polymerase to pass through
Ultraviolet inducer
Gene for cro
Detructive
More complicated than prokaryotic gene expression with several mechanisma for control
Eukaryotic gene expression
Eukaryotes have a
Nuclei
Histones
Chromosomes
RNA undergoes
Post transcriptional process
Eukaryotes transcription
Not simple on and off switch
B globin gene is in the active chromatin in
Reticulocyte
B globin gene is in the inactive chomatin in
Muscle cell
Decreases binding of histone to DNA allowing access to transcription factors
Acetylation
May cause gross changes in chromatin which inhibits transcription
Methylation of deoxycitiine residues
Distrupt nucleosomal structure
Binding of specific transcription factors
DNA sequences that different fom pomoters
Enhancers/silencers
Active only when it exist within the same DNA moleule asthe promoter
Enhancers
Locus control region
Enhncers
B globin gene is in the active chromatin in
Reticulocyte
B globin gene is in the inactive chomatin in
Muscle cell
Decreases binding of histone to DNA allowing access to transcription factors
Acetylation
May cause gross changes in chromatin which inhibits transcription
Methylation of deoxycitiine residues
Distrupt nucleosomal structure
Binding of specific transcription factors
DNA sequences that different fom pomoters
Enhancers/silencers
Active only when it exist within the same DNA moleule asthe promoter
Enhancers
Locus control region
Enhncers
Organism in Helix turn helix
E coli
Phage
Mammals
Organism in zinc finger
E coli Yeast Drosophila Xenopus Mammals
Organism in leucine zipper
Yeast
Mammals
Used in immunoglobulins
Alternative polyadenylation sites
Used to create 7 unique alpha-tropomyosin mRnas in seven different tissues
Alternative splicing and processing
mRNAs are stabilized or destabilize through interaction of ____________ in the cytoplasm
Proteins
During development or in response to drugs, hundred of rRNA and tRNA genes can be used to produce hundreds of copies
Amplification
Organized into loops that are anchored by a nuclear scaffold containing several proteins
Aka nuucleosome or nucleofilament
Polynucleosome
DNA + histones
Chromatin
5 classes of positively charged proteins ( h in arginine and lysine ) that form ionic bonds with negatively charged DNA
Histones
2 molecules
H2a, h2b, h3 h4
1 molecule attach to linker DNA
H1
Dna is further packed due to
Hydrophobic
Densely packed and transcriptionally inactive chromatin during interphase
Heterochromatin
Non densely packed transcriptionally active chromatin
Euchromatin
Organized into loops that are anchored by a nuclear scaffold containing several proteins
Aka nuucleosome or nucleofilament
Polynucleosome
DNA + histones
Chromatin
5 classes of positively charged proteins ( h in arginine and lysine ) that form ionic bonds with negatively charged DNA
Histones
2 molecules
H2a, h2b, h3 h4
1 molecule attach to linker DNA
H1
Dna is further packed due to
Hydrophobic
Densely packed and transcriptionally inactive chromatin during interphase
Heterochromatin
Non densely packed transcriptionally active chromatin
Euchromatin
Organized into loops that are anchored by a nuclear scaffold containing several proteins
Aka nuucleosome or nucleofilament
Polynucleosome
Involved in gene expression, DNA replication, DNA repair, gene activation and supression
Core histones
Beads on a string appearance
Core histones
Coding regions
Exons
Non coding intervening sequences
Introns
Mammalian genome
<25,000 protein
Unique and nonrepetitive sequences 50%
Eukaryotic organism
Repetitive sequences 30%
Centromeres and telomeres
1% of cellular DNA is in
Mitochondria
Stop codons
Uga encodes w aga and agg
Occured in gonads
Meiosis
Protein NH2 DNA replication
Met Gly Leu Ser Asp
DNA replication occurs during the ______ of cell cycle
S phase
Prokaryotic DNA synthesis beginsat an
Origin of replication
One in prokaryotes
Meltiple in eukaryotes
Strands separate locally forming two
Replicaion forks
Replication of double stranded DNA is
Bidirectional
Group of proteins that recognizethe origin of replication
Denaturation/ unwinding of A-T rich group
DNA and Protein step 1
Unwind the double helix ahead of the advancing replication fork
Step 2 helicase
Maintain the separation of the parental strands
Single stranded DNA binding proteins step 3
Removal of supercoils that interfere with the further unwinding of the double helix
DNA topoisomerases step 4
Prokaryotic DNA synthesis beginsat an
Origin of replication
One in prokaryotes
Meltiple in eukaryotes
Strands separate locally forming two
Replicaion forks
For lagging strands
Syhtesize short stretches of RNA called primers (10-200 base pairs long)
Needed by DNA polymerase to begin DNA chain elongation
Step 5 primase
Group of proteins that recognizethe origin of replication
Denaturation/ unwinding of A-T rich group
DNA and Protein step 1
Unwind the double helix ahead of the advancing replication fork
Step 2 helicase
Maintain the separation of the parental strands
Single stranded DNA binding proteins
Removal of supercoils that interfere with the further unwinding of the double helix
DNA topoisomerases
Catalyzes chain elongation in a 5-3 direction
Step 6 DNA polymerase III
DNA polymerase III uses____________ as substrates
5 deoxyribonucleotide triphosphates
Lagging strand
Okazaki fragments
Removes RNA primers using 5-3 exonuclease activity, then fills in the resulting gaps
DNA polymerase I step 7
Seals th nicks between okazaki fragments by catalayzng the final phospholipid ester linkage
Step8 ligase
Newly replicated DNA is assembled into nucleosomes
Reconstitution of chromatin structure
Highly repetitive DNA at the ends of linear chromosomes
Telomeres
Replace telomeres in cells taht do not age
Telomerase
Makes DNA copy of the RNA genome, then integrates this into host cells
Reverse transcriptase
Mismatched strand
Polymerase I and DNA ligase
Hereditary nonpoyposis colon cancer
Abnormal bases
Specific glyoslases
Apyrimidinic or apurinic site
Deoxyribose- phosphate lyase
DNA polymerase and DNA ligase
Damaged DNA
UV specific endonucleases
DNA polymerase I
Xeroderma pigmentosum
