Lectures 13-15 Flashcards
What are the 3 components of Nucleotides?
- Fine-carbon sugar
- Nitriginous Base - 5th carbon is outside of ring
- Phosphate
Base + Sugar =
nucleoside (adenosine)
Two types of sugar (5C)
Ribose and deoxyribose
Base + Sugar + phosphate =
nucleotide, adenosine triphosphate (ATP)
Purine
Has two rings (Adenine (A), and Guanine (G))
Pyramine
Only one ring (Uracil (U), Cytosine (C), and Thymine (T))
What base pairs make up DNA?
AGCT
What base-pairs makeup RNA?
AGCU
How many bonds in A with T?
2 hydrogen bonds
How many bonds in G with C?
3 hydrogen bonds
How long is a helical turn?
3.4nm long with 10bp
How long is a DNA strand (chromosome)?
about 2in
What is a karyotype?
An individuals complete set of chromosomes
Mendel’s Law of Segregation
the two alleles for each trait separate during gamete formation
Mendel’s Law of Independent Assortment
alleles for different traits assort independently
Assumptions of Mendel’s Model of Inheritance
-each trait is controlled by a single gene
-each gene has only 2 alleles
-there is a clear dominant-recessive relationship between the alleles
Polygenic Inheritance
occurs when multiple genes are involved in controlling the phenotype of a trait
these traits show continuous variation and are referred to as quantitative traits
ex; human height
Incomplete Dominance
The dominant allele is not fully dominant
a cross between two heterozygous parents results in __1:2:1____ ratio (instead
of 3:1)
Codominance:
each allele of the gene expressed and determines the phenotypes
1. human blood types is determined by the __sugar__ molecules on the surface
of red blood cells
Multiple Alleles
may be more than 2 alleles for a gene in a population
Human ABO bloodtype
Environmental Influence
temperature-sensitive allele of genes
What enzyme in Himalayan rabbits and siamese cats allows pigment production at a temp below 33 degrees?
Tyrosinase
Deamination causes what mutations?
Point mutations
Depurination causes what mutations?
deletion
What makes a T-T dimer?
covalent bond between two Thyamines
What happens when UV is too high?
accidental double-strand break. Repair leads to deletion
What is base paring in DNA replication?
- Both strands are used as templates
- semiconservative
What is replication origins?
The positions at which double-stranded DNA is open for replication
About how many base pairs are replication origins?
about 100
What kind of proteins do sequences attract?
initiator proteins
What kinds of base pairs are replication origins made of?
A-T rich stretches of DNA
How many replication origins are in Eukaryotes?
around 10,000
How many replication forks are formed at each replication origin?
Two
In what direction can replication forks move?
In both directions
At what rate do replication forks move in humans and bacteria?
Bacteria: 1000bp/sec
Humans: 100bp/sec
Do leading strands grow continuously or discontinuously?
continuously
Do lagging strands grow continuously or discontinuously?
discontinuously - Okazaki fragments
What does helicase do?
unzips the double helix ahead
What do double-strand DNA binding proteins do?
prevent DNA from re-forming base pairs
What does DNA primase do?
makes primers (about 10 base pairs long) for DNA replication
What does DNA polymerase III do?
adds nucleotides to the __3’__ end of a growing DNA
DNA synthesis goes uni-directionally, i.e. __5’3’___
What does DNA polymerase I do?
replaces the RNA primers with DNA
What does DNA ligase do?
joins the Okazaki fragments
What are the ends of chromosomes called?
Telomeres
What repetitive 6-bp DNA sequences are at Telomeres?
TTAGGG
How long are telomeres?
around 10-15 kb long (become shorter after each DNA replication
What makes up the telomerase complex?
reverse transcriptase and telomere RNA
What fixes replication mistakes?
_3’5’ exonuclease ____activity of DNA polymerase III
What can unrepaired mutations do?
cause diseases such as sickle cell anemia
What is the function of restriction enzymes or restriction endonucleases?
found in bacteria and archaea that provides a defense mechanism against invading viruses
Where does restriction enzyme cut double-stranded DNA?
Specific recognition sequences known as restriction sites
What is the palindromic sequence for EcoRI?
GAATTC
What does a zig-zag cut generate?
overhang (protruding) ends -by most res
What does DNA ligase do?
joins DNA fragments in the presence of ATP
What is a plasmid?
A plasmid is an extra chromosomal DNA molecule which is capable of replicating
independently from the chromosomal DNA.
What is an Ori?
A replication origin on a plasmid
What are multiple restriction sites in a gene called?
LacZ
What are artificial chromosomes made for?
larger insert and large-scale analysis of genome
4 steps of DNA cloning
- DNA cleavage
- Ligation of the gene into the vector
- Transformation
- Screening
What are the gene fragment and vectors digested by?
Restriction enzyme
Ligation of the gene into the vector is done by:
DNA ligase in the presence of ATP. Now the recombinant plasmid is made
What is transformation?
introducing the recombinant plasmid into bacteria
What is an antibiotic used in screening?
Ampicillin - clones that contain the plasmid will grow in the medium with amplicillin
What is the substrate for LacZ called?
X-gal - clones that have the gene fragment inserted in the LacZ gene will turn White
What does 94C do in the thermocycler program?
denature the DNA template
What does 55C do in the thermocycler program?
primers to anneal to the template
What does 70C do in the thermocycler program?
for DNA synthesis (primer extension)
What is the central dogma of gene expression?
Transcription and translation
What is the chemical structure of RNA?
- ribose instead of deoxyribose
- U instead of T; U pairs with A
What is the base pairing rule of RNA?
- Read and derive the complimentary sequences
- only one strand of the DNA is used
What is the name of the template strand?
antisense strand
What is the name of the coding strand?
sense strand
What is the function of mRNAs?
code for proteins made by rRNAs
What is the function of rRNAs?
form part of the structure of the ribosome
What is the function of tRNAs?
carry amino acids for protein synthesis
What is the promoter of transcription?
-35 and -10 sequences
What is the terminator of transcription?
stretch of GC that forms into a __hair-pin__ structure
RNA poly I is for:
rRNAs
RNA poly II is for:
mRNAs and small nuclear RNAs
RNA poly III is for:
tRNAs and small RNAs
What does the TFIID complex do?
first complex to bind to DNA - TBP: TATA Box binding protein (binds to the promoter)
What dies TFIIH do?
phosphorylates RNA polymerase II and initiates transcription
What does monocistronic mean?
one mRNA for one peptide
RNA modifications
- 5 prime cap (7-methylguanosine, 5’-5’ triphosphate bridge)
- 3 prime adenylations (poly-A tail) (150-250 As)
- Splicing
What does spliceosome contain?
small nuclear RNAs and proteins
What is the intermediate structure in RNA splicing?
lariat
What is alternative splicing?
combinations of different exons from the same primary
RNA to generate a tissue-specific versions of proteins
Redundancy
most amino acids are encoded by multiple codons
What is the start codon?
AUG
What are the stop codons?
UAA, UAG, UGA
Tetracycline
blocks binding of aminoacyl-tRNA to A site.
Cycloheximide
blocks translocation of ribosome
Exocytosis
ER->Golgi-> transport vesicle-> cell surface
Use COP-coated & clathrin-coated vesicles
Lysosome Pathway
ER->Golgi->endosome-> lysosome
Use COP-coated & clathrin-coated vesicles
Endocytosis
cell surface->endosome->lysosome
Use clathrin-coated vesicles
ER signal sequence
eight or more hydrophobic amino acids
ER signal sequence aided by:
- Signal recognition particle (SRP)
- SRP receptor embedded in membrane
Clathrin Coated Vesicles
- Cargo molecules bind to cargo receptors at the transport signals
- __adaptins___ select cargo molecules for transport by trapping
the cargo receptors. - clathrin-coated pit
- __dynamins_ assemble as a ring around the neck of each coated pit.
- dynamin ring constricts & pinches off the vesicle.
- vesicles shed the coat
Phagocytosis
phagosome to engulf an entire cell, e.g. bacteria or dead cell
Autography
form autophagosomes to engulf organelles
anticodon
3-nucleotide sequence on tRNA complementary to codon in mRNA
Where are amino acids attached to on the tRNA?
the OH end of the 3 prime
corresponds to anticodon
aminoacyl-tRNA synthetase
enzymes attach specific amino acid to
corresponding tRNA
Transformation
DNA uptake by bacteria
Transfection
DNA uptake by animal (Eukaryotic) cells
Transduction
injection of DNA into host cells by virus
Conjugation
DNA transfer between two cells via direct contact
What enzyme does LacZ encode?
B-galactosidase
3 components of a plasmid
- the origin of replication
- selectable marker (easily identifiable)
- Multiple Cloning Sites (LacZ)
Materials required for PCR
template, L&R primers, dNTPs, Mg, Taq DNA polymerase
Deamination leads to
point mutation
Depurination leads to
deletion
Exceptions of Mendel Law
- Polygenic Inheritance
- Incomplete Dominace
- Codominance
- Multiple Alleles
- Environmental Influence
- Traits determined by sex genes
Peptidyl transferase
builds peptide bonds during RNA translation
Aminoacyl-tRNA synthesis
the enzyme has a binding site for amino acid and tRNA
-linkage of amino acid to tRNA through hydrolysis (releases 2 phosphates)
