Midterm 1 Flashcards
photograph 51
an x-ray crystallography exposure taken in 1952
why was photograph 51 so important
it was a key piece of data supporting the model that DNA was a helix
Who took photograph 51?
Dr. Rosalind Franklin but she didnt receive appropriate credt from Watson and Crick
famous quote from Watson and Crick
it has not escaped our notice that the specific base-pairing was have proposed immediately suggests a possible coping mechanism for the genetic material
what happens if we start with a souble stranded molecule and make a complement of each strand
we end up wth 2 double helical daughter molecules that are identical copies of their mother
Each DNA daughter strand contains …
one strand from mother and one newly synthesized strand
What happends to the mother DNA
she has been ripped in half and lives on only in her daughters
DNA replication is describes as what ( a specific word about the strand)
SEMICONSERVATIVE
what does the first cycle of semiconservative replication look like
two DNAs with each a new daughter strand and a new mother strand –> two combos old and new
what does the second cycle of semiconservative replication look like
two new DNAs with completely new dNA (daughter DNA) and two DNAs with combo DNA (mother and daughter half half )
How is the new DNA strand sythesized
new strand is synthesized one nucleotide at a time, and NTPs are used
why NTPS and not NMPs
NTPS are thermodynamically favorable
what is the direction of polyermization
5’ to 3’
nucleotides are added to which side of the strand
the 3’ OH of the growing strand
the 5’ end of the strand has what attached
a phosphate
what is the enzyme that synthesizes DNA
DNA polymerase
DNA polymerase needs what to start polymerization
a DNA or RNA primer is required
PCR benefits …
revolutionized medicine forensics, and experimental biology
what does PCR stand for
polymerase chain reaction
what is PCR
DNA replication in a test tube
what is interesting abt the number of copies in PCR
the number of molecules thats being replicated doubles each cycle/ chain reaction
what are some applications of PCR
- pre implantation genetic diagnosis as an appplication of PCR
- Forensics
- Screening blood products for diseases
- viral infections in wild monkeys by collecting feces
- test for presence of SARS-CoV-2 (virus that causes COVID-19)
what does PCR require
requires a sequence specific primers
special polymerase
IN PCR what is the primer made of
primer made of DNA not RNA
Three steps of PCR
- denaturation
- Annealing
- Extension
What is denaturation
All the DNA duplexes melt into single strands
what is the temp of denaturation
95 degrees celcius
what happens in annealing
the primers anneal (bind) to complementary sequence on the template strands
what is the temp of annealing
50 degrees celcius
what is extension
the polymerase does its thing
what is the temp of extension
72 degrees celcius
Why do we need PCR
because we need more DNA
because we want to measure the size of a piece of target DNA
Chain terminating bases are the key
to Dideoxy DNA sequencing
Dideocy nucleotide is what
a nucleotide without the Oh attached to the 3’ carbon
sequencing reactions utilize
florescent chain terminating nucleotires
In Cells what is used as the primer
RNA
in cells enzymes do what to the DNA duplex
they unwind the DNA duplex
replication origins
sites where DNA synthesis initiates in cells
eukaryotic chromosomes have what when it comes to replication origins
have multiple replication orgins
the human genome contains more than _______ origins , ________ base pairs apart from each other
10,000, 50,000`
DNA is generally replicated in which direction
BOTH directions at once
what are the SIMILARITIES between DNA replication in cells vs PCR/DIDeocy sequencing
in cells and PCR : need template primers, DNA polymerase and nucleotides
CONTRAST DNA replication in cells and in PCR
in cells: RNA primer is used, enzymes unwind the DNA duples, rpelication origins, replication forks, leading strand, lagging strand, multiple enzymes and other proteins are involves
in pcr: DNA primers are used, heat is used to unwind the DNA, no rep origins or forks, no leading strann/lagging strand, only one enzyme needed
The central dogma explains
how DNA genotype becomes a phenotype
central dogma
DNA –> RNA –> protein
proteins give us our …
phenotype
DNA controls our ….
phenotype by encoding proteins
what other than DNA can CONTROL our phenotype
non coding RNAs such as TRNAs, rRNA…
GENE EXPRESSION IS …
the conversion of a gene into its product( generally a protein bis an RNA intermediate)
when we say a gene is being expressed we mean…
its being transcribes and translated into protein
many genes are not….
expressed all the time
many genes are only expressed some of the time… in
response to external or interal conditions or signals
many genes are not…
expressed in ALL cells
each cell of a multicellular organism contains
the same DNA = same genes
different cells
express different genes
genes that are expressed virtually in all cells
housekeeping genes
cell-type specific genes
expressed genes in only certain cells ex neurons, muscle cells, blood cells
regulated gene expression
only a subset of genes are expressed in any given cell type
transcription refers to
the process of RNA being synthesized from a DNA template
where does translation take place in the central dogma
from DNA to RNA
RNA is synthesized by
RNA POLYMERASE USING DNA AS A TEMPLATE
RNA strands are synthesized in which direction
in the 5’ to 3’ direction just like DNA strands are
DNA is composed of
dNMPS
RNA is composed of
NMPs
DNA is synthesized from
dNTPS
RNA is synthesized from
NTPs
DNA is copied into
nto messenger RNA before it becomes protein
coding strand is the
nontemplate strand
The DNA coding and the mRNA transcript
have the same polarity and sequence substituting U in mRNA for T in DNA
RNA polymerase binds to the …
promoter sequences in DNA to initiate transcription
the promoter consists
of two short sequences
what are the two sequences in a promoter sequence
the -10 and -35 sequence
RNA polymerase binds to what sequence
the -35 and -10 sequence of the promoter
Are the sequence of -10 and -35 boxes the same in different genes
the boxed are different in each gene
How can we find a consensus sequence for each box
by aligning the promoter regions of multiple genes
the level of gene expression can be affected by
how similar the 10 and -35 sequences are to the consensus sequence
what can regulate gene expression in eukaryotes
enhancers and silencers
silencers and enhancers are found where
they can be found close to the promoter or far upstream or downstream
enhancer ans silencers have binding sites ….
for specialized proteins called transcription factors
the promoter determines
where transcription starts and the direction in which it proceeds
RNA polymerase do not require
a primer to initiate transcription
termination sequences determine
where an mRNA ends
each eukaryotic mRNA encodes a
SINGLE protein
each prokaryotic mRNA can be
polysictronic (codes for multiple proteins)
polycistronic
codes for multiple proteins
the primary transcript is processed
into mRNA in eukaryotes
what is added to the primary transcript to become mRNA
5’cap and polyA tail
mRNA splicing occurs where
at the the sites determined by consensus sequences & IN NUCLEUS
mRNA requires many
proteins
what happens to spliced out introns ..
degraded and the nucleotides are recycled
splicing patterns can…
very under different conditions
Alternative splicing of the same transcript
can give ride to different proteins
introns are usually much larges than
exons
alternative splicing can produce
forms of protein that have different functions
splicing links up exons from within
given gene, not exons from different genes
alternative splicing results in the inclusion of an exon OR exclusion of an exon BUT
but it doesnt change their order
alternative splicing does’nt result in
the duplication of an exon in the mature mRNA
Replication GOALs
to copy a cells genome so that the two copies can be partitioned to the two daughter cells during cell division/mitosis
transcription GOAL
to copy the instructuon that are present in genes into an intermediate messenger molecule , mRNA
TRANSLATION GOAL
to take the instruction s in mRNA and use them to build proteins
building blocks for replication
DNA nucleotides are the nuilding blocks of new DNA strands
TRANSCRIPTION BUILDING BLOCKS
RNA nucleotides are the building blocks of mRNAs
TRANSLATION BUILDING BLOCKS
amino acids are the building blocks of proteins
proteins are composed of
amino acids
what are the three parts of an amino acid
amino group Nh2
carboxyl group
a side chain/ R group
how many amino acids are there
20 amino acids
what makes each amino acid unique
the side chain/ r group
proteins=
amino acids linked in a chain by peptide bonds
a typical protein is how many amino acids long
450 amino acids long
although proteins are linear chains of AA’s…
they fold into complicated 3D structures
in proteins what are the amino acids linked by
peptide bonds
like the phophodiester bond formation, the peptide bind formation is
a dehydration synthesis reaction
the peptide bond ties the
carboxy terminus (carbon) and the amino (nitrogen)
the new amino acid is added to which terminus
the carboxyl terminus
how is protein sequence encoded inn DNA/RNA
the protein coding region of mRNA is made up of non-overlapping nucleotide triplets (codons) each of which corresponds to an amino acid
codon
nucleotide triplets
with some minor expections, all living organisms on earth
use this same genetic code
ATG/AUG =
signals the start of protein synthesis with M=Met= methionine
Methionine other than start codon can also be
used internally in proteins
how many stop codons are ther
3 stop codons
what are some key players in translation
ribosomes, tRNAs, aminoacyl tRNA synthetases
ribosomes
machine compoesed of 3-4 rRNAs and over 50 proteins
what are the two parts of ribosomes
large and small subunits
Ribosomes have channels that hold
the RNA and nascent polypeptide
what are the three key functions of the ribosome
- bind mRNA and identify the start codon for translation
- help bring about complenetary pairing between mRNA codons and tRNA anti-codons
- catalyze peptide bond formation between amino acids
transfer RNAs (tRNAs) pair codons with
with amino acids
aminoacyl tRNA synthetases are enzymes that
recognize both the anticodon and the cognate (correct amino acid) and then attach this amino acid to the tRNA
what is the cognate
the correct amino acid
what is a charged tRNA
a tRNA attached to an amino acid
translations 3 steps
initiation
elongation
termination
the initiation complex binds to
5’ cap on mRNA
the initiation complex scans along the
mRNA 5’ to 3’ until it finds an AUG
peptidyl - p site
holds the tRNA to which the growing polypeptide chain is attached
A site (acceptor)
binds tRNA carrying the next amino acid to be added
E (exit) site
empty tRNAs leave from here after their amino acid has been added
Elongation steps in translation
new tRNA enters the A site
peptide bond is formed between amino acids in the P and A site
Ribosomes moves down onw codon
tRNA in E site exits
next tRNA enters the A site; repeat
when the ribosome moves down one codon the tRNA in P site moves to
E site
when the ribosome moves down one codon the tRNA in A site moves to
P site
termination steps in translation
release factors are recruited when a stop codon occurs at the A site , eRF fills the A site, triggering the release of the polypeptide by hyddrolysis of GTO, ribosome dissociation and mRNA release
what is the portion of the mRNA after the stop codon
3’ UTR
there is no tRNA for a stop codon, instead
instead release factors bind
the anticodon is a apart of the
tRNA
in eukaryotes where are proteins translated
mRNA is processed in the nucleaus then exported to the cytoplasm where it is translated
where are proteins translated in prokaryotes
in prokaryotes, transcription and translation are coupled and occur in cytoplasm
what are polysomes
many ribosomes simultaneously on a single mRNA
researchers can isolate polysomes from cells and
figure out which mRNAs are being actively translated
RNA polymerase reads template DNA strand in which direction
3’ to 5’ direction
DNA polymerase reads a template DNA stran in which direction
3’ to 5’
DNA polymerase builds a new DNA strand in which direction
5’ to 3 direction
RNA polymerase builds new RNA strand in which direction
5’ to 3’
The ribosome reads the codons in mRNA in which direction
5’ to 3’
the ribosome builds a new protein in which direction
NH2 to COOH
what does the aa-tRNA synthetases do?
it pairs the amino acid with the tRNA to create a chareged tRNA
In DNA replication the genome is copied …
exactly once per cell
Ribosomes choose _____ ____ that have _______ to form complementrary base pairs to the codons in the mRNA
charged tRNAs, anticodons
many mRNA molecules are typically produced from each
actively transcribed gene
mRNA time per gene and hour in eurkayotes
2mRNAs/gene/hour
How many proteins are typically produced from each mRNA
MANY MANY
chromosomes are …
single very long DNA molecules
how many base pairs are on a chromosome
150 million base pairs
chromatin is
DNA + protein
humans have how many chromosomes and what types
46 total
22 pairs of autosomes
1 pair of sex chromosome
DIPLOID
karyotype
image of stained metaphase chromosomes
the two arms of the chromosomes are seperated by a
centromere
what is the p and q in a chromosome
p= short arm
q= long arm
in a pair of chromosme which comes from dad and mom
1 from dad and one from mom
ideogram
shows a chromosomes relative size and banding pattern
banding pattern=
the characteristic pattern of dark and light bands that appear when a chromosome is stained with a chemical solution then viewed under a microscope
describe E. coli
a bacterium
a prokaryote
2um Long
has compacted DNA in the nuceleod
the E coli genome is ———– than E coli
the e coli genome is 1000 x longer than e coli
Bacterial chromosmes are what shape
circular
Bacterial DNA is densely packed toform a region called
nucleoid
what are two features that allow bacterial DNA compaction
- proteins help organize the DNA into a series of tight loops
- the circular DNA undergoes supercoiling
The human genome is how many base pairs long
3 billion base pairs
human DNA is about ____ more tightly packed than in E coli
10 x
unwound DNA in a single cell would stretch to
6 feet
chromatin is the material of which —— are composed of
chromosomes
when is chromatin visible
only visible by light microscpy during mitosis when the NA is at its most compacted ( condensed)
what doesnt play a major role in compaction in eukaryotes
supercoiling
Each chromosome is half …
DNA and half protein
types and ratio of proteins in chromosomes
half histone and half non histone proteins
histones are …
small basic proteins that tightly bind DNA
what are the 5 major types of histones in eukaryotes
H1, H2A H2B, H3, and H4
lysine and arginine are important in what and why
20-30 % of the amino acids in histones are lysine and arginine which are positively charged amino acids
what charge does DNA have
negative charge
what is the nucelosome
146 bp of DNA wrapped around an octamer of histones
when do chromosomes condense
during mitosis and meiosis
euchromatin
areas of active expression, not tightly compacted
where are most euchromtin genes found
in the middle of the chromosme arms
heterochromatin
a few active genes, tightly compacted
what are the two typed of heterochromatin and what do they mean
facultative (mostly condensed )
constitutive (always condensed)
the centromere consists of several
types of repeated DNA sequences
centromeres are what type of chromatin
heterochromatin
telomeres are the
end of linear chromosomes
telomeres are what type of chromatin
heterochromatin
telomere replication requires what
a specialized polymerase called telomerase
without telomerase, every chromosome would get ….
SHORTEr
somatic cells
cells of the body
what type of cells are somatic cells
diploid
gametes
haploid cells used in reproduction
what type of cells are gametes
haploid cells
germ cells
gametes plus the germline stem cells that differentiate into gamestes
sex linked genes/loci
are genes that are on one of the sex chromosomes
where are autosomal genes/loci
on the other, non-sex chromosome (1-22)
heterozygous genotype means what phenotype
dominant phenotype
what is selfing in plants
plants have female parts (ovule) and male parts (pollen) thus they can fertilize themselves = selfing
what is a true Breed
when two Homozygous dominate mate together or when two Homozygous recessive mate together
Mendelian Genetics
the theory of knowedege that allows us to use approches such as Punnet squares to predict the genotypic and phenotypic outcome of crossed
what did mendel want to answer
How are the traits inherited?
How are the traits of parents transmitted to their offspring?
blend theory of inheritence
it viewed the traits in offspring as a mixture of the parental traits
what were the 5 experimental design of Medels experiments
- traits with clearly distinguisgable phenotypes
- controlled crosses between plants
- Pure breeding stains
- Quantification of results
- replicate, reciprocal and Test cross analysis
explain a little bit about controlled crosses between plant?
plants have female parts and male parts, this allows for both self–fertilization and cross fertilization
are pure breeding strains homozygous or heterozygous
homozygous
F1 is
called a hybrid
hybrid=
progeny of a cross between 2 pure-breeding strains
mono hybrid
a hybrid of only one gene
