Exam 1 Molecular Flashcards
Biology’s unifying principles
All organisms use genetic systems that have a number of features in common
Central Dogma
DNA->transcription->RNA->translation->amino acids-> protein
Molecular genetics focuses on
the level of the gene
Divisions of genetics
Molecular genetics, transmission genetics, and population genetics
Transmission genetics focuses on
heredity and how traits are passed from one generation to the next
Population genetics focuses on
the collection of genes within populations
Genome
complete set of genetic instructions for any organism
all genomes are composed of
nucleic acid, DNA or RNA
What makes a good genetic model
short generation time
large but manageable number of progeny
adaptability to laboratory environment
ability to be housed and propagated inexpensively
Two basic cell types
prokaryotic
eukaryotic
Prokaryotic cells
lack nuclear membrane, generally lack organelles
eukaryotic cells
posses nucleus and organelles
Fundamental unit of heredity
gene
Alleles
multiple forms of a gene
what determines the phenotype
genetics+environment
Genetic information is carried in
nucleic acids
Genes are located on
chromosomes
Chromosomes separate through the processes of
mitosis and meiosis
Mutations
permanent changes in genetic information that can be passed from cell to cell or from parent to offspring
Traits are affected by
multiple factors
Evolution is
genetic change
What is needed for inheritance
information storage
information copying (replication)
Information retrieval (translation)
Ability to vary
DNA was identified
before 1900 but it wasn’t until 1940s-1950s that we knew that DNA and not protein was the genetic material
DNA is a molecule composed of
repeating subunits (nucleic acids)
Three parts of DNA/RNA
Pentose sugar
Base
Phosphate
Pentose sugar is used as
an anchor
-DNA uses deoxyribose
-RNA uses ribose
Nitrogenous Bases
Purines-Adenine and Guanine
Pyrimidines- Cytosine, Thymine, Uracil
Purines
Adenine and Guanine
Pyrimidines
Cytosine
Thymine- only in DNA
Uracil- only in RNA
Nucleosides
base linked to sugar by 1’ carbon of pentose sugar
Nucleotides
phosphate group attached to the 5’ carbon
Phosphodiester bonds
covalent bonds between a phosphate group of one nucleotide and the 3’ carbon of the next nucleotide’s sugar (5’ to 3’ linkage)
The two ends of the polynucleotide chain are
not the same
the 5’ end has a phosphate group attached to the 5’ carbon of the pentose sugar
the 3’ end has a hydroxyl group attached to the sugar’s 3’ carbon
A polynucleotide chain has
polarity
Base pairings
A-T
C-G
A-U RNA only
A-T bonding
two H bonds
C-G bonding
Three H bonds
Which nucleotide bonding is the strongest?
C-G bonding
Watson and Crick investigated the structure of DNA by
using all available information about the chemistry of DNA not by collecting new data
DNA is what type of structure
double helix
DNA strands are
antiparallel
What types of bonds are between the complimentary base pairs
hydrogen
The strands are arranged helically meaning
10 base pairs between each turn of the helix
If 10 bp per turn= 3.4 nm what is the distance between each pair
0.34 nm
If a single chromosome is 2.058 bp how long is it in meters
200 million bases
Genetic material must contain
all of the information for the cell structure and function of an organism- storage
1C Value
a single set of genes (or the number of unique DNA bases)
what we contribute to our offspring
Diploid
two copies of every base pair/gene
2C
Haploid
sperm and egg cells have only 1 copy
1C
What does N stand for
the number of chromosome molecules in a cell
DNA is _____ for compaction
supercoiled
Supercoiling relies on
topoisomerases
topoisomerases
enzymes that break the double helix
- rotate the ends then rejoin
Eukaryotic chromosomes have additional levels of compaction-
multiple linear chromosomes
also supercoiled
proteins including histones compact further
Chromatin
DNA with a protein scaffold
Histones
a group of basic proteins found in chromatin
Histones have
a net positive charge thus bind to negatively charged DNA
Histone sequences across species
is very similar
linker between nucleosomes
H1
Histones have two copies of _____ thus an octamer
H2B, H4, H3, and H2A
The fundamental repeating unit of chromatin
nucleosome
what is the structure of chromatin
beads on a string
Karyotype
a chart of chromosomes
how many chromosomes do humans have
23 pairs
Diploid eukaryotic cells have
two sets of chromosomes
Types of chromatin
euchromatin
Heterochromatin
Euchromatin
stains slightly, uncoiled except during cell division
holds active genes
Heterochromatin
stains darkly, more condensed
genetically inactive
found near centromeres, telomeres, and species-specific locations
Types of heterochromatin
Constitutive
facultative
Constitutive heterochromatin
involved in maintaining chromosome structure
includes centromeres and telomeres
Facultative heterochromatin
has the potential to become condensed, e.g. X chromosome inactivation
Centromeres
used by the cell during cell division to make sure that each daughter cell gets a copy of each chromosome
sites at which chromosomes attach to the mitotic and meiotic spindle
Where do kinetochores form and spindle microtubules attach
centromeres
Centromeres are responsible for
accurate segregation of the replicated chromosomes during meiosis and mitosis
Telomeres are located
at the ends of the chromosomes
Telomeres
short tandemly repeated sequences and other repeated sequences further in from the ends
What is the job of telomeres
adds new copies of the repeat so the chromosome isn’t destroyed by the loss of material after each round of synthesis
Circular genome
a form of closed -loop DNA that has no end
uniparental inherited
offspring inherit genotype from only one parent
Replicative segregation can lead to
both heteroplasmic and homoplasmic cells
Semiconservative
one strand of double helix is conserved, the other is new
Dispersive
each strand is a mix of old and new DNA
Conservative
one double helix is unchanged by the process, the other is completely new
Three proposed models of DNA replication
Conservative
dispersive
semi-conservative
DNA structure was discovered in
1953
Why do we use heavy nitrogen (N) in the experiment that demonstrated that replication is semi-conservative
?
Raw materials of DNA synthesis
template
enzyme
substrates (raw materials)
Mg2+ ions
What is the role of DNA polymerase in DNA synthesis
catalyzes the formation of phosphodiester bonds
DNA polymerase joins the ______ group of the last base in the DNA chain to the incoming ______ of a dNTP
3’-OH
5’ Phosphate
Synthesis is
5’ to 3’
How is it decided which dNTP to use
selected by the DNA polymerase 1 using the opposing base on the template strand
When new DNA is synthesized from deoxyribonucleoside triphosphates (dNTPs) the newly synthesized strand is
complementary and antiparallel to the template strand
5 key elements of each replication fork
- helicase to unwind the DNA
- SSBP to protect ssDNA
- Gyrase to remove stain ahead of fork
- Primase to synthesize RNA primer
- DNA polymerase
Okazaki fragments
?
lagging strand
?
leading strand
?
Describe the process that happens at the DNA fork during DNA replication
?
key factors of DNA replication in Eukaryotes
occurs in the nucleus during S phase of the cell cycle
is initiated by RNA primers
occurs in the 5’ to 3’ direction
semiconservative
initiated at the same time at many points (origins of replication) along the chromosome
Packaging of newly replicated DNA
histones must first disassemble to allow DNA synthesis
synthesis of new histones is coordinated with DNA synthesis
Then must reassemble on two new chromosomes
Main polymerases have a _____ activity
Why?
3’ to 5’
?
Once DNA replication is complete, how do we package one copy of the DNA into one daughter cell and the other into another daughter cell
Mitosis
5 phases of a cell life-cycle
G1
G0
S
G2
Mitosis
What happens in the G1 stage
chromosome morphology changes from condensed to dispersed due to a change in the coiling fibers
the cell also prepares for S by producing RNA and protein
Contains the checkpoint
Once a cell reaches the checkpoint in G1 can it go back?
no it must enter the S phase
What happens in G0
quiescent phase of neither growing nor progressing to S
Mature muscle cells and neurons go into this phase
What happens in the S phase
DNA untwists and replicates
What happens in the G2 phase
DNA condenses- generally a short phase
Mitosis is
the formation of two cells from one cell
Mitosis has how many phases
5
result of mitosis
2 daughter cells, each with a complete copy of the genome
Phases of mitosis
Interphase
Prophase
Metaphase
Anaphase
Telophase
What happens in interphase
the cell grows, replicates its chromosomes, and prepares for cell division
What happens in Prophase
Chromosomes condense
Two sister chromatids become detectable
Mitotic spindle assembles outside the nucleus and the envelope begins to break down
At what stage in a cell’s lifecycle is the DNA replicated
S phase
what happens during metaphase
chromosomes line up on the metaphase plate
centrosomes at opposite poles
microtubules from centrosomes to kinetochore
most condensed phase
the number of chromosomes per cell equals the number of
functional centromeres
What happens during anaphase
sister chromatids separate
chromosomes move towards opposite poles
The number of DNA molecules per cell equals the
number of chromosomes when the chromosomes are unreplicated and twice the number of chromosomes when sister chromatids are present
Product of meiosis
four daughter cells; each has half the genetic material of the parent cell (reduction)
Number of chromosomes in a diploid cell
2N
Number of chromosomes in a haploid cell
N
Parts of Meiosis
Meiosis I
- prophase I, Metaphase I, anaphase I, Telophase 1, cell division
Meiosis II
- prophase II, Metaphase II, anaphase II, telophase II, cell division
Meiosis includes how many cell divisions
two
the original cell is diploid with four chromosomes, after two meiotic division, each resulting cell is
haploid (1n) with two chromosomes
Why are brothers and sisters so different if they have the same parents
we don’t get a complete copy of our mom’s mom’s chromosome or our mom’s dad’s chromosome
chromosomes cross-over during prophase I
Chromosome crossover
when chromosomes line up they can switch parts
Independent assortment
the random distribution of chromosomes in meiosis that produces genetic variation
when the cell starts meiosis II it already has
two daughter cells, each one with a replicated copy of each chromosome
In order for the cell to move past Metaphase II
fertilization has to take place
Regulatory promoter is located
upstream of core promoter
regulatory promoter
the binding site for transcription apparatus- RNA polymerase and it’s cofactors
Transcription factors
bind at the regulatory promoter and affect the rate of transcription
Enhancers
distal location that can enhance transcription
Initiation
if the promoter (core and regulatory) and enhancers ‘say so’ a protein- coding gene is transcribed
Elongation
keep adding nucleotides
Termination
for RNA polymerase II there is no specific termination sequence
transcription can continue for 100s-1000s bp
What is a gene
the fundamental unit of heredity
Big picture of RNA processing
Start at a DNA template
RNA message- complimentary and antiparallel
Protein product
With colinearity
the number of nucleotides in the gene is proportional to the number of amino acids in the protein
Introns are found in
most eukaryote organisms
Introns
a non-coding region of DNA that doesn’t code for a protein in between two regions that do
Exon
region of DNA that codes for a protein
In eukaryotes, intron size and number is related to
organism complexity
Some introns have
regulatory roles
introns tend to be _____ than exons
longer
in order to have collinearity,
introns are spliced out by snRNPs in a spliceosome
snRNPs
small nuclear nuclear ribonucleoproteins
All sequences in DNA are transcribed into
a single RNA molecule
mRNA
messenger RNA
role of mRNA
carries the instructions to make a protein
three primary regions of mature mRNA are the
5’ untranslated region
protein-coding region
3’ untranslated region
5’ untranslated region
does not code for protein, ribosomes bind to 5’ end of transcript
3’ untranslated region
not translated
affects stability of mRNA
RNA transcribed in the
nucleus to produce primary transcript
post-transcriptional modifications that can be made
addition of 5’ CAP
addition of Poly-A-Tail
introns spliced out
5’ CAP
addition of extra guanine to 5’ end of primary transcript
addition of methyl groups to G and sometimes other bases
5’CAP occurs
rapidly after transcription initiation
Function of 5’ CAP
functions in initiation of translation
increases stability of transcript and influences splicing of introns
Poly-A-Tail
plays a role in transfer of mRNA into cytoplasm
functions to alter the half-life of transcript
RNA pol II does not have a
transcription sequence it keeps going
primary transcript is
cleaved based on consensus sequence (AAUAA) in 3’ UTR, Polyadenylation signal
polyadenylation signal
the consensus sequence in 3’ UTR that tells when to cleave the primary transcript
Splicing
removes the introns so the DNA and Proteins can be colinear
5’ splice donor site
GU (GT in DNA)
3’ splice donor site
AG
Splicesome
large, complex structure almost 300 proteins plus snRPS
removes introns from pre-RNA to generate mature RNA
Process of splicing
- the mRNA is cut at the 5’ splice site
- the 5’ end of the intron attached to the branch point
- a cut is made at the 3’ splice site
- the intron is released as a lariat
- and the two exons are spliced together
- the bond holding the lariat is broken, and the linear intron is degraded
- the spliced mRNA is exported to the cytoplasm and translated
Process of alternative splicing/ cleavage in thyroid cells versus brain cells
- in thyroid cells, cleavage and polyadenylation take place at the end of exon 4
- producing an mRNA that contains exons 1,2,3,4
- translation produces the hormone calcitonin
Brain cells - in brain cells, 3’ cleavage takes place at the end of exon 6
- during the splicing, exon 4 is eliminated with the five introns
- producing an mRNA that contains exons 1,2,3,4,5,6
- translation yields calcitonin-gene-related peptide
where is the enhancer compared to an intron promotor
typically upstream
why is there extra nucleotides on the end of a gene
room for error
What are proteins
Functional molecules of the cell
Enzymes
proteins that act as biological catalyst
Structural proteins
membranes, filaments
transporter proteins
allow things to move
Regulatory proteins
transcription factors that bind to DNA
Like DNA and RNA, protein
has a linear sequence and an alphabet
repeats similar but not identical units
have directionality
Units that make up a protein
20 amino acids
Amino end of an amino acid
has a free amino group (NH3)
Carboxyl group of an amino acid
has a free carboxyl group (COO-)
R group
differs in each amino acid
Protein structures
Primary
secondary
tertiary
quaternary
primary protein structure
sequence of AA
secondary protein structure
interactions between AA (beta sheets, alpha helix)
tertiary protein structure
structures after folding
overall 3-D structure
quaternary
more than one polypeptide
Domains
groups of AA that form a discrete functional unit
Codon
three bases
degenerate
redundancy
more than one codon for each AA
First AA being translated
Met start codon
can occur internally as well
Wobble
typically the 3rd base of the codon can vary
synonymous
change in DNA sequence does not change AA
non-synonymous
change in DNA sequences changes AA
Nonsense
change in DNA introduces a stop codon
AUG
start codon
methionine
three stop codons
UAG
UAA
UGA
reading frame
a way of dividing the sequence of nucleotides in a nucleic acid molecule into a set of consecutive, non overlapping triplets
Each codon specifies the same AA in
almost all organisms, nearly universal
The genetic code provides the
logic
machinery that makes proteins
ribosomes
Four phases of protein synthesis
- tRNA charging- binding tRNA to AA
- Initiation- start of translation
- elongation- synthesis of polypeptide chain
- termination- ending synthesis
aminoacyl-tRNA synthetase
enzyme that attaches an amino avid to a tRNA
Each aminoacyl-tRNA is
specific for a particular amino acid
what forms the initiation complex recognizing the 5’ CAP
ribosome small subunit
initiation factors
initiator RNA
When is the initiation complex added
just after transcription
What does the initiation complex do
scans the mRNA until it finds the start codon
translation stops when it encounters a __. Why?
stop codon
no incoming tRNA to match it to AA
three sites that a ribosome can occupy
Aminoacyl A site- where charged tRNA enter ribosome
Peptidyl (P) site- where peptide bond is formed
Exit (E) site
only codon to start in the P site
initiation codon met-tRNA
