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Prokaryotic DNA shape:
Circular, double stranded, supercoiled
where is DNA found in a prokaryotic cell?
in the nucleoid
Folding of DNA is facilitated by what proteins in a prokaryotic cell?
nucleoid-associated proteins (bind to and fold DNA)
Folding of DNA is facilitated by what proteins in a eukaryotic cell?
histone proteins (bind to and fold DNA)
Eukaryotic DNA shape:
Linear, double stranded, supercoiled
Where is DNA found in eukaryotic cells?
in the nucleus
All the cells in a eukaryotic organism (except __________) have the same DNA.
gametes
What makes cells and tissues different from eachother?
which sets of genes are expressed
What does the genes that are expressed determine?
types of proteins and functional RNAs produced, and phenotype and function of cell
What is the reason that fertilized eggs become complex multi-cellular organisms?
Gene expression
_______ _________ is the process of controlling which genes in a cell's DNA are expressed.
gene regulation
What is the default state for most genes?
"OFF"
Muscle cells differ from nerve cells mainly because they:
express different genes
What are the main 3 steps that gene regulation occurs at?
transcription, translation, and post-translation
What are additional levels of control for gene regulation?
chromatin remodeling, RNA processing, mRNA stability
In Chromatin remodeling, cells detect chemical signals for 2 reasons:
short term cellular responses and gene activity regulation
Short term cellular responses in chromatin remodeling include:
changes in membrane permeability and activation/deactivation of enzymes/proteins
reasons for gene activity regulation in chromatin remodeling include:
producing specific proteins and to trigger transcription
Why is chromatin remodeling necessary?
DNA is packed tightly in the nucleus and RNA polymerase cannot access it, so the chromatin around the gene must be remodeled
Chromatin consists of:
DNA complexed with histones and other proteins
Histones are
the most abundant DNA associated proteins
Nucleosome is
about 200 bases of negatively charged DNA wrapped around a core of 8 positively charged histone proteins, repeating beadlike structures spaced with linker DNA
nucleosomes form 30 nm fibers that are attached to scaffold proteins to:
hold entire chromosome in place
When chromosomes condense before cell division, they are:
more tightly packed
Chromatin's elaborate structure is important because...(2 reasons)
it allows the DNA to fit in the nucleus and it plays a key role in regulating gene expression
What is the product of chromatin remodeling?
a chromosome(sister chromatids) in its condensed form
Eukaryotic DNA has _________ where RNA polymerase binds to initiate transcription.
promoters
chromatin must be ___________ to expose promoter for RNA polymerase to bind.
decondensed
What are the 2 ways to remodel chromatin?
DNA methylation and histone modification
Is methyl polar or nonpolar?
nonpolar
Methylated DNA is __________ DNA.
condensed
unmethylated DNA is ___________ DNA
Decondensed
What causes DNA to become decondensed/unmethylated?
acetylation
DNA condensation is triggered by
the addition of methyl groups (-CH3) to cytosine (CpG islands) in the promoter of genes
The addition of methyl groups to trigger DNA condensation is called
methylation
What enzyme recognizes CpG islands?
DNA methyl transferase
Reversal of methylation is done by which enzyme?
demethylase
Why do actively transcribed genes usually have few methylated CpG sequences near the promoter?
because they don't want to be condensed, condensation prevents replication process
Methylation when you should have demethylated and vise versa can cause what?
cancer (depends on what the DNA is coding for)
Enzymes can add a variety of chemical groups to histones with different effects. What are these chemical groups?
Methyl groups, acetyl groups, phosphate groups and short polypeptide chains
Histone modifications can promote either __________ or ___________.
condensation, decondensation
More acetyls and fewer histones means that DNA is likely ______.
decondensed/open
True or false: histone methylation does not necessarily condense DNA.
True
Histone acetylation ___________ DNA.
decondenses
Removal of acetyl and addition of methyl functional groups to histone tails __________ DNA.
condenses
More methyl = (more/less) likely that DNA condenses.
more
True or false: DNA and histone methylation condense DNA and make a gene inaccessible to RNA polymerase.
False
True or false: In those sections of DNA where histones are resistant to acetylation, gene transcription will be decreased.
true
What does variation of chromatin modification patterns between cells allow for?
differential gene expression in different tissues and cells
When a cell divides what is passed on to the daughter cells?
patterns of methylation and acetylation
Epigenetic inheritance
any inheritance mechanism that is not due to differences in DNA sequences
____________ _____________ can record life events that influence phenotypes of offspring.
epigenetic mechanisms
Examples of lifestyle factors with epigenetic effects
nutrition, physical activity, smoking, alcohol use, pollutants, emotions/stress, working nights
How many general transcription factors are there and what determines where they bind?
6 and the promoter sequence
What sequence is unique to each gene?
promoter-proximal elements
proximal =
closer
distal =
further
Binding of ___________ ____________ ________ promote or inhibit transcription.
regulatory transcription factors
What provides a mechanism for eukaryotic cells to express certain genes but not others?
promoter proximal elements
General transcription factors is used in eukaryotes instead of ________ in prokaryotes.
sigma
____________ _____________ elements are specific to certain areas/parts of the body.
promoter proximal
What is a distal control element? Where are they located?
Regulatory sequences, can be hundreds of thousands of bases upstream OR downstream from the promoter
Which regulatory sequences increase the rate of transcription?
enhancers
How many regulatory sequences are there?
2, enhancers and silencers
what is the effect of binding the repressor TF?
Decreasing rate of transcription, silencer
What transcription factor is needed to start transcription in all cells?
General (Basal) transcription factor
What transcription factor binds to DNA region called enhancers, silencers or promoter proximal elements?
Regulatory transcription factors
What transcription factor binds to core promoter?
General (Basal) transcription factor
Which transcription factor can increase or decrease levels of transcription?
regulatory transcription factors
Basal TFs together with RNA polymerase form ______ _________ _________ that assembles near the start site on the promoter.
Basal transcription apparatus
Which transcription factor is responsible for expression of particular genes?
regulatory transcription factors
What is sufficient to initiate minimal levels of transcription?
basal transcription apparatus (RNA polymerase + Basal TFs)
TF stands for...
transcription factors
What are the 3 regulatory mechanisms that must occur before the final product appears?
different ways of splicing the same primary transcript
altering availability of mRNAs (translate or destroy)
altering protein activity after translation has occurred
These proteins bind to genes at sites known as enhancers and speed the rate of transcription.
activators
these proteins bind to selected sets of genes at sites known as silencers and thus slow transcription.
repressors
These adaptor molecules integrate signals from activators and perhaps repressors.
coactivators
in response to injunctions from activators, these factors position RNA polymerase at the start of the coding region.
basal transcription factors
post translational regulation allows cells to respond to:
new conditions rapidly
Cells keep an _________ protein waiting.
inactive
inactive proteins can quickly activate in response to:
altered conditions
In eukaryotic gene expression, the step that most prokaryotes do not use is:
RNA processing
A mutation occurs that reduces the effect of an enhancer for a set of genes. What would be reduced?
the amount of protein produced by the set of genes
Alternative splicing during gene expression occurs only inside the nucleus in:
eukaryotes
Rats that are the offspring of parents that were raised with poor nutrition have a greater chance of developing disorders similar to type 2 diabetes, regardless of the alleles they inherit. This shows that __________ ____ ______ ___________ may be inherited.
patterns of gene expression
Which of the following types of gene expression regulation occurs in eukaryotes but is rare or non-existent in prokaryotes?
a.coordinating transcription by organizing genes into operons
b. alternative splicing of primary transcripts
c. phosphorylating proteins to activate them
d. using proteins to help RNA polymerase bind and start transcription
alternative splicing of primary transcripts
Evolution explains how life __________, not how life __________.
changes, started
Theory of evolution states that:
all species are related and gradually change over time confirmed through observations and experiments
Macroevolution:
major changes among living organisms over long periods of time
microevolution
changes in population of a species over a shorter time period
Charles Darwin described evolution as:
descent with modification
Who created the theory of evolution?
Charles Darwin
The branching evolution history of species or other major groups of organisms is called ___________.
phylogeny
A ____________ ________ is a simplified diagram of the branching evolution history of species or other major groups of organisms.
phylogeny tree
What is a species?
classification of organisms
___________ is the scientific method of classifying and naming organisms by grouping them by shared traits or characteristics.
taxonomy
taxonomic unit in the biological system of classification
taxon
examples of taxons:
species or genus
Categories of taxonomic hierarchy in order from largest to smallest:
Domain Kingdom Phylum Class Order Family Genus Species
Human Domain
Eukarya
Note
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