BIO 151 exam 4 content Beate Wone

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?

1. different ways of splicing the same primary transcript
2. altering availability of mRNAs (translate or destroy)
3. 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