bio exam 4

mutations are…

heritable changes to genetic sequence

heritability can either be to the _____ or passed on from parent to offspring by _____

body cells that are produced by mitosis, sexual reproduction

mutations in genes will change the…

sequence of the mRNA made from it

since proteins are made by reading the mRNA sequence, mutations…

change the sequence of the proteins

because the function of a protein is determined by its amino acid sequence, mutations can…

alter protein function

to become a fully functional protein, a protein chain must…

fold into a complex 3D shape

the folding into a complex 3D shape happens through multiple levels of interaction between the…

amino acids in the protein change

sine every protein has a unique sequence of amino acids…

every single protein will fold into a unique 3D shape

a proteins amino acid sequence will determine how it folds and…

any changes to that sequence will change its folding

the process if protein folding is important because…

1) a protein’s 3D shape is required for it to function properly

2) changes a protein’s 3D shape change the function of that protein

proteins that bind to microbes

antibodies

binding of an antibody to a microbe…

tags it for destruction by the immune system

mutations to microbial proteins can change the shape of those proteins:

• sometimes enough to make antibodies unable to bind to them

• allows the microbe to hide from the immune system

the 3 major types of mutations:

1. deletions

2. insertions

3. substitutions

deletions:

• one or more nucleotides in the genetic sequence are permanently removed

• the gene sequence become shorter than normal

insertions:

1. one or more nucleotides in the genetic sequence are permanently added

2. the gene sequence becomes longer than normal

substitutions

1. one nucleotide base is replaced with another

2. the gene sequence stays the same length

effect of mutation can vary from invisible to catastrophic depending on…

the type and location of the mutation

substitution mutations can have 3 different kinds of effects:

1. silent mutations

2. missense mutations

3. nonsense mutations

silent mutations:

occur when a substitution does not result in a change in a proteins sequence

missense mutations:

occur when a substitution changes one amino acid to another in the proteins sequence: which also changes the stop codon to an amino acid

nonsense mutations:

occur when a substitution changes one amino acid to a stop codon

frameshift

what insertions and deletions often result in

codons

3 letter groups read by the ribosome

reading frame

grouping of all codons in an mRNA

insertions and deletions…

shift the genetic sequence within its reading frame

2 ways that mutations can occur:

1. spontaneous mutations

2. induced mutations

spontaneous mutations

• permanent changes to DNA caused by normal cellular processes

• can be errors in the processes of DNA replication and DNA repair

• can also occur when cellular processes cause chemical damage to DNA

induced mutations

• caused by the presence of intense radiation or chemicals that can damage DNA structures

• like x-rays, UV radiation, carcinogenic molecules

methyl-directed mismatch repair

“back-up system” cells have if DNA polymerase does not catch an error in proofreading

after replication, enzymes add…

methyl (-CH3) groups to A and C bases

DNA methylation has a variety of functions, but during replication it…

identifies the parental DNA strands

for a short period oftime after replication, the newly replicated DNA stand has no methyl groups because…

they haven’t been added yet

proteins in methyl directed mismatch repair can identify newly replicated DNA strands by their…

lack of methyl groups

Mut proteins work together form a large “complex” that…

scans the DNA in search of backbone distortions

(mismatched bases cause shape distortions in the DNA backbone)

when mismatches are identified, Mut proteins work with another protein to unwind the DNA and….

cut the DNA backbone of a large region of the unmethylated DNA strand

the cut region is removed when the base pairing in the region is broken by the…

DNA helicase enzyme called UVRD

special gap-filling DNA polymerases will bind to the gap and…

synthesize new DNA to replace the mismatch

DNA damage often occurs due to…

chemical change not caused by replication

an important system of repair for chemical damage is…

nucleotide excision repair

nucleotide excision repair only works on…

regions of damaged DNA with a distorted backbone

how does nucleotide excision repair work:

1. DNA repair proteins bind to and slide along the DNA backbone, scanning for backbone distortions

2. when a distortion is identified, the DNA backbone is cut on both sides of the damage

3. the section of DNA on each side of the DNA nicks (cuts or breaks in the DNA backbone) is destroyed by nuclease enzymes

4. the gap-filling DNA polymerase comes in and makes new DNA using the sequence on the undamaged cell

5. the nicks on either side of the new DNA must be connected to the rest of the strand by forming new covalent bonds

nucleases

enzymes that can break down DNA and RNA molecules into individual nucleotides

proofreading and DNA repair cells typically only make one error for every…

10⁹-10¹⁰ bases that they copy

viruses are much more error prone, making one mistake every…

DNA viruses: 1-10 million bases

RNA viruses: 10,000-100,000 bases

even though human cells and microbial cells have roughly the same mutation rate, microbes…

experience genetic change much faster than humans do

mutations only pass on when the organism…

reproduces itself

bacteria can reproduce in cell division; for many bacteria this happens…

every 30 mins to 2 hours

bacteria can evolve new traits within only a few months or years, for example…

antibiotic resistnace

important for development of traits:

timing and volume of gene expression

timing

when is a gene expressed in the lifetime of a cell

volume

how much of that gene’s mRNA and protein are made

the timing and volume of gene expression is…

tightly controlled by the cell’s physiology and environment

In the gene there are small parts of the system that….

Contribute to how the gene is controlled

Define Chromatin remodling

When the cell regulates how tightly or loosely chromosomal DNA folds in the nucleus

Define Transcription control

When the cell can control timing and volume of transcription of individual genes

Define RNA Processing

After transcription RNA must be modified before it exits the nucleus and the differences in processing can alter both timing and when it leaves the nucleus which can also alter its genetic sequence

Define mRNA Stability

It is when the cell controls the life span of the RNA, shorter levels mean lower levels of proteins and vice versa

Define Translation control

When the cell regulates the timing and volume of translation of induvidual mRNA molecules

Deifne Post translation control

When the cell uses Proteins(Chaparones) that control the folding of proteins

Eukaryotes typically have _____ chromosomes

Multiple linear in shape

Chromosomes only look like a X during….

Cell division

DNA of eukaryotic chromosomes are wrapped around…

Histones

A combination of DNA wrapped around a Histone is called….

Nucleosome

When not in cell diviosn chromosomes are found…

In loosely packed balls of fiber called chromatin

How are chromatin fibers formed?

By the bundling and wrapping of nucleosomes by proteins

Define Mitotic Chromosomes

The X shaped structures that form during cell division

the histone core is made of…

histone proteins (H2A, H2B, H3, and H4)

in each core there are ___ of each protein

2

histone H1 binds to both the DNA and the core to…

lock the DNA strand and core together

between each nucleosome is a small piece of…

linker DNA with no histones attached

the partially-wound DNA that looks like “beads on a strong” is…

10 nm fiber

after the nucleosome is formed the 10-nm fiber is then formed into loops of 8-10 nucleosomes called…

topologically associating domains (TADs)

multiple TADS are associated together via proteins into…

chromatin compartments

the strength of interaction between compartments can give the cell…

control over gene expression in each compartment

the cell can modify the strength if interaction by…

chemically modifying DNA and histones

each of the chromosomes is located within a designated part of the nucleus called its…

chromosomal territory

strongly-interacting chromosomal compartments are referred to as…

condensed chromatin or heterochromatin

condensed chromatin…

inhibits transcription and gene expression

weakly-interacting chromosomal compartments are referred to as…

decondensed chromatin or euchromatin

“looser” arrangement of chromatin allows enzymes like RNA polymerase to bind, which…

activates transcription and gene expression

the cell can control gene expression by controlling the…

condensation of chromatin

to activate gene expression we need proteins that can…

unwind and decondense chromatin

to inhibit gene expression we need proteins that can…

wind and condense chromatin

-CH3

methyl group

cells have enzymes called DNA methytransferases that…

add methyl groups to cytosine bases with covalet bonds

specifically, cytosine bases where the next base in the chain is guanine; these are called…

CpG sites

cellular signals can cause DNA to become methylated; methylated CpG sites become…

binding sites for enzymes that increase chromatin condensation

methylated DNA is…

much more condensed and gene expression is inhibited

unmethylated DNA is…

decondensed and gene expression is activated

while DNA is typically methylated, histones can be…

modifies by several different kinds of chemical groups

each histone protein has a long extension at one end called…

a histone tail

a histone tail is frequently…

modified by multiple kinda of chemical groups

hypothesis: there is a histone code similar to the genetic code where certain patterns of modification are “translated” into…

specific kinds of changes to gene expression

the most well-understood system is…

histone acetylation

histone acetylation uses acetyl-CoA from cellular respiration to add chemical groups called____ to histone tails

acetyl groups

the enzymes that add the acetyl groups to the histone tails are called…

histone acetyltransferases (HATs)

in response to cellular signals, HATs add acetyl groups to histone tails, which…

causes chromatin to condense

decondensed chromatin can now…

activate transcription of its gene

a different enzyme can remove acetyl groups from histones…

histone decetylases (HDACs)