Gene Regulation

Part 2 After The Quiz

What does the nucleus of eukaryotic cells contain

Chromosomes

How is the 3D Structure of DNA formed

Formed of 2 polynucleotide strands twisted together

Histones

Proteins that associate with DNA and help it pack and condense it

What holds nitrogenous bases together

Hydrogen bonds

What’s DNA made of

Deoxyribose sugar, phosphate group, nitrogenous base

What holds the deoxyribose sugar and phosphate groups together

Phosphodiester bond

Polynucleotide

Polynucleotides are long chains of nucleotide monomers

Why does cells need to do DNA Replication

To prepare for cell division. Each new cell will require its own DNA.

DNA replication is described as semi-conservative because…

the new DNA is composed of one strand from, the original parent. DNA and one strand that is newly synthesized.

Replication (Formation)

Parent DNA has 2 identical strands, and then it splits and makes a new strand each.

Helicase

This enzyme unzips DNA like a zipper, creating two single strands of DNA.

Topoisomerase

This enzyme relaxes the super coiled structure of DNA.

Primase

This enzyme primes the DNA, creating a starting point for DNA Polymerase

DNA Polymerase

This enzyme synthesizing new strands of DNA by adding DNA nucleotides

Exonuclease

This enzyme cuts out RNA primers and DNA that needs fixing.

Ligase

The new DNA strands have breaks between fragments, so this enzyme joins the DNA together.

Each stage of DNA Replication

1 - unzipping

2 - stabilizing

3 - priming

4 - building and extending

5 - replacing

6 - gluing

7- proof reading

1 - unzipping

Helicase unzips the double stranded DNA by breaking the Hydrogen bonds between complementary base pairs, separate it into single strands.

SSB

Single Stranded Binding Proteins

2 - stabilizing

SSB proteins attach to the unzipped DNA, stopping it from joining back together. The enzyme Topoisomerase relieves tension in the DNA by relaxing it from its super coiled structure.

3 - priming

An enzyme that attaches RNA primers to the DNA, providing a staring point for DNA polymerase.

4 - building and extending

DNA Polymerase associates with the DNA and build the new DNA strand by adding new DNA nucleotides. It can only build the new strand in the 5’to 3’ direction, creating a leading strand and a lagging strand.

5 - replacing

The primers have to be removed by exonuclease because they are made of RNA. DNA Polymerase then replaces them with DNA nucleotides.

6 - gluing

The enzyme ligase joins or glues DNA fragments together

7 - proof reading

Another type of DNA Polymerase scans the DNA for any errors and fixes any that are found.

Which direction does the DNA Polymerase build a new strand?

5’ to 3’ direction only.

Leading strand

The original strand that goes 3’ to 5’ that’s building a new strand that goes 5’ to 3’, so once a primer is placed, it keeps building built straight.

Lagging strand

The original strand that goes 5’ to 3’ that’s building a new strand that goes 3’ to 5’, so once a primer is placed, it goes backwards and bumps into a different primer.

So the primers are continuing to be built as the DNA relaxes into two strands, and the lagging strand starts at the primer and keeps going backwards over and over again, creating small broken segments.

Why is it called lagging strand?

Because it’s built slower and in short, separate pieces rather than one smooth line.

Okazaki Fragments

Short pieces of DNA that are formed on the lagging strand during DNA replication.

How do you patch/connect Okazaki Fragments?

With Ligase, which takes care of the gaps between the fragments.

Chemically, how does ligase glue everything?

It uses ATP to activate 5’ phosphate group and welds everything with a strong phosphodiester bond.

Why is replication called “semi conservative”?

The two copies of DNA contain one old original strand, and one newly made one.

What could happen if DNA Polymerase matches the wrong DNA bases?

You could end up with an incorrect protein, or no protein.

What is DNA Polymerase III

It’s the thing beginning to form from the primers placed that start DNA Replication.

What is DNA Polymerase I

It removes temporary RNA primers (laid down by primase to start DNA synthesis) from the lagging strand and replaces them with DNA nucleotides.

Why does DNA Polymerase only replace RNA primers of lagging strands?

because the lagging strand has hundreds of temporary RNA primers that must be removed, whereas the leading strand only requires a single primer at the very beginning.

What is the purpose of DNA Replication

It makes an exact copy of a cell’s DNA before it divides, so that each daughter cell receives a complete/identical set of genetic information.

What are mutations

A change in an organism’s genetic material.

How does mutations happen?

Mutations occur at random.

Mutagens

Factors that increase the risk of a mutation occurring.

Mutagen examples

Gamma rays, UV-lights, sun, tar (from cigarette smoke).

Substitution Mutation

This is when one base is exchanged or swapped for another base.

Insertion Mutation

This is when one or more bases are inserted into the DNA strand, making it longer.

Deletion Mutation

This is when one or more bases are deleted from the DNA strand, making it shorter.

How can DNA mutations impact protein that are made in a cell

mRNA synthesis is based off of the DNA for the process of transcription.

If the DNA is mutated, the mRNA made will all end up with an altered base sequence (mutation).

If the codons are altered and it codes for a different animo acid, this COULD affect the structure and function of the protein.

How many mRNA bases are read at a time and what’s it called

It’s called codons, and it reads in groups of three.

Silent mutation

Has no effect on the amino acid that is coded.

Eg. UUA and UUG are both Leu, so if there’s an altered base for that, it wouldn’t do anything,

Missense mutation

Causes a codon to code for a different amino acid than the original one.

Frameshift mutation

Causes the “reading frame” of the mRNA codons to shift forwards or backwards, changing many amino acids.

Nonsense mutation

Causes a STOP codon in the middle, which terminates it early, often resulting in a non-functional protein.

Impact of a mutation

Depends on if it affects a protein’s structure and function. While many mutations have no effect (eg. silent mutation), some mutations alter proteins, affecting the organism’s phenotype (physical) and genotype (gene).

Eg. beneficial phenotype

A white hare living in snowy mountains, being able to hide from predators.

Eg. neutral phenotype

Causes a dog to have a spotted coat instead of a solid coat. Does not affect its chances of survival.

Eg. “Deleterious mutation”

A mutation in the CFTR gene causes Cystic Fibrosis in humans.

Because of a misfolded protein, sticky mucus forms in the lungs and digestive system.

Chromosomes

Molecules of DNA that are tightly bound by histones.

Chromosomal Mutations

During Mitosis and Meiosis, DNA is replicated then divided into daughter cells. Errors during these processes can result in chromosomal mutations.

Duplication chromosomal mutations

Extra copies of genes are added to a chromosome

Inversion chromosomal mutations

A section of the chromosome gets flipped/reversed.

Deletion chromosomal mutations

A piece of the chromosome breaks off and is lost.

Translocation

A piece of one chromosome breaks off and attaches to another chromosome. (If two chromosomes are too close to eachother, they’ll swap.)

Errors in the numbers of chromosomes in the body’s cells.

Having less/more chromosomes: Lead to Aneuploidy or down syndrome.

Organisms many have all kinds of gender chromosomes like (XX, XY, XXX, XYY, XXY, X)

What is gene expression

The process where a cell reads the instructions stored in a gene to build a functional product, usually a protein or an RNA molecule.

Why is it important to regulate gene expression

Not all proteins are needed for all cell types, so it’s important that genes can be switched on and off.

Regulating gene expression allows cells to become specialized.

Transcription factors

Regulatory proteins that can help to increase or decrease the rate of transcription.

Activators

Positive transcription factors.

They attach to the promoter upstream of the target gene and help RNA Polymerase to bind and begin transcription.

Repressors

Negative transcription factors.

They attach to the promoter and block RNA Polymerase from binding to the promoter, or they can make it more difficult to.

-It can either STOP transcription, switching the gene off, or just have the rate of transcription be decreased.

Interfering RNA

siRNA (Short Interfering RNA) and miRNA (micro interfering RNA)

How does siRNA and miRNA interfere

By targeting the mRNA. siRNA (and miRNA in plants) has base sequences that are complementary to the target mRNA, so they can bind to it. Then the proteins of the siRNA cut up the mRNA so it can’t be translated.

miRNA in mammals

It only partially matches the mRNA, so instead of attaching + cutting it up, the proteins of the miRNA physically block ribosomes from accessing the mRNA.

Operon

A cluster of genes in a PROKARYOTIC cell.

They are coregulated- so if one gene is expressed, then the other genes are too.

eg. Lactose and operons

If there’s an absence of lactose, a repressor binds to the operator. The RNA can bind to the promoter, but it cannot move along the DNA because the repressor is blocking it.

If there’s a lactose present, some lactose will be converted to ALLOLACTOSE. This molecule attaches to the pressor and causes its shape to change, forcing it to release from the operator.

RNA Polymerase is now able to transcribe to operon, expressing the genes for lactose enzymes. This allows the cell to break down lactose.

Histone Acetylation

Histones are proteins associated with DNA- they wrap the DNA around themselves, condensing into chromatin.

The more condensed the DNA is, the harder it is to transcribe.

Increased acetylation (addition of acetyl groups) makes the DNA less condensed so that the target genes can be expressed.

DNA Methylation

Methyl groups can be added to DNA at specific sites called CpG sites (where Cytosine and Guanine are next to each other, joined by a phosphodiester bond).

The addition of methyl groups causes the DNA’s structure to change, making it more difficult to transcribe, preventing gene expression.

Epigenetics

DNA methylation and histone acetylation are both examples of epigenetic markers.

(Things that affect an organism’s phenotype WITHOUT changing its DNA sequence that can be inherited.)

DNA Replication involves the breaking of bonds between

Bases

What describes a DNA Molecule?

Double chain of nucleotides joined by hydrogen bonds

If the nucleotide sequence of an anticodon was AUC, the DNA triplet would be

ATC

Where is a codon found

Found on mRNA (Messenger RNA)

Where is an anticodon found

Found on tRNA (Transfer RNA)

Function of a codon

Carries the DNA's genetic code from the nucleus

Function of an anticodon

Decodes the mRNA to deliver the correct amino acid

Origin of codon

Copied directly from the DNA template

Origin of anticodon

Built into the specific tRNA molecule

Role of codon

Acts as the lock or the instruction manual

Role of anticodon

Acts as the key that matches the loc

DNA can be tightened and loosened when wrapped around a histone protein. When tightened, gene expression in this area…

Is decreased, the gene is less accessible

How does a codon and an anticodon work together?

The ribosome reads the mRNA codon (e.g., AUG). A tRNA molecule with the exact opposite anticodon (UAC) docks into place, bringing the specific amino acid required for that code.

Modifications to gene expression, but not the actual gene, refers to

Epigenetics

The number of adenine bases in a DNA molecule equals the number of thymine bases because

Adenine on one strand bonds to thymine on the other strand

Which of the following is a POST TRANSITIONAL modification of mRNA that removes introns and joins exons together to create a mature mRNA molecule?

Splicing

Does Transcription come first or Translation?

Transcription. It has a C in it, and Translation has a L in it. C comes before L in the alphabet.

During protein synthesis, peptide bonds are formed at the

ribosomes

What following statement best describes DNA replication?

DNA nucleotides, by complementary base pairing with DNA, produce DNA.

A function of the tRNA is to

Carry amino acids to the growing polypeptide chain.

The lagging strand is synthesized from a series of short fragments. Why fragments rather than a continuous strand?

DNA Polymerase can only synthesize new DNA in one direction

In gene expression, repressors

Block and or reduce gene transcription

A change in the sequence of bases in a strand of DNA that occurs as a result of exposure to X-rays is an example of

Mutation

What accurately describes the genetic code used in protein synthesis

Each codon corresponds to a specific amino acid

Which of the following would not occur during complementary base pairing?

U-G