Genetics

What occurred in the Avery Macleod Mcarty experiment?

used a bacteria called streptococcus pneumonia

• S strain = harmful and has protective capsule

• R strain harmless and lacks a capsule

They took dead S bacteria and broke them open. This gave them a mixture containing things from the S bacteria, including:

DNA + RNA + proteins + other molecules. They then separated the different components.

Dead S bacteria

↓
Break them open
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Get their cellular contents
↓
Treat the contents with different enzymes
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Mix the contents with live R bacteria
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See whether the R bacteria become S bacteria

What was the conclusion from this experiment?

• Protease → destroys protein → transformation still occurred

• RNase → destroys RNA → transformation still occurred

• DNase → destroys DNA → transformation stopped

Conclusion: DNA, not protein or RNA, carries the genetic information responsible for transformation.

What did the Hershey–Chase experiment show?

• Bacteriophages → made of DNA + protein

• ³²P (radioactive phosphorus) → labels DNA because DNA contains phosphorus

• ³⁵S (radioactive sulfur) → labels protein because proteins can contain sulfur

Made one batch of phages with ³²P-labelled DNA. Made another batch with ³⁵S-labelled protein. Allowed both types of phages to infect E. coli bacteria.

• ³²P (DNA) was found inside the bacteria.

• ³⁵S (protein) remained outside the bacteria with the phage coats.

What are the requirements for genetic information?

1. stable over time

2. faithfully replicated

3. make proteins (essential to carry out life)

4. change in a controlled way (so evolution can occur)

What did Rosalin Franklin discover?

she used X ray crystallography to study the structure of DNA. This X-ray diffraction photograph showed:

• DNA has a helical (spiral) shape.

• The helix has a constant width.

• The bases are on the inside of the molecule.

• The phosphate backbone is on the outside

What is the structure of DNA?

DNA is a polynucleotide, this means it comprised of many nucleotides joined together via phosphodiester bonding

• a nucleotide contains a phosphate, sugar and a base (thymine, adenine, guanine and cytosine)

How is the double helix formed?

the double helix is held in place by hydrogen bonding between complementary base pairs (C and G 3 hydrogen bonds) and (A and T 2 hydrogen bonds)

Explain the antiparralel strands of DNA

DNA has two strands that run alongside each other, but they run in opposite directions. This is called antiparallel

The numbers refer to carbon atoms in the sugar (deoxyribose) of each nucleotide.

• 5′ end = the end with the phosphate attached to the 5′ carbon

• 3′ end = the end with an available OH group on the 3′ carbon

DNA polymerase can only add a new nucleotide to the 3′ OH, so new DNA is always made 5′ → 3′.

What are minor and major grooves?

Gaps formed by DNA's twisted double helix. The major groove is wider, while the minor groove is narrower. Proteins can bind to them

What is the genome?

A genome is all of the genetic material (DNA) in an organism.

What are chromosomes and homologous chromosomes?

A chromosome is one long, organised piece of DNA wrapped around proteins

two chromosomes that carry the same types of genes, but these can be different versions of the same genes (alleles) this is what provides individuals with different characteristics.

• one chromosome from mother

• one chromosome from father

What is a chromatid?

A chromatid is one copy of a chromosome.

Before DNA copies itself:

1 chromosome → 1 chromatid

After DNA copies itself:

1 chromosome → 2 identical sister chromatids

They are joined together in the middle via the centromere

What are histones?

Hstones are proteins which DNA wraps around

there are 4 main types:

• H2A

• H2B

• H3

• H4

Two copies of each form a group of 8 histone proteins called a histone octamer. the DNA wraps around each histone twice in order to form the nucleosome

Histone 1 = H1 is called a linker histone. This brings nucleosomes together to form chromatin fibres. It sits on the linker DNA between each nucleosome and holds the arrangement together tightly and compactly

What is the role of scaffold proteins?

Chromatin forms loops, these loops then attach to scaffold proteins and this helps keep the chromosomes highly condensed

What are the types of chromatin?

• Euchromatin - less compact DNA form, contains genes that are frequently expressed (genes switched on)

• heterochromatin - highly packed DNA, therefore DNA cannot be transcribed (gene switched off)

What did the pulse chase experiment conclude?

RNA only discovered in 1950s

Uracil was made radioactive and therefore could be tracked.The RNA moved from the nucleus to the cytoplasm in order to make proteins

This suggested that RNA was a messenger

What is the central dogma?

Central dogma - describes the flow of genetic information

DNA --> transcription --> RNA --> translation --> protein

How does RNA and DNA differ?

DNA	RNA
Ribose sugar	Deoxyribose sugar
Double helix	Single stranded
Thymine	Uracil
Chemically less reactive as deoxyribose contains one less hydroxyl group on the carbon 2' of the sugar	Chemically more reactive as ribose contains one more hydroxyl group on the carbon 2' of the sugar

What are promoter and termination regions?

Promoter region - specific sequence of DNA that is located upstream of a gene, this determine where transcription actually begins (TATTA RNA polymerase binds and starts transcription)

Terminator region - section of DNA that tells RNA polymerase to stop transcription

What are NTPs?

NTP - nucleoside triphosphate

For RNA NTPs include:

• Adenine ATP

• Guanine GTP

• Cytosine CTP

• Uracil UTP

 

Each one of these NTPs has 3 phosphate groups

• Alpha

• Beta

• Y

During transcription, RNA polymerase uses NTPs to build an RNA strand

How is pre-mRNA synthesised?

1. An enzyme called RNA polymerase binds to the DNA at a specific region called the promoter.

2. RNA polymerase reads the template DNA strand in the 3′ → 5′ direction. It builds the new RNA strand 5′ → 3′

3. This is important because RNA polymerase can only add new nucleotides to the 3′ end of the growing RNA

4. The NTP loses two of its phosphates when it is incorporated, and the released energy helps form the phosphodiester bond between nucleotides.

How does splicing occur and what is the spliceosome?

The pre-mRNA contains:

• Exons = sections that are kept

• Introns = sections that are removed

The spliceosome is a large complex made mainly of:

• Proteins

• snRNAs = small nuclear RNAs

Together these form snRNPs ("snurps"), which recognise the intron and help cut it out.

The spliceosome basically acts like the molecular scissors + machinery for splicing.

What is an amino acid?

An amino acid is a protein monomer, these join via peptide bonds to form a polypeptide. there are 20 amino acids and each one contain 3 triplet of bases known as a codon

What are the rules of the genetic code?

universal - same codons specify the same amino acid in all organisms

degenerate - more than one triplet of bases can code for the same amino acid

non overlapping - each base is part of only one codon

What did Crick, Brenner experiment conclude?

Helped to show that groups of 3 bases are known as codons.

Bacteriophage - virus that infects bacteria

• They used a mutation called frameshift mutation. They added or removed an individual base from a gene (r11 in bacteriophages genome)

• If there was a mutation in this gene it would make plaques which are distinctive and large

• If there were no mutation in this gene it would make smaller normal plaques

they generated mutants in the R11 gene of bacteriophages T4 using Proflavine - a chemical mutagen which can add or remove a single nucleotide from DNA

This proflavine molecule is planar (flat) this means it is able to slide in between base pairs, then this causes a single nucleotide to be added or deleted. --> frameshift effect and therefore changes how the genetic code is read

• If you add or remove ONE nucleotide then it shifts the entire reading frame. However if you make 3 nucleotide changes then the reading frame is restored.

What is the structure and role of rRNA in translation?

It is RNA that makes up a major part of the ribosome, the structure that makes proteins. rRNA + proteins → ribosome → makes proteins

The ribosome has two subunits:

• Small subunit (33 proteins and 1 RNA molecule)→ holds and reads the mRNA

• Large subunit (49 proteins and 3 RNA molecules)→ helps join amino acids together

rRNA is found in both subunits and has two main jobs:

1. Provides the structure of the ribosome.

2. Helps form peptide bonds between amino acids

What is the structure of a ribosome?

The ribosome has two subunits:

• Small subunit (33 proteins and 1 RNA molecule)→ holds and reads the mRNA

• Large subunit (49 proteins and 3 RNA molecules)→ helps join amino acids together

rRNA is found in both subunits and has two main jobs:

1. Provides the structure of the ribosome.

2. Helps form peptide bonds between amino acids

The ribosome has three important sites:

A → P → E

Site	Meaning	What happens
A site	Aminoacyl	New tRNA enters carrying an amino acid
P site	Peptidyl	Holds the tRNA carrying the growing polypeptide
E site	Exit	Empty tRNA leaves

What is the structure and function of a tRNA molecule?

tRNA molecules are made up of important sites:

1. Anticodon

• A sequence of 3 RNA bases

• Binds to a complementary codon on mRNA

2. Amino acid attachment site

• The other end carries one specific amino acid

So tRNA basically acts like a delivery vehicle:

tRNA = brings the correct amino acid → to the ribosome

Explain the initiation process of translation?

1. The small ribosomal subunit, translation initiation factors and initiator tRNA join

2. This complex then binds to the mRNA molecule

3. The small subunit moves along the mRNA searching for the first AUG start codon

4. Once AUG is found, the translation iniation factor dissociates and the large ribosomal subunit binds

5. Charged tRNA binds to the a site and the first peptide bond forms between the 2 adjacent amino acids

Explain the elongation process of translation?

Step 1

• Newly bound charged tRNA binds to the a site

• The growing polypeptide chain is held by the tRNA sitting in the p site

Step 2

• The ribosome catalyses the joining of the amino acids and forms a peptide bond

• The polypeptide chain is now transferred to the tRNA sitting in the a site

Step 3

• The large ribosomal shifts

• This movement shifts the new tRNA into new positions within the larger subunit, the uncharged tRNA (without an amino acid) moves into the E site and the tRNA carrying the growing polypeptide moves into the p site

Step 4

• The small subunit shifts to realign with the larger subunit, this pulls the mRNA along by one codon (3 bases)

• The uncharged tRNA in the e site is ejected and the a site is now empty again

Explain the termination process of translation?

1. The ribosome reaches the stop codon UAG at the site A. since no tRNA matches this codon translation is halted

2. A release factor then binds to this a site where the stop codon is

3. The release factor then triggers a hydrolysis reaction using h20 in order to break the bond between the polypeptide chain and the tRNA. This frees the polypeptide chain

4. The entire complex breaks apart, the mRNA, small and large ribosomal subunits and last tRNA and release factor all separate so they can be recycled