Genetics ch 14

what is a peptide bond 

is the covalent bond between amino acids in a polypeptide, that forms between the carboxyl end of an amino acid and the amino end of the next 

what forms between the carboxyl end of an amino acid and the amino end of the next

peptide bond

where is calmodulin present in

all eukaryotic cells

what is a calmodulin

It is a small protein that consists of a single polypeptide, and has tertiary structure. The helical portions are alpha helices.

What is an alpha helices

a type of secondary structure observed in many proteins

what do many proteins consist of

a single polypeptide

• ex. calmodium 

what is an exampled of a protein with multiple polypeptides

Hemoglobin (Hb)

what is hemoglobin (Hb)

is the protein inside the red blood cells that carries oxygen in the bloodstream. 

• 4 polypeptides

• 2 a-globins 

• 2 b-globins 

• has quaternary structure 

what is the primary structure of a protein

its sequence of amino acids

Secondary structure of a protein

interactions between amino acids cause the primary structure to fold into a secondary structure 

tertiary structure of proteins 

the secondary structure folds further into a tertiary structure 

quaternary structure

two or more polypeptide chains may associate to create a quaternary structure

What is this 

a primary structure of a protein 

• polypeptide: sequence of amino acids 

• 1ry structure 

what is this

Secondary structure of a protein

• Alpha helix: partial folding

• 2ry structure 

what is this

Tertiary structure of a protein

• Globin: complete folded polypeptide

• 3ry structure 

what is this

Quaternary structure of a protein

• Hemoglobin

• 4ry structure 

Sickle cell anemia

a single amino acid substitution in B-globin reduced the affinity of Hb for O2 and impairing the solubility and absorption of oxygen.

• the polypeptide forms large polymers that distort the shape of red blood cells, affecting blood flow and oxygen transport

What is a codon

a three-base (nucleotides) sequence of DNA (a triplet) that codes for an amino acid

The genetic code is usually expressed on the table as what

mRNAs in the 5 → 3 orientation

Start codon

AUG → also codes for methionine

Stop codons

UAA, UAG, UGA (these do not code for any amino acids)

What is a reading frame

a linear sequence of codons in a nucleic acid defined by a start codon and ending with a stop codon

What does degenerate genetic code mean

multiple codons can code for the same amino acid

codon for methionine (Met)

AUG (start codon as well)

what are the characteristics of the genetic code

• unambiguous

• degenerate

• universal

• commaless

• non-overlapping

Unambiguous

each of the 61 triplets code for only one of the 20 amino acids

degenerate 

most amino acids are encoded by more than one codon 

Universal

most living organisms use the same code, but exceptions exist

Commaless

there are no breaks between the codons in the reading frame (all the bases of the translated sequences are part of codons)

non-overlapping

in triplets in a reading frame are in a tandem sequence and do not overlap

what is the flow of genetic information

DNA → mRNA → protein

(transcription → translation)

How do the template strand and mRNA relate

The template (antisense) DNA strand:

• runs 3 → 5

• Used by RNA polymerase to make mRNA

• mRNA is complementary to this strand 

• example: DNA 3 - TACCACAACTCG - 5

mRNA strand

• runs 5 → 3

• sequence matches the DNA coding (sense) strand except U replaced T

• example: mRNA 5 - AUGGUGUUGAGC - 3 

Translation

• ribosome reads mRNA codons (triplets) 

• AUG = start codon → met

• each codon → one amino acid 

example protein 

met - val - leu - ser

what is this

the flow of genetic information

what can spontaneous mutations result in

permanent changes

What causes spontaneous mutations

they are not caused by errors in DNA replication. DNA exists inside of the cell, which is an open system. DNA is then exposed to radiations and molecules that can react with it and cause chemical alterations. 

What is this 

the deamination of cytosine

• spontaneous mutations 

• original C-G base pair and then after deamination → U-A

• The result in a C → T transition mutations after replication  

• to fix: the cells use uracil-DNA glycosylase (base excision repair) to remove uracil from DNA

What is this 

a spontaneous mutation resulting in a permanent base pair substitution in the top right as G has been turned to A to pair with U, and the bottom right has transformed C back to U and G stays the same. 

When a base is replaced by a different base in DNA, the result is a permanent single codon change 

substitution mutations in protein coding genes 

Type of substitution mutations in protein-coding genes

• silent

• missense

• nonsense 

what is a silent substitution mutation

the resulting new codon codes for the same amino acid as the original codon

what is a missense substitution mutation

the new codon codes for a different amino acid

what is a nonsense substitution mutation

the new codon is a stop codon, resulting in a shorter polypeptide

what might cause mutations

errors in DNA replication

where do mutations occur and where may they be copied to

they occur in DNA and may be copied to mRNAs

example of a silent mutation

wild type codon: AGU → ser

mutation: AGC (U→C)

amino acid stays Ser

example of a missense mutation

wild type: AGU → ser

Mutation: AAU → Asn (G→ A)

This changes the amino acid (ser → asn)

Example of a nonsense mutation

wild type: AGU → ser

mutation : UGA → stop (A→ U)

translation ends early → truncated protein 

What is the wildtype

mRNA: AUG ACA CGG AGU AGA UAU UAA

Protein: Met - Thr - Arg - Ser - Arg - Tyr - Stop

what is the silent mutation 

AGG (ser) was AGU (ser)

• U → C

What is the missense mutation 

AAU (asn) was AGU (ser)

• G → A

What is the nonsense mutation

UGA (stop) was AGU (ser)

• A → U 

what does the insertion of a single base result in 

a frameshift mutation 

what are insertion due to

errors in DNA replication

• all the codons from the insertion site on are changed, resulting in frameshift

• the deletion of single bases by errors in DNA replication also occur and also result in frameshift mutations 

what is this 

the insertion of a single base resulting in a frameshift mutation 

What is huntington’s disease

A neurodegenerative disorder

• an autosomal dominant disease caused by the expansion of trinucleotide CAG repeats, which code for glutamine in the mRNA, in the huntingtin gene, resulting in polyglutamine huntingtin proteins 

what does the number of CAG repeats mean

In trinucleotide repeat expansions the number of CAG repeats determines if someone has the phenotype disease 

Number of CAG repeats    phenotype

11-35                                  normal 

36-39                                  borderline

40 and over                        disease 

What is this explain 

Trinucleotide repeats expansion 

1) the DNA molecule has 8 copies of a CAG repeat

2) the two strands separate

3) and replicate 

4) In the course of replication, a hairpin forms on the newly synthesized strand 

5) causing part of the template strand to be replicated twice and increasing the number of repeats on the newly synthesized strand 

6) the strand of the new DNA molecule separate 

7) and the strand with extra CAG copies severs as a template for replication

8) The resulting DNA molecule contains 5 additional copies of the CAG repeat

Translation basic requirements

• mRNA 

• charged transfer RNAs (tRNAs) 

• ribosome

• other requirements: initial factors, elongation factors, and energy sources

• no primers of any kind 

What is this 

Shine Dalgarno sequence in prokaryotes only 

what is this 

Transfer RNA (tRNA)

• an amino acid is attached to the 3 end of the tRNA and is ALWAYS CCA

• The anticodon loop base-pairs with a codon in an mRNA 

The post-transcriptional modification of bases in tRNA result in what

unusual bases

what is inosine

is a modified adenine

what are unusual bases found in tRNAs

• Inosinic acid (I)

• 1-Methyl inosinic acid (I^m)

• 1-Methyl guanylic acid (G^m)

• NM-dimethyl guanylic acid (G^m)

• Pseudouridylic acid

• Ribothymidylic acid

what is the wobble hypothesis

The interaction between the third position of the codon in the MRNA and the first position of the anticodon in the tRNA is less critical and less constrained 

• some tRNA bases can pair with multiple mRNA bases at this position

• this allows translation to occur without the need for the cell to synthesize all 62 tRNAs

• inosine is a post-transcriptionally modified adenine that can occur at the wobble site of tRNAs

how many tRNAs are there

61

how many amino acids are there

20

what is this 

degeneracy and the wobble hypothesis 

During anticodon and codon base paring why are the codon and anticodon antiparallel

because tRNA binds mRNA in opposite orientations:

• mRNA is read 5 → 3

• tRNA anticodon binds 3 → 5 

This ensures correct base pairing during translation 

what is the wobble position

The 3rd base of the mRNA codon and 1st base of the tRNA anticodon

• allowing flexible pairing, meaning one tRNA can recognize multiple codons

how do the base-pairing of the codon and anticodon pair

anti-parallel

what are the essential amino acids for humans

• valine, leucine, isoleucine, phenylalanine, tryptophan, lysine, histidine, methionine, threonine 

what is charging catalyzed by

20 different aminoacyl tRNA synthases

• the enzymes recognize the amino acids by their R groups, and the tRNAs by their shapes and base sequences

• energy is spent in this process in order to eventually make a new peptide bond in the ribosome

what is charging a tRNA

the carboxyl group of the amino acid is covalently attached to the 3 end of a tRNA

what is this 

the charging of a tRNA 

What is this 

recognition of tRNAs by Aminoacyl tRNA synthases 

1) positions in blue are the same in all tRNAs and CANNOT be used to differentiate among tRNAs

2) Positions red are important in the recognition of tRNAs by one synthetase 

3) Positions in yellow are used by more than one synthetase 

step 1 of charging of a tRNA

Amino acid activation:

• the amino acid (AA) is converted to an aminoacyl adenylic acid (AA-AMP)

• This is the energy-consuming step on the process of eventually making a new peptide bond

• requires ATP 

Step 2 of the charging of a tRNA

Charging:

• the aminoacyl adenylic acid loses the AMP and the carboxyl group of the amino acid is attached to the 3 end of a tRNA

• the result is an aminoacyl tRNA (a charged tRNA)

Ribosome

• the large particle of rRNA and proteins where translation occurs

• two subunits: small and large

what is the svedberg unit (S)

is not a measure of molecular weight, but a measure of the rate at which particles sediment in a centrifugal field

• this rate depends on weight, shape, and size

• this unit can be used for measuring large molecules or large cell components such as ribosomes and organelles  

whare are the Svedberg values for prokaryotic ribosomes 

• small subunit: 30S

• large subunit: 50S

• complete ribosome: 70S

what sites in the ribosome are translation components

• peptidyl (P)

• aminoacyl (A)

• exit (E)

What are the steps in the initiation of translation 

1) mRNA binds to the small ribosomal subunit with the AUG codon positioned on the P site

2) f-Met-tRNA (in prokaryotes) binds to the AUG codon

3) the large ribosomal subunit joins the complex

this whole process requires GTP for a source of energy plus a series of initiation factors (IF proteins) 

What is this 

Prokaryotic translation initiation 

during prokaryotic translation initiation which molecule binds to the small ribosomal subunit to prevent premature large-subunit binding 

initiation factor IF-3

during prokaryotic translation initiation what amino acid does the first bacterial tRNA carry 

formyl-methionine (fMet)

During prokaryotic translation initiation which factor brings the first tRNA (fMet-tRNA) to the P-site

IF-2 + GTP

During prokaryotic translation where does the first tRNA (fMet-tRNA) bind in the ribosome 

The P-site 

What happens when GTP is hydrolyzed during initiation

initiation factors dissociate, allowing the large subunit to join

What is the final product of initiation

a 70S initiation complex ready for elongation

Do eukaryotes use formyl-methionine

No → only bacteria + mitochondria/chloroplast use fMet

but eukaryotic organelles (mitochondria and chloroplasts) do

what does EF-Tu and GTP do during elongation

facilitate the binding of the second tRNA to the second codon at the A site

what forms during elongation when the amino acid on the first tRNA is transferred to the second tRNA

A peptide bond forms and dipeptide forms

during elongation Where does the first tRNA move after the peptide bond forms

to the E-site

during elongation what happens to the mRNA after the first peptide bond is formed

the mRNA is shifted to place the second codon in the P site and bring the third codon into the A site 

during elongation what binds to the third codon

the tRNA carrying the third amino acid binds to the third codon on the A site 

What forms during elongation when the dipeptide is transferred from the second tRNA to the third tRNA

a tripeptide attached to the third tRNA 

What happens to the second tRNA after the tripeptide is formed

the second tRNA moves to the E site with the help of EF-G and GTP

Where does the third codon move after EF-G shifts the ribosome during elongation

the third codon moves to the p Site

after elongation steps what happens 

translation continues

What is this

elongation of the polypeptide chain