BIo Test 4

Dr. Lydia Villa Komaroff

* Molecular and cellular biologist
* 3rd Mexican-American woman to receive Dr. in science
* Completed PhD at MIT in 1975
* Post doctorate research at Harvard medical school
* Taught of UMMS and Harvard Medical School
* Discovered insulin can be produced by bacteria

One gene, one polypeptide hypothesis

Hypothesized that each gene contains the information to make one enzyme

What is Neurospora crassa?

A type of bread mold

What did the one gene, only polypeptide hypothesis focus on?

The metabolic pathway that synthesizes arginine

What is arginine?

a key amino acid needed for proteins

What are the three enzymes in the arginine pathway?

Enzymes 1,2 and 3 - help produce Ornithine, Citrulline, and Arginine respectively.

How was the arginine study set up?

The scientists isolated 3 mutant N. Crassa that were deficient in one of the three enzymes in the arginine pathway?

What did the arginine study conclude?

* Mutants for certain genes lacked specific enzymes needed for the pathway.
* Concluded that each gene coded for one “enzyme”

What do scientists now know about the one gene, one polypeptide hypothesis?

Genes contain instructions for not only enzymes but any protein

What is the central dogma?

The flow of information from DNA to proteins

How does the central dogma work?

Sequences of bases in DNA specify the sequences of bases in mRNA which specifies the sequences of amino acids in a protein

Protein account for how much dry mass in cells?

More than 50%

Functions of proteins:

* Speed up chemical reactions
* Defense
* Storage
* Transport
* Cell communication
* Movement
* Structural support
* hormones (insulin)

Proteins are \[Blank\] with \[blank\] as their monomers.

Polymers, amino acids

Peptide bonds form between

each amino acid

polypeptide chains are

the polymer form of a protein

What is the link between DNA and protein?

Messenger RNA (mRNA)

DNA codes for

RNA sequence

RNA codes for

sequence of amino acids in a protein

transcription

uses DNA template to make complementary RNA

translation

use information in mRNA to synthesize proteins

Organism’s genotype (DNA) determines the

phenotype (Proteins)

Where does transcription take place?

the nucleus of a eukaryotic cell

Where does translation occur?

the cytoplasm, specifically within a ribosome (either free-floating or in the RER)

How are these processes different in a prokaryotic cell?

A prokaryotic cell has no nucleus, so they both take place in cytoplasm.

Three-base code referred to as

triplet code

Codon

group of 3 bases that specifies a particular amino acid

Start codon

only one (AUG), codes for methionine and will be important for the beginning of translation

Stop codon

three stop codons (UGA, UAA, UAG), do not code for an amino acid and result in the end of translation

In order for the code to work, the correct…

reading frame, or sequence of codons is needed.

Genetic code is: redundant-

all but two amino acids are encoded by more than one codon

Genetic code is: unambiguous-

one codon never codes for more than one amino acid

Genetic code is: non-overlapping

codons are read one at a time

Genetic code is: Nearly universal

all codons specify the same amino acids in all organisms

Genetic code is: conservative

if several codons specify the same amino acid, the first two bases are usually identical

Mutations are…

changes in the genetic information of the cell

What are point mutations?

changes in just one nucleotide pair of a gene - can lead to production of an abnormal protein

Mutations can be

Beneficial- increase fitness

Neutral - do not affect fitness

Deleterious - decrease fitness

Silent mutations -

have no effect on the amino acid produced by a codon because of redundancy in the genetic code

Missense mutations

still code for an amino acid, but not the correct one

Nonsense mutations

change an amino acid codon into a stop codon, most lead to a nonfunctional protein

Frameshift mutation\*

add or delete a nucleotide, almost always deleterious

Sickle cell anemia

affects the shape of RBCs and leads to low RBC count, pain, swelling, infections, etc.

What type of mutation is present in the Sickle Cell gene?

Missense mutation

Chromosome mutations: Deletion

segment of chromosomes is lost

Chromosome mutations: inversion

segment of chromosome breaks off, flips around and rejoins

Chromosome mutations: Duplication

segment of chromosome is present in multiple copies

Chromosome mutations: translocation

section of chromosome breaks off and becomes attached to another chromosome

Chromosome mutations can be

Beneficial, Neutral, or deleterious

Cancer cells exhibit

numerous deleterious chromosome mutations

Dr. Venki Ramakrishhnan

* Indian-born British and American structural biologist
* BS in physics
* Completed PhD in Physics in US
* Transferred to biology at UCSD
* Worked on ribosomes at Yale
* Work for determining 305 subunit of the ribosome
* Shared Nobel prize in chemistry

In what direction do RNA polymerases make mRNA from a template DNA strand?

5’ to 3’ direction

What makes RNA polymerase different from DNA polymerase?

RNA polymerase does not require an RNA primer

Prokaryotic cells have how many RNA polymerases?

One

How many RNA polymerases do eukaryotic cells have?

Three

Three stages of transcription.

1. Initiation
2. Elongation
3. Termination

Where does transcription occur in a prokaryotic cell?

holoenzyme

What is the holoenzyme made up of?

The core enzyme which is a RNA polymerase and sigma

How does initiation begin in prokaryotes?

Sigma recognized a promoter in the DNA

What are promoters?

* Segments of DNA that are 40-50 base pairs long
* Will be recognized by sigma within the holoenzyme and allow the start of transcription

/Once bonded to the holoenzyme, RNA polymerase will…

* Open up the double helix
* begin adding new nucleotides

During prokaryotic elongation…

the RNA polymerase will add new nucleotides to the growing 3’ end of the RNA

Prokaryotic termination happens when

the RNA polymerase transcribes a “transcription-termination signal”

What happens when the “transcription-termination signal” is transcribed?

The RNA polymerase will separate from the RNA transcript

What is different about the promoters in eukaryotic transcription?

The promoters are larger, including TATA box

What recognizes the promoter in place of the sigma protein?

Transcription factors

What leads to the termination of eukaryotic transcription?

A poly-A signal is transcribed

What type of cells will require RNA processing?

Just eukaryotic cells

What needs to occur to the primary transcript within eukaryotic cell?

1. Splicing
2. Addition of caps and tails

The 5’ end of the primary transcript receives….

a modified nucleotide, known as 5’cap

The 3’ end of the primary transcript receives…

a poly-A tail

Why do caps and tails need to be added?

* Facilitate export of mRNA to the cytoplasm
* protect the mRNA from hydrolytic enzymes
* help ribosomes attach to the 5’ end

What is the purpose of RNA slicing?

creates an mRNA molecule with a continuous coding sequence

In RNA splicing, introns must be…

removed

In RNA splicing, exons must be…

joined

What is the site that mRNA is translated into protein?

Ribosomes

What is unique about transcription and translation in a prokaryotic cell?

Ribosomes can begin translating before transcription is complete

How do transcription and translation run in a eukaryotic cell?

Separately

What does each transfer RNA (tRNA) carry?

A specific amino acid on one end

What is present on the other end of a tRNA molecule?

An anticodon

What is an anticodon?

three base pairs that attach to a complementary codon on mRNA

What do ribosomes allow for?

tRNA anticodons to recognize mRNA codons

What are ribosomes made up of?

ribosomal RNA (rRNA)

Translation initiation occurs when…

the start codon (AUG) signals

During initiation of translation…

small ribosomal subunit binds with mRNA and a special initiator tRNA

Translation elongation

amino acids are added one by one to the end of the growing chain

What direction does elongation proceed in translation?

Along the mRNA in the 5’→3’ direction

Elongation continues until….

a stop codon is read

What do stop codons code for?

release factors

Dr. Tracy L. Johnson

* American geneticist
* BA in Biochemistry and cell biology form UCSD
* PhD in Biochemistry and Molecular Biology from UC
* Studied RNA splicing at Cal IT
* Focuses on gene regulation, chromatin modification, and RNA splicing
* Known for work in diversity, equity, and inclusion in STEM

operon

set of operator and promoter sites and the structural genes they control

operator

acts as a go or a stop signal for transcription

promoter

segment of DNA where RNA polymerase initiates transcription

Negative regulation

1. Repressor protein
2. Repressor can bind to segment of DNA and block transcription from occurring
3. Includes both repressible and inducible operons

Positive regulation

1. Activator protein
2. Activator binds to segment of DNA to turn on transcription

Repression operon

Trp

Induction operon

Lac

Trp is short for

Tryptophan

What is feedback inhibition used for in this unit?

Starting and stopping the production of enzymes

Repression:

decreases gene expression and decreases enzyme synthesis