Biology 189 Ch.7 DNA Structure and function

mRNA vaccine example

Covid vaccine consists of COVID-19 spike (coat) protein mRNA and lipids (similar to cell membrane lipids)

Where does translation occur?

Cytoplasm

DNA can be tightly bound to histone proteins that can prevent gene expression. Chemical modifications of histones can open up (or close off) DNA for transcription

DNA availability

What are the 6 mechanisms for regulating gene expression in eukaryotes?

DNA availability, Transcription factor availability, mRNA processing (alternative splicing), mRNA transport from nucleus, RNA degradation, and Protein processing and degradation

Polymers made up of nucleotide monomers

Nucleic acids

Where does Transcription take place in the nucleus and what is it performed by?

Nucleus, performed by RNA Polymerase.

Protein-based infectious particles

Prions

In humans, how many genes spread across how many chromosomes?

25,000 genes spread across 23 chromosomes

Chromosome pairs are called what? what do they contain?

homologous chromosomes, they contain the same genes in the same locations

Short RNA molecules that fold into a unique "t" shape

tRNA

What happens in the attachment step in viral replication?

virus binds to host cell surface receptors

What happens in the penetration step in viral replication?

virus genome enters the host cell - Phagocytosis - Injection

How many circular chromosomes do prokaryotes typically have?

a single circular chromosome

Define start Condon

a specific codon that starts amino acid incorporation

Define genome

all of the DNA inside of a cell

The strands of DNA run

anti-parallel

In Elongation, RNA polymerase then begins to move along what and reads what?

begins to move along the DNA strand and "reads" the DNA template

Bacteria can turn genes on or off depending on what?

depending on what resources are available

Sugar and phosphate groups make the rails aka the...

"sugar-phosphate backbone"

-Misfolded proteins that cause other proteins to misfold - Result in massive accumulation of misfolded proteins resulting in cell death - Mad cow disease is caused by prions- typically from eating nervous tissue of previous infected cows

"zombie proteins"

What happens in the elongation step of translation?

- After Met, the ribosome moves the mRNA down one codon - The next codon is read and the appropriate tRNA enters the ribosome - Ribosome makes covalent peptide bond between amino acids then kicks tRNA out as ribosome moves down one codon -Next codon is read, new tRNA enters, and next amino acid is added

What happens in the termination step of translation?

- Specific "stop codons" indicate where the protein ends - Protein release factors bind to the stop codons and cause ribosomes to release from mRNA

What happens when the ribosome "reads" the mRNA codon?

- The appropriate tRNA enters the ribosome - Codon-anticodon base pairing (RNA-RNA base pairing: C-G; A-U) -The new amino acid is covalently bound to the previously-added amino acid in the growing polypeptide chain

All eukaryotic polypeptide sequences have Met as what?

1st a.a

1 parent cell =

2 daughter cells

What are the three steps in translation?

1. Initiation 2. Elongation 3. Termination

Transcription takes place in the nucleus in 3 steps, what are those steps?

1. Initiation 2.Elongation 3.Termination

How much energy is spent on gene expression?

90%

A segment of DNA that contains instructions to make a specific protein or RNA molecule

A gene

What is the start Condon for eukaryotic?

AUG and codes for the amino acid Methionine (Met)

What are the 4 different nucleotides (different nitrogenous bases)?

Adenine (A) and Guanine (G), Cytosine (C) and Thymine (T): Pyrimidines

What does not work against viruses?

Antibiotics

What are the 5 stages of viral replication?

Attachment, penetrations, synthesis, assembly, and release

The sequence of one strand can be used to determine the sequence of the other strand

Complementary base pairing

which step in transcription adds complementary RNA nucleotides to a growing RNA molecule as it moves down the gene

Elongation

Segments joined together to make mature mRNA

Exons

The 20+ different amino acids provide proteins with a huge variety of molecular interactions such as?

H-bonds, hydrophilic, hydrophobic, charged, uncharged, etc.

Segments removed from pre-mRNA- trash RNA

Introns-

A group of genes that function to break down lactose sugar but are expressed only in the presence of lactose sugar

Lac operon

What happens when lactose is present in regulating gene expressions in prokaryotes?

Lactose physically binds to the repressor and the repressor falls off of the operator

Viral genome incorporated into host genome (prophage) - Viral genome maintained within host until conditions trigger entry into lytic phase - Stressful conditions can cause this transition - Sometimes host genes can be incorporated into viral genome

Lysogenic phase

What are the two potential lifecycle phases?

Lytic and Lysogenic phases

Rapid viral replication which causes infected cells to die - Massive release of new viral particles into the organism/ environment

Lytic phase

Any external agent that induces mutations

Mutagens

Describe a tRNA molecule

One end binds to a specific amino acid, the other end has 3 nucleotides that are complementary to the codon= anticodon

A DNA sequence between the promoter and the protein-coding genes and serves as a regulatory region

Operator

A clustered group of genes related to a specific function that can be turned on or off as needed

Operon

Code the required proteins

Operon genes

Site where RNA polymerase binds

Promoter

Acts as a signal for where the gene starts and what strand to use as template

Promoter region

Just like mRNA, proteins can be regulated at the level of production and degradation. Some proteins get degraded as they are transcribed while others can be maintained long after production.

Protein processing and degradation

Adenine (A) and Guanine (G):

Purines

Cytosine (C) and Thymine (T):

Pyrimidines

Enzymes in cell actively degrade RNA. mRNA can be chemically modified which can change its "lifespan" and the likelihood that a transcript will be made into a protein or not.

RNA degradation

Proteins known as transcription factors recruited to promoter and guide RNA polymerase to bind with what?

RNA polymerase binds with template DNA strand at the correct location

What happens when no lactose is present in regulating gene expressions in prokaryotes?

Repressor proteins bind to the operator and physically stops RNA polymerase and operon gene expression

What is translation performed by?

Ribosomes

In translation, what do the ribosomes read?

Ribosomes read 3 bases at a time (Condon)

Point mutations that do not change the protein's amino acid sequence • Genetic code redundancy tolerates mutations in the third base (wobble) position of a codon

Silent mutations

Mutations can affect what?

Single DNA base, a few bases, or large portions of chromosomes

The process of removing introns and connecting exons from pre-RNA to form mature mRNA

Splicing

which step in transcription recognizes the termination sequence and releases from the DNA • mRNA molecule released

Termination

What happens in the step of initiation in translation?

The mRNA cap helps mRNAs associate with ribosomes but does not specify any amino acids

Specialized RNA molecules called "transfer RNA" (tRNA) carry specific amino acids to what?

The ribosome

What happens in the assembly step in viral replication?

The viral particles assemble and the genetic information moves inside

A gene's DNA sequence is rewritten into a messenger RNA (mRNA) molecule in the nucleus

Transcription

Proteins that bind to promoter regions of DNA and help direct RNA polymerase to gene• No transcription factor - no gene expression

Transcription factor availability

Converting the mRNA code into a polypeptide (protein) sequence

Translation

The mRNA molecule leaves the nucleus and enters a ribosome (free or bound) where the mRNA codes for the specific amino acids in a polypeptide chain

Translation

Very small protein shells that contain genetic material made of either DNA or RNA

Viruses

What describes the flow of information from DNA to RNA to protein molecules

central dogma

What do Polysomes increase?

increase protein synthesis efficiency

Removal of certain introns/ exons can have dramatic effects on downstream protein products (see earlier slide)

mRNA processing (alternative splicing)

Segments of RNA are removed and the remaining segments are joined together

mRNA splicing

If mRNA is not specifically transported from the nucleus, it will not become a protein

mRNA transport from nucleus

What does alternative splicing + post-translational modifications increase?

massively increase total number of proteins a cell can make vs. # genes

How many linear chromosomes do prokaryotes typically have?

multiple linear chromosomes

In sexually reproducing organisms- chromosomes come in pairs, from where do they come from?

one chromosome from the mother and one chromosome from the father

Paired nitrogenous bases joined with hydrogen bonds

rungs

What happens in the synthesis step in viral replication?

the host cell is hijacked to produce millions of copies of the viral genome and viral proteins - Host cell provides all of the resources- ATP, ribosomes, nucleotides, amino acids, enzymes

What happens in the release step in viral replication?

the host cell releases the newly formed viral particles - Some viruses kill host cell during release (lysis) while others are released via exocytosis (vesicles)