Biology 204 Chapter 9 Quiz

Nucleic Acid

Monomer: Nucleotide

Polymer: Nucleic Acid

• 1’ Nitrogenous base

• 5-Carbon Sugar

• 5’ 3 phosphate group

• 2’ OH (RNA) or H (DNA)

DNA

-Double stranded

-Thymine (ATCG)

-Deoxyribose sugar (2’ H)

-High replication stability, replicates more accurately than RNA → due to 2’ H’

-Blueprint for cell division (DNA replication)/Involved in DNA replication & protein synthesis (Transcription → Translation)

-Genetic material → involved in heredity

RNA

-Single Stranded

-Uracil (AUCG)

-Ribose sugar (2’ OH)

• 2’ OH leads to instability (very electronegative oxygen that wants to steal electros, causing oxidative stress and base damage → mutations)

-Low stability of RNA limits it to <1000 nucleotides

-RNA viruses mutate faster than DNA viruses, which is why RNA viruses require booster shots

DNA vs RNA stability

DNA is more stable because:

• 2’ H (No electronegative oxygen)

• Hydrogen bonding between DNA bases (2 OH groups face each other in RNA leading to instability)

• DNA is double stranded → Chemicals cannot access bases which minimizes chemical damage

-DNA genome is less prone to mutation so it can be millions to tens of millions of nucleotides

Protein

-20 Amino Acids

Very good catalytic stability

-More structurally diverse than nucleic acids (4 nucleotides and same basic structure) with wide range of properties & 20 amino acids → leads to more possible functions

-More diverse catalysts than RNA

RNA Evolution Supported Early Life

Original RNA → Ribozyme → more RNA + Catalysts → More mutations → Natural Selection → Evolution

Central Dogma

DNA → Transcription → mRNA → Translation → Protein

DNA Replication

-Semiconservative (Each double stranded molecule has one old strand and one new strand)

-Goal is 2 identical DNA molecules

-Separates by unzipping hydrogen bonds between base pairs

• Each strand exposed to nucleotides

-New strand synthesized from 5’→3’

• Strands are antiparallel (Starts at 3’ end of template)

-AT, CG

-Occurs at series of replication bubbles (occurs on both sides of replication bubble)

-Leading Strand: 3’→5’

-Lagging Strand: 5’→3’

Origin of Replication

Point at which DNA first unzips

-DNA unwinds in both directions from the origin to form replication bubble (DNA replicates through a series of replication bubbles)

-2 halves of replication bubble have opposite stranded-ness (One is 5’→3’ on one end, lagging strand, one is 3’→5’, leading strand.

Leading Strand

3’→5’ Template from origin to edge of the bubble.

-Synthesized continuously because DNA polymerase can extend 5’→3’ due to 3’→5’.

Lagging Strand

5’→3’ Template from origin to edge of the bubble

-Okazaki fragments

-Synthesizes discontinuously because DNA polymerase cannot extend 5’→3’ (due to 5’→3’ template)

Replication Fork

Where DNA double helix unwinding occurs with helicase

Helicase

Unwinds parental double helix at replication forks

-Moves away from origin of replication and unwinds DNA in both directions by breaking hydrogen bonds between complementary bases, creating replication bubble

-2 Helicase enzymes create replication bubble

Primase

Synthesizes RNA Primer at 5’ end of leading strand (3’ end of template) and at 5’ end of each Okazaki fragment of lagging strand (3’ end of template)

-Loading dock for other enzymes (no enzyme that can bind single stranded DNA and add DNA nucleotides)

DNA Pol III

Using parental DNA as template, synthesizes new DNA strand by adding nucleotides to an RNA primer or a pre-existing DNA strand

-Extends 5’→3’

DNA Pol I

Removes RNA nucleotides of primer from 5’ end (3’ end of template) and replaces them with DNA nucleotides

-Binds to RNA primer and replaces RNA nucleotides with DNA nucleotides from 5’→3’

DNA Ligase

-Joins Okazaki fragments of lagging strand & DNA of primer to DNA extended by DNA Pol III

-Joins 3’ end of leading strand DNA that replaces primer to rest of leading strand DNA (DNA extended by DNA Pol III) through a phosphodiester bond

Eukaryotic Replication Bubbles

Eukaryotes have multiple replication bubbles

-Each bubble replicates separately, but they eventually run together

-Dramatically increases speed of replication

End result of DNA Replication

-2 new, identical DNA molecules → semiconservative (one original and one new strand per DNA molecule)

Transcription

DNA→mRNA

-DNA Template

-Transcribes portions of DNA that encode proteins (genes) into mRNA for later translation, small portions of DNA (genes) are transcribed at any given time

Template Strand: 3’→5’, transcribed by hydrogen bonding of complementary bases

Coding Strand: 5’→3’, same sequence as mRNA except for Thymine & Uracil

-RNA Polymerase unwinds DNA and functions as “helicase”

Initiation: RNA Polymerase binds at promoter and unwinds DNA, transcription starts at TSS (Transcription start site) following promoter, RNA transcript forms along template strand DNA

Elongation: RNA Polymerase moves down the DNA, RNA transcription continues.

Termination: RNA transcript creates GC hairpin and polyU tail, RNA polymerase falls off, RNA transcript completed → transcription ends

DRAW

Initiation

RNA Polymerase binds at promoter, transcription starts at TSS (Transcription start site) following promoter, DNA unwinds and RNA transcript forms along template strand DNA

• Genome has many genes/coding regions as well as regions that do not encode protein

DRAW

Promoter

Signals start of mRNA transcript

Elongation

RNA Polymerase moves down the DNA, RNA transcription continues.

• RNA polymerase continues unwinding DNA and transcribing DNA into mRNA using complementary base pairing.

• Hydrogen bonds between DNA-DNA are stronger than DNA-RNA so RNA bases separate from DNA and DNA begins to rewind

DRAW

Termination

RNA transcript creates GC hairpin and polyU tail, RNA polymerase falls off, RNA transcript completed → transcription ends

• RNA Polymerase stops transcription after a GC hairpin with a polyU tail has been transcribed

• After RNA polymerase falls off DNA, DNA rewinds

• Transcription machinery can be used to transcribe same gene again or different gene

• mRNA goes to be translated in translation

DRAW

GC Hairpin with polyU Tail

Series of G-C repeats followed by a string of U’s

-G-C repeats: Spontaneously form hairpin structure (G-C hairpin made up of Hydrogen bonds)

• Gets stuck in RNA Polymerase → prevents it from continuing to travel across DNA → Stops transcription

-PolyU Tail: U binds to A on DNA, A-U Bonds are weak and cause release of mRNA

What type of bonds holds nucleotides in place before they have been connected to the growing chain?

Hydrogen bond (hydrogen bond to template strand)

What types of bonds does RNA polymerase create to connect RNA nucleotides to the growing transcript

Covalent bonds (monomer to monomer)

Replication vs Transcription

Differences:

• RNA polymerase unwinds DNA in transcription, Helicase unwinds DNA in replication

• mRNA uses Uracil instead of Thymine, DNA uses Thymine when replicated

• 5’→3’ DNA template is called the coding region in transcription, 5’→3’ DNA template is called lagging strand in replication

Similarity:

• Both use DNA as a template

• Template strand is 3’→5’

Translation

mRNA → Protein

-Nucleotide sequence used as template for sequence of amino acids that create a protein

-mRNA → tRNA complementary binds & brings amino acid

Completed in ribosome

mRNA

Photocopy of genetic message that encodes the protein (Copy of original DNA coding strand)

Codon

Series of three nucleotides that encodes an amino acid found on mRNA

Transfer RNA (tRNA)

Decodes nucleotide sequence into amino acids (“decoder ring”)

-Complementary binding to mRNA & brings amino acid (use codon chart to find proper amino acid)

Ribosome

Protein factory that creates proteins as directed by mRNA sequence

-Polypeptide chain created → Protein

Genetic Code Translation

Codon Chart

64 possible codons encoding 20 amino acids

-Unambiguous: Every codon only codes one specific amino acid

• Ex: AUG only codes for Met

-Redundant: Some amino acids encoded by more than one codon

• Ex: Val coded by GUU, GUC, GUA, GUG

Start Codon: AUG → Met (amino acid) (AUG encodes Met & Signals start of translation, following AUG are not a start, just a Met)

Stop Codons: UAA, UAG, UGA → Stop (NOT an amino acid), do not encode an amino acid, tell translation when to stop

5’ UTR is the untranslated region before the start codon

3’ UTR is the untranslated region after the stop codon