BIS 2A Midterm 3

Britt 2022

What are the three constituent molecules of a nucleotide?

Phosphate group, ribose or deoxyribose sugar, nitrogenous base

Which carbon atom is attached to the nitrogenous base?

1' carbon

Which carbon atom is attached to the phosphate group?

5' carbon

What is the purpose of DNA?

Storing genetic information
Stored in the nitrogenous base

What are the four nitrogenous bases in DNA?

Adenine, guanine, cytosine, thymine

What are the four nitrogenous base sin RNA?

Adenine, guanine, cytosine, uracil

What is the difference between the 5' end and the 3' end?

3' carbon in the pentose sugar with hydroxyl group
while 5' carbon is attached to the phosphate group

DNA is a

double stranded molecule
runs anti parallel

What is the name of the bond that connects two nucleotides?

phosphodiester bond (polar)

What is the function of DNA Polymerase I?

removes RNA primer and replaces them with DNA nucleotide

What is the function of DNA polymerase III?

Synthesizes daughter strands

Function of Helicase ?

separates parent DNA strands

Function of Ligase?

connects Okazaki fragments

Function of primase?

generates RNA primer

Function of telomeres?

lengthens telomeres

Function of single stranded binding proteins?

Reduces super-coiling of DNA,
which allows helicase to operate
Keep the strand separated by
holding them in place

Where does DNA replication take place?

Origin of replication

How does Helicase operate?

Breaks down hydrogen bonds between nucleotides which allows double-helix to separate

What direction does the DNA Polymerase III move along the template strand?

3' - 5'

What direction does the DNA polymerase III move along the daughter strand?

5' - 3'

mismatched proteins

detect mismatches and excise patch of nucleotides

What reduces spontaneous mismatches?

mismatch repair and proofreading by DNA polymerase

Another source of mutation?

UV induces crosslinks between adjacent primidines (C and/or T)

Why do UV induce mutation need to be repaired?

Because neither DNA polymerase nor RNA polymerase can get past them.

What allows repair on damaged base pairs?

the double stranded nature of DNA

mutation

new allele
crick base pairing

damaged nucleotide

example include accidentally methylated base
It will be detected and the methyl group will be removed
by O6methylguanine methyltransferase

DNA damage can be

mutagenic (can cause mutations)

mutation can not be

repaired

Error-free repair of a degraded double strand break

homologous recombination
unbroken sister chromatid is used as a template

What if a double strand break occurs but no sister chromatid is available?

the broken ends may simply be rejoined- which might result in a deletion mutation, if any bases were damaged or lost.

This is called a nonhomologous end joining

In eukaryotes...

there are 3 different RNA polymerases

In eubacteria and Archeans...

there are one RNA polymerases

rRNA

Ribosomal
- transcribes from ribosomal RNA genes
- makes up most of the ribosome
- stable

mRNA

- transcribed from protein-coding genes
-carries copy of coding region of gene
- translated to protein
- unstable

tRNA

- transcribed from tRNA genes
- an adaptor that recognizes sequences of nucleic acids on mRNA and pairs them with the correct amino acids
- stable, recycled

RNA is like DNA, but

ribose instead of deoxyribose (NTPs vs dNTPS)
Uracil instead of Thymine

Requirements for Transcription

DNA template, the appropriate RNA polymerase, Ribonucleotide triphosphate: ATP, UTP, CTP, GTP

Steps include:
1. Initiation
2. Elongation
3. Termination

Initiation and Promoter

Promoter is a DNA sequence that binds and directs RNA polymerase to initiate transcription

Specifies location, orientation, and fréquence of initiation

1st step of Initiation

RNA polymerase binds to DNA at the promoter

RNA polymerase unwinds and separates the DNA

2nd step of initiation

The 2nd strands of DNA separate within RNA polymerase, transcription begins (upstream)

RNA synthesis (elongation)

Synthesis is anti-parallel to the

template strand

RNA sequence matches that of the "coding strand"

Rules of RNA Transcription

- RNA polymerase moves toward the 5' end of the template strand
- mRNA is built antiparallel to the DNA, in the 5' to 3' direction
- new nucleotides are added to the 3' end of the strand
- RNA Pol. does not need a primer to start synthesis

Polymerase moves which way on the template strand

3' to 5'

termination =

dissociation of RNA polymerase from the DNA

Eukrayotic mRNAs must be processed from preRNA to mRNA in 3 steps

1. Capping of the 5' end
2. Polydenylation (adding many A's to the polyadenylation site)
3. Splicing which removes introns - noncoding sequences - from pre-mRNA

codons

sixty four - three letter 'words' spelled by RNA basses
sense = correspond to an amino acid

How is the information from the genetic code converted into the language of amino acids?

There must be an adapter molecule (tRNA)

Where do tRNAs come from?

They are encoded by genes, transcribed by RNA Polymerase III (in eukaryotes)

More tRNA facts

They are recycled - amino acid carriers
enzyme double checks that the correct amino acid is attached to the tRNA

A charged tRNA has

had the correct amino acid attached to its 3' end

Animoacylation of tRNA

adding an amino acid to the 3' end of a tRNA = "charging"

What do adapter molecules do?

Hold amino acids and interact with mRNA codons

What happens when RNA polymerase hits a nonsense mutation?

Transcription continues until a transcription termination site is reached.

Circular DNA is found in which type of cell?

Both prokaryotic and eukaryotic cells

Strong Promoter means

RNA Polymerase binds very tightly, so the transcription rate is high

In what type of cells doe genes contain exons, which are interrupted by introns, which are spliced after transcription?

Eukaryotic cells

Which of the following represents a change that CANNOT be passed on
to the next generation?
A. Changes in gene expression due to increased production of a hormone.
B. Changes in DNA packaging leading to gene silencing.
C. Changes in DNA sequence due to exposure to radiation.
D. None of the above, as they are all heritable changes.

A. Changes in gene expression due to increased production of a hormone.

Eukaryotic DNA is packed into nucleosomes due to the action of:

Histones

Does RNA polymerase require help to bind to weak promoters?

Yes

The role of ligase is to

seal nicks (single strand breaks in the backbone) in DNA

What is the role of DNA Pol I in DNA replication?

Replaces primers required for DNA synthesis with DNA

DNA double strands breaks are intentionally generated by the cell during ... and are repaired via ...

Meiosis, homologous recombination

The promoter tells RNA polymerase:

where to begin transcription
How often to being transcription
Which strand to transcribe

RNA splicing

eliminate internal noncoding sequences from mRNA

Horiztontal gene transfer includes

Examples:
Insertion of a gene from a jellyfish into a mouse
The generation of the first eukaryotes from a bacterium and an archean

Positive regulation

Transcription factor increases transcription by binding to a regulatory element (activation)

Negative regulation

Transcription factor blocks transcription by binding to a regulatory element (repression)

What are the layers of gene regulation?

1) Promoter strength: weak or strong
2) transcription factor: activator or repressor
3) regulation of the transcription factor

What are regulatory sequences?

Regions of DNA with specific sequences that can, when bound by a transcription factor, help increase or decrease gene expression

What is an enhancer?

Regulatory sequence that helps enhance (increase) gene expression

silencer

regulatory sequence that helps inhibit (decrease) gene expression

effector

a molecule that binds transcription factors to change transcription

inducer

a molecule that binds to repressors to deactivate them (prevent binding to DNA) or binds to activators to activate them (allow binding to DNA)

inhibitor

a molecule that binds to activators and prevents from binding to DNA (opposite of inducer)

operator

a regulatory sequence to which a repressor can bind
These are found in Prokaryotic cells

The majority of DNA in bacterial cells is synthesized from:

DNA polymerase

Without primase...

Replication would be unable to start

DNA FACT

DNA is negatively-charged and migrates from the negative end to the positive end

Which of the RNA molecules can be described as a copy of the gene that codes for a protein?

mRNA (carries the genetic information necessary to build a protein)

Hydrogen bonds between nitrogenous bases

A and T = 2
G and C = 3
A and U = 2

Where does DNA replication and transcription occur in eukaryotes?

The nucleus

Where does translation occur in eukaryotes?

The ribosome

Where does DNA replication occur in prokaryotes?

Cytoplasm

Where does transcription and translation occur in prokaryotes?

Cytoplasm

What sites must be present in DNA so that RNA polymerase can transcribe the DNA to RNA?

RNA binding site
transcription start site
transcription stop site

What two things does the promoter determine?

where RNA polymerase binds to DNA

What is the -10 sequence in the promoter known as?

TATA box

How does a base-pair change in the promoter affect transcription?

Base-pair changes affect the ability of RNA polymerase to recognize and bind to the promoter

Transcription: Elongation

Double stranded DNA that enters from the front of the enzyme is unwound and the template strand is made available for complementary base pairing

Two DNA strands reunite at the trailing end of the transcription bubble while the single-stranded RNA emerges alone

The bubble generated by RNA polymerase is small

In transcription elongation, when joining nucleotides together, what is the exergonic reaction?

Breaking of the phosphoanhydride bond

What is the purpose of the 5' cap?

Regulation of nuclear export
prevention of degradation by exonucleases
promotion of translation
promotion of 5' proximal intron excision

What is splicing?

Splicing removes introns and splices exon together
Multiple proteins can be obtained from one gene
Exon exit the nucleus, whereas the introns stay

initiation summary

the ribosome assembles around the mRNA. The first tRNA is attached at the start codon

Elongation Overview

The tRNA transfers an amino acid to the tRNA corresponding to the codon. The ribosome then moves to the next mRNA codon to continue the process, creating an amino acid

termination overview

When a peptidyl tRNA encounters a stop codon, the ribosome folds the polypeptide into its final structure

Which direction does tRNA attach to mRNA?

Antiparallel
IF mRNA is read 5'-3', the tRNA will be 3'-5-

What enzyme attaches amino acid to tRNA molecules?

Aminoacyl tRNA syntestases attach amino acids to the tRNA molecules

Missense Mutation

A mutation that results in a different amino acid in the peptide chain