Unit 2 Material Bio 116

describe the structure of a nucleotide

a 5-carbon sugar connected to 1 or more phosphate group(s) (via 5' carbon) and a nitrogenous base

What is the difference between a purine and pyrimidine base?

Purine- Has 2 carbon-nitorgen rings
Pyrimidine- Single carbon-nitrogen ring

How is a polynucleotide formed?

Via 5'-3' phosphodiester linkage- The phosphate group connects to the 5' carbon of one sugar and connects to the 3' carbon of the sugar on the next nucleotide

What is the function of a nucleic acid?

Carries hereditary information and instructions for cells function

What are the differences in nucleic structure of DNA vs RNA?

1. Dna is made of the sugar deoxyribose whereas RNA is made of the sugar Ribose
2. the pyrimidines of DNA are Thymine (T) and Cytosine (C) whereas in RNA its Uracil (U) and Cytosine (C)

How does the simple primary and secondary structure of DNA hold the information needed to code for the many features of multicellular organisms?

The base sequence of DNA carries coded information.

What is the difference between a ribonucleotide and a deoxyribonucleotide?

Ribonucleotides have a hydroxyl group on the 2 carbon of their sugar subunit.

explain how nucleic acids have directionality and polarity?

because one end has an unlinked 3' carbon; the other end has an unlinked 5' carbon.

Which direction are nucleic acids written in?

5' to 3'

What is the complimentary strand to the following sequence:

5'-ACCGGTATC-3'

5'-GATACCGGT-3'

when a DNA strand is heated, which base-pair will break first? why?

Adenine-Thymine because there is only two hydrogen bonds between them (G-C has 3)

What bonds hold together the single sequence of DNA?

Covalent Bonds (phosphodiester bonds)

what bonds hold together the double helix of DNA?

Hydrogen bonds between base pairs

what bonds hold together the higher order structure of DNA?

Electrostatic (ionic) interactions

What is the product of DNA replication?

2 strands: each contains one parental strand and one daughter strand (strand made from replication). because in replication each strand replicates itself.

If a molecule contains 20% Adenine, how much Thymine and Guanine respectively does it contain?

20% Thymine, 30% Guanine. (Recall Chargaffs rule: equal amounts of A & T, equal amounts of G & C but the two pairs don't have to be equal to each other)

What provides the energy for the polymerization reactions in DNA synthesis?

the deoxyribonucleotide triphosphate substrates

A, B, C or D?

B. (the 3' end )

In double-stranded DNA why are certain purines base-paired with certain pyrimidines?

Because only certain purine-pyrimidine base pairs have the same geometries

Which bases are Purines?

Adenine and Guanine

Which Bases are Pyrimidines

Thymine and Cytosine

Semiconservative replication involves a template. What is the template?

one strand of the DNA molecule

True or False: An error is the same as a mutation.

Support your answer

False
An error- occurs during replication
mutation- an error becomes a mutation if it is not fixed before the next round of replication

What is the origin of replication?

The specific nucleotide sequence where replication begins. Helicase bonds to the origin of replication and breaks hydrogen bonds to unwind DNA creating the replication fork as DNA opens into a Y-shape.

In detail describe the process of replication

1. DNA unwinds at the origin of replication

2. Helicase opens up the DNA by breaking H bonds, forming replication forks

3. Single-stranded binding proteins (SSBP) coat the DNA around the replication fork to prevent rewinding of DNA

4. Topiosomerase binds at the region upstream of the replication fork to prevent supercoiling

5. Primase synthesizes RNA primers complementary to the DNA strand

6. Dna polymerase III starts adding nucleotides to the 3'-OH end of the primer (recall its read 3'-5' so the product is 5'-3') 7.Elongation of both the lagging and leading strand continues

7. RNA primers are removed

8. Gaps are filled by DNA pol I

9. the strand fragments reconnected by DNA ligase catalyzing phosphodiester bonds

What is the function of the protein Helicase in replication?

Breaks hydrogen bonds, unwinding DNA double helix

What is the function of the protein Topiosome in replication?

Binds upstream of replication fork and ensures that DNA does not supercoil. Relaxes supercoiled DNA

What is the function of the protein primase in replication?

Synthesizes RNA primers on leading and lagging strand

What is the function of the protein Single-stranded binding proteins in replication?

coats single-stranded DNA to prevent rewinding

What is the function of the protein DNA polymerase I in replication?

Replaces RNA primers with DNA nucleotides

What is the function of the protein Polymerase III in replication?

adds nucleotides in the 5'-3' direction

What is the function of the protein Ligase in replication?

Catalyzes phosphodiester bond formation to fix any damage caused to the strands during replication

Describe Okazaki fragments

because polymerase extends in the 5'-3' direction the lagging strand (3'-5' strand) is broken into fragments and each requires a primer to start synthesis

True or False: The leading strand is synthesized towards the replication fork

True, the leading strand is 5'-3' so it is read 3'-5' (to produce a product that is 5'-3') therefore towards the replication fork

Explain DNA pol "proofreading function)

as DNA pol moves along is can feel any bumps caused by the wrong base being in that spot which causes the geometric shape to be incorrect. When is feels a bump it will remove that base and replace it with the correct base, smoothing the bump

Describe the 4 types of mutation

1. Frameshift: result of insertion or deletion, All bases in the sequence are shifted over
2. Nonsense: Mutation that produces a stop codon within a gene sequence resulting in a portion of the gene not being read that was supposed to be.
3. Missense: when a base is miscoded (e.g. supposed to be GAA but instead is CAA) resulting in a codon that codes for a different (the wrong) amino acid
4.Silent: when a mutation occurs but the result has no affect because the produced codon codes for the same amino acid

Describe the 4 Chromosome-level mutations

1.Inversions: Section of chromosome break, rotate and rejoin
2.Translocation: Section of chromosome breaks and attaches to another chromosome
3.Deletion: When section of chromosome is lost
4.Duplication: when DNA is copied and inserted next to the old one

True or False: If a chromosome level mutation occurs during mitosis it only affects one cell, if it occurs during meiosis it will affects all cell offspring

True

True or False: If a chromosome level mutation occurs during meiosis it only affects one cell, if it occurs during mitosis it will affects all cell offspring

False

If DNA poly does not correct an error what else can?

Mismatch repair mechanisms can be activated (base-pair excision repair for short sequences errors, nucleotide excision repair for long errors)

The size of a genome is measured by...?

number of base pairs

How do you predict which organism will have a larger genome?

It is impossible! There is no rhyme or reason to it.

What is the function of telomerase?

Solves the issue of the directionality of lagging strand synthesis (away from replication fork) causing the loss of DNA, shortening of the telomere (end cap of chromosome) Telomerase can reverse these effects, restoring lost DNA

Fill in the blanks:
Each chromosome is made of .______. During replication, the chromosome splits into two ______ _______

1. Chromatin
2.Sister Chromatids

what is a genome?

contains all genetic information in the cell. Contains all coding and non-coding DNA components

True or False:
A genome contains only the coding components of DNA

False

True or False:
A genome contains both non-coding and coding components of DNA

True

Define Ploidy

the number of sets of chromosomes in a cell

Define Haploid

one set of chromosomes

Define Diploid

two sets of chromosomes (e.g. one set of chromosomes from each parent)

What is a gene?

A region of DNA that codes for proteins, Contains a regulatory region (other regulatory regions + promoter sequence) and a transcribed region (the region being read and used to synthesize RNA)

What is the +1 site? Where along the gene is it located?

the transcription start site. Located at the very start of the transcribed region.

What does the theory of Central Dogma state?

genetic information only flows in one direction
DNA ----> RNA ----> Protein

what 2 things is genetic code?

1. Degenerate: amino acids are encoded by nucleotide triplets and the given amino acid can be coded by more than one codon

2.Universal: Virtually all species use the same genetic code for protein synthesis

DNA is read _____(direction) and synthesized _______ (direction)

1. 3'-5'
2. 5'-3

What is the promoter sequence?

The DNA sequence that the transcription machinery & RNA poly bind to to start transcription

Describe the stages of Transcription in prokaryotes

1.Sigma (o) binds to the promoter region
2. The holoenzyme assembles
3. The helix is opened and the DNA template strand is threaded through the interior of RNA polymerase
4.Transcription begins, incoming RNA nucleotide triphosphates can come in & base pair with the DNA template
5. Sigma is released
6.Pressure builds as RNA elongates giving RNA pol the energy to escape the promoter and continue down the template strand
7. Termination occurs either as a result of Rho-dependant or Rho-independant

Describe rho-dependant termination

Caused by rho protein. The protein follows behind RNA pol and when the pol runs into a series of G nucleotides it slows down, the rho protein crashes into pol causing the RNA pol to release from the transcription bubble

Describe rho-independant termination

controlled by DNA sequences. When RNA pol runs into a series of G nucleotides, the mRNA folds back on itself (called a stable hairpin formation) and pol stalls when it reaches an A-T rich region and the interaction caused by the stable hairpin causes enough instability that pol breaks off.

How do you locate the -10 box?

count 10 bases upstream of the +1 region (it is not exactly 10 bases up but within the region)

Fill in the blanks:
Stable hairpin is made of _____ bonds and is an example of nucleic acid _______ level structure

1. Hydrogen/Base pair
2.Secondary

How can you tell which strand is the template strand and which is the non-coding strand for transcription?

Template-opposite code to mRNA
Non-coding- Same as mRNA

What is a difference between prokaryotic and eukaryotic initiation of transcription?

In eukaryotes, proteins called transcription factors must bind to the promoter region first and help recruit the correct polymerase (depending on type of gene). Prokaryotes do not need/have transcription factors

When does translation take place in Eukaryotes and Prokaryotes?

Eukaryotes- after the completion of transcription, mRNA exits the nucleus and translation begins
Prokaryotes- can occur at the same time as transcription

What is splicing?

In eukaryotic genes, splicing occurs which is the process of removing the introns from the genetic sequence, leaving only the exons. Introns are non-

What benefit does splicing have?

Removing introns from the genetic sequence means you are removing

What is 5' capping? When does it occur?

5' capping- when a 7-methylguanosine cap is added to 5' end to start the assembly of ribosomes. This proccess occurs during mRNA synthesis

What is 3' poly-A tail? When does it occur

3' poly-A tail: an enzyme adds a poly-A tail to the 3' end to create a binding site for the protein that comes to move mRNA to the cytoplasm for translation. Adding this poly-A tail occurs after the completion of mRNA synthesis.

What is the role of mRNA in translation?

carries message (code for protein synthesis)

What is the role of tRNA in translation?

acts as an adaptor between mRNA (ribosomes) and amino acids.

What is the role of rRNA in translation?

stitches amino acids together in the correct order inside the ribosome

What is the role of ribosomes in translation? Where are ribosomes found in eukaryotes and prokaryotes

the site of protein synthesis, catalyzes peptide bond formation. Found in the rough endoplasmic reticulum of eukaryotes and the cytoplasm of prokaryotes

What is the role of Aminoacyl tRNA synthesase?

attach amino acids to correct tRNA

True or False:
each mRNA template can be coded many times

true

explain the process of translation, be specific.

1. Initiation: the ribosome anchors to mRNA upstream of start codon. tRNA interacts with start codon

2.Elongation: mRNA template provides binding specificity for tRNA. The ribosome moves along the template, registering each codon and binding with a charged tRNA anticodon occurs. tRNAs enter and leave the ribosome as each new amino acid is added to the polypeptide chain

3.Termination: a stop codon is encountered, a protein called the release factors binds to ribosome (like a tRNA) and without the charge from a tRNA the ribosome is unable to catalyze the formation of peptide bonds. Peptide chain gets released and the ribosomal complex falls apart

What is the difference between prokaryotic and eukaryotic translation?

1.Eukaryotic mRNA undergoes post-transcriptional modifications (5' cap, 3' poly-A tail, splicing)

2. Difference is in initiation, for ribosome binding in bacteria there is a ribosome binding site that is complimentary size/shape to the ribosome that the ribosome binds to. In eukaryotes the ribosome recognizes the 5' cap and scans along the mRNA from there looking for the start codon (AUG)

True or False:
Genes are expressed when needed

True

True or False:
Genes are always expressed

False. Genes are only expressed when needed

What is an operon?

a region of bacterial DNA that encodes for a series of functionally related genes, that are transcribed using a single promoter sequence.

When does gene regulation occur in eukaryotes vs prokaryotes?

Eukaryotes: basically at any stage
Prokaryotes: Regulation at transcription only

Why is gene regulation necessary?

To ensure that only the genes needing to be expressed at that specific time are expressed. If all genes were being expressed at once (no regulation) it would be impossible to maintain or pinpoint the needed gene at that time

How are prokaryotic genes regulated?

With the use of operons at the transcriptional level

Choose all that apply:
Which method is utilized by eukaryotes to control their gene expression that is not used in bacteria?

-Control of transcript processing
-epigenetic control (i.e. control of DNA packing)
-translational control
-transcriptional control

-Control of transcript processing
-epigenetic control (i.e. control of DNA packing)
-translational control

What does it mean when an operon is "inducible"?

An inducible operon is one that is usually turned off and requires an inducer to turn it on

Explain negative vs positive regulators. Include an example from the lac operon.

When a negative regulator binds, transcription is turned off. (e.g. when lac I binds to the negative regulatory site (which overlaps the promoter site) it blocks the promoter site and RNA pol is unable to bind to begin transcription)

When a positive regulator binds it promotes or turns on transcription. (e.g. the CAP in the lac operon binds to the positive regulatory site and helps RNA pol bind to the promoter)

Define Enhancer

A regulatory region of DNA that controls when a specific gene is activated

Why are operons useful?

They allow for gene regulation at transcription and they save space by creating multiple needed proteins from the same mRNA template.

Explain what is going on in the lac operon in the following scenarios:

1. No lactose in the cell
2. lots of lactose in the cell
3. lactose is running out (being used up)

1. Lac I is produced and has no lactose to interact with so binds to promoter region. Transcription is blocked
2. Lac I interacts with lactose, changing shape, making it unable to bind to the promoter region. Transcription occurs
3. Once lactose gets used, Lac I changes back to its original shape and is able to bind to the promoter region. Transcription becomes blocked

Describe transcription factors and the 2 types

Transcription factors are proteins that regulate where and when genes are expressed in eukaryotes.

1.General: bind to core promotor region and help RNA pol bind
2. Specific: Bind to enhancer regions outside of core promoter region and interact with proteins at core to enhance or repress activity of RNA pol

True or False:

a single transcription factor can regulate for many genes in different places

True

True or False:

a single transcription factor can regulate only one gene

False.
a single transcription factor can regulate for many genes in different places

True or False:

Eukaryotes have operons

False

What are epigenetic changes

Epigenetic mechanisms control access to the chromosomal region to allow genes to be turned on or off. These mechanisms control how DNA is packed into the nucleus by regulating how tightly the DNA is wound around histone proteins. Transcription cannot occur if DNA is tightly wound

What is the difference between a ribonucleotide and a deoxyribonucleotide

Ribonucleotides have a hydroxyl group on the 2 carbon of their sugar subunit.

Imagine a case in which the start codon of a gene is deleted. Which of the following processes would subsequently be affected?

Translation

Various species of Chrysanthemum have 18, 36, 54, 72 and 90 chromosomes. This variation is likely due to:

polyploidy

In comparison to a functional mRNA, how large is the primary transcript in a 1. eukaryote 2. prokaryote? why?

1. Eukaryote primary transcript is larger
2. Prokaryote primary transcript is the same size

this is due to the process of splicing that occurs only in eukaryotes where half the gene sequence (the introns) are removed.

Fill in the blank:
There should be a strong positive correlation between the rate of protein synthesis and _______ in the cell.

Number of ribosomes

What molecule/feature ensures that the correct amino acid is added when reading a specific codon during translation?

the charged anticodon of aminoacyl tRNA

What is the primary difference between an error and a mutation is...?

an error can still be fixed, a mutation is permanent