BIOL1400A Second exam

Role of nucleus

command center, stores genetic instructions that encode DNA, DNA directs protein synthesis

DNA organization

DNA is coiled with proteins into chromosomes, when not dividing DNA+protein=chromatin before division chromatin coils into visible chromosomes

Nuclear envelope

double membrane, controls material flow in/out of nucleus, contains protein lined pores that regulate molecular traffic and connect the endoplasmic reticulum

nucleolus function

synthesizes ribosomal RNA, combines rRNA with cytoplasmic proteins to form ribosome subunits, subunits exit nucleus → assemble into functional ribosomes in the cytoplasm

Messenger RNA

mRNA transcribes protein making instructions from DNA, mRNA exits the nucleus → translated by ribosomes into proteins

Nucleotides

monomer of DNA/RNA

Nitrogenous bases A,C, G, T(U in RNA), sugar, phosphate group

covalent bonds between sugar and phosphate from backbone

purines

double ring, A and G

pyrimidines

one ring T,C,U

DNA

lacks one O2 atom (-H instead of -OH)'

double helix, Watson and Crick(1953), Roslind Franklin X-Ray

Stores genetic info, passed during cell division and reproduction

Chargaff’s rules

A=T C=G in DNA

A=T 2 hydrogen bonds

C=G 3 hydrogen bonds

Semiconservative model

contains one parental strand and one newly synthesized strand

Replication process of DNA

DNA separates, free nucleotides align with base pair enzymes link nucleotides → new strands

it can start in different origins in eukaryotic chromosomes → faster replication

Orientation of DNA

antiparallel, DNA polymerase only adds to the 3’ end daughter strand grows 5’-3’

strands run opposite to each other

one runs 3’-5’ other runs 5’-3’

Okazaki fragments and enzymes

leading strand- synthesize continuously

lagging strand- synthesize in short pieces

DNA ligase- joins fragments into continuous strand

DNA polymerase- synthesizes DNA, proofreads and corrects errors, repairs damage from radiation/toxins

genotype→ phenotypes

DNA based sequence → physical traits

DNA→RNA→Protein

Transcription: DNA→RNA

Translation: RNA→ polypeptide

occurs from nucleus →cytoplasm in eukaryotic cells

Historical foundations of genes

Archibald Garrod(1902): genes→enzyme→traits

Beadle+Tatum(1940s): bread mold mutants lacked enzymes each defective gene→ missing enzyme led to “one gene-one enzyme” hypothesis

Modern understanding of genes

genes code for all proteins, some proteins = multiple polypeptide → multiple genes. Alternative splicing→functional RNAs

Current definition of gene

DNA region that can be expressed to produce a functional product: either a polypeptide/RNA molecule

Transcription (Prokaryotes)

Copy DNA → RNA

RNA polymerase

Start site: promoter sequence

End site: terminator sequence

Template: 1 DNA strand used

A-U, C-G (U replaces T in RNA)

RNA Processing (Eukaryotes)

occurs in nucleus before mRNA exits

5’ cap: modified G nucleotide

3’ tail: 50-250 A nucleotides which protects mRNA, aids export, helps ribosome binding

Introns, Exons

Introns

removed in RNA processing (noncoding)

Exons

joined in RNA processing (coding)

Result and Benefit of Introns and Exons

Result: continuous coding sequence

Benefit: one gene → multiple proteins via exon variation

Flow of genetic information

Central dogma: DNA → RNA→ protein

Transcription: DNA is copied into RNA

Translation: RNA codons are decoded into amino acids

5’ end

phosphate group

3’ end 

hydroxyl group (-OH)

codon

3 base RNA sequence that specifies the amino acids

triplet codon

64 possible codons; enough to code for 20 amino acids

start codon

AUG (methionine)

Stop codon

UAA, UGA, UAG

Redundancy

multiple codons can code for the same amino acid

universaltiy

genetic code is shared across nearly all organisms

GMOs

genes artifically inserted

transgenetic

GMO with foreign DNA from another species

tRNA

transfer RNA, transfer amino acids to ribosomes during protein synthesis, picks up specific amino acids, matches mRNA codons via its anticodon. Single RNA strand, clover leaf shape, contains modified bases, anticodon region pairs with mRNA codon, amino acid attachment site on opposite end, 20 aminoacyl-tRNA synthases, use ATP to bind correct amino acids to match tRNA

Ribosomes

coordinate with mRNA and tRNA to synthesize polypeptides. 2 Subunits: small (binds mRNA) and large (binds tRNA). Made of proteins and rRNA. P site- growing polypeptide. A site- accepts incoming aminoacyl-tRNA

initiation of translation

mRNA binds to small ribosomal subunit, inhibitor tRNA(anticodon UAC) pairs with start codon (AUG) carrying methionine (met), large subunit joins forming functional ribosome

Elongation of translation

1. tRNA anticodon pairs with mRNA codon at A site

2. Peptide bond forms between polypeptide at P site and new amino acid at A site

   1. Empty tRNA exits; ribosomal shifts tRNA with polypeptide from A → P site

Termination of Translation

stop codons (UAA, UAG, UGA) signal the end

polypeptide released; ribosome disassembles

energy source of translation

GTP powers elongation

mutations in translation

wrong codon can make wrong protein and can be spontaneous or mutagens

transcription

DNA→mRNA happens in eukaryotes nucleus and prokaryotes cytoplasm

translation

mRNA→ polypeptide cytoplasm, initiation, elongation, termination

protein folding

polypeptide fold into tertiary/quaternary structures

silent mutation

no change in protein

missense mutation

one amino acid changes

nonsense mutation

codon becomes stop → funky protein

frameshift mutation

insertion/deletion → dysfunctional

Roles of cell division

transmits gene information for reproduction, genetically identical daughter cells, asexual, sexual, zygote→ adult, repair of tissues

Asexual reproduction

involves 1 parent → clone offspring, yeast, sea stars, house plants

sexual reproduction

fusion of gametes, half the chromosome number, gene variation

mitosis

growth, Maintenace, asexual reproduction

meiosis

gametes, sexual reproduction

binary fission in prokaryotes

chromosome duplicates, cell elongates, membrane pinches inward, cell wall forms → daughter cells. Single cellular, asexual

How many chromosomes in humans

46 chromosomes

Chromatin= DNA +protein

long thin fibers, proteins help regulate gene activity

chromosome compaction

before division chromatin coils, efficient sorting and transport

chromosome duplication

each chromosome duplicated into identical sister chromosomes, sister chromosomes are joined at centromere

cell division outcome

sister chromatins separate, become full chromosome, each receive identical set of chromosomes

Why did scientists initially propose that either DNA or protein was the information carrying molecule, and not carbohydrates or lipids?

DNA and proteins are complex and variable enough to store genetic information; carbs and lipids are not.

Review the first experiment we discussed where mice were injected with various mixtures of S. pneumoniae bacteria.  What conclusions (if any) could have been drawn if mice injected with heat-killed pathogenic bacteria had died of pneumonia?  If you were doing the analysis, what would you do next?

It would suggest heat didn’t destroy the virus; further tests would be needed to isolate the active molecule.

Imagine that mice injected with a mixture of heat-killed pathogenic and live harmless bacteria had NOT died of pneumonia.  Propose at least one hypothesis to explain this alternative result.

Possibly no transformation occurred; maybe DNA was degraded or uptake failed.

Review the second experiment we discussed where mice were injected with cellular molecules removed from heat-killed pathogenic bacteria treated in various ways and mixed with harmless bacteria.  What specific results allowed them to conclude that RNA was not necessary for transformation?  That proteins weren’t necessary for transformation?  That DNA was essential for transformation?

Scientists injected mice with cellular molecules from heat-killed pathogenic bacteria that had been treated with enzymes to destroy specific molecules. When RNA was destroyed using RNase, the mice still developed pneumonia. This showed that RNA was not necessary for transformation. When proteins were destroyed using protease, the mice still developed pneumonia. This showed that proteins were not necessary for transformation. When DNA was destroyed using DNase, the mice remained healthy. This showed that DNA was essential for transformation. These results proved that DNA was the molecule responsible for carrying genetic information

For each of the two experiments we discussed, list the control conditions that were essential to include.  For each control condition, explain what information it provided (i.e. why it was important to include) and describe results that would indicate the results obtained for the experimental condition could be used to accurately assess the hypothesis (i.e. the experiment was working as expected).

Griffith’s Experiment Controls

Live R strain only: Confirms it's non-pathogenic; mice should survive.

Heat-killed S strain only: Confirms heat destroys virulence; mice should survive.

Live S strain only: Confirms S strain causes disease; mice should die.

Mixture of R + heat-killed S: Tests transformation; mice should die if transformation occurs.

Avery’s Experiment Controls

Untreated extract + R strain: Confirms transformation is possible; mice should die.

RNase-treated extract + R strain: Tests RNA’s role; mice should die if RNA isn’t required.

Protease-treated extract + R strain: Tests protein’s role; mice should die if protein isn’t required.

DNase-treated extract + R strain: Tests DNA’s role; mice should survive if DNA is essential.

Each control ensures the experiment works as expected and isolates the role of each molecule.

Explain why scientists were so interested in determining the structure of DNA once evidence accumulated suggesting it was the information carrying molecule

Scientists wanted to understand how DNA could store, copy, and transmit genetic information. Knowing its structure would reveal how traits are inherited, how mutations occur, and how cells replicate DNA accurately. The structure was key to unlocking the mechanism of heredity.

List the three components (parts) of nucleotides.  What components differ between nucleotides?  What’s the difference between DNA vs. RNA nucleotides?

Three parts: phosphate group, sugar (ribose or deoxyribose), nitrogenous base.

Differences: DNA has deoxyribose and thymine; RNA has ribose and uracil.

Are the bonds that connect DNA nucleotides in a strand the same as the bonds that connect nucleotides in a strand of RNA?

Both use phosphodiester bonds to link nucleotides in a strand.

Explain what it means that nucleic acid strands have a direction.

Strands run 5′ to 3′, based on the orientation of the sugar-phosphate backbone.

Describe the structure of a DNA molecule (DNA helix).  What type of bond connects nucleotides within a strand?  What type of bond forms between the two strands of a DNA molecule to hold it together?

DNA is a double helix with antiparallel strands.

Phosphodiester bonds connect nucleotides in a strand.

Hydrogen bonds hold the two strands together (A–T has 2, G–C has 3).

A DNA helix that is mainly A-T base pairs is easier to separate than a helix with the same number of base pairs, but mostly G-C pairs.  Based on what you know about the structure of DNA, explain why this is true.

A–T pairs have 2 hydrogen bonds, G–C pairs have 3.

Fewer bonds in A–T make those regions easier to separate.

You isolate a DNA molecule from a cell and find that 35% of the nucleotides are A’s.  Based on that, can you figure out the percentages of T’s?  G’s?  C’s?  If so, what are the percentages?  If not, why not

If A = 35%, then T = 35%.

G and C share the remaining 30%, so G = 15%, C = 15%.

Describe the differences between the DNA present in prokaryotic vs. eukaryotic cells.  List ALL features of DNA common to BOTH prokaryotic and eukaryotic cells.

Differences:

Prokaryotic: circular, no nucleus, few/no histones.

Eukaryotic: linear, in nucleus, wrapped around histones.

Shared features:

Double-stranded helix, made of nucleotides, uses A, T, G, C, stores genetic info.

You isolate an RNA molecule from a cell and find that 35% of the nucleotides are A’s.  Can you figure out the percentages of U’s?  G’s?  C’s?  If so, what are the percentages?  If not, why not?  Hint – Think about the differences in the structures of DNA and RNA.

If A = 35%, you can’t determine U, G, or C percentages.

RNA is single-stranded, so base pairing rules don’t apply consistently.

Make a table to compare the structures of DNA and RNA.  List all the similarities and differences you can remember without looking at your notes.  Then go back through your notes and the slides to check yourself.  Correct and/or add to your lists if necessary.

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Bases	A, T, G, C	A, U, G, C
Strands	Double-stranded	Single-stranded
Stability	More stable	Less stable
Location	Nucleus	Nucleus & cytoplasm
Function	Genetic storage	Protein synthesis, info transfer

Describe the roles of the three information processing pathways that occur in all cells

Replication – Copies DNA so cells can divide and pass genetic material to daughter cells.

Transcription – Converts DNA into RNA, which carries instructions for protein synthesis.

Translation – Uses RNA to build proteins by assembling amino acids in the correct order.

What’s a gene?  What does it mean to express a gene?

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

To express a gene means to transcribe it into RNA and (usually) translate it into a protein.

Describe how the structural differences of DNA and RNA relate to their respective roles in biological information processing

DNA is double-stranded and stable, ideal for long-term storage of genetic information.

RNA is single-stranded and more flexible, suited for short-term tasks like carrying messages and helping build proteins.

RNA’s ribose sugar and uracil base make it more reactive and less stable than DNA.

Identify the feature of DNA’s structure that allows a DNA helix to be copied in cells to form two new, identical DNA helices

Complementary base pairing and double-stranded structure allow each strand to serve as a template for making a new strand.

If a change in the DNA sequence of a prokaryotic chromosome introduced an additional origin of replication (ORI), how would that affect DNA replication?

It would speed up replication, allowing the chromosome to be copied more quickly

A change in the DNA sequence of the ORI in the chromosome of a prokaryotic cell alters the sequence so that DNA replication proteins can no longer interact with the ORI.  How will this affect the cell?  What if the sequence of an ORI was altered on a chromosome in a eukaryotic cell?

In prokaryotes, replication may fail entirely since they usually have only one ORI.

In eukaryotes, replication may still occur using other ORIs, but could be slower or incomplete.

Why do the two strands of a DNA helix need to be separated in order for DNA to be copied?

DNA strands must be separated so enzymes can access bases and build complementary strands during replication.

Describe the roles of the DNA replication enzymes that we discussed.  Explain why there are two DNA polymerases at each replication fork.

Helicase: Unzips the DNA strands.

DNA polymerase: Builds new DNA strands.

Ligase: Seals gaps between fragments.

Two DNA polymerases are needed because each works on one strand—one on the leading strand, one on the lagging strand.

In what direction are DNA strands read/written by scientists?  In what direction do DNA polymerases form new DNA strands?

Scientists read/write DNA 5′ to 3′.

DNA polymerases also build new strands 5′ to 3′, reading the template 3′ to 5′

A cell is treated with a drug that decreases the activity of DNA ligases in a cell.  Will replication of both strands of a DNA helix at a replication fork be equally affected?  What if a drug decreased the ability of DNA polymerases to function?  Decreased the activity of DNA helicases?  Explain your answers.

Ligase inhibition: Affects lagging strand more (can’t seal Okazaki fragments).

Polymerase inhibition: Stops replication on both strands.

Helicase inhibition: Prevents strand separation, halting entire replication.

What would happen if a drug was added to a cell that inhibited the proofreading ability of DNA polymerases?

 Increases mutation rate because DNA polymerase can’t correct errors during replication.

A cell is treated with a drug that prevents formation of RNA primers.  How will this affect DNA replication?

DNA polymerase can’t start replication without primers, so replication won’t begin.

Two cells have exactly the same amount of DNA (same number of base pairs), but one cell has 1,000 genes and the other cell has 3,000 genes.  Will the difference in the number of genes affect DNA replication?  Explain your answer

No. DNA replication copies all base pairs, regardless of how many are genes. Gene count affects expression, not replication speed.

Choose three of the words below and write a sentence that describes their relationships. Now do the same thing with a different set of three words. genome, DNA, chromosome, protein, amino acids, mRNA, gene.

Set 1: DNA, chromosome, genome

Sentence: DNA is tightly packed into structures called chromosomes, and all of your chromosomes together make up your genome.

Set 2: gene, mRNA, protein

Sentence: A gene is a segment of DNA that is transcribed into mRNA, which is then translated into a protein.

If you compared the genome of one of your skin cells to the genome of one of your eye cells, would all the genes be the same? What if you compared the genes expressed in the two cells? Explain your answers

Yes they would be the same. All cells that make up multicellular organisms have the same genome. Different types of cells express different sets of genes. Some genes are never expressed while others are expressed many times.

Explain why the ability of a cell to change which genes get expressed when, and to control how much particular genes are expressed is important

Under different conditions, different genes can be expressed. The ability of a cell to change which genes are expressed is crucial for several reasons:

Adaptation: Cells can adjust their gene expression based on environmental conditions, allowing them to respond to changes in their surroundings. 

Development: Gene regulation is essential for normal development, as it ensures that cells express the appropriate genes at the right times. 

Functionality: Different cells in a multicellular organism may express varying sets of genes, which is necessary for their specific functions. This ability enables cells to function effectively in dynamic environments and supports the complexity of multicellular organisms.

If you looked at the DNA sequence of one small part of one of your chromosomes, is it likely that the sequence is part of a gene? Why or why not?

No, because most of your DNA isn't part of a gene. Only about 2% of your DNA actually codes for proteins, and even fewer genes are active at any given time. A lot of the rest helps control how genes work, and some parts we still don’t understand. So if you look at a random piece of DNA, it’s probably not part of a gene. Introns and exons impact this!

Can transcription occur without translation? Translation without transcription? Explain your answers

Transcription can occur without translation because it is just DNA being turned into RNA which doesn’t need RNA beforehand. Translation cannot occur without transcription because it needs mRNA in order to be read by a ribosome and a protein to be made.

If the DNA sequence of the promoter of a gene was altered such that RNA polymerase could no longer interact, how would that affect transcription? What if the terminator was changed to a different sequence?

If the promoter was changed, RNA polymerase might not bind properly, so transcription might not start at all. That means the gene wouldn’t be expressed, and no protein would be made. It wouldn’t usually cause a frameshift, since frameshifts happen during translation, not transcription.

If the terminator was changed, RNA polymerase might not stop where it should. This could lead to a longer RNA strand than normal, possibly including extra sequences that aren’t supposed to be part of the gene. That could result in a faulty or nonfunctional protein.

Be able to transcribe a gene given the coding and/or template DNA strands. You do not need to be able to identify specific promoter or terminator sequences; they’re different for different genes.

Transcription always builds mRNA in the 5' to 3' direction.

The template strand is read 3' to 5'. If you're given the template strand (also called the antisense strand):

This is the strand that RNA polymerase reads.

Transcribe it directly into mRNA by pairing bases:

A → U

T → A

C → G

G → C If you're given the coding strand (also called the sense strand):

This strand has the same sequence as the mRNA, except it uses T instead of U.

So, just copy it, but replace T with U.

RNA polymerase interacts with the promoter sequence of a gene. What needs to happen before the enzyme starts forming an RNA strand

Binding to the promoter, unwinding of DNA, and initiation complex formation. 

1. Binding to the promoter

RNA polymerase must recognize and bind to the promoter region of the DNA.

In eukaryotes, this usually requires help from transcription factors—proteins that guide RNA polymerase to the right spot.

2. DNA unwinding

The DNA around the promoter must be unwound so RNA polymerase can access the template strand.

This creates a small open region called the transcription bubble.

3. Initiation complex formation

RNA polymerase and other helper proteins form a stable initiation complex.

Once everything is in place, RNA polymerase can begin synthesizing RNA by matching RNA nucleotides to the DNA template.

Explain how expression of a specific eukaryotic gene can produce proteins with different amino acid sequences. Do you expect the proteins produced by expression of the gene to have components of their structures that are similar? Why or why not?

 Alternative splicing(Introns and exons) leads to eukaryotes to produce different proteins with different amino acid sequences from one gene. Yes, at least some parts. This is because they’re all derived from the same gene, so they tend to have some overlapping sequence and structure, especially if those parts are essential for the protein’s function.

Explain why expression of one particular prokaryotic gene cannot produce proteins with different amino acid sequences

 In prokaryotes, there are no alternative splicing(Introns and exons), the mRNA is fixed and the ribosome reads the mRNA the same each time.

In prokaryotic cells, a gene can be transcribed and translated simultaneously. Explain why this is not possible in eukaryotic cells (there are two reasons).

One reason is because transcription happens in the nucleus and translation happens in the cytoplasm. Also, alternative splicing happens in between transcription and translation in order for introns to be taken out and exons can stay. It also adds the cap to the phosphate end(5’) and the poly-a tail to the end(3’).

Make a table to summarize the similarities and differences between DNA replication and transcription.

Feature	DNA Replication	Transcription
Purpose	Copy entire DNA for cell division	Make RNA from a gene to produce proteins
Enzyme involved	DNA polymerase	RNA polymerase
Template used	Both DNA strands	One DNA strand (template strand)
Product	Two identical DNA molecules	Single-stranded RNA (usually mRNA)
Base pairing	A-T, C-G	A-U, C-G (U replaces T in RNA)
Location (in eukaryotes)	Nucleus	Nucleus
Timing	During S phase of cell cycle	Anytime a gene needs to be expressed
Resulting molecule	Stays in nucleus	Moves to cytoplasm for translation