Exam 2 Mocell Study Guide

1. Describe Griffith’s transforming principle.

Frederick Griffith studied two strains of Streptococcus pneumoniae:

• S strain — had a capsule and caused disease.

• R strain — lacked a capsule and did not cause disease.

He injected mice with different combinations of these bacteria. The important result was that heat-killed S bacteria + living R bacteria killed the mice, and living S bacteria were recovered.

This showed that something from the dead S bacteria had transformed the living R bacteria into disease-causing S bacteria.

Transforming principle: Griffith showed that some substance from dead bacteria could transfer a heritable trait to living bacteria. He did not know that the substance was DNA.

2. How did Avery, MacLeod, and McCarty determine that DNA is the genetic material?

Avery, MacLeod, and McCarty followed up on Griffith's experiment.

They isolated different substances from heat-killed S bacteria and treated the extracts with enzymes that destroyed:

• Protein

• RNA

• DNA

They found that transformation of R bacteria still occurred when protein or RNA was destroyed, but transformation stopped when DNA was destroyed.

Therefore, they concluded that DNA was the transforming principle and the genetic material.

3. Understand/describe the Hershey and Chase blender experiment

Hershey and Chase used bacteriophages, viruses that infect bacteria.

A bacteriophage contains:

• DNA

• Protein

They labeled DNA with radioactive ³²P and protein with radioactive ³⁵S.

The phages infected E. coli. They then used a blender to separate the virus particles from the bacteria.

Results:

• ³²P (DNA) entered the bacteria.

• ³⁵S (protein) stayed outside the bacteria.

Therefore, DNA—not protein—is the genetic material because DNA entered the cells and directed production of new viruses

4. Describe the composition of DNA – subunits, bonds that hold the subunits together, bonds that hold strands together.

Each nucleotide contains:

1. A phosphate group

2. A deoxyribose sugar

3. A nitrogenous base

The four DNA bases are:

• Adenine (A)

• Thymine (T)

• Guanine (G)

• Cytosine (C)

Within one DNA strand:

Nucleotides are connected by phosphodiester bonds between the sugar and phosphate.

Between the two DNA strands:

The bases are held together by hydrogen bonds:

• A pairs with T using 2 hydrogen bonds

• G pairs with C using 3 hydrogen bonds

5. What are Chargaff’s rules of base pairing?

Chargaff discovered that in double-stranded DNA:

• A = T

• G = C

Therefore:

• Purines = Pyrimidines

• Adenine pairs with thymine.

• Guanine pairs with cytosine.

The amount of A and T may differ from the amount of G and C, but within a particular double-stranded DNA molecule, A and T are equal and G and C are equal.

6. What is chromatin? What are chromosomes? What is a gene?

Chromatin: DNA combined with proteins, especially histones, inside the nucleus.

Chromosome: A long, organized DNA molecule associated with proteins. Before cell division, chromosomes become highly condensed and visible under a microscope.

Gene: A segment of DNA that contains information used to produce a functional product, usually a protein or functional RNA.

Think of it as:

DNA → organized into chromosomes → chromosomes contain genes

7. What is an origin of replication? A telomere? A centromere?

   
   

Origin of replication: A specific DNA sequence where DNA replication begins.

Telomere: Repetitive DNA sequences at the ends of chromosomes that protect chromosomes from losing important genetic information.

Centromere: A chromosome region where sister chromatids are held together and where proteins attach that help move chromosomes during cell division.

8. What is the nucleolus?

The nucleolus is a region inside the nucleus where:

• Ribosomal RNA (rRNA) is produced.

• Ribosomal subunits are assembled.

It is not surrounded by a membrane.

9. What is a nucleosome? How do nucleosomes pack within the nucleus?

A nucleosome is DNA wrapped around a group of histone proteins.

The basic structure is approximately:

DNA → wraps around histones → nucleosome

Histones help package DNA so that a very long DNA molecule can fit inside the nucleus.

Nucleosomes can interact with one another and form increasingly compact structures. This allows DNA to become highly organized and condensed into chromosomes.

10. What is heterochromatin? Euchromatin?

Heterochromatin:

• Tightly packed DNA

• Generally less accessible

• Genes are usually less actively expressed

Euchromatin:

• Loosely packed DNA

• More accessible to transcription machinery

• Genes are generally more actively expressed

Easy memory trick:

Hetero = hidden/tight

Eu = easy access

11. How are histones modified? What effect does it have on the DNA with which they interact?

Histones can be chemically modified by adding or removing groups such as:

• Acetyl groups

• Methyl groups

• Phosphate groups

• Ubiquitin

One important example is histone acetylation.

Adding acetyl groups to histones generally decreases their interaction with negatively charged DNA. This makes chromatin less condensed and more accessible, usually increasing gene transcription.

Histone modifications can therefore help determine whether genes are accessible for expression.

12. What is a Barr body?

A Barr body is an inactivated X chromosome found in cells with more than one X chromosome.

For example, in typical XX cells, one X chromosome is largely inactivated to prevent the cell from producing twice as much X-linked gene product.

The inactive X becomes highly condensed and forms a Barr body.

13. What is semiconservative replication? How was it determined to be the method of DNA replication?

semiconservative replication means that each new DNA molecule contains:

• One original/parental strand

• One newly synthesized strand

The classic experiment was performed by Meselson and Stahl.

They grew bacteria in nitrogen containing ¹⁵N, which made their DNA heavy. They then transferred the bacteria to ¹⁴N.

After replication, the DNA showed patterns that supported the semiconservative model.

After one round:

¹⁵N–¹⁴N

After two rounds:

¹⁵N–¹⁴N + ¹⁴N–¹⁴N

This matched the predictions of semiconservative replication.

14. What is generated from the replication of DNA? What method is used? Describe the process. What are Okazaki fragments? Where does this take place in the cell? What enzymes are used?

DNA replication produces two identical DNA molecules, each containing one original strand and one newly synthesized strand.

Replication is semiconservative.

DNA replication occurs:

• In the nucleus of eukaryotic cells

• In the cytoplasm/nucleoid region of prokaryotes

Important steps:

1. Helicase unwinds the DNA double helix.

2. Single-strand binding proteins stabilize the separated strands.

3. Topoisomerase helps relieve twisting and tension.

4. Primase makes a short RNA primer.

5. DNA polymerase adds DNA nucleotides.

6. DNA is synthesized 5′ → 3′.

7. DNA ligase connects DNA fragments.

Because the two DNA strands are antiparallel:

• The leading strand is synthesized continuously.

• The lagging strand is synthesized discontinuously.

The short pieces made on the lagging strand are called Okazaki fragments.

Important enzymes:

Enzyme	Function
Helicase	Unwinds DNA
Topoisomerase	Relieves DNA twisting
Primase	Makes RNA primers
DNA polymerase	Adds DNA nucleotides
DNA ligase	Joins DNA fragments

15. What does telomerase do?

Telomerase is an enzyme that extends the ends of chromosomes.

It adds repetitive DNA sequences to telomeres.

This helps prevent important DNA from being lost during replication.

Telomerase is particularly active in:

• Germ cells

• Stem cells

• Many cancer cells

Most normal somatic cells have relatively low telomerase activity.

16. How are mistakes fixed during replication?

DNA polymerase has a proofreading ability.

If DNA polymerase adds the wrong nucleotide, it can:

1. Detect the incorrect base.

2. Remove it.

3. Add the correct nucleotide.

Additional DNA repair systems can fix mistakes that escape proofreading.

This helps maintain the accuracy of DNA replication.

17. How is DNA damaged? How is damaged DNA repaired?

DNA can be damaged by:

• UV radiation

• Ionizing radiation

• Chemicals

• Reactive molecules

• Replication errors

• Spontaneous chemical changes

Examples include:

• Incorrect bases

• Missing bases

• Broken DNA strands

• Thymine dimers caused by UV radiation

Cells use several repair mechanisms.

Mismatch repair: Fixes errors that remain after replication.

Nucleotide excision repair: Removes a damaged section of DNA and replaces it.

Base excision repair: Removes individual damaged bases.

Double-strand break repair: Repairs breaks in both DNA strands through mechanisms such as homologous recombination or nonhomologous end joining.

18. What is a mutation?

A mutation is a permanent change in the DNA sequence.

Mutations can result from:

• DNA replication errors

• DNA damage

• Environmental factors

Examples include:

• Substitution

• Insertion

• Deletion

Mutations can be:

• Harmful

• Beneficial

• Neutral

19. What is homologous recombination?

Homologous recombination is a DNA repair/recombination process in which DNA sequences with significant similarity are used to exchange or repair genetic information.

During meiosis, homologous recombination also allows chromosomes to exchange DNA, creating genetic variation.

During DNA repair, an undamaged homologous DNA molecule can serve as a template for repairing a damaged region.

20. What is the central dogma of molecular biology?

The central dogma describes the flow of genetic information:

DNA → RNA → Protein

The major steps are:

DNA → transcription → RNA

RNA → translation → protein

DNA can also be copied through replication:

DNA → DNA

21. Describe the composition of RNA – subunits and the bonds that hold the subunits together.

RNA is made of nucleotides.

Each RNA nucleotide contains:

1. Ribose sugar

2. Phosphate group

3. Nitrogenous base

RNA contains:

• Adenine (A)

• Uracil (U)

• Guanine (G)

• Cytosine (C)

Unlike DNA, RNA contains uracil instead of thymine.

Nucleotides within an RNA strand are connected by phosphodiester bonds.

RNA is usually single-stranded but can fold into complex shapes through hydrogen bonding between complementary bases.

22. What enzyme is used in transcription?

The enzyme responsible for transcription is RNA polymerase.

RNA polymerase reads a DNA template and produces an RNA molecule.

23. What are the three major types of RNA? What enzyme is used to make each?

The three major types are:

mRNA — messenger RNA

• Carries information from DNA to the ribosome.

• Made by RNA polymerase II in eukaryotes.

rRNA — ribosomal RNA

• Makes up part of ribosomes.

• Made primarily by RNA polymerase I and III, depending on the rRNA.

tRNA — transfer RNA

• Carries amino acids to the ribosome.

• Made by RNA polymerase III in eukaryotes.

24. What are general transcription factors? What is a TATA box? What binds there?

General transcription factors are proteins required for transcription of many or most protein-coding genes.

They help:

• Position RNA polymerase.

• Identify the promoter.

• Begin transcription.

The TATA box is a DNA sequence found in some eukaryotic promoters.

A general transcription factor called TBP (TATA-binding protein) binds to the TATA box.

TBP is part of TFIID.

25. Describe transcription – direction of synthesis, enzymes used, location within the cell.

Transcription is the process of making RNA from a DNA template.

RNA polymerase:

1. Binds to the promoter.

2. Opens a small section of DNA.

3. Uses one DNA strand as a template.

4. Adds RNA nucleotides.

5. Produces RNA in the 5′ → 3′ direction.

In eukaryotes, transcription occurs in the nucleus.

The main enzyme is RNA polymerase.

The RNA sequence is complementary to the DNA template strand.

26. How/where is mRNA processed?

In eukaryotic cells, pre-mRNA is processed in the nucleus before leaving for the cytoplasm.

Three major processing steps are:

1. 5′ cap is added.

2. Introns are removed through splicing.

3. Poly-A tail is added to the 3′ end.

The result is mature mRNA, which can leave the nucleus and be translated.

27. What is differential splicing?

Differential splicing, also called alternative splicing, allows one pre-mRNA molecule to produce different mature mRNAs.

Different combinations of exons can be included or excluded.

Therefore:

One gene → multiple mRNAs → multiple possible proteins

This allows cells to produce different proteins from the same gene.

28. The genetic code is degenerate – what does that mean?

A degenerate genetic code means that more than one codon can specify the same amino acid.

For example:

GCU, GCC, GCA, and GCG all code for alanine.

There are 64 possible codons but only 20 standard amino acids, so multiple codons must specify the same amino acid.

29. How was the genetic code determined?

Scientists determined the genetic code by using experiments involving mRNA sequences and cell-free translation systems.

Marshall Nirenberg and Heinrich Matthaei showed that an RNA molecule containing only uracil:

UUUUUU...

produced a protein containing only phenylalanine.

Therefore:

UUU = phenylalanine

Other researchers, including Har Gobind Khorana and Robert Holley, helped determine additional codons and the role of tRNA.

Eventually, scientists determined all 64 codons.

30. . How does a tRNA interact with mRNA?

A tRNA contains an anticodon that pairs with a complementary codon on mRNA.

For example:

mRNA codon: 5′-AUG-3′

tRNA anticodon: 3′-UAC-5′

The tRNA also carries a specific amino acid.

During translation, the ribosome matches tRNAs to mRNA codons and uses their amino acids to build a protein.

31. What is a wobble base? What is a codon? What is an anticodon?

    
    

Codon: A three-nucleotide sequence on mRNA that specifies an amino acid or a stop signal.

Anticodon: A three-nucleotide sequence on tRNA that pairs with an mRNA codon.

Wobble base: A position where non-standard or less strict base pairing can occur between a codon and anticodon, allowing one tRNA to recognize multiple codons.

The wobble position helps explain why cells do not need a different tRNA for every codon.

32. How are amino acids linked to tRNAs?

An enzyme called aminoacyl-tRNA synthetase attaches the correct amino acid to its corresponding tRNA.

This process is called tRNA charging.

The enzyme recognizes:

• The correct amino acid

• The correct tRNA

The amino acid is attached to the 3′ end of the tRNA.

33. Describe the composition of ribosomes.

Ribosomes are made of:

• rRNA

• Proteins

They have two subunits:

Small subunit: Helps position and read the mRNA.

Large subunit: Helps form peptide bonds between amino acids.

In eukaryotes, cytoplasmic ribosomes are 80S, consisting of:

• 40S small subunit

• 60S large subunit

In bacteria, ribosomes are 70S, consisting of:

• 30S small subunit

• 50S large subunit

34. Describe the four-step cycle of translation.

The basic translation cycle can be described as:

1. Aminoacyl-tRNA entry

A charged tRNA enters the ribosome's A site and matches its anticodon with the mRNA codon.

2. Peptide bond formation

The amino acid on the tRNA in the A site is joined to the growing polypeptide chain.

3. Translocation

The ribosome moves one codon along the mRNA.

The tRNA holding the growing chain moves from the A site to the P site.

4. tRNA release

The empty tRNA moves to the E site and leaves the ribosome.

The cycle repeats until a stop codon is reached.

35. What is a ribozyme? Why are ribosomes ribozymes?

A ribozyme is an RNA molecule that can catalyze a chemical reaction.

Ribosomes are considered ribozymes because the rRNA in the large subunit catalyzes the formation of peptide bonds.

Therefore, RNA—not protein—is directly responsible for the ribosome's peptide bond-forming activity.

36. What is the translocation step of translation?

Translocation is when the ribosome moves one codon along the mRNA.

During translocation:

• The tRNA carrying the growing peptide moves from the A site → P site.

• The empty tRNA moves from the P site → E site.

• The A site becomes available for the next charged tRNA.

This allows translation to continue.

37. How does translation terminate?

Translation ends when the ribosome reaches a stop codon:

• UAA

• UAG

• UGA

Stop codons do not have corresponding tRNAs.

Instead, a release factor binds to the stop codon.

The completed polypeptide is released, and the ribosome separates from the mRNA.

38. What is a polyribosome?

A polyribosome, or polysome, is a group of multiple ribosomes translating the same mRNA molecule at the same time.

This allows a cell to produce many copies of the same protein quickly.

39. How do antibiotics work (related to prokaryotic gene expression)?

Many antibiotics target bacterial gene expression, particularly translation.

Bacterial ribosomes are 70S, while human cytoplasmic ribosomes are 80S.

Some antibiotics specifically interfere with bacterial ribosomes.

Examples:

• Tetracyclines: Interfere with tRNA entering the bacterial ribosome.

• Macrolides: Interfere with bacterial ribosome function/translocation.

• Aminoglycosides: Cause errors in translation.

• Chloramphenicol: Inhibits bacterial peptide bond formation.

Because bacterial ribosomes differ from human ribosomes, these drugs can selectively interfere with bacterial protein production

40. What is a proteasome? How does it work?

A proteasome is a large protein complex that breaks down unwanted or damaged proteins.

Proteins destined for destruction are often tagged with ubiquitin.

The process is:

Protein → ubiquitin attached → proteasome recognizes protein → protein is unfolded → protein is broken into peptides

The resulting small peptides can be further broken down into amino acids.

The proteasome helps control:

• Protein quality

• Protein levels

• Cell cycle regulation

• Removal of damaged proteins

41. What is the RNA world hypothesis?

The RNA world hypothesis proposes that early life may have relied heavily on RNA before DNA and proteins became dominant.

RNA could potentially have performed two important jobs:

1. Store genetic information.

2. Catalyze chemical reactions.

Therefore, RNA could have served as both a primitive genetic molecule and enzyme.

42. What aspects of RNA make it a possible first organic molecule in prebiotic Earth?

RNA is a good candidate because it can:

• Store genetic information through its nucleotide sequence.

• Form complex three-dimensional structures.

• Act as a catalyst.

• Base-pair with complementary sequences.

• Potentially copy or assist in copying genetic information.

The discovery of ribozymes provides evidence that RNA can have catalytic activity.

43. Are all genes found in all cells? Are all genes expressed in all cells?

For cells in the same multicellular organism, most cells contain essentially the same genome, meaning they generally have the same genes.

However, not all genes are expressed in all cells.

Different cells turn different genes on and off.

For example:

• Muscle cells express genes important for muscle function.

• Neurons express genes important for nervous system function.

• Liver cells express genes important for liver functions.

This is called differential gene expression and allows cells with the same DNA to develop different structures and functions.

44. At which levels can gene expression be controlled?

Gene expression can be regulated at many levels:

1. Chromatin remodeling

2. DNA methylation

3. Transcription

4. RNA processing

5. mRNA transport

6. mRNA degradation

7. Translation

8. Protein modification

9. Protein degradation

This allows cells to control gene expression at multiple checkpoints.

45. What are specific transcription factors? How do they control transcription? Describe DNA-binding motifs found in regulatory proteins.

    
    

Specific transcription factors are proteins that regulate particular genes.

They bind specific DNA sequences near or within regulatory regions.

They can:

• Activate transcription

• Repress transcription

They can recruit or block proteins involved in transcription and can influence chromatin structure.

Common DNA-binding motifs include:

Zinc fingers

• Use zinc ions to help stabilize the protein structure.

• The protein contacts specific DNA sequences.

Leucine zippers

• Contain repeating leucine residues.

• Help transcription factors form dimers and bind DNA.

Helix-turn-helix

• Contains alpha helices connected by a turn.

• One helix interacts with DNA.

Homeodomain

• A specialized DNA-binding domain found in many developmental transcription factors.

46. What is an operon?

An operon is a group of bacterial genes that are controlled together and transcribed as a single RNA molecule.

An operon typically contains:

• Promoter

• Regulatory DNA region

• Multiple genes

Operons allow bacteria to coordinate expression of genes involved in the same biological pathway.

Examples include:

• lac operon

• trp operon

47. How does the lac operon work?

The lac operon allows E. coli to use lactose as an energy source.

It contains genes needed to metabolize lactose.

When lactose is absent:

A repressor protein binds the operator.

This prevents RNA polymerase from efficiently transcribing the lac genes.

Lactose absent → repressor active → genes OFF

When lactose is present:

Lactose is converted to allolactose, which binds the repressor.

This changes the repressor's shape and prevents it from binding the operator.

The genes can then be transcribed.

Lactose present → repressor inactive → genes can turn ON

Glucose also affects the lac operon.

When glucose is low, cAMP increases.

cAMP binds CAP, allowing CAP to help RNA polymerase bind the promoter.

Therefore, the lac operon is expressed most strongly when:

Lactose is present + glucose is low

48. How does chromatin structure contribute to regulation of gene expression?

Chromatin structure controls how accessible DNA is to transcription machinery.

Tightly packed chromatin:

• DNA is difficult for transcription factors and RNA polymerase to access.

• Gene expression is generally lower.

Loosely packed chromatin:

• DNA is more accessible.

• Transcription factors and RNA polymerase can bind more easily.

• Gene expression is generally higher.

Histone modifications and chromatin-remodeling proteins can change how tightly DNA is packaged.

49. How do transcription regulators control cell fate?

Transcription regulators control which genes are expressed in a cell.

During development, different transcription factors become active in different cells.

This causes cells to express different sets of genes even though they contain the same DNA.

For example:

Different transcription factors → different genes expressed → different proteins → different cell characteristics

This allows cells to become specialized, such as:

• Neurons

• Muscle cells

• Blood cells

• Skin cells

50. Can DNA methylation patterns be inherited? Can histone modifications be inherited?

DNA methylation patterns can sometimes be inherited through cell division.

When DNA is replicated, methylation patterns can be copied onto the newly synthesized DNA strand by maintenance DNA methyltransferases.

Therefore, DNA methylation can contribute to epigenetic inheritance.

Histone modifications can also contribute to epigenetic inheritance.

During DNA replication, histones are distributed to daughter DNA molecules, and existing histone modifications can help guide restoration of chromatin states.

However, both DNA methylation and histone modifications can also be removed or reprogrammed, so they are not necessarily permanent.

51. What is miRNA? What is RNA interference? How do each of these contribute to post-transcription control of gene expression?

miRNA (microRNA) is a small, noncoding RNA molecule that helps regulate gene expression after transcription.

A miRNA can bind to a complementary sequence in an mRNA.

This can cause:

• Reduced translation

• mRNA degradation

Therefore:

miRNA → binds mRNA → less protein produced

RNA interference (RNAi)

RNA interference is a gene-regulation mechanism in which small RNA molecules guide cellular machinery to specific RNA molecules.

The small RNA helps a protein complex, such as RISC, identify a complementary mRNA.

Depending on how closely the RNA matches the target:

• The mRNA may be degraded.

• Translation may be inhibited.

RNAi therefore provides a way for cells to silence or reduce gene expression after transcription.

Simple comparison:

DNA methylation → controls access to DNA

Transcription factors → control transcription

miRNA/RNAi → control mRNA after transcription

Proteasomes → control proteins after translation