Bio Chapters 16-17

What discovery is Edwin Chargaff responsible for? How does his discovery help determine the percentages of nucleotides found in a sample of DNA and the structure of DNA?

DNA composition

DNA from any species will have 

A=T and G=C

A pyridamine (T and C) must bond with a purine (A or G) to account for the 2nm diameter

1. 2 purine = too wide

2. 2 pyridamine = too narrow

The sequence of bases carry a vast amount of hereditary information

Why does replication in prokaryotes differ from replication in eukaryotes?

Prokaryotes - one origin of replication (circular)

Eukaryotes - multiple origins of replication (linear)

What did Griffith observe in his transformation experiments?

Transformning principle

Transformation is a change from genotype to phenotype from taking in different DNA, Something in heat-killed bacteria could still transmit disease-causing properties

He mixed a heat killed pathogenic strain of bacteria with a living nonpathogenic strain some living cells were converted into the pathogenic form

Which enzyme catalyzes the elongation of a DNA strand in the 5’--->3’ direction

DNA polymerase three

What does “antiparallel” mean with regard to the DNA molecule?

Nucleotides in DNA backbone are bonded from phosphate to sugar between 3’ and 5’ carbons

Sugar phosphate backbones of the double helix

Complementary strand runs in opposite directio

Why do eukaryotic telomeres replicate differently from the rest of the chromosome

There is a gap left at the 5’ end of the lagging strand 

Different type of replication to fill in the gap

In which order do the enzymes work to repair a thymine dimer by nucleotide excision repair?

1. Cells continuously monitor DNA and make repairs

2. NUCLEASES-DNA cutting enzyme removes errors (removes one or a few bases and hydrolyzes DNA)

3. DNA POLYMERASE ONE fills in the gaps with nucleotides

4.  LIGASE is a linking enzyme that catalyzes the covalent bonds of a 3’ end to a 5; end

What is the difference between ATP and the nucleotide triphosphates used during DNA synthesis?

The sugar molecule and the type of base they contain is different. 

1. ATP: Contains the sugar Ribose and the base Adenine. Used primarily for energy.

2. Nucleotide: Contains the sugar Deoxyribose and one of four bases (A, T, C, G). Used as building blocks for DNA.

How do the leading and lagging strands differ?

Lagging Strand

1. Okazaki fragments are joined by ligase

2. Moving AWAY from the replication fork

3. Discontinuous

Leading Strand

1. Continuous synthesis

2. Moving TOWARD the replication fork

Why is it that the DNA strand elongates only in the 5’ to 3’ direction?

Can only add nucleotides to the free 3’ end of a GROWING DNA strand

Strand only grows 5’ ---> 3’

What is the function of topoisomerase?

Protein that breaks, swivels, and rejoins DNA strands, Relaxes supercoiling in front of the replication fork

Function of DNA ligase

joins the sugar phosphate backbones of all the okazaki fragments into continuous DNA strands, the glue 

Function of SSBP

Binds to and stabalizes single stranded DNA, hold the DNA strands apart

Function of Helicase

Unwinds part of the DNA helix at the replication fork and seperates the two strands making them available as template strands , Stabalized by single-stranded binding proteins

Function of DNA pol 3

Synthesizes new DNA strands by adding nucleotides to a pre-existing nucleotide chain 

Function of DNA pol 1

Removes sections of RNA primer and replaces with DNA nucleotides. But, DNA polymerase 1 can ONLY build onto the 3’ end of an EXISTING DNA strand

Function of primase

Synthesizes an RNA primer at the 5’ end of the leading strand and the 5’ end of each okazaki fragment of the lagging strand

In what way are the cells of individuals with xeroderma pigmentosum different from normal cells?

They can’t repair thymine dimers (covalent linkings of thymine bases)

1. Causes the DNA to buckle and it interferes with DNA replication

2. Inherited defect in nucleotide excision repair 

Mutation in DNA enzymes that repair UV damage in skin cells

1. Can’t go out in sunlight

2. Increased skin cancers and cataracts

 describe how mRNA is translated into a protein.

mRNA is translated into a protein during the process of translation, which occurs at a ribosome in the cytoplasm. The ribosome binds to the mRNA and reads its sequence in groups of three nucleotides called codons. Each codon specifies a particular amino acid. Transfer RNA (tRNA) molecules carry amino acids to the ribosome, and each tRNA has an anticodon that is complementary to a codon on the mRNA. As the ribosome moves along the mRNA, tRNAs match their anticodons with the codons, and the corresponding amino acids are linked together by peptide bonds to form a growing polypeptide chain. This process continues until a stop codon is reached, at which point the completed protein is released and folds into its functional shape.

Why do histones bind tightly to DNA? What are nucleosomes?

DNA is negatively charged and histones are positvely charged. The attraction lets them bind tightly together. A nucleosome is a DNA segment that is wound around a protein core (DNA wrapped around histones)

Why is it thought that RNA probably evolved before DNA?

1. DNA replication requires RNA to function while RNA is simpler 

2. DNA polymerase uses an RNA primer which implies the RNA primer came prior to the DNA

What elements make up DNA

 CHONP (carbon hydrogen oxygen nitrogen phosphorus)

What elements make up proteins

CHONS (carbon hydrogen oxygen nitrogen sulfur)

Since the genetic code is essentially the same for all organisms, what conclusions can be drawn from this information?

All organisms share a common ancestor

Common origin of all life, since we all use the same genetic code

Evolutionary significance as this language is shared by all living things operated very early on in life

What is the function of the three different types of RNA polymerases?

RNA Pol 1: Only transcribes rRNA genes, makes ribosomes

RNA Pol 2: Transcribes genes into mRNA

RNA Pol 3: Only transcribes tRNA genes

What is alternative splicing?

Alternative mRNAs produced from same gene

Allows for the production of proteins of different sizes from a SINGLE mRNA

Gene regulation at the RNA processing level where you can get different mRNAs from the same primary transcript and it is dependent on which segments are treated as exons and introns 

What is the function of GTP in translation?

Provides the energy for the formation of the initiation complex and it uses initiation factors to do so

Why are there 61 mRNA codons but only 45 tRNAs?

Several codons for each amino acid

3rd base “wobble”

1. Codon and tRNA is flexible in the base pairing for the third nucleotide base

Which event takes place first in translation in eukaryotes?

Small subunit of the ribosome will recognize and attatch to the 5’ cap of the mRNA

For translation to occur in both eukaryotes and prokaryotes, what factors are required?

mRNA, Ribosomomal subunits, tRNA, GTP, amino acids, polypeptide factors (initiation factors)

Which type of mutation has the most serious effect on protein formation?

Insertion or deletion of one or two nucleotides (anything not a multiple of three) because it will throw off the reading frame rather than just a codon because then it would be missing an amino acid but doing two nucleotides will change the entire reading frame to have different amino acids after

nonsense mutation

introduce a premature stop codon in the mRNA and it causes a premature termination so the protein may not be fuly completed or malfunctioning

point mutation

only one base of the DNA is copied incorrectly

silent mutation

 no observable effect on the phenotype. May change the wobble but still translates into the same amino acid

missense mutation

substitution that changes one amino acid to another amino acid

frameshift mutation

one or two bases are added or deleted to the DNA which changes all the amino acids after it because the reading frame will be shifted

Cystic fibrosis causes what type of mutation? What effect does this have on the protein?

Deletion of a single codon, which results in the amino acid being deleted 

This mutation prevents the protein from folding into its correct 3D shape, leading to its destruction by the cell before it reaches the cell membrane.

How is translation different in prokaryotes than in eukaryotes?

Prokaryotes: the DNA is in the cytoplasm so translation and transcription can happen simultaneously. Ribosomes read the RNA as its being transcribed

Eukaryotes: DNA is in the nucleus so transcription happens in the nucleus and translation happens in the cytoplasm. RNA editing happens in eukaryotes but not prokaryotes (poly-A tail, 5’ cap, introns, exons, splicing

What must occur for transcription to begin in eukaryotic cells?

Several transcription factors must bind to the promoter

How does a tRNA molecule correspond to an mRNA molecule?

The anticodon of a tRNA molecule will be complementary to the corresponding mRNA molecule

What occurs during RNA processing?

5’ cap is going to consist of a modified guanine nucleotide that is added to the 5’ end

Poly-A tail consist of up to 215 adenine nucleotides and is attached to the 3’ end

Spliceosomes cut out the introns and splice the exons together

What is the “Central Dogma” in biology? Who proposed this flow of genetic information in the cell?

Flow of genetic information in a cell

1. How do we move information from DNA to proteins

2. DNA ---> RNA ---> Protein ---> Trait

   1. DNA → RNA is transcription

   2. RNA →  Protein is translation 

Proposed by Francis Crick

What is the function of a signal peptide?

AKA “Address label”

Sequence of about 20 amino acids at the leading or amino end of the polypeptide and it targets it for where it needs to go within the cell

Translocate polypeptides across the ER membrane

What is the most current definition of a gene?

A gene is a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule

What are anticodons?

An anticodon is a three-nucleotide sequence located on a transfer RNA molecule that is complementary to a specific codon in messenger RNA

Central Dogma SHORT FRQ

The central dogma describes the flow of genetic information in a cell from DNA to RNA to protein. During transcription, a segment of DNA is used as a template to produce messenger RNA (mRNA). This mRNA then travels to a ribosome, where translation occurs. During translation, transfer RNA (tRNA) brings amino acids that are assembled into a polypeptide chain based on the sequence of codons in the mRNA. This process links genotype to phenotype because the DNA sequence (genotype) determines the structure of proteins, and proteins are responsible for an organism’s traits (phenotype) by performing functions such as catalyzing reactions and forming cellular structures.

Chargaff’s Rules SHORT FRQ

Chargaff’s rules state that in DNA, the percentage of adenine equals thymine and the percentage of guanine equals cytosine. These relationships occur because adenine pairs with thymine and guanine pairs with cytosine through complementary base pairing. This pairing is essential to the structure of the DNA double helix because it ensures a consistent width and allows the two strands to twist into a stable helical shape. Additionally, complementary base pairing allows each strand to serve as a template during DNA replication, ensuring accurate copying of genetic information.

Leading vs Lagging strand in DNA replication SHORT FRQ

During DNA replication, the leading and lagging strands are synthesized differently due to the structure of DNA and the direction in which DNA polymerase operates. DNA polymerase can only add nucleotides in the 5’ to 3’ direction. The leading strand is synthesized continuously toward the replication fork, requiring only one RNA primer. In contrast, the lagging strand is synthesized discontinuously away from the replication fork in short segments called Okazaki fragments. Each fragment requires its own RNA primer, and the fragments are later joined together by DNA ligase. This difference results in continuous synthesis on the leading strand and fragmented synthesis on the lagging strand.

Prokaryotes vs Eukaryotes in translation SHORT FRQ

Translation differs between prokaryotes and eukaryotes primarily due to the location of their chromosomes. In prokaryotes, DNA is located in the cytoplasm, so transcription and translation can occur simultaneously. Ribosomes can begin translating mRNA while it is still being transcribed. In eukaryotes, DNA is enclosed within the nucleus, so transcription occurs in the nucleus and the mRNA must be processed and transported to the cytoplasm before translation can begin. This separation allows for greater regulation of gene expression in eukaryotic cells, while prokaryotic cells can produce proteins more quickly.

Post-transcription modification, Translation, Process of secretion of the protein

LONG FRQ

Before mRNA leaves the nucleus, it is processed from pre-mRNA into mature mRNA.

• 5’ Cap (GTP Cap): A modified guanine nucleotide is added to the 5’ end. It acts as a "start" signal for ribosomes and protects the mRNA from degradation by hydrolases in the cytoplasm.

• 3’ Poly-A Tail:

  adenine nucleotides are added to the 3’ end. This increases stability, helps export the mRNA from the nucleus, and protects it.

• Splicing (Introns & Exons):

  • Introns: Non-coding, intervening sequences are removed.

  • Exons: Coding sequences are "spliced" (joined) together by the spliceosome (a complex of snRNPs).

  • Alternative Splicing: Different exons can be joined together, allowing one gene to code for multiple unique proteins.

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2. Translation (Protein Synthesis)

The process of creating a polypeptide chain from the mRNA template in the cytoplasm.

• Components:

  • Ribosome: Composed of large and small subunits (rRNA + protein). Has A, P, and E sites.

mRNA: Template containing codons (3 nucleotides).

• tRNA: Transfers amino acids. Contains an anticodon that is complementary to the mRNA codon.

• Steps:

  1. Initiation: Small ribosomal subunit binds to 5’ cap, scans for start codon (AUG). tRNA carrying Methionine (Met) binds to P site. Large subunit binds.

  2. Elongation:

     • Codon recognition: Next tRNA binds to the A site.

     • Peptide bond formed: The ribosome (specifically rRNA acting as a ribozyme) creates a peptide bond between amino acids, transferring the chain to the A-site tRNA.

     • Translocation: Ribosome moves down. Empty tRNA moves to E site and leaves.

  3. Termination: Stop codon (UAA, UAG, UGA) enters A site. A release factor binds, hydrolyzing the bond and releasing the polypeptide.

• Genetic Code: Redundant (multiple codons for one amino acid) but not ambiguous (1

  codon never codes for 2 different amino acids).

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3. Secretion of Protein & Endomembrane System

If a protein is designed to be secreted (e.g., insulin) or membrane-bound, it follows a specific path.

• Signal Peptide: The first few amino acids of the polypeptide act as a "zip code."

• Signal Recognition Particle (SRP): Binds to the signal peptide and pauses translation.

• Rough ER: The ribosome/mRNA/SRP complex binds to the Rough ER. The protein is translated into the ER lumen.

• Modification: Inside the lumen, enzymes add sugars (glycosylation) or phosphates to the protein (Post-translational modification).

• Transport: Protein is packaged into a transport vesicle and buds off the ER.

• Golgi Apparatus: Vesicle fuses with the Golgi (cis face). The protein is sorted, modified further, and concentrated.

• Secretory Vesicle: Protein buds off the trans-Golgi and moves to the plasma membrane.

• Exocytosis: Vesicle fuses with the plasma membrane, releasing the protein outside the cell.

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4. Post-Translational Modifications (HW Packet Specifics)

Once the protein is folded, it is rarely fully functional. Further modifications are necessary.

• Sugars (Glycosylation): Carbohydrates are added to proteins, critical for cell-to-cell recognition (glycoproteins).

• Phosphates (Phosphorylation): Phosphate groups are added by kinase enzymes, often acting as an "on/off" switch for protein function.

• Cleavage: Certain proteins must be cut to become active (e.g., proinsulin to insulin).

• Folding: Proteins may require chaperone proteins to reach their functional 3D conformation.

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