AP Penguins Unit 6 Study Guide

How is genetic information stored?

In the sequence of nucleotide bases in DNA (and RNA in some viruses)

How is genetic information passed from one generation to the next?

Via semi-conservative replication of DNA prior to cell division

How is prokaryotic DNA shaped?

Circular and typically contained within a single chromosome in the nucleoid region

How is eukaryotic DNA shaped?

Linear, multiple chromosomes packaged with histone proteins

How is the amount of DNA different between a prokaryote and a eukaryote?

Eukaryotes typically have much larger amounts of DNA organized into multiple linear chromosomes

What is a plasmid?

A small, circular, extrachromosomal DNA molecule capable of autonomous replication

What is NOT a function of a plasmid

They carry essential genes used for replication and for life.

Identify two biotechnical uses for plasmids

Vectors for gene cloning and recombinant DNA production

Why is DNA a better hereditary material than RNA?

Deoxyribose is chemically more stable than ribose and double-stranding provides error-repair back-ups

What are the nucleotide base pairing rules?

Apples in the Trees, Cars in Garage

What is the structure of a purine?

A double-ring nitrogenous structure consisting of a 6-membered ring fused to a 5-membered ring

What is the structure of a pyrimidine?

A single 6-membered nitrogenous ring structure

Which of the nitrogenous bases are pyrimidines?

Cytosine, Thymine, and Uracil

Why does a purine always pair with a pyrimidine?

To maintain a constant double-helix width (3 rings wide) and proper hydrogen bonding potential

If there is 20% thymine in a DNA strand, how much cytosine is there?

30%

Which of the nitrogenous bases are purines?

Adenine and Guanine

What direction is DNA synthesized?

5' to 3' direction

What direction does the DNA polymerase READ the DNA template?

3' to 5' direction

What is the function of helicase?

Unwinds and unzips the double-stranded DNA helix by breaking hydrogen bonds

What is the function of topoisomerase?

Relieves strain and prevents supercoiling ahead of the replication fork by cutting and rejoining DNA strands

What is the function of DNA polymerase?

Synthesizes new DNA strands complementary to a template by adding dNTPs to the 3' OH end

What is the function of RNA primers and primase?

Primase synthesizes short RNA primers that provide a free 3'-OH group for DNA polymerase to start synthesis

Why are RNA primers required for DNA replication?

DNA polymerase can only elongate an existing strand and requires a free 3'-OH group to add nucleotides

How does the leading and the lagging strand differ?

Leading strand is synthesized continuously 5' to 3'

What is the function of DNA ligase?

Joins Okazaki fragments by catalyzing phosphodiester bonds in the sugar-phosphate backbone

Describe the process of DNA replication using the enzymes described above (helicase, topoisomerase, DNA polymerase, primase, RNA primers, and DNA ligase)

Helicase unwinds DNA while topoisomerase relieves strain

What determines RNA function?

Its specific sequence of nucleotides and resulting secondary/tertiary folded structure

What is the function of mRNA?

Carries genetic code from DNA in the nucleus to the ribosome for translation

What is the function of tRNA?

Delivers specific amino acids to the ribosome by matching its anticodon to the mRNA codon

What is the function of rRNA?

Forms the structural and catalytic components of the ribosome (catalyzes peptide bond formation)

How does the mRNA, tRNA, and rRNA all interact?

mRNA carries the code

How does the DNA sequence determine the RNA sequence?

RNA polymerase uses base-pairing rules to build complementary RNA from the DNA template strand

What is transcription?

The process of copying a segment of DNA into a complementary RNA sequence by RNA polymerase

What is the starting material for transcription?

A single-stranded DNA template (within double-stranded genomic DNA)

What is the product of transcription?

A primary RNA transcript (such as pre-mRNA, tRNA, or rRNA)

What is the function of RNA polymerase?

Binds DNA at promoters, unwinds the helix, and synthesizes complementary RNA in the 5' to 3' direction

Which strand is the template strand?

The 3' to 5' DNA strand that RNA polymerase reads to synthesize complementary 5' to 3' RNA

Which direction does transcription take place (which direction is the RNA synthesized)?

5' to 3' direction

Which direction is the template strand READ?

3' to 5' direction

What is the function of the poly-A tail?

Protects mRNA from enzymatic degradation in the cytoplasm and aids in export and translation efficiency

What is the function of the GTP cap?

Protects 5' end of mRNA from degradation and helps the ribosome recognize and attach to mRNA

What is the function of RNA splicing?

Removes non-coding introns and joins coding exons to form mature mRNA

How can multiple proteins be synthesized from the same mRNA transcript?

Alternative splicing includes or excludes different combinations of exons

What is translation?

The synthesis of a polypeptide chain from an mRNA sequence by a ribosome

Where does translation take place?

At ribosomes in the cytoplasm or on the rough endoplasmic reticulum

How does the location of translation differ between a prokaryote and a eukaryote?

In prokaryotes translation occurs concurrently in cytoplasm

How does the location of translation affect gene expression in a prokaryote?

Allows coupled transcription-translation, enabling rapid cellular response to environmental changes

Describe the process that takes place during transcription

RNA polymerase binds promoter, unwinds DNA, synthesizes complementary pre-mRNA 5' to 3', and terminates

Identify three post-transcriptional modifications that alter the pre-mRNA prior to its release from the nucleus

Addition of 5' GTP cap, addition of 3' poly-A tail, and RNA splicing (intron removal)

Describe the process that takes place during transcription

RNA polymerase unwinds DNA template strand and builds a complementary RNA transcript in 5' to 3' direction

Identify three post-transcriptional modifications that alter the pre-mRNA prior to its release from the nucleus

5' GTP capping, 3' poly-A tail addition, and intron splicing

What are the three steps of translation?

Initiation, elongation, and termination

What happens in the initiation step of translation?

Small ribosomal subunit, mRNA, initiator tRNA (Met), and large ribosomal subunit assemble at start codon (AUG)

Where does translation start?

At the start codon (AUG) near the 5' end of the mRNA transcript

What is a codon?

A sequence of three consecutive mRNA nucleotides that codes for a specific amino acid or stop signal

How many nucleotides make up a codon?

3

Practice using a codon chart:

Codon charts match 3-letter mRNA codons to their specific amino acids

What amino acid is coded by UAU?

Tyrosine

What codons code for lysine?

AAA and AAG

How are multiple codons able to code for the same amino acids?

Due to degeneracy/redundancy in the genetic code (wobble position at 3rd base)

True or False: One codon can code for more than one amino acid

False (the genetic code is unambiguous)

What are the three sites found on a ribosome and what is their function?

A site (accepts incoming tRNA), P site (holds tRNA with growing peptide chain), E site (exit site for uncharged tRNA)

What happens in the elongation step of translation?

tRNAs deliver amino acids corresponding to codons, forming peptide bonds and extending the polypeptide chain

What happens in the termination step of translation?

A stop codon reaches the A site, binding a release factor that cleaves the polypeptide and disassembles the ribosome

What chemical process releases the growing polypeptide?

Hydrolysis reaction catalyzed by a release factor

How does the genetic code demonstrate common ancestry?

Nearly all living organisms share the same universal genetic code (same codons specify same amino acids)

What is the central dogma?

Genetic information flows from DNA to RNA to protein

What is the function of reverse transcriptase?

Synthesizes double-stranded DNA from an RNA template (used by retroviruses)

How does a virus incorporate its viral genome into a host genome?

Integrase enzyme inserts reverse-transcribed viral DNA into host chromosome

How does a virus form progeny viruses?

Uses host cell machinery (ribosomes, ATP, enzymes) to transcribe, translate, and assemble viral parts

How does a retrovirus violate this process?

Transcribes genetic information backward from RNA to DNA using reverse transcriptase

Identify two examples of retroviruses

HIV and Human T-lymphotropic virus (HTLV)

What are regulatory sequences?

Non-coding DNA segments (promoters, enhancers, silencers) where regulatory proteins bind to control transcription

What is the promoter region?

A specific DNA sequence upstream of a gene where RNA polymerase and transcription factors bind to initiate transcription

What is the TATA box?

A conserved DNA sequence within eukaryotic promoters that helps position transcription factors and RNA polymerase

What is the enhancer region?

A DNA sequence that can be far from the promoter, binding activator proteins to significantly increase transcription rates

What are epigenetic changes?

Heritable changes in gene expression that do not alter the underlying DNA nucleotide sequence

How is DNA modified to initiate transcription (to regulate gene expression)?

Demethylation of DNA allows chromatin to relax and transcription factors to access promoters

How is DNA modified to inhibit transcription (to regulate gene expression)?

DNA methylation (adding methyl groups to cytosines) condenses chromatin and represses transcription

How are histones modified to initiate transcription (to regulate gene expression)?

Histone acetylation neutralizes positive charges, loosening chromatin structure (euchromatin) for polymerase access

What is cell differentiation?

The process by which stem cells become specialized in structure and function through differential gene expression

Why can different phenotypes result from different levels of gene expression?

Different sets or amounts of proteins are produced, altering cellular structure and function

What is the function of transcription factors?

Proteins that bind to specific DNA sequences to assist or block RNA polymerase binding, regulating transcription

How do gene products affect the phenotype of organisms?

Proteins and functional RNAs carry out cellular processes that dictate physical and functional traits

How do the amount of gene products affect the phenotype of organisms?

Higher or lower concentrations of functional proteins change trait intensity, metabolic rate, or cell fate

How is prokaryotic gene expression regulated?

Primarily at the transcriptional level using operons controlled by repressors, activators, and inducers

What is an operon?

A cluster of prokaryotic genes with related functions regulated by a single promoter and operator

What is a repressor?

A regulatory protein that binds to the operator DNA sequence to block RNA polymerase transcription

What is a promoter?

A DNA sequence where RNA polymerase attaches to initiate transcription of downstream genes

Describe the interaction between repressors and promoters

Repressors bind to the operator adjacent to/overlapping the promoter, physically blocking RNA polymerase access

How does the repressor interact with the promoter?

Binds to the operator site, sterically hindering RNA polymerase from binding or moving past the promoter

Is this operon repressible or inducible?

Operons like lac are inducible (off until substrate activates)

How is eukaryotic gene expression regulated?

At multiple levels: chromatin structure, transcription initiation, post-transcription processing, translation, and post-translation

How do transcription factors affect the binding at the promoter?

Activators facilitate RNA polymerase recruitment

Describe the difference between a promoter or enhancer

Promoter is adjacent to the gene where core transcription machinery binds

What is the function of transcription factors?

Regulate gene expression by assisting or inhibiting RNA polymerase binding to promoter regions

What is the function of RNA polymerase?

Transcribes DNA sequences into complementary RNA molecules

What is the function of the promoter?

Serves as the binding site for RNA polymerase and transcription factors to initiate transcription

How do negative regulatory molecules inhibit gene expression?

By binding to operators/promoters or mRNA to block transcription or translation

What is differential gene expression?

The expression of different sets of genes by cells with identical genomes, driving specialization