Biology Genetics Quiz

Genes, Chromosomes, & DNA Metabolism

•  Chapters 24-25 cover genes, chromosomes, and DNA metabolism
•  The universal problem: DNA is extremely long, needing compact storage in cells.
• 1 human cell contains 2 meters of DNA, 3.1 billion base pairs.

Chapter 24: Genes & Chromosomes

• Chromosomes are the carriers of genetic information.
• Fundamental structural hierarchy includes sequence, double helix, and supercoiling.
• This supercoiling of DNA is essential for packing into a cell, minimizing space needed.

Chromosomal Structure

• DNA is extremely long, requiring precise organization within the cell.
• Supercoiling allows for tight packing of DNA.
• Chromatin fibers in eukaryotic cells involve DNA and proteins (histones).
• Key structural DNA packaging units are nucleosomes.
• Histones are Arg- & Lys-rich (25%) and positive charge.
• Packaging levels help package DNA into small cell structures.

Universal Problem

• DNA is too long to fit in cells without compacting
• Packing into cells occurs through coiling of coiling (supercoiling)

Super Coiling

• Coiling of a coil = supercoiling
• DNA has a structural hierarchy
• Primary-sequence
• Secondary-double helix
• Tertiary-supercoiling
• Underwinding'

Chromatin - Eukaryotes

• Chromatin consists of protein and DNA in roughly equal proportions, and a small amount of RNA.
• Histones are positively charged proteins in eukaryotes that help package the DNA into nucleosomes.
• Arginine and Lysine (Arg- & Lys-) are rich (25%) in positively charged proteins.
• Nucleosomes = DNA + associated proteins = basic packaging unit

Epigenetic Mechanisms

• Epigenetic processes: Development, Environmental chemicals, Drugs, Aging, and Diet.
• Epigenetic Factors affect DNA methylation or histone modification.
• DNA methylation and histone modification affect gene expression.

Human Chromosomes

• Humans have 23 pairs of chromosomes in their cells.
• Male DNA contains an X and a Y chromosome.
• Female DNA contains two X chromosomes.

Size of Genomes

• Chromosome = nucleic acid repository of genetic information
• E. coli chromosome is circular, contains 4,300 genes for proteins and 157 genes for RNA
• Human chromosomes are linear, have 41,000 genes, and 3.1 billion base pairs.

Genes

• DNA that encodes the primary sequence of a final biological product, including mRNA and proteins.
• Includes those with structural and catalytic functions.
• Historically, a gene was a unit of DNA that controlled a phenotype.
• One gene-one enzyme, and one gene-one protein hypotheses were proposed

Regulatory Sequences

• DNA sequences define the beginning or end of genes.
• These sequences influence gene transcription and act as initiation points for transcription and replication.

Viruses

• They are not free-living organisms.
• Generally not considered living.
• Infectious parasites, using host machinery to replicate.
• Many consist of genome (DNA or RNA) surrounded by a protein coat.

Viral Genomes

• RNA genome = present in almost every plant, some bacteria, and animal viruses. Some examples - HIV and Bacteriophage QB.
• DNA genome = many are circular for at least some part of the life cycle
• Vary in size greatly

Bacterial Genomes (E. coli)

• Circular, 4,639,675 bp, contour length 1.7mm.
• Cell generally 1 x 2 µm.
• May contain plasmids in cytoplasm.
• Genes for own replication and extra genes for resistance.

Bacterial Chromosomes

• Generally, bacteria contain only one chromosome.
• Almost all DNA is colinear with amino acid sequence that it encodes.
• Only one copy of genes.

Eukaryotic Chromosomes

• Structurally and functionally more complex than prokaryotic chromosomes.
• Only about 1.5% of the DNA encodes functional protein, rRNA, or tRNA.
• Many genes contain introns (intervening sequences) and exons (coding sequences.)

Eukaryotic Genomes

• Yeast has 2.6 times more DNA than E. coli.
• Drosophila has 35 times more DNA than E. coli, while humans have 700 times more.
• Many plants and amphibians have much more DNA than E. coli.
• Humans have 46 chromosomes.

Diploids

• Genetic material in eukaryotes into chromosomes.
• Diploid number (2n) depends on the species
• Humans have 46 chromosomes (23 pairs), large duplex DNA molecule.
• Each chromosome is single, large, duplex DNA molecule.
• Length of human chromosomes vary over 25-fold.

Eukaryotic Organelles

• Contain their own DNA. Mitochondria generates energy for the cell, and chloroplasts are photosynthesis sites.
• mtDNA is circular, 16,569 bp in humans, with copies ranging from 2 to 10 per cell.
• cpDNA is circular.

Eukaryotic Chromosomes

• Structurally and functionally more complex than prokaryotic chromosomes.
• Only about 1.5% of the DNA codes for functional protein, rRNA, or tRNA.
• Genes contain one or more segments of DNA that do not code for amino acids of polypeptide products.
• Intervening sequences (introns) are removed through RNA splicing.
• Coding segments (exons) remain in the final product.

Other DNA

• Transposons (jumping genes) = transposable elements.
• Alu element & Simple sequence repeats (SSR) = highly repetitive elements (10-15% human genome).
• Centromere is a region of DNA that links the chromosomes to the mitotic spindle.
• Telomeres are sequences at the ends of chromosomes that help to stabilize them.

DNA Replication

• DNA is semiconservative; one old strand & one new strand.
• Replication begins at the origin of replication.
• Replication proceeds bi-directionally.
• DNA polymerase can synthesize DNA only 5′→3′; creating Okazaki fragments on the lagging strand.

DNA Polymerase

• Can only add nucleotides in the 5′→3′ direction.
• Capable of proofreading.
• Different polymerases have different proofreading abilities.
• Some are more accurate than others (higher fidelity).

Degradation

• Nucleases-work on both DNA and RNA
• DNase and RNase are enzymes to degrade DNA and RNA respectively.
• Exonucleases - remove nucleotides from an end
• Endonucleases - begin degradation at a specific internal site.

DNA Repair

• Corrects damaged DNA and prevents mutations.
• Examples include mismatch repair, base excision repair, and nucleotide excision repair.

Mutations

• Permanent changes in DNA.
• Types include substitution, insertion/deletion, and duplication.
• Mutations can be linked to disease and cancer.
• Ames test is used for identifying mutagens.

DNA Repair

• Very inefficient, bioenergetically speaking; organisms do not spend as much energy repairing DNA.
• Small price to pay for preventing mutations.

Base-Excision Repair

• Removes damaged bases.
• DNA glycosylases remove damaged base.
• AP endonuclease removes sugar.
• DNA polymerase fills gap, and ligase seals nick.

Nucleotide-Excision Repair

• Repair's damaged DNA, large distortion types.
• E. coli has 12 cut bases and 13 for 2 mistakes.
• Eukaryotes cut out more bases.

SOS Response - Desperation

• Response when both DNA strands are damaged.
• Error-prone translesion DNA synthesis replaces DNA damage.
• Special polymerases are used to replicate past the damage.
• Error rate 1 in 1000.

DNA Recombination

• Homologous and site specific recombination events.
• Meiosis (chromosome alignment-swap-genetic diversity)
• Transposition elements (move from one site to another.)

RNA Metabolism

• Chapter 26 covers all of the processes involved with RNA.

Brief Introduction to Mendelian Genetics

• Early ideas on offspring inheritance vs. modern understanding.
• Offspring resemblance to one parent or a mix is discussed.

Blending Inheritance

• Offspring traits are a blend of parent traits, where traits are lost of diluted from generation to generation.

Gregor Johann Mendel

• Father of genetics, documented and documented experiments with pea plants.

Model Organism: Pea Plants

• Organism chosen to study heredity due to short generation times, numerous traits, and cross-breeding capabilities.
• Traits observed and identified

Studied 7 Traits

• Round/wrinkled seed shape, yellow/green seed color, purple flower color, axial/terminal flower position, inflated/constricted pod shape, yellow/green pod color, tall/dwarf stem height

First Law: Law of Segregation

• Specific units are passed down from parent to offspring, come in pairs, and offspring get one from each parent.
• Dominant factors can sometimes overshadow recessive ones in giving rise to a trait.

Terminology

• Gene = region of DNA encoding RNA or proteins.
• Allele = variant form of a gene.
• Pea plants examples: gene controls pea color, yellow allele (dominant - Y), and green allele (recessive - y)

Genotype vs. Phenotype

• Genotype = all of the genes that an organism has.
• Phenotype = observable characteristic
• Pea plant example: Homozygous=YY or yy, Heterozygous=Yy, yellow, or green peas are the phenotypes.

Reginald C. Punnett

• Devised a Punnett square method for predicting outcomes.
• Squares focused on genotype.

Punnett Square

• Predicting outcomes of cross-breeding experiments.
• Genotype-phenotype ratios

Law of Independent Assortment

• Factors responsible for different traits are inherited independently.
• Pea colors (yellow/green) and flower color (purple/white) are inherited independently.

### Punnett Squares with Multiple Traits

• Predicting outcomes of cross-breeding experiments with more than one trait.
• Multiple genes determine a trait, where each gene gives rise to an allele

Other Types of Inheritance

• Non-standard patterns of inheritance, including Incomplete Dominance and Co-Dominance.

Incomplete Dominance

• Heterozygous phenotypes blend the homozygous phenotypes, or a unique trait.

Co-Dominance

• Both alleles are expressed in heterozygous individuals as unique or distinctive traits.

Boveri-Sutton Chromosome Theory

• Chromosomes are basis for Mendelian genetics (chromosomes carry hereditary information.)
• Chromosome number reduced to half during gamete production in ova and sperm cells.

Cellular Basis of Mendelian Genetics?

• Chromosomes (23 pairs)
• Sex characteristics (XX or XY)
• Cell processes and chromosomes are central to Mendelian genetics or genetics in general.

### RNA Synthesis & Transcription

• Section on the processes of RNA synthesis and transcription; fundamental processes in molecular biology.

RNA vs. DNA

• RNA has additional hydroxyl group (-OH) on the 2nd carbon.
• RNAs are typically single-stranded.
• RNAs are more structurally diverse than DNAs and transmit information & catalyses (catalyze.)
• RNAs are synthesized from a DNA template, except in the case of RNA viruses.

RNA Polymerase

• DNA-dependent RNA polymerase (DdRp).
• Uses the 3' hydroxyl to attack a-phosphate of incoming nucleotide.
• Binds to specific promoter sequences.
• Transcription bubble to synthesize RNA.
• 17 bp in E. coli.

Step 1: Open the double helix

• Helicase unwinds DNA. This forms a transcription bubble.

Step 2: RNA polymerase synthesizes the RNA complement to the template strand.

Step 3: Bonds between DNA template strand reform and new RNA leaves.

Where to Start? Promoters

• RNA polymerases bind to promoter sequences.
• Variable but consistent DNA sequence elements that allow RNA polymerases to begin transcription.

The Two Strands

• Template strand serves as a template; this strand of DNA is antiparallel and complementary to the mRNA molecule.
• Coding strand is parallel and identical (not complimentary) to mRNA; all Ts substitute for Us.

Where to End? Terminators

• RNA polymerase will continue until it reaches a specific sequence terminator, and additional proteins involved in the termination.

RNA Polymerases in Eukaryotes

• Eukaryotes have 3 RNA polymerases; involved in specific steps in RNA synthesis.

Disruption of Transcription

• Some antibiotics, intercalating agents- preventing DNA movement disrupting transcription.

RNA Processing

• Occurs with almost all eukaryotic RNA.
• Enzymes include: RNA-based (ribozymes) & Protein-based processing.
• Primary transcript to RNA splicing, which removes introns.

Primary Transcript

• Newly synthesized RNA molecule; undergo extensive processing.
• Prokaryotes have different processing methods than eukaryotes.
• Pre-mRNA, heterogeneous nuclear RNA (hnRNA).

End Processing

• Protection from degradation, 5' cap added, 3' end removal & poly(A) tail added.
• Mature mRNA is the final product.

Introns & Exons

• Both introns and exons are transcribed, but introns are removed.
• Eukaryotic genes have introns to remove; prokaryotes do not!
• Introns vary in size, from simple to complex.

Introns: Groups I and II

• Rare & self-splicing; do not require proteins.

Introns: Groups III and IV

• Largest group.
• Uses spliceosome; includes small nuclear RNAs (snRNA).
• Requires ATP and endonuclease.

Differential mRNA Processing

• Introns are removed; exons stay.
• Alternative splicing occurs with different proteins being generated from mRNA.

rRNA & tRNA Processing

• Pre-rRNA and tRNA are modified at specific residues and contains introns.
• They vary greatly in structure and length.

Special RNA

• Small nuclear RNA (snRNA)
• Small nucleolar RNA (snoRNA).
• Micro RNA (miRNA).

Catalytic RNA = Ribozymes

• RNA molecule with catalytic activity.
• Group I introns can self-splice.
• RNase P cleaves RNA (tRNA).
• Ribosomes have rRNA that catalyze protein synthesis.

RNA Viruses

• Genetic material is RNA, not DNA
• Retroviruses (HIV) use ssRNA and reverse transcriptase.
• Genome typically 10,000 nucleotides long, with errors in replication cycles ranging from 1-2 per cycle.
• Examples include HIV, containing 6 separate proteins/mRNA; Gag, Pol, and Env genes or groups.

RT is a Good Drug Target

• AZT is reverse transcriptase inhibitor, or RT inhibitor.

Common Origin

• Transposons, retroviruses, and introns.
• Structural similarities between these elements suggest a common evolutionary origin.
• Retrotransposons are viruses that lost genes and are trapped in cells, similar to HIV.

RNA & Biochemical Evolution

• RNA could have been first informational molecule and catalyst for primordial metabolic function.
• RNA viruses, retrotransposons, &ribozymes are vestiges of RNA world.
• RNA catalysts are important for protein synthesis and self-replication.

Targeting structural dynamics of the RNA-dependent RNA polymerase for antiviral strategies

• RNA-dependent RNA polymerase (RdRp) is a main target for antiviral drugs.
• RdRp is crucial for genome duplication.
• Mutations in RdRp can alter properties.

RNA-dependent RNA polymerase

• RdRp responsible for genome duplication and maintenance in RNA viruses.
• Cycles through conformational changes while incorporating nucleotides.
• Mutations can affect amino acid sequence and properties of the enzyme.
• Examples, such as G64S substitution (reduced virulence.)

Poliovirus

• RNA virus in Picornaviridae family.
• Single-strand positive-sense RNA genome.
• Small, well-studied model for RNA viruses

PV RdRp

• Proteins of the RdRp.
• Amino acid motifs (A, C, F, G, D) are absolutely conserved in the RdRp.

Structural Dynamics

• Combination of NMR spectroscopy and MD simulations to study conformational changes in the RdRp.
• Checkpoints are critical to understanding the structure of the RdRp.
• Important to understanding how RNA is replicated and the steps involved; including replication, and fidelity checkpoints.

Motif D

• Key motif on the RdRp characterized by conserved amino acids (Lys359.)
• Acts as a general acid.
• MD simulation demonstrated conformational changes upon NTP binding.
• Possible fidelity in RdRP by conformational checkpoints.

Antiviral Strategies

• RdRp is among the most conserved proteins in RNA viruses.
• Vaccines attempt to reduce or manipulate error rates of RdRps
• Mutations in RdRP can alter the production of RNA and proteins produced from an RNA template.

Test your knowledge on DNA replication and inheritance patterns in this engaging quiz. Covering topics like Okazaki fragments, chromosome theory, and phenotypic traits, this quiz is perfect for biology students. Challenge yourself with questions on alleles, genotypes, and Punnett squares.