Module 4 Exam BIOCHEM 352

Chapters 24-28

Central Dogma of Molecular Biology

Describes the flow of genetic information from DNA to RNA to protein.

DNA Replication

Information that flows from DNA to DNA. From parental DNA copied to daughter DNA with high accuracy. Proceeds in the 5’ to 3’ direction

RNA Transcription

Information flow from DNA to RNA. Uses DNA as a template to synthesize RNA

Protein Translation

Information flow from RNA to proteins. Uses information stored in mRNAs to synthesize protreins

Reverse Transcription

Information flow from RNA to DNA and replication at the RNA level

Gene

A segment of a chromosome that contains the instructions for synthesizing a specific protein or RNA molecule.

Genetic Information

A sequence of nucleotides in RNA or DNA

Translation

triplets of nucleotides in mRNA - codons - bind to complementary triplets in tRNA to form a specific amino acid sequence, ultimately synthesizing proteins.

Genome

A set of all genes of a given organism and its non-coding sequences, representing the complete genetic blueprint.

Prokaryotes

Bacteria and archea. They have circular, single double-stranded chromosomes and are associated with non-histone proteins in the cytoplasmic nucleoid region

Eukaryotes

Animals, plants, and fungi. They have multiple, linear chromosomes and are associated with histone proteins and restricted to the cell nucleus

Plasmids

Circular DNA that are easily exchanged between bacteria and carry no essential genes

Eukaryotic chromosome

Consists of one linear DNA and 1 associated protein

Karyotype

A constellation of all chromosomes in a somatic cell of a given species

Telomeres

Sequences at the ends of eukaryotic linear chromosomes that are needed for DNA replication and cell division.

Hayflick Limit

A cell can divide ~52 times before losing the ability to divide again

Centromere

A sequence of DNA that functions as an attachment point for spindle fibers during cell division.

Exons

Expressed regions of the genes that are translated into amino acid sequences, only accounts for 1.5% of human DNA.

Introns

Regions of genes that are transcribed but not translated.

Splicing

The process by which introns are removed from RNA transcripts and exons are joined together to form a mature mRNA molecule.

Endosymbiotic Theory

Mitochondria and chloroplasts originated as free-living bacteria that were engulfed by ancestral eukaryotic cells. Explains the dual genetic origins and the symbiotic relationship between these organelles and host cells.

Viral Genomes

made of DNA/RNA surrounded by protein coat called capsid which is limited on the inside

DNA Compaction

The process by supercoiling DNA (prokaryotes) or involving histone proteins and chromatin structure (eukaryotes)

Topoisomerases

Required for DNA unwinding and rewinding during transcription and replication.

Type 1 DNA Topoisomerases

One transient cut in one DNA strand, removed negative supercoils (relaxes), and doesn’t need energy in the form of ATP

Type 2 DNA Topoisomerases

A transient cut in both DNA strands, enabling the passage of another double helix through the break, requiring ATP for the process.

DNA Gyrase

A type of Type 2 DNA Topoisomerase found in bacteria, which introduces negative supercoils into DNA and is essential for DNA replication.

Chromatin

the material of a eukaryotic chromosome. DNA + Proteins + a little bit of RNA

Chromatin (Structure)

Changes over the course of a cell cycle. It condenses during mitosis to form visible chromosomes and decondenses during interphase to allow for transcription and replication.

Nucleosome

Fundamental organizational units of chromatine that form “Beads of a string” structure. DNA is wrapped around histons.

Amino-Terminal Histone Tail

Sticks out of nucleosome core and protude between DNA turns, sites for regulatory covalent modifications that regulate gene expression and chromatin structure.

DNA metabolism

A set of tightly regulated processes that govern DNA replication, repair, and recombination.

Watson-Crick base pairs

Base Pairs: A-T, G-C.

Semi-conservative

refers to the method of DNA replication in which each new double helix contains one original strand and one newly synthesized strand.

DNA Synthesis

Addition of new nucleotides to the 3’ end

Leading Strand

Top strand. the DNA strand that is synthesized continuously in the direction of the replication fork during DNA replication.

Lagging Strand (Okazaki Fragments)

Bottom Strand. the DNA strand that is synthesized in short, discontinuous segments away from the replication fork during DNA replication.

Nucleases

Enzymes that cleave the bonds between nucleotides in nucleic acids

Exonucleases

Cleaves bonds that remove nucleotides from the ends of DNA

Endonucleases

Cleaves bonds withing a DNA sequence

DNA Polymerases

Enzymes that synthesize DNA molecules from nucleotides using a template strand.

Processivity

The number of nucleotides added before dissociation

Deoxynucleoside Triphosphate

Serves as a substrate in DNA strand synthesis

Primer

Required base-paired 3’ end for DNA polymerases to begin.

Exonuclease activity

3’ to 5’. Responsible for the correction of errors during synthesis. Proofreads DNA by removing incorrect nucleotides.

DNA Polymerase 1

Hydrolyzes polynucleotide strands ahead of the enzyme, 5’ to 3’ eonuclease activity

Replisome

The entire macromolecular complex for DNA replication

DNA Helicasas

Uses ATP to unwind/separate DNA strands in DNA Replication

DNA Topoisomerasa

Relieve the stress caused by unwinding in DNA Replication

DNA-binding proteins

Stablizes separated strands in DNA Replication

DNA Primases

Makes RNA primers in DNA Replication

DNA Ligases

Seals single-stranded breaks in DNA Replication

DNA Lesion

DNA Damage

Mutation

DNA lesions that remained unrepaired. They can be substitutions, deletions, additions. The daughter DNA carries the changed sequence

Silent Mutation

A mutation that has no effect on gene function

Types of DNA Damage

Mismatch, Abnormal bases, Pyrimidine dimers, Backbone lesions

Mistmatches

Are errors in DNA replication where the wrong nucleotides are paired, leading to potential mutations if not corrected.

Abnormal bases

are from spontaneous deamination, chemical alkylation or exposure to free radicals

Pyrimidine Dimers

Formed when DNA is exposed to UV light

Backbone Lesions

Occur from exposure to ionizing radiation, free radicals.

DNA Repair Systems

Mismatch repair, Base-excision repair, Nucleotide-excision repair, and Direct Repair

Mismatch Repair

Corrections replication errors and relies on Methylation of DNA to identify the correct DNA strand for repair.

Base-excision Repair

Repairs deaminated nucleotides and relies on specific glycosylases

Nucleotide-excision Repair

Repairs lesions that cause large distortions and relies on excinucleases

Direct Repair

“Undoes” damage to nucleobases

Methylation-Directed Mismatch Repair

A system that will cleave the unmethylated strand in the initial part of the repair system

DNA glycosylases

Cleaves N-glycosydic bond between sugar and base and creates apurinic/apyrimidinic (AP) site

Uracil glycosylase

Removes uracil from DNA to precent C from spontaneously deaminating to U in DNA

Excinucleases

Cleaves DNA backbone in two places to remove a damaged segment of DNA during nucleotide excision repair. Requires DNA polymerase I and DNA ligase to replace the DNA and seal the gap

DNA Recombination

Segments of DNA rearrange their location within a chromosome or from one chromosome to another

Types of DNA Recombination

Homologous Recombination, Site-specific Recombination, DNA transposition

Homologous Recombination

Occurs during the first meiotic division in Meiosis between the chromatids. These recombined chromosomes are then segregated into daughter cells

Chiasmata

A region in the chromosome where the strand breaks and rejoining occurs for recombination

Transposons

Some DNA sequences that can move around within the genome of a single cell

Transposons (continued)

Their ends contain terminal repeats that hybridize with the complementary regions of the target DNA during insertions and carry genes for transposases that catalyze insertion

Ribonucleic Acid - RNA

contains ribose sugar, uracil instead of thymine, and is typically single-stranded.

Messenger RNAs (mRNAs)

Encode the amino acid sequences of all the polypeptides found in the cell

Transfer RNAs (tRNAs)

Matches specific amino acids to triplet codons in mRNA during protein synthesis

Ribosomal RNA (rRNAs)

Constitute the ribosome — a molecular machine that is responsible for synthesis of all proteins in a cell

DNA Template Strand

Serves as template for the RNA Polymerase

DNA Coding Strand

Has the same sequence as the RNA transcript

RNA Elongation

DNA serves as a template for RNA synthesis and primer is not required to start

RNA polymerase 1

Synthesizes pre-ribosomal RNA

RNA Polymerase 2

Is responsibly for synthesis of mRNA. It’s very fast, specifically inhibited by muchsroom toxin alpha-amanitin, and can recognize thousands of promoters

RNA Polymerase 3

Transcribes tRNAs, 5S rRNA, RNA components of spliceosome and other smal RNA products

Processing RNA Polymerase 2

splices out introns and rejoining any exons, adding a 5’ cap, adding a 3’ poly(A) tail

5’-cap of Eukaryotic mRNA

Linked by 70methylguanosine, protects mRNA from nucleases, forms binding site for the ribosome. W/o it, mRNA is not translated efficiently and is degraded by cellular ribonucleases

Group 1 and Group 2 introns

Are self-splicing, requires no additional proteins or ATP, and are found in some mitochondrial, chloroplast, and nuclear genes. Have different splicing mechanisms

tRNA Introns

Spliced by protein-based enzymes, are the primary transcript cleaved by endonuclease, exons are joined by ATP-dependent ligase

Group 1 splicing mechanism

3’OH of guanosine acts as a nucleophile and attacked P at the 5’ splicing site. 3’OH of the 5’ exon becomes the nucleophile, completing the reaction

Group 2 splicing mechanism

2’OH of a specific adenosine in the intron acts as nucleophile and attacked the 5’ splice site to form a lariat structure. 3’OH of the 5’ exon becomes the nucleophile, completing the reaction

Retroviruses

Can do reverse transcriptase. Degrades the RNA from the DNA-RNA hybrid and replaces it with DNA

Composition of RNA

Ribonucleotides, contains uracil, usually single-stranded, and has multiple cellular functions

Protein Metabolism

Protein synthesis, folding, targeting, processing, degradation

Protein Synthesis

Very energy demanding, can use up to 90% of chemical energy, tightly regulated, are targeted to cellular locations, and degradation of proteins keeps pace with their synthesis

Protein Synthesis (cont.)

synthesized on the ribosomes, amino acids activated for synthesis via aminoacyl-tRNA synthetases, tRNA acts as an adapter to translate mRNA

Messenger RNA (mRNA)

primary product of structural genes, brings structural information from genes to ribosomes. They code for polypeptide chains

tRNAs

Act as decoders to translate sequences of nucleotides in mRNA into sequence of amino acids in protein

Genetic Code

Consists of Nucleotide Triplets. 20 common proteinogenic amino acids

Genetic Code Features

Consists of condons, each codes for a specific amino acid. The code is directional, contiguous, and non-overlapping