BIOB11

Winter 2023

Central Dogma of Biology

DNA to RNA to Protein

Dominant Allele

Determines the phenotype

Homozygous

Same copy (AA or aa)

Heterozygous

Different copy (Aa)

Law of Segregation

An Individual’s two alleles segregate from one another during gamete formation

Law of Independent Assortment

Segregation of a pair of alleles for one trait has no effect on the segregation of alleles for another trait

Walter Flemming

Discovery of chromosomes

Walter Sutton

Concept of *homologous* chromosomes

Crossing Over’/Recombination

Homologous chromosomes when paired (bivalent) can break and exchange pieces with each other to allow for reshuffling of genes

Chiasma

Point at which homologous chromosomes are crossed

Photo 51

Rosalind Franklin’s X ray diffraction image of DNA in 1952 was key to figuring out the double helix model

Pyrimidines

Cytosine, Uracil, Thymine

Purines

Guanine, Adenine

Phosphodiester Linkages

Connects nucleotides

3’ end

hydroxyl

5’ end

phosphate

Chargaff’s Rules for DNA base composition

\[A\] = \[T\] and \[G\] = \[C\]

Functional Requirements of DNA Structure

1. Storage of Genetic Information
2. Replication and Inheritance
3. Expression of Genetic Message

Eukaryotic genomic DNA

Membrane-enclosed Nucleus

Prokaryotic genomic DNA

No distinct nuclear compartment

Heterochromatin

Portions of DNA found in a condensed form

Introns

Do not code for proteins

Exons

Protein-coding sequences

RNA splicing

Removes introns from RNA

Transposons

mobile elements that can move around in the genome and duplicate themselves, leading to repetitive sequences

Supercoiling

Double-stranded, double helix DNA molecule twists on itself

Positive Supercoils

Helix is __over__wound

Negative Supercoils

Helix is __under__wound

Histones

Highly conserved proteins rich in basic amino acids

Chromatin

Eukaryotic DNA associates with histones and other proteins to form chromatin that forms chromosomes

Nucleosomes

Repeating subunits of negatively supercoiled DNA + 8 histones

Lowest level of chromatin organization

30 nm fiber

Level of chromatin organization above nucleosomes

Made of histone H1 + core nucleosome

Histone H1

Linker histones - binds linker DNA that connects one nucleosome to another

Scaffolds

Supercoiled loops of 30 nm fiber

Euchromatin

Less compacted, functionally active sections of DNA

Heterochromatin

Always compacted, little to no functional activity sections of DNA

Constitutive Heterochromatin

Compact at all times, surrounds telomeres and centromeres, contains DNA repeats and relatively few genes

Facultative Heterochromatin

Inactivated during certain phases of organism’s life

Epigenetics

Inheritance that can occur without changes to nucleotide sequence in DNA

The Histone Code

Acetylation leads to more open structure and transcription

Methylation leads to less

Histone Acetyltransferase (HATs)

acetylates proteins

Histone Deacetylases (HDACs)

removes acetyl group from proteins

Histone Methyltransferases (HMTs)

adds methyl groups to lysine or arginine

Histone Demethylases

Removes methyl group

Position Effect

Silencing of genes by heterochromatin occurs in regions and is inherited after cell division

DNA Methylation

proteins that bind to methylated DNA can recruit enzymes involved in promoting a repressed chromatin state

CpG

C-phosphate-G

Epigenetic marker created by DNA methylation

Genomic Imprinting

some methylation patterns are passed on to offspring

Reader Complex

Protein complex that “reads” the histone code and positions and activates enzyme “writers” that can act on the DNA/histone

Barrier Proteins

Create physical barriers or actively recruit opposing chromatin modifying enzymes

Point Mutation

Switching one nucleotide for another

Tandem Repeats

DNA that repeats themselves over and over without interruption

Satellite DNAs

5-500 bp in tandem repeats of up to 100 kb

Minisatellite DNAs

10-100 bp with up to 3k repeats

Microsatellite DNAs

1-5 bp in clusters of 10-40 bp scattered evenly throughout genome

Microsatellite Instability

Regions of repeated DNA that change in length when mismatch repair is not working properly

Intrachromosomal duplications

Usually in euchromatic regions, predisposed to large mutations

Interchromosomal duplications

common in pericentriomeric or subtelomeric regions

Regions of Synteny

Blocks of DNA in conserved order

Mobile DNA

DNA that moves from one place to another in the genome

Reverse Transcriptase

Used by Transposable elements with LTRs (long-terminal repeats) to copy themselves

Inverted DNA Repeats

Required for recognition by transposase and excision from donor DNA

Direct DNA repeat

Generated in recipient DNA

Retrotransposon

“copy-and-paste” mechanism that involves an RNA intermediate

Exon Shuffling

Transposition altering gene sequences

Ortholog

Mutation of a gene in an ancestral organism causes speciation and gives rise to two separate species

Paralog

Gene duplication and divergence within the same species

Unequal Crossing Over

Misalignment in two genes causing deletion in one gamete and duplication in the other

Multigene Families

Closely related sequences which may encode related polypeptides that have a similar function

Pseudogenes

“Genes” that have a similar sequence to their gene family but have accumulated so many mutations that they are now non-functional

Single Nucleotide Polymorphism (SNP)

Single nucleotide difference in protein coding/non-coding sequence, causes alleles

Copy Number Polymorphism (CNP)

Difference in the number of copies of a particular sequence

Structural Variation

Changes in segments of the genome that alters chromosome structure

Haplotypes

A particular combination of alleles on a chromosome that are inherited together

Base Composition and Denaturation

Higher the G/C content, higher the Tm

G/C has more h-bonds and more base-stacking interactions

Speed of Renaturation

Smaller the genome, the faster

Replication Fork

points where a pair of replicating segments come together and join the non-replicated segments

DNA Helicase

Opens up DNA double helix ahead of replication fork

Single-strand DNA-binding (SSB) Proteins

Bind and stabilize single stranded DNA after helicase unwinds double helix

DNA Polymerase

Family of enzymes that carry out new DNA synthesis

RNA Primer

Synthesized by primerase, required to by DNA Polymerase to being synthesis

Topoisomerase

generates temporary single-strand breaks in DNA to relieve torsional stress of DNA unwinding

Topoisomerase I

‘Nicks’ one DNA strand to allow free rotation of DNA

Topoisomerase II

Catalyzes a double stranded break to detangle DNA

3’ to 5’ Exonuclease activity

Removes incorrectly added nucleotide

Strand-Directed Mismatch Repair

Distortions of the double-helix are used for recognition of mismatched base-pairing

Okazaki Fragments

Small fragments that are synthesized into the lagging strand

DNA Ligase

Covalently connects the Okazaki fragments into a continuous strand

Sliding Clamp

Clamps DNA Polymerase onto DNA template during synthesis

S Phase

DNA Synthesis Phase

Histone Chaperones

Adds back histones to re-established nucleosomes behind the replication fork

Replicons

Eukaryotic cells replicate their DNA in small portions

Telomeres

Sequences at the end of chromosomes that are composed of tandem repeats

Telomerase

Extends the template strand with repetitive DNA

Depurination

Removes base from DNA

Deamination

Most commonly converts cytosine to uracile

Nucleotide Excision Repair (NER)

Removes bulky lesions

Transcription Coupled NER Pathway

repairs DNA being actively transcribed

Global Genomic NER Pathway

repairs DNA in the remainder of the genome

Excision Nuclease

Cut the damaged strands on either side of the lesion (as separated by DNA helicase)