Ch. 11 Flashcards by Julia Nauman

Primary Structure of DNA
Secondary Structure of DNA
Tertiary Structure of DNA

1- Nucleotide sequence
2- Double-stranded helix
3- Higher-order folding

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Supercoiling

Type of tertiary structure

When DNA is strain by over (postitive)/under (negative) wounding.

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What are the enzymes that add/remove rotations from DNA helix by temporarily breaking the nucleotide strands, rotating the ends around each other, and rejoining the broken ends?

topoisomerases

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Most DNA is ___ supercoiled, or relaxed?

negatively supercoiled, because it makes the separation of the two strands easier during replication. Also, supercoiled DNA can be packed into a smaller space

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Chromatin

protein + DNA

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Euchromatin

Undergoes normal condensation and decondensation.

Less condensed
On chromosome arms, Unique sequences
Many genes
Replicated throughout S phase
Transcription occurs often
crossining over is common

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Heterochromatin

more condensed
located at centromere/telomeres
repeated sequences
few genes
replicated late in S phase
transcription is infrequent
crossing over is uncommon

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Most abundant protein in chromatin? What do they do?

Histones- small, + Charge
H1, H2A, H2B, H3 & H4
+ charge attracts the negative charge on the phosphates of DNA.

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DNA diameter

2nm

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Nucleosomes consist of __ histone proteins around which DNA wraps __x.

1.65 times

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Length of histone is ___nm.

The nucleosomes fold up to produce ___nm fiber that forms loops averaging ___ nm in length.

11nm

30 nm

300 nm in length

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The 300 nm loops are compressed to produce __nm wide fiber that is ___ nm high.

250 nm wide

700 nm high

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Simplest level of chromatin structure

nucleosome
8 histones (2x H2A, H2B, H3, &amp; H4)  
DNA in direct contact is 145-147 bp long.

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What is H1 good for?

binding to 20-22 bp of DNA where DNA joins and leaves the histone octamer. Helps lock DNA in place

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Linker DNA is normally

30-40bp in length

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Chromatosomes

Nucleosome + histone 1

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Nuclease

Cleave linker DNA leaving 200bp bits. then continues to destroy unprotected DNA leaving the 145-147 bp .

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What part of histone has + charge? What part of DNA has - charge?

Tail

Phosphates

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polytene chromosomes

giant chromosomes

occur when repeated rounds of DNA replication take place without Cell divisions

chromosomal puffs

localized swellings of the chromosome. Each puff is chromatin with more relaxed structure. Regions of active transcription

DNase 1 digests DNA. How does sensitivity vary?

when DNA tightly bound to histone proteins, it is less sensitive to DNase 1. unbound DNA is more sensitive.

Correlated with gene expression, suggesting chromatin changes during transcription

CenH3

Variant histone that takes place of H3 at centromeres.
Required for assembly of kinochore proteins. Alters nucleosome and chromatin structure, allowing kinetochores proteins to bind and spindle microtubules to attach.

Centromere is constricted region of ______ where ___ attached

heterochromatin

spindle fibers

Telomere structure

Stabilize chromosome and provide means to replicate the ends of chromosomes.

5’T end/3’ A end to centromere

5’ T or A (1-4) then G (2+)

G rich single stranded sequences

Special proteins bind to protect telomere from degradation and prevent chromosomes from sticking together. Longer than C-rich strand. 50-500 nucleotides. Folds and pairs with short stretch of DNA to form t-loop, which prevents degradation.

Shelterin

multiprotein that binds to telomeres and protects DNA for being inadvertently repaired as doubled stranded break

C-value

amount of DNA per cell

C-value paradox

why do eukaryotic cells have extra DNA if not for complexity

Denaturation or melting

Two strands separate completely , hydrogen bonds weekend. Melting temp depends on base sequences. G-C pairs takes more energy

Renaturation or reannealing

reversal of denaturation by cooling.

unique-sequence DNA

sequences present only one, or at most, a few times in the genome

Repetitive DNA. Most common type is....

exists in many copies Moderately repetitive, typically 150-300 bp long

Moderately repetitive divisions

1. Tandam repeats- appear one after another and tend to be clustered at particular locations on the chromosomes 2. Interspersed repeats- scattered throughout genome.

Types of interspersed repeats: 1. SINEs 2. LINEs

SINE: ex: Alu sequences, LINE: 1000-2000 bp long

Highly repetitive DNA

Less than 10 bp long, but in hundreds of thousands to millions of copies in tandem clustered in certain regions. Also called satellite DNA.

Evidence for Endosymbiotic Theory

1. Modern day single-celled eukaryotes (protists) are hosts to endosymbiotic bacteria 2. M&C are similar in size to eubacteria, and have their own DNA/ribosomes 3. Antibiotics that inhibit protein synthesis in eubacteria but not in eukaryotic cells do affect organelles. 4. Sequences mtDNA and cpDNA are more closely related to sequences in the genes of eubacteria than they are to those found in eukaryotic nucleus.

Uniparental inheritance of organelle traits

in animals, 100% female (mostly). Paternal mitochondria selectively eliminated by autophagey

heteroplasmy

Organelle: 2 distinct varieties of DNA in single cell

Homoplasmy

Organelle: 1 type

Traits encoded by mtDNA

petite mutations in yeast, Neurospora, human diseases, cytoplasmic male sterility in plants

Human mtDNA size

``` Circular 16,569 bp 2 rRNAs 22 tRNAs 13 proteins Own replication/transcription initiation site. Economical- few noncoding nucleotides between genes, almost all mRNA encodes proteins ```

Yeast mtDNA

``` 5x as large as human 2 rRNAs 25 tRNAs 16 polypeptides Lots of noncoding sequences found within and between genes ```

Flowering plant mtDNA

Size variation- due to presence of long sequences that are direct repeats Direction cross over and separation cycles

Why are mitochondria ideal for reconstructing patterns of evolution in humans and other organisms?

1. small size and abundance 2. rapid evolution of mtDNA sequences 3. Maternal inheritance of mtDNA and lack of recombination makes it possible to trace female lines of descent 4. Abundance of mtDNA, thousands of copies per cell

Damage to mitochondrial DNA and Age

mtDNA disease are late in life ATP synthesis declines with age mechanisms unknown

Chloroplast genome

Many exhibit cytoplasmic inheritance | Sequence very similar to DNA in cyanobacteria.

Many proteins found in modern mitochondria and chloroplasts are encoded by ____ genes.

Nuclear genes | more stable as nuclear DNA, less mutations