MCB 701 Exam 2 FULL SET

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401 Terms

1
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Griffith's experiment

- used pneumonococci and infected mice

- infected mice with a deadly (live) and non-deadly (heat killed or non-virulent) virus

- mice with virulent virus: died

- mice w/heat treated or non-virulent virus: lived

- mice w/ a mix of dead virulent and non-virulent virus: died

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After seeing that infected mice with a mix of dead virulent and non-virulent virus died, Griffith then

- took samples from those mice to culture

- found that the mice had living virulent strains of virus in the samples

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Griffith's experiment concluded that

- something from the dead virulent virus can transform living cells to cause infection

- the concept of transformation

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Transformation (of pathogens)

- components of pathogens are capable of using DNA to communicate genetic information for infection

- proteins are NOT hereditary material

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Base pairs occurring in a 1:1 ratio with each other means

the amount of A = T

the amount of G = C

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Structural features of DNA

- Double stranded

- anti-parallel

- complementary base paired

- major and minor grooves

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Minor groove

- the more constricted groove in the double helix

- harder to gain access too; likely to contain genes that aren't actively/frequently transcribed

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The minor groove is partially blocked by

deoxyribosyl moieties (this is likely what keeps it restricted/ compact

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Major groove

- the more open groove in the double helix

- can more easily bind DNA-specific proteins to the DNA (NT specific)

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AT regions/base pairings in DNA are important because

- AT regions melt and lower temps compared to GC regions

- allows DNA to be denatured and opened for other processes (ex. replication)

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Why do AT regions melt at lower temperatures in comparison to GC regions in DNA?

- AT bps are connected by two H-bonds, and GC bps are connected by three H-bonds

- AT bps are easier to dissociate since they only have two H-bonds

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TATA box (promoter)

- a region in the DNA specifically w/high accumulations of AT base pairing

- it is easily melted, which allows DNA to unwind for gene expression

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Nuclear DNA

- the bulk of all DNA in the cell organized into chromosomes

- 46 chromosomes, 23 chromosome pairs

- chromosomes contain between 48-240 billion bps

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A nucleotide (NT) consists of

- a 5 carbon sugar

- a phosphate group

- a nitrogenous base

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DNA strands always run from

5'-3'

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The backbone of DNA consists of

the phosphate group and the sugar (phosphate-sugar backbones)

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Mitochondrial DNA

- a small circular genome found only in the mito

- encodes for a small number of mitochondrial specific proteins

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Examples of mitochondrial proteins encoded by mitochondrial DNA

- NADH dehydrogenases

- cytochrome B

- oxidases and ATPases

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The synthesis of mitochondrial proteins takes place in

the mitochondria, with similar replication machinery

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Telomeres

nucleoprotein complexes that cap the end of 3' DNA to ensure cell viability after each replicative cycle

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Telomeres are composed of

tandem repeats of G-rich oligonucleotides (TTAGGG)

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telomerase

a ribonucleoprotein complex that elongates telomeres on the ends of DNA

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RNA

a single stranded nucleic acid composed of ribose

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RNA structures

- single stranded

- contains uracil instead of thyamine

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Since RNA is single stranded, it cannot

self replicate (no template for self replication)

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Primary, secondary, and tertiary structures of RNA

- primary: chain of NTs

- secondary: folded into functional unit (ex. tRNA)

- tertiary: multiple folded RNAs working together as a unit (ex. ribosomal RNA)

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rRNA

- ribosomal RNA

- a large complex of RNA molecules that are the structural and functional components of ribosomes

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Nucleotide functions (6)

- building blocks for DNA/RNA

- activated intermediates of glycogen and lipids

- 2ndary messengers in signal transduction

- energy currency for ATP and GTP

- enzymatic function (Ribozymes)

- structural components of co-factors (NAD/NADH+)

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Purine and pyrimidine carbon ring structure

- Purines: 2 carbon rings

- Pyrimidines: 1 carbon ring

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Nucleobase

the nitrogenous base all by itself

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Nucleoside

the nitrogenous base (nucleobase) + a phosphate group

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A nucleotide is a nucleoside with

one or more phosphate groups (PO-)

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Examples of nucleosides

- NMP: nucleoside 5' monophosphate

- NDP: nucleoside 5' diphosphate

- NTP: nucleoside 5' triphosphate

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Deoxyribose differs from ribose in that

the placement of an -OH or -H on the 2' carbon

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Deoxyribose has a _________ on the 2' carbon

-H

(deoxy: no oxygen)

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Ribose has a _________ on the 2' carbon

- OH

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Since RNA has a -OH in its carbon sugar, it prevents

long double helix regions from forming

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How do NTs function as metabolic intermediates?

- contain phosphate groups that allows them to be/become energetic intermediates

- can transfer Ps to do work or use Ps to join a growing strand

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Metabolic "forms"/examples of metabolic NTs

- NAD+

- FAD

- Coenzyme A

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NAD+, FAD, and coenzyme A are all formed by

ATP phosphate donation

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NAD

- nicotinamide adenine dinucleotide

- a pyrimidine NT formed from niacin (vit. B)

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NAD+ is metabolically involved in

- redox rxns

- carries of reducing equivalents of hydride (H-) transfer rxns

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NAD+ is also as a

cofactor for redox enzymes

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Purine synthesis

the process of synthesizing purine carbon sugars

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Purine synthesis occurs via what two pathways?

- De Novo

- Salvage

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De Novo purine synthesis

- process of taking raw materials and a lot of ATP to produce a purine carbon sugar

- energetically expensive (11 enzymes; 7 ATPs required)

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Raw materials for De Novo purine synthesis

- CO2

- NEAA (Asp, Glu, Gly)

- folic acid derivatives

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Steps of De Novo synthesis

- starts w/Ribose 5'-P (synthesized from the PPP: pentose phosphate pathway

- Purines start as PRPP (Purine Ribose Pentose Phosphate)

- go from Inosine monophosphate to Adenosine or Guanine monophosphate

- N9 is added to complete the pathway

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De Novo synthesis pathway is most active during ___________ and ___________;

De Novo synthesis pathway is also active in ___________ and ___________ tissues

the S-phase of the cell cycle

bone marrow and cancer

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The 1st committed step of the de novo pathway is

the addition of the N9

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Salvage pathway of purine synthesis

- the process of acquiring purines from food sources/endogenous NTs from ingestion/the environment

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Which purine synthesis pathway is the most preferred?

- the salvage pathway

- especially when there is a presence of free floating NTs

- De Novo synthesis is very energetically taxing, which is why the salvage pathway is most preferred

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Gout

- a disorder of purine catabolism

- purines cannot be broken down, leading to increased concentrations of urate and uric acid in the blood, urine, and joints

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On a cellular level, gout results from ____________

On a metabolic level, gout results from ___________

- massive necrosis of tissue with insufficient purine catabolism

- insufficient enzymatic activity to clear uric acid

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Xanthine oxidase

an enzyme responsible for the production of uric acid as a product

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Treatments for gout use

xanthine oxidase inhibitors

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Lesch-Nyhan Syndrome

- X-linked disorder characterized caused by a lack of the HGPRT gene

- leads to gouty arthritis, neuropathologies, mental retardation and aggressive behaviors

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The HGPRT gene is responsible for

the conversion of PRPP into inosine monophosphate

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the lack of HGPRT in Lesch-Nyhan syndrome causes

- an over-accumulation of PRPP

- increased purine biosynthesis

- increased accumulation of uric acid

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Drugs that target NTs and nucleic acid metabolism

- cancer drugs

- antiviral drugs (base, nucleoside, and NT analogues

- anti-folates

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Base-analogs alter

the nucleobases

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Nucleoside analogues alters

- the nucleobases

- the sugar component

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NT analogues alter/contain

a nucleic acid alteration with a normal sugar and phosphate group

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Histones

- protein subunits that come together to allow for DNA organization

- fully formed histones allow DNA to wrap around it to form the nucleosome

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Nucleosomes

- organizational structure of DNA

- comprised of DNA wrapped around histone proteins

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Chromatin

further condensation of nucleosomes into fibers

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Chromatin is commonly referred to as

beads on a string

- beads: nucleosome

- string: DNA; regions of DNA not wrapped around nucleosome called linker DNA

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Chromatin organizes DNA specifically so

the right genes/areas of DNA are accessible for transcription

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the accessible/transcribable areas of chromatin are

the regions of DNA NOT wound around a histone

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DNA compaction/organization from small scale to big scale:

DNA strand > DNA wrapped around histones > nucleosomes > coiled into chomatin > chromatin condensed into chromosome

(DNA > nucleosome > chromatin > chromosome)

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Nucleases

enzymes that break down nucleic acids

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In chromatin, nucleases target __________ for digestion

linker DNA

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Nucleases can't digest the DNA in a nucleosome because

the histone unit protects DNA from digestion

74
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Histone units can be digested/dissociated by

- putting DNA in high salt concentrations

- disrupts histone into individual subunits

75
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The core histone is comprised of

4 subunits that form an octamer

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Histone subunits

H2A

H2B

H3

H4

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process of forming the histone octamer

1. H3 and H4 dimerize , H2a and H2b dimerize unit)

2. H3-H4 dimers form tetramer

3. H3-H4 tetramer binds to DNA

4. H2a-H2b dimer binds to H3-H4-DNA complex

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The ________ term tails of the histone stick out when bound to DNA

the N term elongated tails

79
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Histones can associate tightly with DNA because

- Histones are positively charged

- DNA is negatively charged

- H-bonds form b/w the two

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When the DNA associates with the histone, what regions of the DNA are more favorable?

- the minor groove

- regions with AT, AA, TT dinucleotide regions in the minor groove

- allows the DNA in these regions to be closer together/more compressed

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In other words, the minor groove and regions of the DNA with AT,TT,AA di-NTs are

the more energetically efficient/favorable option for histone association

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Histone H1

- a histone subunit not apart of the core histone

- "linker histone": binds to the DNA wrapped around the core histone to lock it into place in the nucleosome

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Structural states of the nucleosome

- tetrasome

- hexasome

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Tetrasome nucleosome state

DNA wrapped around an H3-H4 tetramer (abt 80 bps)

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Hexasome nucleosome state

DNA wrapped around an H3-H4 tetramer and 1 H2a-H2b heterodimer

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Structural states of the nucleosome can lead to/allow

transient DNA breathing

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Transient DNA breathing

- a transient state of the nucleosome where the last 10-20 penultimate bps of DNA dissociate from the histone octamer

- allows these sites to be exposed (proteins can bind, transcription can occur, ect.)

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The canonical nucleosome is

a left handed supercoil

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Other than the structural states of nucleosomes, nucleosome structure can vary with

- direction of handedness of the DNA coil (L vs R hand)

- stoichiometry

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The chromatin filament itself if mainly comprised of the

interactions of the N-tails of neighboring histones interacting

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The chromatin filaments specifically organize into what shape?

a solenoid structure (a spring)

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Solenoid structures in chromatin filaments are stabilized head to tail by

H1 histone subunits

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Chromatin filaments further organize into chromosomes by using the

nuclear scaffold

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Nuclear scaffold

- non-histone proteins that assemble to form a scaffold for chromatin to bind to/wrap around

- the innermost core of the chromosome

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Primary, secondary, and tertiary structure of chromatin

1': "ball and string" motif: individual nucleosomes

2': nucleosomes condensing into solenoid structures; binding of H1 subunits

3': condensation of nucleosome solenoids into chromatin fibers

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What factors alter the primary structure of chromatin?

- spacing b/w nucleosomes (due to DNA sequence, remodeling enzymes, and protein binding)

- post-translational modification of histones

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What factors alter the 2ndary/tertiary structure of chromatin?

- long range interactions b/w nucleosomes in 1' structure

- stabilization of via architectural proteins (ex. H1)

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The 2' and 3' structure of chromatin is important because

Its structure is what makes DNA functional and accessible in a cell

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In the form of a chromosome/chromatin filaments, DNA can be accessed by/due to

- spontaneous unwraping from nuclesomes (mainly experiments)

- transition states of the nucleosome

- dynamic DNA-protein interactions that are reversible and highly regulated

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Chromatin can be categorized as

euchromatin

heterochromatin