Exam 1 (Lectures 2-7)

Biology 0500 with Atwood/freiman at Brown University

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By: Alyssa Kahn
Created: 2011-02-17
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Nucleotide Structure

Nitrogenous Base, Sugar, and phosphate

Phosphodiester Bonds

Links together nucleotides
Between nucleotides that are right next to each other- Covalent bond between 3' to 5'

Differences between DNA and RNA

RNA is single stranded and DNA is double stranded
RNA has Uracil to replace DNA's Thymine
RNA has ribose sugar (2'C has OH) and DNA has deoxyribose sugar (2'C has H)

Chromatid

Replicated chromosome strand

Chromatin

DNA + Proteins
Beads on a string.
Chromosomal DNA
Nucleosome: core histones H2A, H2B, H3, and H4 (octamer)
Liner Histone H1 and non-histone chromosomal proteins
30 nm condensed
10 nm decondensed via salt
DNA replication, DNA repair, Transcription, Recombination

Genetic

Coded within the nucleotide sequence of the genome.

Mendelian inheritance of genes from parent to progeny

Epigentic

Coded outside the nucleotide sequence

a.) DNA methylation: genes can be inherited with Me marks

b.) Chromatin Modification: Histone marks can be inherited

Heterochromatin

Chromatin is more highly compact. Silencing.

Telomeres and centromeres

Spreads if not stopped.

Euchromatin

Chromatin is more extended. Gene activation.

Chromatin Remodeling Complex

Protein machine that can move the nucleosomes around. Can open up a whole region of chromatin or move away. They use ATP hydrolysis to move chromatin/ move histones. Move nucleosome to get access to DNA.

Genetic Inheritance

When DNA sequences are copied quickly and correctly.

Effects how we look, act, behave, etc.

Epigenetic Inheritance

Histones and their modifications must also be replicated.

Each daughter chromosome will inherit about half of its parent's collection of modified histones. The remaining stretches of DNA receive newly synthesized, not yet modified histones. Proteins that recognize a particular modification can bind to the chromatin and catalyze the formation of the same modification on the new histones. Restores parental modification pattern and allows inheritance of parental chromatin structure.

DNA polymerase

Synthesizes new DNA using one of the old strands as a template. This enzyme catalyzes the addition of nucleotides to the 3' end of a growing DNA strand by forming a phosphodiester bond between this end and the 5'- phosphate group of the incoming nucleotide.

Built from 5' to 3'.

-Backstitches the Okazaki fragments to get the 2nd strand.

-Prokary: 1000 nucleotides/ sec

-Eukary: 100 nucleotides/ sec (chromatin makes packaging tighter and more regulate)

Replication Origin

Where DNA is first opened and marked by a particular sequence of nucleotides. Initiator proteins will initiate the complex with the help of DNA helicase (separates strands).

Lagging Strand DNA Replication Cascade

DNA Primase synthesizes new RNA primer.
RNA Primer is started on the new strand. DNA polymerase continues where RNA Primer left off to finish the DNA fragment (until it hits the next RNA primer).
RNase (nuclease) will digest the RNA parts and DNA polymerase will repair, meaning make the RNA into DNA.
DNA ligase comes in and links the Okazaki fragments together.

Telomerase

Replicates the ends of chromosomes.

-If DNA primase wants to add the DNA primer, cant replicate the end of the strand like it can in the middle of the strand. If it could, nuclease would digest

-Requires a length of template RNA that is beyond the DNA that is copied. Telomerase adds a series of repeats of a DNA sequence to the 3' end of the template, which then allows the lagging strand to be completed by DNA polymerase. This is done with RNA sequence complementary to DNA repeat seq.

Huntington's Disease

A model of triplet repeat expansions. Mutation in DNA replication- making more repeats. If have more than CAG 42 repeats. Neurological disorder.

Late onset genetic disorder (40s and 50s)
Transmitted as a vertical, autosomal dominant allele
Severe depression, cognitive defeats and chorea (movement disorder)
Progressive neurodegeneration that is ultimately fatal
If understood the slips and uncorrect replication, then maybe could help

Thymine Dimer

Chemical lesions caused by UV radiation.

-Repaired by nucleotide excision repair (NER) proteins that remove the specific proteins that are wrong and add the correct bases.

Xeroderma Pigmentosa

Cannot repair thymine dimers because of an inherited defective gene for mutation in NER genes and proteins. NER disruption

-People will develop severe skin lesions, skin cancer because of the accumulation of thymine dimers in cells that are exposed to sunlight and the consequent mutations that arise in the cells that contain them.

Nonhomologous End Joining

Double stranded break in the DNA perhaps by xray. Broken ends are recognized by cell and gamma H2AX recognizes the double stranded breaks to process them via nuclease. Will reattach the two ends together. Deletions of nucleotides at the repair sites. Leaves a gap while homologous doesn’t. Not as accurate as homologous. Lose whatever you had originally.

RNA polymerase

The enzyme that synthesizes RNA copy of template strand in the 5’ to 3’ direction

-Doesn't need a primer to start synthesizing.

-Signals in DNA tells it where to start (promotors) and finish (terminals).

mRNA

Code for proteins

rRNA

Form the core of the ribosome and catalyze protein synthesis

miRNA

Regulate gene expression

tRNA

Serve as adaptors between mRNA and amino acids during protein synthesis

Other small RNAs

Used in RNA splicing, telomere maintenance, and many other processes

RNA Polymerase I

Type of RNA: Ribosomal RNA

Cellular localization: Nucleolus

RNA Polymerase II

Type of RNA: mRNAs and miRNAs

Cellular Localization: Nucleoplasm

RNA Polymerase III

Type of RNA: tRNAs and snRNAs

Cellular Localization: Nucleoplasm

Humans vs. others

Large size and number of introns.

Less difference in exons.

aminoacyl- tRNA synthetase

couples a particular amino acid to its corresponding tRNA AKA charging

Wobble Position

The third position in a codon that can have any of the nucleotides. Doesn’t need 3^rd base pair to be perfect. Large number of codons to be read from a single tRNA

Initiation Site

Sets the reading frame. Where protein synthesis begins.

Cytosol

Contains many metabolic pathways
Protein synthesis occurs here
Makes up 54% of the total cell volume
i.e. Red blood cells are mostly this and very very small nucleus.

Nucleus

Contains main genome
DNA and RNA synthesis occurs here
i.e. Lymphacytes are mostly nucleus and little cytosol

Endoplasmic Reticulum (ER)

Synthesis of most lipids
Synthesis of proteins for distribution to many organelles and to the plasma membrane

Golgi Apparatus

Modification, sorting, and packaging of proteins and lipids for either secretion or delivery to another organelle

Lysosomes

Responsible for Intracellular degradation with a low pH.

-Degrade material usually from outside that are coming into the cell.

-Enzymes don't get chewed up by the low pH because they are covered in glycosilated or coated in sugar- not accessible to acid.

-300 per cell

Endosomes

Responsible for sorting of endocytosed material

-200 per cell

Peroxisomes

Responsible for oxidation of toxic molecules

Mitochondria

ATP synthesis by oxidative phosphorylation

-Makes up 22% of the total cell volume

-1,700 per cell

Chloroplasts (in plant cells)

ATP synthesis and carbon fixation by photosynthesis

Evolution

Nuclear membranes and ER evolved through invagination of the plasma membrane. Nucleus regulates splicing of messengar RNA and removal of entrons.

Nuclear Pore Complex

Forms a gate through which molecules enter and exit from the nucleus.

-Proteins bound for the nucleus are actively transported through the nuclear pore. Can work in reverse the export mRNA.

-Nuclear localization signal tell the protein to go to the nucleus.

-Nuclear proteins bound with nuclear transport receptor actively transport through the pore, released then transport receptor is recycled.

-Uses GTP hydrolysis. See slide 13 on ER lecture.

Signal- Recognition Particle (SRP)

In the cytosol, binds to the ER signal sequence when it is exposed by the ribosome.

SRP Receptor

Embedded in the membrane of the ER, recognizes the SRP.

Clathrin molecule

Form basketlike cages that help shape membranes into vesicles.

-Bud from golgi apparatus on the outward secretory pathway and from plasma membrane on the inward endocytic pathway.

-Starts off as Clathrin- coated pit. Cathrin molecules assemble into basketlike network on the cytolic surface of the membrane and starts shaping the membrane into vesicle.

-Dynamin assembles as a ring around the neck of coated pit. Helps the ring to constrict: pinching off vesicle from membrane.

Dynamin

(GTP- binding protein)

-Assembles as a ring around the neck of each deeply invaginated coated pit.

-Helps the ring to constrict by undergoing GTP hydrolysis: pinching off vesicle from membrane.

Clathrin Molecule: Selected Cargo

-Cargo receptors, with their bound cargo molecules, are captured by adaptins, which also bind clathrin molecules to the cytosolic surface of the budding vesicle.

-Dynamin helps to pinch off the vesicle.

-An uncoating ATPase later removes the clathrin

-Endocytosis but can go both ways.

SNARE

Direct vesicles to their targets

-v-SNARE occur on vesicles; t-SNAREs occur on Target membranes

-v-SNARE on vesicle binds to a complementary t-SNARE on target membrane.

-Rab provides initial recognition btwn them, the complementary pairing ensures that the vesicle goes to the correct location.

Rab

Helps vesicles to dock on the appropriate membrane.

Golgi Apparatus

-Modify, sort, and package material from ER

-Cis Cisterna: materials get processed.

-Trans cisterna: Pinched off/ making new membranes.

-Constitutive Secretion: Operates continuously to supply lipids and proteins.

-Regulated Secretion: Selected proteins in trans Golgi are diverted into secretory vesicles, accumulate, that are signal to release when stimulated by hormone or NT

Golgi Modification

As proteins pass through the Golgi, sugars may be removed from the oligosaccharides that were added in the ER. Conversely, additional sugars may be added to the oligosaccharides

-Adding: carbohydrates

Sorting: phosphorylated

Golgi Packaging

-At the trans Golgi network, secretory proteins are packaged into secretory vesicles with clathrin or COP coats.

-Signal sequences on the proteins direct them to the appropriate vesicle. This allows the Golgi to produce several products at once.

-Microtubules and motor proteins MAY be involved in movement of vesicles

About this deck

By: Alyssa Kahn
Created: 2011-02-17
Size: 54 flashcards
Views: 65

About StudyBlue

“Simply amazing. The flash cards are smooth, there are many different types of studying tools, and there is a great search engine. I praise you on the awesomeness.”
Dennis