cell and molec test 2 review

Nucleoside

Where the base is attached to the sugar

Guanine

Adenine

Thymine

Cytosine

Purine Bases

Guanine, Adenine

Pyridmadines

Thymine, cytosine, uracil

Wavelength used to observe DNA absorbance

260 nm

how wide is DNA

2 nm

Regions of the Chromosomes

telomere, replication origin, centromere

chromatin-remodeling complexes

Proteins that

telomere

Repetitive nucleotide sequence that caps ends of linear chromosomes

DNA Helicase

Uses the energy of ATP hydrolysis to pry apart the DNA double helix ahead of the replication fork

Single-strand DNA-binding protein

Binds to single-stranded DNA exposed by DNA helicase, preventing base pairs from re-forming before the lagging strand can be replicating

DNA topoisomerase

Produces transient breaks in one strand of the DNA double heliz to relieve the tension buit up by the unwinding of DNA ahead of the DNA helicase; reseals breaks after DNA has relaxed

Sliding Clamp

Keeps DNA polymerase attached to the template, allowing the enzyme to move along without falling off as it synthesizes

Clamp loader

Uses the energy of ATP hydrolysis to lock the sliding clamp into DNA

Primase

Synthesizes RNA primers, does not proofread

DNA ligase

Uses the energy of ATP hydrolysis to join Okazaki fragments made on the lagging-strand template

DNA polymerase III

• Synthesizes leading and lagging strand of DNA

• Proofreads nucleotides added to newly synthesized DNA and removes incorrect pairings

DNA polymerase I

• Removes RNA primers and replaces it with DNA

• Proofreads nucleotides added to newly synthesized DNA and removes incorrect pairings

amt of genes in genome

21000

Protease

Enzyme that degrades proteins by hydrolyzing their peptide bonds and recognizes damaged and misfolded proteins

Centromere

Specialized DNA sequence that allows duplicated CMA to be separated

Histone-Modifying Enzymes

Enzyme that catalyzes the covalent addition of a small molecule, including methyl/acetate group to an amino acid side chain on a histone

Heterochromatin

highly condensed region of an interphase chromosome, gene poor and transcriptionally inactive

Euchromatin

Gene rich area of the cell where transcription proteins can access genes

Cohesin

A ring-shaped SMC protein complex that organizes interphase chromosomes into a long series of large chromatin loops

Condensin

A ring-shaped SMC-protein complex that compacts duplicated chromosomes for segregation by forming loops and loops within loops

How is the chromatin structure established and maintained?

By different sets of histone tail modifications

Epigenetic inheritance

The transmission of a heritable pattern of gene expression from one cell to its progeny

What is the stronger bond: C-G or A-T

C-G

What structure does DNA have? (conservative, semiconservative, etc.)

Semiconservative

What nucleic bases are found in replication origins?

T and A

In the Meselson and Stahl experiment, what did the DNA look like after being centrifuged?

A mix of ‘heavy’ and ‘light’ DNA, was in the center of the tube

RNA Polymerase

Enzyme that synthesizes RNA using DNA as a template

Which strand (leading or lagging) would be more effected by primase mutation?

Lagging strand

‘Replication machine’

Clamp loader added, Lagging strand template is covered by single strand DNA binding proteins, lagging strand is looped such that it is closer to the leading strand polymerase, polymerases held together by clamp loader arms

‘End replication problem’

DNA on lagging strand in eukaryotes cannot be fully reproduced

Telomere

Repetitive nucleotide sequence that caps the ends of linear chromosomes

Telomerase

Enzyme that elongates telomeres synthesizing the repetitive nucleotide sequence found at ends of eukaryotic chromosomes

Depurination

When a purine base is removed from a nucleotide due to Brownian motion

Deamination

Loss of an amino group from cytosine, causing it to form uracil

What damage does UV radiation do to DNA?

Promotes linkage between two pyrimidine bases, causing thymine dimers to form

What is the basic procedure for DNA repair for single-strand damage?

• damaged DNA is spotted and removed by nucleases that cleave DNA backbone around the damage

• Repair DNA polymerase binds to 3’ hydroxyl of cut strand and fills in the gap

• Break is sealed by ligase

Nonhomologous end joining

An error-prone mechanism for repairing double strand breaks in DNA by rejoining two broken ends. Often results in the loss of genetic information

Homologous Recombination

• Recombination-specific nuclease chews back 5’ ends of two broken strands

• one of the broken 3’ ‘invades’ unbroken homologous DNA duplex and searches for complementary sequence through base pairing

• Invading strand is elongated by repair polymerase, which uses the undamaged strand as a template

• invading strand passes break point and is disconnected from the template strand

• Repair is completed by additional DNA synthesis at 3’ ends of strands

mRNA

RNA molecule that specifies the amino acid sequence of a protein

rRNA

RNA that forms the core of ribosome structure

Sigma Factor

Subunit of RNA polymerase is bacteria that is released at the start site and reattached at termination

Region for bacterial promoter

-10 and -35

RNA Polymerase I

Codes for most rRNA, is found only in eukaryotic DNA

RNA polymerase II

Codes for all protein coding genes, miRNA, and other noncoding RNA. Found only in eukaryotes

RNA polymerase III

Codes for tRNA, 5S rRNA, other small RNAs. Found only in eukaryotes

General Transcription Factors

Proteins that assemble on the promoters of eukaryotic genes near the start site of transcription and load the RNA polymerase in the correct position

Transcription initiation complex

TFIID, TATA box, and RNA polymerase II

TBP

TATA binding protein

TATA box

About 30 nucleotides upstream form the transcription start site

Transcription factors that begin transcription

TFIID and TBP

TFIIH

Transcription factor that opens the double helix at transcription start point, initiates start of transcription

Elongation factors

Form a wedge that pries DNA off of histone core, is bonded after general transcription factors leave to unpack DNA from nucleosomes

Processes of mRNA processing

RNA Capping, Polyadenylation

RNA Capping

5’ end of RNA is bonded to 7-methylguanosie which protects it from the cytosine

Polyadenylation

3’ end trimmed at specific nucleotide sequence, then a lot of A’s are added to create a poly-A tail

Introns

Non-coding, intervening sequences

Exons

Short portion of eukaryotic genes that are used to code for proteins

RNA splicing

Process by which intron sequences are excised from RNA molecules in the nucleus during formation of mature mRNA

SnRNPs

Small nuclear ribonucleoproteins, cause direct breaking of RNA intron and exon, orders and catalyzes exon linkage

Spliceosome

Large assembly of RNA and protein molecules that splices introns out of pre-mRNA in the nucleus of eukaryotic cells

Alternative splicing

the production of different mRNAs from the same gene by splicing its RNA transcripts in different ways.

Nuclear Pore Complexes

Connect nucleoplasm to cytosol

Codon

Group of three consecutive nucleotides that specifies a particular amino acid. 20 are commonly used and/or found in proteins

Start Codon

AUG

tRNA

Small RNA molecule that serves as an adaptor that ‘reads’ a codon in mRNA and serves as the source of the amino acid added to the growing polypeptide chain.

Anticodon

Set of 3 consecutive nucleotides in a transfer RNA molecule that recognizes the 3-nucleotide codon on a mRNA molecule

What is wobble in tRNA?

The third nucleotide in the anticodon is not correct, however the tRNA can still bind to the mRNA

Aminoacyl-tRNA synthetase

an enzyme that attaches the correct amino acid to a tRNA during protein synthesis

how is an amino acid group attached to tRNA?

by a synthesizing enzyme that is specific to that codon

Ribosome

Large macromolecular complex composed of RNA and proteins. Translates mRNA to polypeptide chain. Made of one small and one large subuint

Small ribosomal subunit

Matches tRNA to codons of mRNA

Large ribosomal subunit

Catalyzes formation of peptide bonds

What are the three different binding sites for tRNA molecule in a ribosome?

A-site, P-site, E-site

A-site

Charged tRNA enters the A-site of a ribosome through base pairing with complementary codon on mRNA molecule

P-site

Amino acid linked to polypeptide chain

E-site

tRNA is ejected

What is the 4-step cycle of translation?

• Charged tRNA is added to vacant A-site

• Carboxyl end of polypeptide chain is uncoupled from tRNA at P site and joined with a peptide bond

• Large subunit shifts, which moves the bound tRNAs to the P/E-site

• Small subunit shifts

What catalyzes the polypeptide bond?

rRNA

How does the rRNA catalyze polypeptide bonds?

the reactants are precisely oriented such that the reaction is favorable

Translation initiator factor

Protein that promotes proper association of ribosomes with mRNA

Ribozyme

An Rna molecule with catalytic activity

Small ribosomal subunit

Scans mRNA until hits first AUG

Polycistronic

mRNAs encode several different proteins on same molecule

Stop codons

UAA, UAG, UGA

Release Factors

Bind to stop codons that reach A-site on ribosome with no amino acid, catalyzes water

Protease

Enzyme that degrades proteins in eukaryotes by hydrolyzing their peptide bonds that hydrolyze the peptide bonds between amino groups

Proteasomes

A large protein machine that degrades misfolded damaged proteins. Target proteins are marked with chain of ubiquitin.

parts of a proteasome

polyubiquitin binding site, central cylinder, stopper

differation

Process by which a pluripotent cell undergoes a progressive coordinated change to a more specialized cell type brought about by large scale changes in gene expression

‘Housekeeping proteins’

Proteins common to all cells of an organization, include RNA polymerase, DNA repair enzymes, ribosomal proteins, enzymes in glycoses, cytoskeleton

Transcription Regulators

Proteins that bind to specific DNA sequences and control gene expression