nucleic acid transcription/translation Flashcards by kaitlyn crist

what is a primary structure?

covalent structure and nucleotide sequence

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what is a secondary structure?

regular, stable structure taken up by some or all nucleotides

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what is a tertiary structure?

complex folding of large chromosomes or the elaborate folding of tRNA or rRNA structures

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What is a phosphodiester linkage?

Covalent bond that joins successive nucleotides of both NDA and RNA

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What is a parallel strand?

3’ , 5’-phosphodiester bonds run in the same direction

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What is an antiparallel strand?

3’ , 5’-phosphodiester bonds run in the opposite directions

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How was antiparallel strands confirmed?

x-ray analysis

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What is Chargaff’s Rules:

A + G = T + C
A = T
G = C

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How many hydrogen bonds between G & C

3 H bonds

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How many hydrogen bonds between A & T

2 H bonds

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What is a palindrome sequence?

has the potential to form a hairpin (single strand) of cruciform (double stranded)

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What is a mirror repeat?

no possibility of self-complementarity (does not lead to secondary structure)

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A form DNA

right handed helix
more common in solutions lacking water
usually outside physiological conditions

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B form DNA

Watson-Crick
most stable
most common in physiological conditions

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Z form DNA

left handed helix
common when C-G pairs are alternating
can be found in physiological conditions but not common

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Hoogsteen pairing forms a:

triplex DNA

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Tetraplex DNA is formed when:

four DNA strands pair
occur readily only for DNA sequences with a very high proportion of G residues

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Is a G tetraplex stable?

very stable

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mRNA structure:

always single stranded
right handed
can base pair with complementary regions of DNA or RNA

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Structure of complementary RNA strands is:

an A-form right handed double helix

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breaks caused by mismatched or unmatched bases result in:

bulges or internal loops

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internal loops form between:

palindromic sequences

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what is the most common RNA secondary structure?

hairpin

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DNA cellular locations:

Nucleus
Mitochondria
Chloroplast

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Nucleus DNA:

primary location, containing all genetic material organized in chromosomes

Mitochondria DNA (mtDNA):

much smaller than nuclear chromosomes codes for mitochondrial tRNA, rRNA, and some mitochondrial proteins

Chloroplast DNA (cpDNA):

even smaller than mtDNA provide chloroplast specific things

New gene definition:

all the DNA that encodes the primary sequence of some final gene product

What is a gene product?

polypeptide or RNA with a structural/catalytic function

one gene-one polypeptide hypothesis:

one protein is produced from one gene (not 100% true)

What are introns?

nontranslated DNA

What are exons?

translated DNA (coding DNA)

What is a codon?

3 consecutive nucleotides in a single strand of DNA that codes for a specific amino acids

In Bacteria DNA is present as a:

Plasmid compacted in the nucleoid

What is a plasmid?

small, circular DNA molecule that are in the cytosol of many bacteria

What are viruses?

a single RNA or DNA molecule and a protein coat not technically living

Genomes are variable across species and the association between number of chromosomes and protein coding genes is:

not associated with more DNA equaling more proteins coded

What is chromatin?

eukaryotic chromosomal material composed of DNA, RNA, and proteins

What are chromosomes?

tertiary packaging of DNA

DNA has regions that are ____ and ____?

underwound and supercoiled

enzymes that increase or decrease the extent of DNA underwinding?

topoisomerases

What is a centromere?

A DNA sequence that functions during cell division as an attachment point for proteins that link the chromosome to the mitotic spindle

What are telomeres

sequences at the ends of eukaryotic chromosomes that help stabilize the chromosome

What are histones?

Proteins that are tightly associated with chromatin and function to package and order the DNA

What base pairs do histones attend to associate with?

regions rich in A/T

What is a nucleosome?

the fundamental structural unit of chromatin composed of a "bead" plus DNA connecting next to the bead

DNA replication occurs during this phase?

Interphase

DNA polymerase reads in what direction and synthesizes in what direction?

reads 3' to 5' and synthesizes 5' to 3'

What is an Okazaki Fragment?

result of lagging strand of DNA

5' end is the end where 5' C is only bound to:

phosphate, not another base pair

3' end is the end where 3'C is:

free

What are the 3 main functions of DNA Polymerase?

Incorporate dNTPs Proofread (exonuclease activity) Replaces RNA primers with DNA

What is the template strand?

3' to 5' strand only the way that the polymerase moves DNA strand that serves as template for RNA synthesis

What is the non template strand?

DNA strand that is identical in base sequences to the transcribed RNA, with U in RNA in place of T in DNA

Bacterial RNA Polymerase sigma subunit does what:

Directs the enzyme to specific DNA binding site

Eukaryotic RNA Polymerases functions: I II III

I - pre-ribosomal RNA, matures to rRNA II - mRNA ncRNA (non-coding RNA) III - tRNA 5S rRNA ncRNA

Eukaryotic Transcription has what that binds promoter sequences to regulate transcription?

Transcription Factors

What is the CTD?

carboxyl-terminal domain of RNA pol II

What is a-amanitin?

compound produced by the death cap mushroom Amanita phalloides

What does a-amanitin do?

disrupts transcription in animal cells by blocking Pol II and, at higher concentrations, Pol III

mRNA processing has what 3 features:

5' cap Intron splicing Poly A tail

What is the 5' cap?

addition of a 7-methylguanosine to the 5' end for blocking of degradation by RNAses

What is Intron Splicing?

an intron can code for noncoding mRNA Facilitated by a spliceosome congregation of proteins most common intron removal can be spontaneous though

What is the polyadenylation enzyme?

Polyadenylate polymerase catalyzes the synthesis of the poly A tail Serves as the buffer from degradation at the 3' end

mRNA processing leaves a smaller or larger length

The final mature mRNA is smaller in length than the full gene coded in DNA

With mRNA processing how does it work in different locations?

Different cell locations, cell types, or different environmental factors can process differently

What is alternative splicing?

Some genes go through alternative splicing depending on specific conditions or different cell types to produce different proteins.