molecular biology Flashcards by mir mir

Define a nucleoside

sugar + base

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What is the linkage between a sugar & base?

B-N-glycosidic linkage (btw 1C of sugar and base)

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Beta sugar linkage mnemonic

It’s better to B Up

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The 3’ of DNA has what group

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The 5’ of DNA has what group

phosphate

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Viral genomes are

circular or linear and can consist of DNA or RNA which can be single or double stranded

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DNA gyrase is a

topoisomerase

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what is the function of a topoisomerase?

cut one or both strands and unwrap the helix releasing excess tension created by the helicases

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DNA gyrases is involved in

compacting prokaryotic genome; supercoils

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Nucleosomes are composed of?

DNA wrapped around an octamer of histones

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Ribosomes are composed of ?

protein + rRNA

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The 3 stop codons are

UGA = U Go Away
UAA = U Are Away
UAG = U Are Gone

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Replication occurs in the

5 to 3 prime direction

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Replication requires

a primer and a template

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How many origins does replication have for eukaryotes and prokaryotes?

eukaryotes - multiple

prokaryotes - single (replication occurs bidirectionally)

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Prokaryoties have how many DNA polymerases?

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DNA Polymerase I

has 5–>3 exonuclease capability for the removal of RNA primers

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Another name for the template strand

noncoding strand, antisense strand

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The complementary strand of the template strand is the

coding, sense strand

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How many RNA polymerases do prokaryotes have?

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How many subunits does the prokaryote RNA polymerase have?

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B-N-Glycosidic

linkage between the sugar and nitrogenous base in nucleic acids

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is the B-N-Glycosidic up or down

up. remember “it is better to B up”

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these amino acids are unusually abundant in histones

arginine and lysine

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DNA is _____ and histones are ______

acidic; basic

telomere repeat

5'-TTAGGG-3'

prokaryotes have telomeres.

FALSE

In DNA replication, the parental strand is read in the

3 to 5 direction

In DNA replication, the daughter strand is written in the

5 to 3 direction

DNA polymerase I has ____ polymerase activity

5 to 3

DNA polymerase I has ____ exonuclease activity

3 to 5 and 5 to 3

DNA polymerase I is important for ________ repair

excision

3 to 5 exonuclease activity is also referred to as

proofreading

DNA polymerase III has high _______

processivity

catalyze consecutive reactions without releasing the substrate

DNA polymerase III has _____ polymerase activity

5 to 3

DNA polymerase III has _____ exonuclease activity

3 to 5 (proofreading function)

DNA polymerase III is important for _______ repair

none; it has no known function in repair; therefore, is considered a replicative enzyme

Compared to DNA, RNA has the following differences

is single stranded (DNA is double stranded) has the base uracil (DNA has thymine) sugar is ribose (DNA is deoxyribose)

monocistronic

one gene one protein

What is the significance of monocistronic when looking at experiments?

of unique proteins = # of mRNA

Monocistronic applies to prokaryotes or eukaryotes?

eukaryotes

Explain why deoxyribose is more stable than ribose

ribose has 2-OH which is nucleophilic and can attack the 5'-phosphate

What is the driving force for replication and transcription in terms of energy?

the hydrolysis of pyrophosphate

Holoenzyme

bound to sigma factor

bacterial promoter sequence

pribriow box: -10 and -35 sequence

when is the sigma factor released? where is it released from?

it is released after a few phosphodiester bonds have been formed (between RNA nucleotides). from the RNA polymerase

Prokaryotic Transcription is

rho / rho-independent (need to look up)

anabolism

biosynthetic repressible only occurs when product is scarce

catabolism

degradation | inducible

Eukaryotes have how many DNA polymerases

Eukaryotes have how many RNA polymerases

RNA polymerase I

transcribes rRNA

RNA polymerase II

transcribes mRNA

RNA polymerase III

transcribes tRNA

what is heterogeneous RNA (hnRNA)

applies to eukaryotes before splicing located in the nucleus primary transcript

Eukaryotic modifications to RNA

1. Splicing 2. 5' Cap - Methylated Guanine 3. Poly Adenine Tail

What is the importance of the 5' Cap - Methylated Guanine

essential for translation

Eukaryotic promoter

TATA box (~25 bp from initiation site)

Eukaryotic promoters contain regulatory sequence elements that are bound by _________ which result in an (increase/decrease) in transcription?

sequence specific transcription factors | either increase or decrease

Enhancers are located where

upstream or downstream from the sequence

Sequence specific transcription factors bind to

both to promoter and enhancer to regulate transcription

what regulates the binding of factors to DNA?

extracellular signals

what is the tertiary structure of tRNA? and how is it stabilized?

stem-and-loop | stabilized by hydrogen bonds between bases of neighboring atoms

Does tRNA nucleotides

tRNA contains several modified nucleotides

tRNA sites consist of

1. Anticodon | 2. AA receptor site

peptide bond formation is (positive/negative) delta G and kinetics are _____

positive | slow

tRNA loading is also called

AA activation

What drives peptide bond formation?

breaking of the aminoacyl bond

loading of tRNA

AA is attached to AMP + 2 high energy bonds are hydrolyzed

Prokaryotic ribosomes

30s, 50s, 70s (odd)

Eukaryotic ribosomes

40s, 60s, 80s (even)

synthetase

use energy from ATP

synthase

do not use energy from trinucleotide

Prokaryotes translation: upstream sequence function of that sequence?

Shine-Dulgarno sequence | ribosomal binding site

Prokaryotic Translation: | Initiation of translation

1 GTP required f-met-tRNA P-site Initiation factor proteins involved

Prokaryotic Translation: | A site versus P site

Aminoacyl-t-RNA site | Peptidyl-tRNA site

Prokaryotic Translation: | elongation involves

several EF (proteins)

Prokaryotic Translation: | Binding of tRNA in A site requires

1 GTP

Prokaryotic Translation: | which ribosomal subunit has the peptidyl transferase

``` Large subunit function of transferase is to catalyze the peptide bond ```

Prokaryotic Translation: | Transduction

1 GTP required

Prokaryotic Translation: | Termination

Release Factor enters A site

Eukaryotic Translation: | N terminal AA is ____

Methonine

Ribosomal binding site

Kozak sequence

Eukaryotic Translation: | Sequence of events in translation:

1. tRNA binds to small subunit 2. mRNA binds to small subunit 3. lg subunit binds

Prokaryotic Translation: | Sequence of events in translation:

1. IF combine with small subunit 2. mRNA binds to small subunit 3. first aminoacyl-tRNA 4. lg subunit binds

Activation of each AA during translation requires

2 ATP