DNA to protein Flashcards by Catriona Grant

nucleoside =

base and sugar

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nucleotide =

nucleoside and phosphate group

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what is the difference between ribose and deoxyribose?

on C2 of ribose there is an OH instead of an H

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what are the two purines?

adenine and guanine

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what are the three pyramidines?

uracil, thymine and cytosine

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in polymerisation a phosphodiester bond is formed between a free 3’ __ group and a 5’ ________

A phosphodiester bond is formed between a free 3’ OH group and a 5’ triphosphate

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polymerisation releases 2 __ enegy bonds

high

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new nucleotides are only added to a free _’ end

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analogues of thymidine (ZDV=AZT=retrovir) can be used as drugs. The analogue is incorporated into the growing viral DNA
Lacks _’ __ group, therefore, chain elongation is terminated

Is incorporated into the growing viral DNA

Lacks 3’ OH group, therefore, chain elongation is terminated

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the nucleotide analogue mechanism only works because viral _____ ______ has higher affinity for ZDV than human DNA polymerases

reverse transcriptase

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Replication is semi-______

conservative

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replication is catalysed by ________

DNA polymerase

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DNA polymerase requires a ____ primer to start replication

RNA

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in eukaryotes Replication starts simultaneously at several points in the genome
and is bidirectional, what is the advantage of this?

ensures that replication can be finished in a reasonable time

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the leading strand template runs from __’ to __’

5 to 3

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the lagging strand template runs from __’ to __’

3-5

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which enzyme synthesises the primer for replication?

primase

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DNA ______ unwinds the double helix

helicase

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after the okazaki fragments have been generated the ____ are degraded and filled in by DNA -_______

primers, polymerase

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DNA polymerase has 3’ → 5’ _______ activity

exonuclease which removes incorrect nucleotide

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RNA is usually ___ stranded with local stretches of _______ base-pairing

single, intramolecular

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what are the three main classes of RNA

ribosomal RNA
transfer RNA
messenger RNA

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what are the stable RNAs?

ribosomal and transfer

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what is the function of ribosomal RNA?

combines with proteins to form ribosomes where protein synthesis takes place

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what is the function of transfer RNA?

carries the amino acids to be incorporated into the protein

what is the function of messenger RNA?

carries the genetic information for protein synthesis

RNA contains __ instead of thymine

uracil

rRNA has __ units to it

in tRNA specific amino acid is attached to the _’ end | depends on _______ sequence

Specific amino acid is attached to the 3’ end | depends on anticodon sequence

RNA is made by ___ _______

RNA polymerases

eukaryotic cells have __ types of RNA polymerase, what are they

3 | - pol I,II,III

how can the different RNA polymerases be distinguished

by their sensitivity to toxins like alpha-amantin

pol__ synthesised all mRNA

the ____ region is foun just upstream of the initiation site for transcription

PROMOTOR

____ ___ is present about 25 nucleotides before the transcriptional start (-25)

TATA box

_____ is a general transcription factor required for all pol ___ transcribed genes

TFIID, II

___ is part of TFIID and is responsible for recognising the TATA box

TBP

TFIID Provides a landing platform for further ____ _____ and for ___ _______

Provides a landing platform for further transcription factors and for RNA polymerase

what part of transcription process allows transcription to happen at low basal rates?

TFIID remains at the promotor region

RNA chain is synthesised in a __ to __ ’ direction

5 to 3

New RNA sequence is ______ to the template strand and it is _____- to the coding strand

complementary, identical

in transcription termination newly synthesised RNA makes a ____ -____ structure followed by a stretch of __

Newly synthesised RNA makes a stem-loop structure | followed by a stretch of Us

when proteins are to be made in response to a signal | they require ‘specific’ ____ ____.

transcription factors

regulatory transcription fatcprs can bind to either the >> 2 things

DNA-binding domain | transcriptional activation domain

the ______ receptors are a family of transcription factors, subset of (much larger) family of nuclear hormone receptors

steroid

they have 3 binding domains, whatare they

- Transactivation domain - DNA-binding domain - Ligand-binding domain

steroid receptors are located in the _____ (inactive). On binding ligand (steroid) move to _____ and bind to DNA at ___ ____ _____ (SREs)

cytoplasm, nucleus, steroid response elements

what is an example of a steroid receptor ?

glucocorticoid receptor

Coding regions _____ are interrupted by non-coding regions ______

exons, introns

introns are removed by ___

splicing

what changes are made to pre-mRNA to make it into mature mRNA?

1. a cap of modified GTP is added to the 5' end 2. specific sequence is recognised and cut by an enzyme 3. a poly A tail is added to the cut 3' end

where is mRNA processing done?

in the nucleus

During translation, _____ of tRNA molecules form base pairs with _____ on mRNA

anticodons, codons

how many different triplet combinations are possible?

the genetic code is ____ meaning that many amino acids have more than one codon

degenerate

the genetic code is ____ meaning that each codon codes for only one amino acid (or a Stop)

unambiguous

what is a start triplet?

AUG

give some examples of stop codons

UAA, UAG, UGA

translation is an ____ reaction

anabolic

___ _____ ______ bind amino acids to their corresponding tRNA molecule(s)

Aminoacyl-tRNA synthetases - this is highly specific

ATP provides energy for the formation of the ___ bond between AAs and the tRNA molecule

covalent

what are the three tRNA binding sites called?

1. exit 2. peptidyl (start) 3. aminoacyl

initiation of translation: ____ is hydrolysed to provide energy for initiation. Small ribosomal subunit binds to __ end of mRNA. Moves along the mRNA until ___ (start codon) is found (ATP-dependent). Special ‘initiator’ tRNA with___ anticodon base-pairs with the start codon- carries ____

GTP, 5', AUG, UAC, methionine

elongation of translation: An ______ ______ brings the next aminoacyl-tRNA to the A site. GTP is hydrolysed, __ is released from tRNA. A second elongation factor (EFβγ) regenerates ____ to pick up the next aminoacyl-tRNA

An elongation factor (EF-1α), brings the next aminoacyl-tRNA to the A site, EF EF1alpha

For EF-1a to be active, it must have a -__ molecules attached to it.

GTP

____ _____ catalyses peptide bond formation between amino acids in the P and A sites

peptidyl transferase

______ moves ribosome along the mRNA

Elongation factor EF-2 moves ribosome along the mRNA

No aminoacyl-tRNA base-pairs with ___ codons. the ___ factor binds to stop codons

stop, release

the _____ is where ribosomes will bind to mRNA wherever they find space

polysome

what is a point mutation?

change in a single base in DNA

what are the two point mutations>

- missense and nonsense

what happens in a missense mutation

there is a change in the amino acid sequence

what happens in a nonsense mutation?

this creates a new termination code

what is a silent mutation?

no change of amino acid sequence due to degeneracy of the genetic code no effect on protein function

what is a frameshift mutation?

addition or deletion of a single base (or two!) not three , doesnt change the frame changes reading frame of translation into protein

chromosomal mutations affect ___ portions of the genome

larger

what are the 4 chromosomal mutations?

deletions duplications inversions translocations

the location of the final protein depends on the presence of specific amino acid sequences within the _-_____ _____

translated protein

what three things can happen to a finished protein?

1. targeting 2. modification 3. degradation

``` ___ ribosomes in the cytosol make proteins destined for: cytosol nucleus mitochondria translocated post-translationally ```

free

``` _____ ribosomes on the rough endoplasmic reticulum make proteins destined for: plasma membrane ER Golgi apparatus secretion translocated co-translationally ```

bound

what is glycosylation/

addition and processing of carbohydrates in the ER and the Golgi

post translational modificaron: - specific proteolytic cleavage in the ER, Golgi, and secretory vesicles e.g insulin - formation of disulfide bonds in the ___

Hereditary form of emphysema results from misfolding of the protein __________ in the ER

Hereditary form of emphysema results from misfolding of the protein α1-antitrypsin in the ER

what happens in I-cell disease?

- proteins normally destined for lysosomes are not properly sorted in the Golgi - end up secreted from cell - lysosomes can not properly digest material, become clogged