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Flashcards in RNA and the Genetic Code Deck (54):
1

Central dogma of molecular biology

Doctrine that states the necessary steps for transfer of genetic information from generation to generation

Steps:
1. Replication
I. Production of DNA copies
2. Transcription
I. Formation of single stranded mRNA from
DNA through complementary and antiparallel
base pairing
3. Translation
I. Formation of proteins from mRNA codons
using ribosomes in a N- to COOH- terminal
orientation

2

Types of RNA

1. mRNA / messenger RNA
I. The most abundant form of RNA
II. Formed in nucleus from complementary and
antiparallel transcription of DNA
III. Contains codons that code for amino acids
IV. Carries its information from nucleus to ribosome
in the cell's cytoplasm to initiate translation
2. tRNA / transfer RNA
I. Second most abundant RNA that converts the
language of nucleic acids to amino acids
II. It contains contains amino acids that upon pairing
of its anticodons with mRNA's codons add to the
polypeptide chain
III. Is found in the cytoplasm of cells
3. rRNA / ribosomal RNA
I. created in nucleolus but a vital part of ribosomal
machinery in the cytoplasm
II. It catalyzes the formation of polypeptide bonds as
a ribozyme

3

DNA Mutations and their Effects on Proteins

Mutations-----------------------Consequent Protein Changes
1. Silent/Degenerate--------None; change in wobble base
2. Point/Missense------------None or change in amino acid
3. Point/Nonsense-----------Premature protein truncation
4. Frameshift------------------Change in amino acid
sequence

4

Important Codons to Remember

Start codon for all eukaryotic proteins
1. AUG--------corresponding to -----Methionine
Stop Codons
1. UAG
2. UGA
3. UAA

5

Codons

--mRNA reading frames in bases of 3 that code for
amino acids
--There are 64 codons--
I. 61 of which code for amino acids
II. 3 of which code for premature ending of protein
translation
--a single amino acid can be coded for by multiple
codons that share identical nucleotides for their first 2
bases, varying only at the wobble position

6

Wobble Position

Variable third base of a codon that allows for a silent mutation, preventing harmful changes in amino-acid sequence

7

Transcription

Process of converting genetic info from DNA to RNA to allow transportation of genetic info to ribosome in the cell's cytoplasm where translation takes place

Reason for transcription:
1. DNA's degradation upon leaving the nucleus

***Does not require a primer for its initiation and does not involve proceeding proofreading of the transcript as opposed to what's seen in DNA replication

8

Template Strand

AKA anti-sense strand
DNA strand that serves as a template for mRNA transcription by RNA polymerase II

9

RNA polymerase II

DNA-dependent RNA polymerase that locates the promoter region on a DNA strand with the help of transcription factors before using the template strand to synthesize/transcribe mRNA

10

Promoter Region for Transcription

Region of DNA template strand with particular set of genes where RNA polymerase can bind to start transcription

****Contains the TATA box****

11

TATA box

Region of DNA template strand with high adenine and thymine content to which RNA polymerase II binds to start the transcription process

12

Various Types of RNA-Polymerases

1. RNA polymerase I: responsible for rRNA [28S, 18S,
5.8S] synthesis in the nucleus
2. RNA-polymerase II: responsible for synthesis of
snRNA & hnRNA in the nucleus
3. RNA-polymerase III: responsible for synthesis of tRNA
and rRNA [5S]


*****No need for primer to start transcription*****
snRNA------->small number RNA
hnRNA-------->heterogenous nuclear RNA

13

hnRNA

heterogenous nuclear RNA is the pre-processed mRNA synthesized by RNA-polymerase II in the nucleus that upon post-transcriptional modifications turns into mRNA

14

Coding/Sense Template

DNA strand complementary to the template strand and identical to the mRNA strand except for including thymine instead of uracil

15

+1 Base of a Gene Region

The first base of a gene transcribed from DNA to RNA

16

Base-Numbering of a DNA Coding Region

1-Negative numbers: #s to the left of +1, upstream and
toward 5'; include -25 which is the
region where TATA box is located
2. +1 #: #of the first base on DNA that gets
transcribed
3. +2, +3, +4, etc #: #s downstream of +1 on which RNA
polymerase II moves until it
reaches a stop sequence, ending
transcription

17

Post-Transcriptional Processes

Define: Processes involved in preparing hnRNA to leave the nucleus and to interact with ribosome to participate in translation

1. Splicing of Introns and Ligation of Exons on hnRNA
by spliceosome
2. Addition of 7-methylguanylate-triphosphate 5'Cap to
hnRNA to
1. protect it against ribosomal
degradation
2. to enable it to bind to ribosome
3. Addition of poly-A-[polyadenosyl] Tail to 3' end of
mRNA to protect it against degradation in
cytoplasm before it reaches the ribosome
[the longer the tail, the longer the mRNA's
survival time in the cytoplasm]

18

Spliceosome

Complexes of small nuclear RNA and small nuclear ribonucleoproteins [snRNA & snRNP] that recognize the 5'to3' ends of introns on hnRNA and splice or snurp them before degrading them post-transcription

19

Introns vs. Exons

Non-coding vs. coding regions of mRNA

20

Evolutionary Significance of Introns

1. Maintenance of genomic size
2. Rapid protein evolution

21

UTRs

Untranslated regions in mRNA's 3' and 5' edges b/c translation starts at start codon (AUG) and ends at one of the stop codons [UAG, UGA, UAA]

22

Alternative Splicing

Potential post-transcriptional process that splices introns and ligates exons in alternative ways, increasing protein diversity in addition to taking role in gene-expression regulation.

23

Translation

Process of protein synthesis that takes place on a ribosome in the cytoplasm with the help of mRNA, tRNA, amino acids, ribosomes and GTP in both prokaryotes and eukaryotes.

It proceeds in three steps of
1. Initiation
2. Elongation
&3. Termination
with help of
1. Initiation factors [IF]
2. Elongation factors [EF]
&3. Releasing factors [RF]


*****All Steps require GTP******

24

Ribosome

Cytosolic structure in a cell composed of rRNA and proteins that bring mRNA and aminoacyl-tRNA together to synthesize proteins.

25

3 Binding Sites on Ribosome for tRNA

1. A [Aminoacyl] site
2. P [Peptidyl] site
3. E [Exit] site

26

Range of rRNA Strands in Eukaryotic Ribosomes

1. 28S rRNA
2. 18S rRNA
3. 5.8S rRNA
4. 5S rRNA

27

Difference b/w Eukaryotic and Prokaryotic Translation

Translation in
1. Prokaryotes: occurs concurrently with
transcription
2. Eukaryotes: occurs post transcription in 3
stages of
1. Initiation
2. Elongation
3. Termination

28

Initiation Stage of Translation

1. small ribosomal subunits bind to
1. a prokaryotic mRNA's Shine-Dalgarno
sequence in its 5' UTR
2. a eukaryotic mRNA's 5' cap
2. the charged initiator tRNA pairs its anticodon with
mRNA's start codon [AUG] at the ribosome's p-site
3. The first amino acid forms as
1. fMet [N-formylmethionine] in prokaryotes
2. Methionine in eukaryotes
4. The small and large ribosomal subunits bind to form
a complete initiation complex with assistance of IF at
the ribosomal site

29

Elongation Stage of Translation

A process of amino-acid addition to the polypeptide-chain in which a charged tRNA's with a particular anticodon recognizes its matching codon on mRNA, after which it binds to the mRNA and to the A-site of the ribosome. In this process, the tRNA then shifts to the P-site where its amino acid forms a peptide bond with the growing polypeptide chain. Finally, the uncharged tRNA gets released from the E-site of the ribosome to pick up another amino acid.

The ribosome moves along mRNA in a 5' to 3' direction while synthesizing a polypeptide chain from its N to its C terminus with the help of EFs that locate and recruit aminoacyl-tRNAs and GTPs.

30

Initiation Factor

Proteins that help bind small and large subunit ribosomes at the site of mRNA to prepare for elongation stage of translation

31

Elongation Factor

Proteins that locate and recruit aminoacyl-tRNA to assist with peptide chain elongation during the elongation stage of translation

32

Termination Stage of Translation

1. Stop codon moves into the A site of a ribosome
2. RF binds to the termination codon & adds H2O to
the polypeptide chain
3. Peptidyl transferase and termination factor
hydrolyze polypeptide chain from the final tRNA in
the P-site
4. the 2 ribosomal subunits dissociate

33

Post-Translational Processing

1. Folding-----------------
2. Cleavage-------------Insulin
3. Subunit addition---Hemoglobin
4. Biomolecule addition
1. Phophorylation
2. Carboxylation
3. Glycosylation
4. Prenylation

34

Chaperone

Category of proteins that assist with protein folding during the post-translational process

35

Phosphorylation

A post-translational modification process that involves addition of a phosphate to a protein by protein kinases to initiate protein activation/deactivation

36

Carboxylation

A post-translational modification process that involves addition of a carboxylic acid group to the protein to form a Ca2+ binding site

37

Glycosylation

A post-translational modification process that involves addition of an oligosaccharide to a protein as it passes through the ER and golgi apparatus to determine its cellular destination

38

Prenylation

A post-translational modification process that involves addition of a lipid group to a protein that serves as a membrane bound-enzyme

39

Prokaryotic Regulation of Gene Expression

Done through:
I. Operons [with 2 types of:
1. Inducible
&2. Repressible

40

Operons

Cluster of
1. structural gene
2. operator site
3. promoter site
& 4. regulator gene

With 2 types of 1. inducible & 2. Repressible

41

Structural gene

Genes that bind RNA polymerase to allow mRNA transcription followed by protein synthesis through translation

42

Operator gene

Non-transcribable sites of DNA upstream of the structural gene site where a repressor protein can bind to block RNA polymerase bound to the promoter from creating a RNA transcript

43

Promoter Site

Site that binds RNA polymerase

44

Regulator Gene

Gene that codes for a repressor

45

Inducible Operon Regulation

System for gene regulation that provides
1. negative control
I. where a repressor binds to an operator
to blocks RNA polymerase from
transcripting DNA
2. positive control
I. where an inducer binds to a repressor,
changes its conformation, and frees the
RNA polymerase to transcript DNA

46

Repressible Operon Regulation

System for gene regulation that provides
1. Negatieve control
I. by having the product of a regulator
gene [repressor] bind to a corepressor
before binding the operator site of an
operon to provide transcription blockage

47

Eukaryotic Regulation of Gene Expression Through:

1. Transcription Factors
2. Gene Amplification
3. Remodeling of Chromatin Structure

48

Transcription Factors

I. Proteins that recognize DNA binding motifs and
initiate/activate transcription after binding to them
II. Have 2 domains
A. DNA-binding domain
I. Bind DNA response element in the
DNA's promoter region to recruit
transcriptional machinery
B. Activation domain
II. Binds transcriptional factors,
regulatory proteins, RNA polymerae,
and histone acetylase

49

Gene Amplification

I. Up-regulation of transcription through
A. Enhancers
B. Gene Duplication

50

Enhancers

Clusters of various response elements outside of a DNA's promoter region that allow upregulation of a single's gene's transcription through multiple signals

51

Gene Duplication

Parallel or In-series duplication of a gene of interest to increase transcriptional activity of the gene

****Parallel duplication of the gene can be accomplished in a single chromosome by opening of the DNA using helicase followed by replication of the response element of interest******

52

Remodeling of Chromatin Structure

1. Condensing Chromatin into Heterochromatin and making it inactive and inaccessible for transcription
1. Via DNA methylation

2. Loosening chromatin into Euchromatin and making it accessible to transcriptional factors and machinery
1. Via Histone Aceylation

53

Histone Acetylation

I. Process that up-regulates transcription through histone acetylation
II. Involves Acetylation of a lysine residue in a histone's amino tail which results in reduction of the lysine's positive charge, causing consequent weakened association b/w DNA and histone, loosening of the chromatin conformation, and increased gene expression due to increased transcriptional machinery access to the chromatin's DNA

****Deacytylation of histone reverses this process****

54

DNA Methylation

I. Process that silences and reduces gene expression by methylating adenine and cytosine nucleotides of DNA, creating heterochromatines that are inactive and inaccessible to transcriptional machinery