presentations hg 2015 for midterm exam

7/24/2019 Presentations HG 2015 for Midterm Exam

1/41

DNA Repair

Prepared by:Denana Sarajlid

Berina Alid

Dijana Sejinovid


2/41

General errors in DNA replication are unavoidable.

DNA polymerases very occasionally insert the wrong

nucleotide, resulting in mispaired bases.

In the great majority of cases, the errors are quickly

corrected by the DNA polymerase itself.

If mispaired bases are not eliminated by the DNApolymerase, a DNA mismatch repair system is activated.

Chemical damage to DNA can be caused by external

mutagens

Various endogenous and exogenous sources can causedamage to DNA by altering its chemical structure


3/41


4/41

According to the type of DNA lesion, one of several

alternative DNA repair pathways is used:

Base excision repair (BER)

Single-strand break repair

Nucleotide excision repair (NER)

Base mismatch repair


5/41

Base excision repair


6/41

Nucleotide excision repair


7/41

Double-strand DNA breaks (DSBs) are normally rare in cells.

DSBs occur by accident, as a result of chemical attack onDNA by endogenous or externally induced ROS .

Unrepaired DSBs are highly dangerous to cells. The break

can lead to the inactivation of a critically important gene.

Two major DNA repair mechanisms can be deployed to

repair a DSB :

- Homologous recombination (HR)-mediated DNA repair

- Nonhomologous end joining (NHEJ).


8/41


9/41

DNA damage may sometimes go undetected. For

example, cytosines that occur within the dinucleotide CG

are highly mutable as a result of inefficient DNA repair.Deamination of 5-methylcytosine, however, produces a

normal DNA base, thymine, that can sometimes go

undetected as an altered base.

DNA lesions may be identified but are not repaired beforeDNA replication (damage tolerance).

DNA lesions that block replication may be bypassed

rather than repaired, and non-classical DNA polymerases

are required to resume DNA synthesis (translesion

synthesis).


10/41

References

T. Strachan, J. Goodship, P. Chinnery, Genetics and

Genomics in Medicine, Garland Science 2014

All figures in this presentation are taken from

Chapter 4 Principles of Genetic Variation of thementioned book.


11/41

Regulation of Transcription in

Eukaryotes 1

Prepared by:

Ahme Osmanovid

Adnan Fojnica


12/41

Control of the gene expression is far more complex ineukaryotes than in prokaryotes

Expression of eukaroyotic genes is regulated primary at

level of initiation of transcription

Regulation of Transcription in Eukaryotes includes :

cis-Acting Regulatory Sequences (Promoters and

Enhancers), Transcription Factor Binding

Sites,Transcriptional Regulatory Proteins, Structure andFunction of Transcriptional Activators


13/41

Cis-Acting Regulatory sequences:

promoters, enhancers & silencers

We can distinguish three classes of elements on the basis of theirrelative locations.

1. Promoters:

a. the core promoter (binding site for the RNA polymerase II)

b. promoter-proximal cis-acting sequences ( binding site for

proteins that assist in the binding of RNA polymerase II to its

promoter)


14/41

Enhancer sequences are regulatory

DNA sequences that, when bound

by specific proteins called

transcription factors, enhance thetranscription of an associated gene.

Enhancers can be located upstream,

downstream, or even within the

gene they control.

2. Enhancers


15/41

3. Silencers

Silencers are cis-acting sequences

that are bound by repressors,thereby inhibiting activators andreducing transcription. Enhancersand silencers are similar topromoter-proximal regions in thatthey are organized as a series of cis-acting sequences that are bound bytrans-acting regulatory proteins.However, they are distinguishedfrom promoter-proximal elementsby being able to act at a distance,

sometimes 50

kb or more, and bybeing able to operate eitherupstream or downstream from thepromoter that they control.Enhancer and silencer elements are

intricately structured.


16/41

Transcription Factor Binding Sites

The binding site of most transcription factors

consist of short DNA sequences, 6-10 base pairs.


17/41

Transcriptional regulatory proteins

Most common transriptional regulatory factors are transcription

factors.

Transcription factor (sometimes called a sequence-specific DNA-

binding factor) is a protein that binds to specific DNA sequences,

thereby controlling the rate of transcription.

Mouse Transcription factor


18/41

Structure and Function of Transcription

activators

Regulatory proteins that bind to DNA sequence and stimulates

transcription.

One region of the protein binds DNA, other part interacts with

proteins.


19/41

https://www.youtube.com/watch?v=nLAF5i1X7DI


20/41

References

1. Cooper, G. M., & Hausman, R. E. (2007). The Cell: A Molecular

Approach.

2. https://www.ndsu.edu/pubweb/~mcclean/plsc731/cis-

trans/cis-trans6.htm3. http://www.nature.com/scitable/definition/enhancer-163

4. http://www.nature.com/scitable/definition/promoter-259

5. https://www.youtube.com/watch?v=nLAF5i1X7DI

6. http://www.ncbi.nlm.nih.gov/books/NBK21780/

7. http://highered.mheducation.com/olcweb/cgi/pluginpop.cgi?i

t=swf::535::535::/sites/dl/free/0072437316/120080/bio28.swf

::Transcription%20Complex%20and%20Enhancers


21/41

Regulation of transcription in eukaryotes

2

Prepared by:

Ilderina Jusufovid

Layla Abdelilah

Selma Demirovid


22/41

1.Eukaryotic Repressors

Repressor is any protein that binds to DNA and thusregulates the expression of genes by decreasing therate of transcription.

Gene expression in eukaryotic cells is regulated byrepressors as well as by transcriptional activators.

In some cases, eukaryotic repressors simply interferewith the binding of other transcription factors toDNA.

Other repressors compete with activators for bindingto specific regulatory sequences.


23/41


24/41

2.Relationship of Chromatin Structure to

Transcription

Chromatin is a complex of macromolecules found in

cells,consisting of DNA,protein and RNA.

Several modifications are characteristics oftranscriptionally active chromatin:modifications of

histones,rearrangements of nucleosomes, and the

association of two ninhistone chromosomal proteins

called:HMGN proteins with the nucleosomes with

actively transribed genes.


25/41

Histone Acetylation neutralizes (+) charges on amino-

terminal tails that are rich in lysine residues andprevents binding to adjacent nucleosome which resultsloose chromatin structure, allowing for increasedtranscription.

Methylation of lysine and arginine residues promotes

repression and chromatin condensation. Phosphorylation of serine residues can prevent

condensation, if phosphorylation is adjacent to methylgroup.

Combinations of histone modifications constitute ahistone coe.


26/41


27/41

3.Regulation of transcription by non-coding

RNA-s

RNA interference- is a biological process in whichRNA molecules inhibit gene expression, typically by

causing the destruction of specific mRNA molecule.

Micro RNA + RISC = destroying mRNA

Micro RNA + RITS = heterochromatin

X chromosome inactivation- Xist


28/41


29/41

4.Methylation

Cytosine residues in

vertebrate DNA can be

modified by the addition of

methyl groups at the 5-carbon position .

DNA is methylated

specifically at the C's that

precede G's in the DNAchain (CpG dinucleotides).


30/41

References

http://themedicalbiochemistrypage.org/gene-regulation.php

http://genesdev.cshlp.org/content/21/1/11.full

http://www.bloodjournal.org/content/93/12/4059?sso-

checked=true

http://www.ncbi.nlm.nih.gov/books/NBK9904/

http://www.news-medical.net/health/What-is-DNA-

Methylation.aspx

Cooper, G., & Hausman, R. (2007). The cell: A molecularapproach (4th ed.). Washington, D.C.: ASM Press


31/41

RNA PROCESSING

Prepared by:

Belma Alispahid

Leila Kekid

Jasin Hoid


32/41

PROCESSING OF rRNAs

Eukaryotic cells 4 rRNAs 5S rRNA from a separate gene

18S, 28S and 5.8S from a common pre-rRNA

Final products 18 S, 5.8S H-bonded to 28S

rRNA processing cleavages + addition of methyl groups

to the bases and sugar moieties of specific nucleotides(function unknown).


33/41

PROCESSING OF tRNAs

Derived from pre-tRNAs

Cleavage at 5 by RNAse Pribozyme

Cleavage at 3 by conventionalprotein RNAse

CCA terminus ae to 3 en

Bases modified (10%):

Uridines modifications:ribothymidine (T)

dihydrouridine (DHU)pseudouridine ()

Guanosines modifications:inosine (I)

methylguanosine (mG)


34/41

PROCESSING OF mRNA

5 terminus cappingwith 7-

methylguanosine

(m7G)

Placing of GTP in

reverse orientation

Methylation of G

residues


35/41

3 Polyadenylation

Polyadenylation signals ; hexanucleotide AAUAAA

Endonuclease cleaves the pre-mRNA CA sequence Poly-A polymerase as As on 3 en

regulate both translation and mRNA stability


36/41

SPLICING MECHANISMS

In vitro splicing

bacteriophage RNA

polymerases

transcription nuclear

extract 2 steps

3 critical sequence

element

snRNAs and snRNPs


37/41

Capability of self-splicing

Revealed self-splicing RNAs in protozoan, mitochondria,

chloroplasts, and bacteria Divided into two classes on the basis of their reaction

mechanisms:

Group I introns

Group II introns


38/41

ALTERNATIVE SPLICING

Alternative splicing-different mRNAs from differentcombinations of 5and 3 splice sites.

Transcriptional regulatory protein ;

Activator VS Repressor


39/41

RNA EDITING

RNA editing refers to RNA processing that alter the protein-

coding sequences of some mRNAs:

deamination of cytosine to uridine

adenosine to inosine

Editing of apolipoprotein B mRNA


40/41

RNA DEGRADATION

rRNAs and tRNAs are very stable (90% in cells) mRNA degradation: shortening of poly-A tails removal of 5

cap degradation of the RNA by nucleases acting from both

ends (mammalian mRNA half-life: 30min-20h)

mRNA stability: Unstable mRNAs: regulatory proteins, transcription factors

Stable mRNAs: in response to extracellular signals

(transferrin mRNA)


41/41

SOURCES



http://www.csun.edu/~cmalone/pdf360/Ch13-

2RNAprocess.pdf

http://study.com/academy/lesson/rna-splicing-of-introns-

exons-and-other-forms-of-rna-processing.html

https://www.youtube.com/watch?v=MblGu1okRuY

https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-

eukaryotes-109/
http://www.ncbi.nlm.nih.gov/books/NBK9864/http://www.ncbi.nlm.nih.gov/books/NBK21563/http://www.csun.edu/~cmalone/pdf360/Ch13-2RNAprocess.pdfhttp://www.csun.edu/~cmalone/pdf360/Ch13-2RNAprocess.pdfhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttps://www.youtube.com/watch?v=MblGu1okRuYhttps://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/rna-processing-in-eukaryotes-109/https://www.youtube.com/watch?v=MblGu1okRuYhttps://www.youtube.com/watch?v=MblGu1okRuYhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://study.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-of-rna-processing.htmlhttp://www.csun.edu/~cmalone/pdf360/Ch13-2RNAprocess.pdfhttp://www.csun.edu/~cmalone/pdf360/Ch13-2RNAprocess.pdfhttp://www.csun.edu/~cmalone/pdf360/Ch13-2RNAprocess.pdfhttp://www.csun.edu/~cmalone/pdf360/Ch13-2RNAprocess.pdfhttp://www.ncbi.nlm.nih.gov/books/NBK21563/http://www.ncbi.nlm.nih.gov/books/NBK21563/http://www.ncbi.nlm.nih.gov/books/NBK9864/http://www.ncbi.nlm.nih.gov/books/NBK9864/

presentations hg 2015 for midterm exam

Documents