Uf Genetics (8/3/15)

Front 1

Central Dogma

Back 1

Transcription to Translation (DNA to RNA to Protein)

Reverse Transcription (RNA to DNA)

Front 2

What parts make up the organization of the Eukaryotic gene and mRNA?

Back 2

Exon- Part of gene encoded in transcribed RNA

Intron- DNA region between eons (unexpressed)

mRNA- mature/messenger RNA (codes for all proteins)

Promoter- regulatory region

Enhancer- distal regulatory element

Poly A tail- Adenines on 3' end of mRNA

5' Cap- Guanine triphosphate

UTR- Untranslated region

Start Codon- AUG

Stop Codon- Terminating sequence

Front 3

RNA Polymerase I

Back 3

Product: rRNA

Location: Nucleolus

Front 4

RNA Polymerase II

Back 4

Product: hnRNA (mRNA)

Location: Nucleoplasm

Front 5

RNA Polymerase III

Back 5

Product: tRNA

Location: Nucleoplasm

Front 6

Phases in Which Transcription Proceeds

Back 6

Initiation- Binging of RNA Polymerase to template DNA

Elongation- Nucleotides complimentary to DNA template are added to the growing RNA molecule

Termination- The Enzyme and RNA is release from DNA template

Front 7

Which direction does Transcription proceed from?

Back 7

In the 5' to 3' direction

Front 8

Requirements on Transcription

Back 8

Does not need primer

Needs: RNA polymerase, DNA template, and four nucleoside triphosphate

Front 9

Splicing Mechanism

Back 9

-Specific proteins bind to the donor and acceptor splice sites

-Two sites then brought together by other components of the Spliceosome

-Donor site cut and the free end of intron binds to branch site within the intron (forms a lariat structure)

-Acceptor site cleaved, releasing the lariat

-Exons are ligated together

http://www.youtube.com/watch?v=aVgwr0QpYNE

Front 10

Alternative Splicing

Back 10

Single primary transcript is able to be spliced in more than one pattern to generate multiple, distance mature mRNAs

This is the main source for generating protein and functional diversity in high organisms

Front 11

Exon Skipping

Back 11

Exon spliced out of the primary transcript or retained

Front 12

Mutually Exclusive Exons

Back 12

One of two exons is retained in mRNAs is retained after spring, but not both

Front 13

Alternative Donor Site

Back 13

An alternative 5' splice juction is used, changing the 3' boundary of the upstream exon

Front 14

Alternative Acceptor site

Back 14

An alternative 3' splice junction (acceptor site) is used, changing the 5' boundary of the downstream exon

Front 15

Intron retention

Back 15

Sequence may be spliced out as an intron or simply retained

Front 16

Cryptic Splice Site

Back 16

A randomly occuring site in the genome that contains consensus sequence for 5' or 3' intron splicing but is not normally used for that purpose

Front 17

Apoptosis

Back 17

Stimulus dependent process of cell death

Front 18

What is apoptosis characterized by?

Back 18

Cellular blebbing and shrinking, nucear fragmentation, chromatin condensation and chromosomal DNA fragmentation

Front 19

What type of virus is HIV?

Back 19

A lentivirus in the retrovirus family

Front 20

What are the steps in the HIV Replication Cycle?

Back 20

1. Fusion of HIV cell to host cell

2. HIV RNA, reverse transcriptase, integrase, and other viral proteins enter host cell

3. Viral DNA is formed by reverse transcription

4. Viral DNA transported and integrated into host DNA

5. New viral RNA is used to make viral proteins

6. New viral RNA and proteins move to cell surface and a new immature HIV virus forms

7. Virus matures by protease releasing individual HV proteins

Front 21

Non-coding RNA (ncRNA)

Back 21

Functional RNA molecule that is not translated into a protein. DNA sequence from which non-coding RNA is transcribed is often called an RNA gene or non-coding RNA gene

Front 22

Xist

Back 22

noncoding RNA gene on the X chromosome of placental mammals that acts as major effector of the X inactivation process

Front 23

miRNAs Function

Back 23

Help regulate gene expression (during development), function as post-transcriptonal regulators that bind to complementary sequences in multiple target mRNAs (usually resulting in translational repression or target degradation and gene silencing

Front 24

siRNA

Back 24

Short double stranded RNA molecules that can be chemically synthesized and are being used in therapeutic gene silencing

Front 25

What are miRNA genes transcribed by and what is produced?

Back 25

miRNA are transcribed by RNA polymerase II or III to produce long primary transcripts that undergo post transcriptional processing like mRNA

Front 26

Where and what are the transcripts processed by?

What happens after processing?

Back 26

The Drosha complex in the nucleus (hairpin like pre-miRNA precursor)

It is exported to cytoplasm by exporting 5

Front 27

What is Dicer's role in the synthesis and mode of action of miRNAs in mammalian cells?

Back 27

It degrades the pre-miRNA into mature miRNA

Front 28

What is the RISC complex composed of?

Back 28

Argonaute and associated proteins

Front 29

What happens after mature miRNA is formed?

Back 29

The RISC complex gets incorporated and the miRNA "guide" strand binds to the target mRNA sequences with partial complementarity, leading to translations inhibition or degradation

Front 30

Describe the composition of DNA

Back 30

DNA is composed of nitrogenous bases (pyrimidines and purines) attached to a ribose or deoxyribose sugar (both pentoses) held together through phosphodiester bonds

Front 31

How are adjacent bases in DNA connected?

Back 31

Connected via phosphate moiety linked to the sugar

Front 32

Chargaff's Rule

Back 32

Amount of A equals the amount of T and the amount of G equals to the amount of C

Front 33

Hydrogen bonds in AT vs GC

Back 33

AT=2

GC=3

Front 34

Structure of DNA

Back 34

Anti-parallel strands

Has major and Minor groove

B DNA= 10 bases per turn

34 Angstroms in one turn

3.4 A between each base pair

Right Handed Helix

Front 35

Spatial Dimensions of DNA

Back 35

Sugar/ phosphate backbone is on the outside, organic bases stack on top of each other in parallel planes and project into the inside of the double helix

Front 36

Transformation

Back 36

Ability to deliver foreign DNA to cells (prokaryotic and eukaryotic)

Front 37

Plasmid

Back 37

autonomously replicating DNA molecule, critical for the mass production of DNA

Front 38

Restriction Endonucleases (enzymes)

Back 38

Molecular scissors to selectively cut DNA

Front 39

Dna ligation

Back 39

the ability to join different pieces of DNA

Front 40

Selection

Back 40

Methods that rapidly select those house cells that contain recombinant DNA

Front 41

Whole Genome Sequencing

Back 41

Determines the complete dna sequenceof an individual's entire genome at a single time

Front 42

Personal Genomics

Back 42

Concerned with sequencing/analysis of an individual's genome where the genotyping stage employs SNP analysis (.02% of genome or partial/full)

Front 43

Predictive Medicine

Back 43

Uses information produced by personal genomics to decide personalized medical treatments.

Front 44

Precision medicine

Back 44

New taxonomy of human disease based on molecular biology

Front 45

What is the centromere and how is it important?

Back 45

Centromeres divide the chromosome into long and short arms. It is required for chromosome segregation where one copy of each sister chromatid is segregated to each daughter cell

Front 46

Kinetochore

Back 46

Part of the centromere that has a repeated sequence (alpha satellite DNA)

Front 47

Telomere

Back 47

Repeating DNA sequence at the end of the chromosome. Controlled by erosion and addition

Front 48

Erosion

Back 48

Part of teller lost after each cell division; leads to apoptosis

Front 49

Addition OF Telomere happens when and is determined by what?

Back 49

Happens during active cell division and is determined by the activity of telomerase

Front 50

How large is human DNA and how is it packaged?

Back 50

roughly 3 billion nucleotide base pairs in 23 chromosome pairs. It is packaged as chromatin.

Front 51

What are the two classes of DNA-binding proteins?

Back 51

The histones ( H1, H2A, H2B, H3, H4) AND that non-histone proteins.

Front 52

Chromosome Translocation is caused by what?

Back 52

Caused by a rearrangement between non homologous chromosomes. A gene fusion may be created when the translocation joins two separate genes (Common in cancer)

Front 53

Two main types of chromosome translocation

Back 53

Reciprocal and Robertsonian (unbalanced)

Front 54

Epigenetics

Back 54

Heritable alterations in gene expression which are not due to structural changes in DNA. May be induced spontaneously, in response to environmental factors, or in response to the presence of a particular allele

Front 55

Types of Epigenetic Processes

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Methylation, acetylation, phosphorylation, Ubiquitylation, and sumolyation

Front 56

Functions of DNA methylation in mammals

Back 56

Transcriptional gene silencing

Chromatin compaction

Genome stability

X chromsome inactivation (females)

Front 57

X- inactivation forms what? What does it also account for?

Back 57

The inactive X forms a discrete body with the nucleus (Barr Body)

It also accounts for equal expression in human females and males normalizing phenotypic expression of X-linked genes

Front 58

What are the different histone modifications and what does it do?

Back 58

Methylation- Turns gene off

Acetylation- Turns gene on

Ubiquination- Targets for Degradations

Sumoylation- Promotes gene silencing

Phosphorylation- Both negative and positive consequences

Front 59

What part of histones protrude from each nucleosome and what does it do?

Back 59

N-terminus tails protrude from each nucleosome. The positively charged tails contact negatively charges patches on neighboring nucleosomes of the backbone of DNA

Front 60

Histone Acetyltransferase

Back 60

Response for histone acetylation. It reduces the positive charge of the tails leading to an open chromatin structure accessible to transcription machinery

Front 61

Histon Deacetylase

Back 61

Reestablishes the positive charge on histone lysine residues leading to a tighter packing on DNA (makes less accessible for basal regulatory factors)

Front 62

DNA Replication

Back 62

Semiconservative process; Existing DNA molecule is separated into two template stands, new nucleotides align and bind to existing strands forming two DNA molecules

Front 63

Proteins and Enzymes Needed for DNA replication

Back 63

DNA polymerase: DNA synthesis

DNA ligase: Phosphodiester bond formation

Helicse: Unwinds DNA helix

Single Strand binding protein: Keeps DNA single stranded

DNA primase: Makes RNA primer that initiates synthesis

Topoisomerase: Removes torsional stress in DNA

Okazaki Fragments: Small segments of newly synthesis DNA on lagging strand

Front 64

What direction does DNA synthesis proceed?

Back 64

5' to 3'

Front 65

What is used to initiate a new strand?

Back 65

RNA PRIMERS

Front 66

What two things bind in DNA replications? How does it occur?

Back 66

A 5' triphoshate bings to a 3'OH of deoxyribose. This happens bidirectionally.

Front 67

What determine the leading strand?

Back 67

The parental strand at the 3' end of the template

Front 68

What produces/ determines the lagging strand?

Back 68

The parental strand at the 5' end of the template

Front 69

Okazaki Fragments

Back 69

Lagging strand fragments

Front 70

What are the Okazaki fragments joined by?

Back 70

DNA LIGASE

Front 71

What is the function and purpose behind each function of topoisomerases?

Back 71

Permite select regions of DNA to untangle (allows for transcription and replication to occur)

Temporarily break DNA (allows for topological changes and then reseals the breaks)