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Biochem Week 1
Genetics
79
Chemistry
Professional
01/24/2009

Additional Chemistry Flashcards

 


 

Cards

Term
1/150 Births
Definition
Frequency of chromosomal abnormalities
Term

1.  Chromosome abnormalities

2.  Single-gene disorders

3.  Multifactorial disorders

4.  Mitochondrial disease

Definition
Classes of Genetic Diseases
Term

50% of trimester 1 spontaneous abortions

20% of trimester 2 spontaneous abortions

Definition
Chromosome abnormalities that occur immediately after conception account for?  (% of spontaneous abortions in trimesters 1 and 2)
Term
10-15% of conceptions
Definition
______ of conceptions result in a chromosomal abnormality. 
Term

1.  Down Syndrome (Trisomy 21)

2.  Klinefelter Syndrome (XXY)

3.  Turner Syndrome (X)

Definition
Three most frequent Chromosome abnormalities at birth:
Term

1.  Expression of a non-functional protein (recessive)

2.  Failure to express protein (recessive)

3.  Altered espression of a proetin with normal function (Dominant)

4.  Expression of protein with altered fxn (Dominant)

Definition
Single Gene disorders may be dominant or recessive and result from:
Term

1/200 to 1/1000

cleft palate

club foot

heart defects

neural tube defects

pyloric stenosis

Definition
Example of Congenital Malformations and frequency
Term

E. coli:  4.2 x 10^6 bp

Human genome:  3.2 x 10^9 bp (1 whole meter!)

 

Definition
Sizes of E.coli and human genomes:
Term

5' 3nd (position 5- not part of the ring)

3' end (position 3)

phosphodiester linkage (positions 5-->3)

gycosidic bond (position 1)

Definition
4 characteristics of DNA primary structure:
Term

width= 20 A

Pitch (rise per one complete turn)= 34 A

Rise per bp= 3.4 A

One complete tun~ 10 bp 

B-DNA is right handed

strands are antiparrallel

Contains major and minor grooves

 

Definition
Features of the DNA double helix (B type)
Term
hyperchromism
Definition
An increase in UV absorbance is called ______ and occurs following DNA strand separation. 
Term
melting temperature.
Definition
When 50% of the DNA is separated, you have reached the ___________. 
Term

1.  Increase the GC base content

2. increase the salt concentration

Definition
DNA stability increases (Tm increases) if you:
Term

Formaldahide

Urea

Acid

Base

(low OR high pH)

Definition
DNA stability is decrease by denaturants such as:
Term
Southern blotting combines agarose gel electrophoresis for size separation of DNA with methods to transfer the size-separated DNA to a filter membrane for probe hybridization.
Definition
Southern blot?
Term

1.  Uracil replaces Thymine

2.  2'-hydroxyl

3.  RNA is single-stranded

4.  RNA has secondary and tertiary structure ("hairpin")

Definition
RNA differes from DNA in 3 ways
Term

Genome type (Euk, Prok, or viral)

Genome size

Phase of Cell Cycle (Euk)

Definition
DNA packing mode depends on:  3 things
Term

G1  prep for replication

S DNA synthesis phase

G2 preparation for cell division

M Mitosis, cell division

G0 non-dividing phase (stationary)

Definition
Cell Cycle stages:
Term

Euchromatin (transcriptionally active or competent)

Heterochromatin (highly condensed, transcriptionally incompetent)

Definition
two types of chromatin:
Term

Constitutive Heterochromatin (permanently condensed)

Facultative Heterochromatin (may decondense, becoming transcriptionally active)

Definition
Two types of Heterochromatin:
Term

1- naked DNA (1.0)

2- "beads on a string" 10-nm chromatin fibril of necleosomes (7-10)

3-30 nm chromatin fibril composed of  superhelical nucleosomes (40-60)

4- non-condensed loop

5- condensed loops

6- metaphase chromosome (8000)

Definition
6 levels of DNA folding (and packing ration)
Term

Nucleosome Core

146

1.75

 

(H2a, H2b, H3 and H4=proteins)

Definition
Histone proteins in an octomer make up the _____ and there are _____ bp of DNA per ___ turns. 
Term

Nucleosome core

Histone H1

180-200 (2 turns of DNA wrapped around it)

Definition
A nucleosome consists of the __________ ____ and _______ __, plus it will hold ___-___ bp of DNA. 
Term

Acetyl group

Lysine

Phosphate

Definition
Positive charges can be removed fromt eh histone tails by adding an ______ _____ which will loosen the DNA from the histone so that it can be transcribed.  This occurs on ______ amino groups and causes loss of positive charge and interactions with DNA _________. 
Term

1-Acetylation (gene transcription and DNA replication)

2- Phosphorylation (chromosome condensation)

3- ADP-ribosylation (DNA repair)

4- Methylation (activation or repression of gene transcription)

5- monoubiquitylation (activation and repression of gene transcription)

Definition
Chomatin can be remodeled by modifying histones via 5 ways: 
Term

5

750

Definition
Humans have _x more genes than bacteria, but they have _x more DNA than bacteria. 
Term

repetative

non-gene

non-structural

Definition
Much Human DNA is __________, ___-____, and ___-__________ (sometimes called "junk DNA")
Term

Telomers; GT

Centromeres; AT

Definition
_________ are at the ends of chromosomes and conatin __-rich repeats.  ___________ join sister chromatids, and contain __-rich repeats.
Term
Kinetochore
Definition
The spindle attachemt site for chromosome segregation is the ________.
Term

1- Highly repetative  (mini-satellites; 5-500 bp),    1-10 x 10^6 copies in total per genome, mainly telomere and centromere.

2-Moderately repetitive, Dispersed DNA (SINES 70-300 bp long, LINES 6000-7000 bp long)

3- micro-satellites (2-6 bp long; commonly repeated up to 50x)

Definition
Three classes of repetative DNA
Term

SINES:  70-300 bp long; more than 100,000 copies total per sequence per genome...ex is the Alu family (5-6% of the genome)

LINES:  6000-7000 bp long; 20,000-50,000 copies per sequence per genome.

Definition
Two types of dispersed repetitive DNA are _____ and _____.
Term

Retrotransposons

Nonsence (stop)

Definition
Pseudogenes are ___________ from mRNA.  Over generations they will produce ____ codons, or cause loss of other critical signals.
Term

semi-conservative

bidirectional

Definition
DNA replication is ____-____________ and _____________.
Term

1- DNA synthesis (uses NTP to add nucleotide to the 3'-OH end of the growing chain releasing PPi)

2- 3'-5' exonuclease (proof-reading)

3- 5'-3' exonuclease (Pol 1, excises RNA primer from lagging strand)

4- Sliding clamp (keeps polymerase on template)

Definition
DNA polymerase is a multi-subunit enzyme with several activities:  (4)
Term

DNA Pol III (homologous to DNA pol gamma)

-makes both leading and lagging strands

-3'-5' exonuclease activity (proof-reads)

DNA Pol I (homologous to DNA pol alpha)

-degrades RNA primer (5'-->3') exonuclease activity

-refills gap with DNA by "nick translation' (5'-->3')

 

Definition
There are two distinct polymerases that participate in replication: 
Term
5'-->3'
Definition
DNA synthesis procedds in the ______ direction.
Term

Helicase

Topoisomerase (gyrase, topoisomerase I)

SSBPs (single-stranded DNA binding proteins)

Primase

DNA ligase

Definition
The replisome consists of 5 accessory proteins
Term

Gyrase (a topoisomerase II)

Topoisomerase I

Definition
There are two topoisomerases, ______, which works by making a double stranded break in DNA, and then using an ATP to unwind DNA, while ________ works by nicking a single strand and allowing the other single strand to unwind by swiveling. 
Term
secondary structure
Definition
SSBPs prevent _____________ formation near fork.
Term

rRNA (80 %)

tRNA (15%)

Definition
The most abundant RNAs are machinery for protein synthesis and they are ____ and ____.
Term

snRNA

siRNA

Spliceosome

Definition
The small RNAs, _____ and _____ are editing RNS. The first is part of the ____________, and is involved in pre-mRNA editing.  The second causes degradration of specific mRNAs.
Term

3'-->5'

5'-->3'

Definition
The template strand is read in the _______ direction and RNA is made in the ______ direction.
Term
3'-OH
Definition
New nucleotides are always added to the _____.
Term

alphaalphaBetaBeta'sigmaomega

two alphas (promoter binding and assist RNAP assembly)

one beta (catalytic, polymerization site)

one beta' (DNA binding site)

sigma (identifies promoter and assists initiation)

omega (unk fxn)

Definition
RNAP has six subunits _______
Term
Promoters
Definition
The RNA transcription complex is assembles at __________.
Term
+1
Definition
RNA transcription starts the the __ position on the DNA template strand. 
Term
5'
Definition
Promoters are regulatory sequences flanking the initiation sites on the __-ends of genes.
Term

Negative

Positive

'upstream'

Definition
________ positions are 'upstream' and ________ positions are 'downstream.  Promoter sequences are ________.
Term

-10 TATA box ("Pribnow Box")

-35 Region

Definition

Typical bacterial promoters? 

Term

cis-sequence elements (CSE)

upstream

downstream

1-Promotors, 2-proximal promoter sites, 3-enhancer and repressor elements, 4-terminators

Definition
DNA contains ___-______ _______ sequences as well as genes!  These lie ________ or __________ and include the following 4 elements. 
Term

holoenzyme

promoter

-10

-35

pre-initiation complex (PIC)

Definition
Bacterial RNAP __________ slides on DNA until sigma factor finds and binds to the ________, recognizing the ___ and ___ consensus sequences and forming the closed ___-__________ _______.
Term
initiation
Definition
When a dinucleotide is elongated to a 10 nucleotide 'primer,' you are in the __________ phase of transcription.
Term

NusA

Promoter

Definition
During initiation the sigma factor dissociates and ____ takes its place, and core polymerase moves away from the ________.  Initiation is now over and Elongation begins.
Term
nucleotidyl
Definition
Chain elongation is a __________-group transfer.
Term

1- DNA template

2- RNA primer strand with 3'-OH group

3- ribonucleoside tripphosphates (ATP, GTP, CTP, UTP)

Definition
Elongation of transcription requires three things:
Term

unwind

rewind

Definition
Topoisomerase activity is required to ______ DNA ahead of transcription bubble, and ______ DNA behind bubble. 
Term

irreversible

replication

transcription

Definition
When a PPi is released it is hydrolyzed to 2Pi, making polymerization ____________ in both ___________ and ___________.
Term

hairpin forming

Rho

Definition
Termination may occur spontaneously via a special _______ _______ sequences followed by weakly base-pairing __-rich sequence.  Termination may also occur via ___-dependent termination. 
Term

ATP

RNA

helicase

Definition
Rho is an ___-dependent, ___-dependent ________.
Term

rRNA

hnRNA (mRNA), miRNA

tRNA, 5SRNA

Definition

RNAP I mainly makes?

RNAP II mainly makes?

RNAP III mainly makes?

*these are in eukaryotic cells*

Term

alpha-amanitin

II

mRNA

Definition
_-________, a potent muschroom toxin, blocks RNAP _ and ____ production.
Term

TBP with TAP in the TFIID complex binds promoter.

 

TFIIA and B stabilize RFIID, select start site, recruit RNAP with the assistance of TFIIF

 

TFIIE recruits TFIIH

 

TFIIH (helicase) unwinds promoter, activates RNAP by phosphorylation of C-term domain (CTD) of RNAP

Definition
Steps of eukaryotic initiation (4)
Term
TBP
Definition
___ specifically recognizes the TATA box during eukaryotic initiation.
Term
RNAP II
Definition
Transcription factors bind proximal promoter in eukaryotic initiation and this activates ______.
Term

promoter

promoter proximal elements

Definition
The ________ determines the position of transcription initiation.  ________ ________ ________ determine the frequency of transcription initiation.
Term

TFIID

Sp1

CTF

Definition
_____ recognizes the promoter and promoter proximal elements are recognized by ___ and ___.  The first recognizes the GC islands, and the second recognizes the CAAT box.
Term

distant

enhancers

silencers

Definition
Transcription of many genes above basal levels is regulated by ______ DNA elements such as _________ and _________.
Term

long

promoter

activating

repressor

independent

Definition
Enhancers and Silencers act at ___ distances from the ________.  Enhancers bind __________ TFs and Silencers bind _________ TFs.  Both can be either upstream or downstream (orientation-___________). 
Term

nucleus

mRNA

Definition

hnRNA (preRNA) is made, spliced, and otherwise processed in the _______, and once all these things are done, it is ____.

Term

addition of the 5' cap

splicing

3' polyadneylation (poly A tail)

transport out of the nucleus

Definition
Four processes that must occur post RNAP II transcription are?
Term

7-methyl G base

5'-->5' GTP attachment

2'-O-methyl on 5'-base

Definition
The 5'-cap has 3 unique features. 
Term

1- Polymerase transcribes past consensus AAUAAA polyadenylation sequence

2-Protein Factors bind and this leads to cleavage of the transcript downstream from the sequence

3- additional factors bind and A residues are added (a few hundred)

Definition
Steps in Polyadenylation? (3)
Term

C-terminal

Splicing

TREX

Definition
The __________ domain of RNAP II localizes ________ by providing a scaffold.  ____ complex assists transport through nuclear pores. 
Term

snRNAs

lariat

Definition
Spliceosomes contating ______ carry out splicing.  SPlicing involves a ______ intermediate. 
Term

1- 3' primary transcript

2-nucleophilic attack at 5' end of intron

3-lariat formation

4- cut at 3' end of intron

5- ligation of 3' end of exon 1 to 5' end of exon 2

6- intron is digested

Definition
Steps in Lariat formation during splicing?  (6)
Term

AGGU

AGG

A

splice acceptor

Definition
The consensus sequences occur at splice junctions and the branch point.  5'-splice site (splice donor)= ____; 3'-splice site (splice acceptor)= ___.  The branch point (site splicing factors recognize it) nucleotide (_)~ 30 nt upstream of ______ ________. 
Term
Ribozyme
Definition
When RNA acts like an enzyme it is called a ________. 
Term
Alternative
Definition
___________ splicing is a route to genetic diversity.
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