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Biochem Week 2
Genetics continued
70
Chemistry
Professional
01/24/2009

Additional Chemistry Flashcards

 


 

Cards

Term

Degenerate- more than one triplet per aa

Redundant- two first bases are same for specific aa

Unambiguus- no codon encodes more than one aa

non-overlapping- codons are read sequentially

not puctuated- no interuptions

universal (almost)

Definition
Properties of the genetic code
Term

AUG

UAA, UAG, UGA

Definition

Start codon= ?

Stop codons= ?

Term

L

aminoacyl accepter

D

T

tertiary

Definition

Key interaction sites of tRNA:

One end of '_' is the anti-codon containing loop for mRNA recognition, the other end of it is the _________ ________ stem with a conserved sequence to charge the tRNA, and finally the _ and _ loop residues are highly conserved for ____ interactions. 

Term
aminoacyl tRNA synthetase
Definition
tRNAs are 'charged' by _________ ____ __________, using ATP-activated amino acid. 
Term

Prokaryotic:  70S (30S and 50S)

Eukaryotic:  80S (40S and 60S)

Definition
Difference between prokaryotic and eukaryotic ribosomes?
Term

rRNA

Nucleolus

tRNA

Nucleus

Definition
RNAP I synthesizes ____ in the _________, while RNAP III synthesizes ____ and other small RNAs in the _______.
Term

TRUE

 

also...RNAP I catalyzes simultaneous synthesis of polycistronic rRNA (45S precursor) 

Definition

True of False?

Multiple rRNA transcripts can be made simultaneously from multiple rRNA genes.

Term

1- 40S subunit binds tRNA (PIC formation (43S))

2- mRNA activation

3- mRNA binds small subunit (48S)

4- Activated 80S ribosome forms

Definition
The four major steps of the initiation of translation?
Term

Initiation factors (elF 1,2,3)

GTP

methionyl-tRNA^met

 

the whole complex is energized by GTP hydrolysis

Definition
WHen the 40S ribosomal subunit binds tRNA, the 40S subunit must bind 3 things:
Term

elF-4

cap

ATP hydrolysis

Definition
During mRNA activation of the initiation of translation, the mRNA is activated by _____ complex and the complex binds at the ___ via ___ __________. 
Term

43S pre-initiation complex (PIC)

hydrolyzed

elF-4

Definition

When mRNA binds the small ribosomal subunit, the elF-4/mRNA complex joins the ___ ___-__________ complex.  Once mRNA translocates the the start codon, ATP is __________ and _____ dissociates. 

Term

elF-5

GTP

Definition
Activated 48S initiation complex joins 60S subunit with the assistance of _____.  During this process ___ is hydrolyzed. 
Term
Insulin
Definition
_______ and growth factors stimulat mRNA activation and translocation. 
Term

1- Binding of aminoacyl-tRNA to the 'A' site

2- Peptide bond formation

3- translocation

Definition

The three steps of Elongation?

Term

EF1A-GTP

A

GTP

EF1A-GDP

Definition
The first step of elongation involves the aa-tRNA binding to the ________ complex.  Once bound, the entire complex will bind the _ site on an activated 80S ribosome.  ___ is hydrolyzed at this step and ________ is released.
Term

peptidyl transferase

28S

Ribozyme

Definition
The peptide bond formed in step two of elonogation is formed by ________ ___________ of ___ rRNA of the 60S subunit.  rRNA is acting like an enzyme, therefore it is called a ________.
Term

EF2-GTP

GTP

Definition
During translocation, the _______ complex binds to and displaces peptidyl tRNA from A site to P site. The deacylated tRNA dissociates.  ___ is hydrolyzed and mRNA translocated forward on codon, leaving a site ope.   
Term

A

UAG, UAA, UGA

RF-GTP

peptide

tRNA

GTP

Definition
Termination occurs when the _ site reaches a stop codon (___, ___, or ___).  Release factor, ______ complex binds, causing the _______ and ____ are released, driven by ___ hydrolysis. 
Term

4

 

Breakdown: 

1ATP in tRNA chargins

1GTP in aa-tRNA delivery

1GTP during translocation

total:  4 ATP equivalent per aa

Definition
Translation requires _ ATP per amino acid
Term

IRES (internal ribosome entry site)

ElF-4F 

IRES

elF-4G

 

Definition
Viruses co-opt host protein synthesis via ____.  This causes the ______ complex to abort, the mRNA cap is not recognized, and viral ____ is recognized instead by ______ causing viral mRNA to be preferentially translated. 
Term
Polysomes
Definition
_________ occur when multiple proteins are made simulatneouslly from a single mRNA. 
Term

1-Folding

2-Signal sequence targeting (to mbs or other locations)

3-selective proteolysis (cleavage leads to active enzyme)

4- Assembly for multi-subunit complexes)

5-Post-translational modification

6-Turnover

Definition
Proteins are processed in 6 ways after synthesis:
Term

hydrophilic

hydrophobic

Definition
Globular proteins are often water-soluble, with primarily ___________ exterior and ___________ interior. 
Term

Domains

Quaternary (4)

Definition
Non-covalently associated subunits in within a protein are called _______ and are very important in a proteins __ structure.
Term

3.6

H-bonds

R-groups

Definition
Aplha helix has ___ aa per one turn.  ______ hold the structure together on the inside, while the ________ point away from the helix. 
Term

Perpindicular

stacking

 

*Natural silk interdigitates oily methyl groups to produce that 'silky' feel*

Definition

In a beta-pleated sheet R-groups are _____________ to the sheet and alternate up and down along each chain (this allows for ________). 

 

 

Term

single

4

alpha helices

prosthetic

Definition

Ribonuclease is a small single chain protein, while Hemoglobin (Hb) is a ______ chain protein with  _ nearly identical subunits.  The secondary structure is composed mostly of _______ _______ and each subunit contains one Heme group which is a __________ group. 

Term

4

disulfide

3

folding motifs

motif

beta-sheets

beta-barrel

Definition
Immunoglobulin G has _ chains with internal _________ bonds and _ domains.  Domains can be characterized in terms of one or more _______ ______.  Note that IgG domains are built on a repeated _____ of __________ folded into a ____ ______.
Term

1- predominately alpha helix

2-predominantly beta-sheet

3- mixed

Definition
There are three general protein folding motifs:
Term

zinc finger

leucine zipper

helix turn helix (HTH)

helix loop helix (HLH)

Definition
Four common sturcture motifs in DNA binding proteins: 
Term

1- Spontaneous (usually small, cytoplasm proteins)

2- Rapid Chaperone-assisted folding

3 Membrane proteins are targeted and assisted in membrane insertion by a signal peptide sequence and signal recognition protein (SRP)

Definition

THere are three types of protein folding mechanisms: 

Term

signal peptide

signal recognition protein

Definition
Membrane proteins are targeted and assisted in membrane insertion by a ______ _______ sequence and ______ ___________ _______(SRP). 
Term
Cooperative.
Definition
Protein folding and unfolding are ___________ processes.
Term

FALSE- proteins are easily unfolded

 

*  unfolded protein is favored unless other forces bring protein parts together.

Definition

True or False?

Proteins are difficult to unfold once they've finished folding.   

Term

weak

non-covalent

Definition
Proteins are stabilized by the sum of a very large number of ____, ___-________ interactions.
Term
Folding
Definition
The hydrophobic effect drives partial protein _______. 
Term

H-bonds

ion pairs

other weak interactions (van der waals etc...)

metal binding (Ca, Cu, Zn, Fe, others)

Definition

Proteins can be further stabilized by these four sources: 

Term

micelle

Definition
Protein hydrophobic effect mimics _______ formation. 
Term

Metal ion coordination

disulfide bond

hydrophobic interaction

hydrogen bonding

electrostatic attraction

Definition
Some examples of weak interactions.
Term

Promotor

LacZ gene (beta-galactosidase)

LacY gene (beta-galactoside permease)

LacA gene (beta-galactoside transacetylase)

Definition
The lactose operon is made of four regions: 
Term

INACTIVE

ACTIVE

glucose

cAMP

Definition
The operon is ________ without lactose.  The operon is ______ when lactose is present.  Transcription of the lac operon will only occur at a high level is _______ levels are low (meaning ____ levels are high). 
Term

Methylation

Phosphorylation

Acetylation

Definition

Genes can be silences through chromatin modifications (3):

1- marks heterochromatin and silenced genes

2-marks chromosomes for condensation

3- marks transcribed genes

Term

BASAL

GC box

CAAT box

TATA box

Definition
_____ expression involves two upstream elements and one proximal element.  The first upstream element, __ ___ is bound by SPI and the other upstream element, ____ ____ is bound by CTF.  The proximal element, ____ ___ is bound by TFIID. 
Term

Enhancers

Repressors

Definition
Regulated expression involves _________ and __________. 
Term

less

yeast

less

 

*e.coli (3-5 min)

*yeast (22 min)

*mammals (10 hrs)

Definition

mRNA half-lives vary significantly for different mRNAs and organisms. 

t1/2 of e.coli is _______ than the t1/2 of _____ which in turn is _______ than the t1/2 of mammals.

Term

IRE-BP

transferrin

ferritin

IREs

IRE

Definition

mRNA translation can be regulated by iron status:

a deficiency in iron causes ______ to be activated.  Once activated, it will prevent mRNA degradation of the ___________ recepter mRNA, which it recognizes by the large amount of ____ on the sequence, and it will inhibit translation of ________ mRNA (which it recognizes by ONE ___ on the mRNA). 

Term

Apo-B

apo-B-100

apo-B-48

Definition
_____ mRNA produced in the liver is translated into the ___-____ protein, but the same mRNA is edited, deaminating ac to au in intestinal cells to make a stop codon and the protein produced is ________. 
Term
Cytogenetics
Definition
____________ is the study of chromosomes and their abnormalities. 
Term
1/150
Definition

The frequency of live births with chromosome abnormalities which lead to disease is ______. 

Term

Mental Retardation

50%

20%

Definition
Chromosomal abnormalities are the leading cause of ______ ___________ and pregnancy loss seen in ___ of the first trimester spontaneous abortions and ___ of the second trimester spontaneous abortions.  (%)
Term
Chiasma (occur in prophase I)
Definition
_______ between homologous chromosomes  allow for genetic exchange to occur via crossing over.
Term
Unequal crossover
Definition
_______ _________ causes a net gain of info on one chromosome and loss of info on the other. 
Term
Aberrant
Definition
________ recombination causes gene (DNA) gains and losses.
Term

jumping genes

Alu

Definition
Transposable elements or _______ _____ may use ___ sequences to target insertion sites where mutations could occur.  Some viral DNA take advantage of this to integrate their DNA into chromosomal DNA.
Term

10-15%

50%

20%

15%

Definition
A minimun of __-__% of all conceptions have chromosomal abnormalities.  __% of those are trisomies, __% are monosomes and __% end up being triploids. 
Term

karyotypes

Acrocentric

Submetacentric

Metacentric

Definition

Chromosomes are sorted in __________ by size and shape.  Chromosomes are further classified byt the position of the centromere:

___________= centromere near tip

____________= centrome between middle and tip

____________= centromere near middle

Term

p

q

centromere

Definition

Short arm of a chromosome is labeled _, and the long arm is labeled _.  Band numbering is from __________ to tip.

Term

G-banding (giemsa stain)

Q-banding (quinacrine stain fluorescent)

 

band

region

long

14

Definition

2 ways to stain chromosomes?

 

Nomenclature?  14q32

Implies second ____ in ____ 3 on the ___ arm of chromosome __.

Term

Polyploidy

Aneuploidy

Definition
__________ means possessing a complete set of extra chromosomes.  __________ means not containing a multiple of 23 chromosomes (for humans).
Term
plant
Definition
Polypoid abnormalities are common in _____ cells, but are rare in humans. 
Term

1/10000

15%

 

fertilization of egg by two sperm

 

Definition

Sex chromosome triploidy (XXX, XXY or XYY) is seen in ____ live births, but nearly all __% of conceptions with this abnormality  are spontaneously aborted.  Survivors die soon after birth. 

 

Most common cause?

Term

Trisomy 21

down

1/800

1/1000

Definition
_______ __ is the most common trisomy in live birthds and causes ____ syndrome.  The frequency is _____ to ______. 
Term

80%

50%

Definition
__% of down syndrome patients live to age 10 and __% of them live to age 50.
Term

Edward's

Patau

1/6000

1/10000 live births

5

Definition

There are two less common trisomies:  Trisomy 18 (________ Syndrome) and Trisomy 13 (_____ syndrome).  Trisomy 18 has a frequency of ______ and trisomy 13 of _______.  For each of these only about _% survive past 12 months. 

Term

Sex

1/400

1/650

X

Definition
___ chromosome aneuploidy is more common than trisomy.  _____ males to _____ females.  These are survivable unless no _-chromosome is present. 
Term

X

1/2500

1/10000

Definition
Turner sydrome karyotype 45 __, has a freqency of _______ to ________. 
Term

Reciprocal (mutal exchange)

Robertsonian (loss of short arms and fusion at centromese fo the remaing long arms into one chromosome- this can only occur with the acrocentric chromosomes- 13-15, 21 and 22)

Definition
There are two types of translocations: 
Term

Deletions

Microdeletions

Definition
_________ are losses of one or more bands.  _________ are losses of chromosome regions too small to be detected by traditional clinical cytogenetics. 
Term

1- recognizable chromosome features (down s.)

2- unrecognizable pattern of 2+ malformations. 

3- ambiguos genitalia

4- MR or developmental delay in children with multiple physical abnormalities.

5- children with parents with chromosome abnormalities.

6- females with short stature and primary amenorrhea

7- males with small testis or significant gynecomastia

8- stillborns with malformations or not recognizable reasons for fetal death.

Definition
Indications for performing chromosome analysis?(8)
Term

Somatic

oncogenes

tumor suppressors

Definition
Many cancers are associated with chromosome rearrangements within _______ cells.  Rearrangements causing cancer often involve altered expresson of _________ or _____ ___________. 
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