Genetics Test 2 Ch 9, 11, 12, 13, 14, 19

nucleotide

building blocks of DNA (AT,GC)

purine bases

Guanine and Adenine

pyrimidine bases

Cytosine, Thymine and uracil

how are nucleotides linked?

phosphodiester bonds - 5’ P of one nucleotide to 3’
OH of another

what direction does the strand run?

5’ to 3’

what is the backbone made up of?

sugar and phosphate

bonds in A-T

two

bonds in G-C

three

who is credited for determining the double helical structure of DNA

James Watson and Francis Crick, 1953

What is necessary for genetic material to be considered DNA

1. Contains information needed to build an organism

2. Can be transmitted from parent to offspring

3. Can be replicated to be passed to next generation

4. Is capable of variation to account for phenotypic differences of a species

Frederick Griffith

transforming principle

Avery, Macleod, Mccarty

DNA responsible for transformation

Hershey and Chase

DNA is genetic material in T2 phase

transforming principle

concluded that something from the dead type S bacteria was transforming type R bacteria into type S

Linus Pauling

proposed alpha helix in proteins (ball and stick models)

Rosalind Franklin

X-ray diffraction of DNA Fibers

• helical, 10 bases/turn, >1 strand

Erwin Chargaff

determined DNA base composition from many
organisms
-% A = % T; % G = % C (Chargaff’s rule)

nucleotide difference in RNA

uracil replaces thymine

what replaces deoxyribose in RNA

ribose

The backbone of the DNA molecule is formed by ________.

phosphodiester bonds

At a neutral pH nucleic acids have a net ________ charge

negative

Going from simple to complex, which of the following is the proper order for the structure of DNA?

nucleotide, DNA strand, double helix, chromosome

A nucleotide is composed of

one phosphate group, a pentose sugar, a nitrogenous base

Adenine and thymine form ________ hydrogen bonds between them, while cytosine and guanine form ________ bonds.

2,3

In a double-helix DNA strand, the adenine on one strand forms a hydrogen bond with a(n) ________ on the other strand.

thymine

How did Avery, MacLeod, and McCarty contribute to our understanding of DNA? 

found that “the transforming principle” is destroyed by DNAase

In an experiment where you have isolated all of a cells nucleotides and you would like to study its RNA, you would add which enzyme to digest the unwanted nucleotide strands. 

DNAase

Why were bacteriophages used in the Hershey–Chase experiment?

• They had a protein coat and an internal DNA molecule

• They injected their genetic material into bacterial cells.

How did Chargaff's rules contribute to Watson and Crick's elucidation of the structure of DNA? 

The rules suggested the base-pairing combinations of A-T and G-C

Which molecule is featured at the 5' end of a DNA backbone?

a phosphate group

The fact that the helixes of the DNA strand are arranged in opposite directions gives DNA its ________ characteristics

antiparallel

How did Rosalind Franklin contribute to our understanding of DNA?

used X-ray diffraction to show that the structure of DNA is helical

Which of the following is NOT a key characteristic that genetic material must possess? 

Genetic material must not gain mutations

conservative model

parental strands stay together after replication

semiconservative model

after replication DNA has one parental strand and one daughter strand

dispersive model

parental and daughter DNA segments interspersed in both strands

how does DNA replication begin?

• begins at origin of replication

• bidirectional

• ends when forks meet

oriC

origin of chromosomal replication

3 regions in oriC (prokaryotes)

• A-T rich region

• DNa A boxes

• GATC Methylation sites

oriC in eukaryotes

• ARS elements (also AT rich)

• consensus sequences ATTTA (A or G) TTTA

• Still not well understood

Initiation of replication

• Dna A proteins bind Dna A boxes and each other

• other proteins recruited, bends DNA

• opens replication fork at AT rich regions

• DNA helicase binds origin with help of DNA C and opens replication forks

  • 5’ to 3’ direction

  • uses ATP

  • multiple subunits

DNA methylation

regulates replication

GATC sites are

methylated on adenine

• Dam enzyme (DNA-adenine-methyltransferase)

initiation can only occur on

fully methylated DNA (hemimethylated DNA has one methylated strand)

DNA helicase

separates DNA strands (breaks H bonds), generates + supercoiling ahead of forks

topoisomerase II (DNA gyrase)

ahead of helicase, relieves supercoils

single-strand binding proteins

bind DNA, keeps strands apart

RNA primase

lays down short (10-12 bp) RNA primer

• one primer in leading strand, multiple in lagging

DNA polymerases

synthesize DNA

DNA polymerase III

primary enzyme for DNA synthesis

DNA polymerase I

removes primer and repairs gaps in DNA

DNA ligase

joins Okazaki fragments (covalent)

DNA polymerase II

DNA repair

alpha enzyme

initiates DNA replication

epsilon enzyme

replicates leading strand

gamma enzyme

replicates lagging

delta enzyme

mitochondrial

DNA polymerase III holoenzyme

• 10 subunits (alpha joins nucleotides)

• resembles right hand, DNA between thumbs and fingers

how rare are errors in replication

extremely rare 1/10^8 bases are errors

stability of base pairing

mismatches are much less stable

DNA polymerase active site structure

mismatches cause distortion of helix and poor fit in active site

DNA polymerases proofreading

removed mismatched base with 3’ to 5’ exonuclease activity - inserts correct base

leading strand

• one primer

• DNA pol III moves towards replication fork

• continuous synthesis

lagging strand

• many primers

• DNA pol III moved away replication fork

• short fragments (1000-2000 bp - Okazaki fragments)

• discontinuous synthesis

• DNA pol I removes primers and fills gap

• DNA ligase joins fragments (phosphodiester bonds)

termination of replication

• 2 termination (ter) sequences opposite oriC (one for each fork)

tus (termination utilization substance) proteins

bind ter sequences and stops replication forks

problem with telomeres

• DNA polymerases cannot initiate DNA synthesis on a bare DNA strand

• at the 3’ ends of linear chromosomes - the end of the strand cannot be replicated

Why is it a problem to replicate DNA at the very ends of linear chromosomes?

It is a problem to replicate DNA at the very ends of linear chromosomes as the DNA cannot be fully copied in each round of replication. This leads to the gradual shortening of the chromosome. The DNA cannot be fully copied because the primer used for strand synthesis is not able to be replaced.

Describe the DNA in the telomere regions.

A telomere is a structure at then end of a chromosome comprised of DNA and proteins. The telomere serves as a cap and helps to protect the chromosome. The DNA in the telomere regions is extremely repetitive and very short. There are hundreds to thousands of the same DNA sequence on every telomere.

Describe the mechanism by which the telomerase enzyme extends the ends of linear chromosomes

First, there is the binding of telomerase, the telomerase RNA component allows the enzyme to bind to the 3' overhand. Second, the enzyme begins polymerization which is the synthesis of a six-nucleotide sequence at the end of the DNA strand. Finally, the enzyme translocates, moving a new end of DNA strand to the six nucleotides that were polymerized.

Which model organism did Dr. Blackburn use in her study of telomeres and telomerases? What made this a good model system for studying this particular research question?

Dr. Blackburn used single-celled organisms in order to study telomeres and telomerases. This is a good model system for her research because these organisms had ample linear chromosomes and therefore, telomeres. By studying a simpler organism with good model DNA, Dr. Blackburn could focus in on the telomere aspect of the DNA.

How is telomere length linked to aging and illness?

Telomere length is linked to aging and illness because everytime cells divide, the strand becomes shorter. That is, until the cells can no longer divide making the cells inactive. When this happens, there has been a higher risk of cancer and death. The shortening of telomeres is also related to aging because it occurs over time and can display itself over time.

How can external circumstances or our internal reactions to these circumstances influence the length of our telomeres?

Telomere shortening can occur as a byproduct of oxidative stress, therefore when someone is under duress for an extended period of time, there is a good chance that that person's telomeres will begin shortening at a faster rate than normal.

Your friend has found a website that sells TA-65, a dietary supplement that contains cycloastragenol, a triterpenoid isolated from various legume species in the genus Astragalus that is purported to have telomerase activation activity. Would you take this supplement? Why or why not?

No, I would not take this supplement because an increase in telomerase activation activity is the same incident that occurs when someone contracts cancer. This supplement could potentially give you illness or rapidly increase your aging.

DNA → RNA

transcription

DNA → mRNA

will proceed to translation to become proteins;
structural genes; >90% of the genes% of genes

DNA → rRNA

associate with proteins to form ribosomes

DNA → tRNA

adaptors used in translation

DNA → regulatory RNA

influence transcription & translation

DNA sequence defines

boundaries of gene

transcription requires that

proteins recognize/interact with DNA

DNA sequence + environmental factors

determine which genes expresses / to what levels (determine phenotype)

regulatory sequence(s)

regulatory proteins bind here, influence rate of transcription

promoter

where RNA polymerase binds to initiate transcription

• DNA sequences that recruit machinery to transcription start site

• recognized by transcription factors

• located upstream of gene, numbered relative to transcription start site

terminator

site that triggers end of transcription

bacterial genes are organized into

operons

mRNA from operons is

polycistronic

Steps of transcription

1. Transcription factors assemble at promoter region of a gene

2. RNA polymerase “unzips” a small portion of the DNA

3. Nucleotides bind complementary to the template strand, then covalently bind together to form their own backbone

4. Build mRNA strand = copy of DNA

initiation (transcription)

transcription factors bind to promoter, recruit RNA polymerase; DNA is denatured into a bubble known as the open complex

elongation (transcription)

RNA polymerase slides along DNA in an open complex to synthesize RNA

Termination (transcription)

terminator is reached, RNA polymerase and RNA transcript dissociate from DNA

template strand (anti-sense strand)

used as template to synthesize RNA - RNA transcript is COMPLEMENTARY to template

sense strand (coding strand, non-template)

not involved in transcription - RNA transcript is SAME as sense strand

core promoter

• Short, TATA box + transcriptional start site

• alone, get low levels of transcription (basal levels)

regulatory elements

• affect binding of RNA polymerase to promoter

• TF’s bind elements, influence rate of transcription

• varied locations, typically -50—-100 region

enhancers

stimulate transcription

silencers

inhibit transcription

basal transcription apparatus

• RNA polymerase II

• 5 general transcription factors (GTF)

Eukaryotic initiation overview

TATA box → TFIID → TFIIB → RNA polymerase → TFIIF → TFIIE/TFIIH

• TFIIH unwinds DNA and phosphorylates RNA polymerase II - flips switch to elongation

Elongation (transcription)

• RNA synthesis ~43 nt/s

• core enzyme slides along DNA, creates open complex as it goes

• direction of synthesis: 5’ to 3’ (new nts added to 3’ end)

• building blocks: nucleotide triphosphates (NTPs)

• U replaces T

• formation of DNA/RNA hybrid

• DNA behind rewinds

• More complex in eukaryotes