Foundations Exam 3 Material - Nucleotide Metabolism, DNA Replication, DNA Repair

What is chronic/delayed toxic exposure?

more than 3 months, repeated doses

What is an informational pathway?

pathway in which genetic information is stored as the nucleotide sequence is maintained and expressed

How is information from parenteral DNA copied to daughter DNA with high fidelity?

DNA replication

How is RNA synthesized using DNA as a template?

transcription

How are viruses able to make RNA and DNA using RNA as a template?

Reverse transcription

Define gene

segments of DNA that code for peptides and RNA; different from regulatory sequences, DNA can be expressed differently to yield different products

How is DNA involved in transcription?

one strand of double-stranded DNA acts as the molecular template for RNA synthesis

What happens in translation?

triplets of nucleotides in mRNA bind complementary triplets in tRNA

What determines biological function?

the protein sequence

Human somatic cells have how many chromosomes?

46 (22 diploid pairs plus X and Y)

Do mitochondria and chloroplasts have DNA?

Yes; double stranded circles

What is the majority of eukaryotic DNA?

non-coding DNA

(T/F) The total length of DNA, nor the number of chromosomes correlates strongly with the complexity of an organism.

False

How is eukaryotic DNA organized?

into a complex called chromatin

How much of the total genome encodes for proteins?

a small fraction (1.5%)

What are some non-protein things that are encoded in the total genome?

things that are involved in regulation of gene expression (promoted, terminations signals, etc), small regulatory RNA, junk DNA (pieces of unwanted genes, remnants of viral infections)

What are exons?

expressed sequences that are translated into the amino acid sequence

What are introns

regions of genes that are transcribed but not translated; do not encode polypeptide sequence

What happens to introns?

they are removed after transcription and the exon mRNA sequences are spliced together; creates mature transcripts

What are transposons?

sequences that can move around within the genome of a single cell

Describe transposon characteristics

ends of transposons contain terminal repeats, these repeats hybridize with complementary regions of target DNA during insertion; account for 50% of human genome

Describe simple sequence repeats (SSRs)

short sequences with millions of repeats also known as satellite DNA, associated with centromeres and telomeres

What are telomere sequences for?

may form special loop structures to keep DNA ends from unraveling

What adds telomere sequences to chromosomes?

telomerase

Describe cellular DNA aging

in many tissues, telomeres are shortened after each round of replication

What is the hayflick limit?

normal human cells divide about 52 times before losing the ability to divide again

What are centromere sequences?

AT-rich repeated sequences essential for equal distribution of chromosome sets to daughter cells; region where two daughter chromosomes are held together during mitosis

What is DNA supercoiling?

the formation of additional coils in DNA due to twisting forces

Why does DNA need to be organized?

packing of large DNA molecules within cells; access of proteins to read the information in DNA sequences

What is non-supercoiled DNA called?

relaxed

Supercoiling has great influence on ________ and ________ of DNA

transcription and replication

Is supercoiling regulated?

Yes

Most cellular DNA is under-wound in what form?

normal B-form

(T/F) Closed circular DNA is rarely relaxed

True

How is linear DNA underwound?

With the help of proteins to prevent strands from rotating

What additional DNA structural changes are facilitated by underwinding?

maintain structure of cruciforms at palindromes (cruciforms rarely occur in relaxed DNA), facilitate formation of stretches of left-handed Z-form

What are topoisomers?

Different forms of DNA that differ only in the degree and nature of supercoiling

What is required for conversion between topoisomers?

a DNA strand break

What type of supercoiled DNA travels faster in agarose gel electrophoresis experiment than relaxed or nicked DNA?

negatively supercoiled DNA

What do topoisomerases do?

cur DNA strands for DNA unwinding and rewinding during transcription and replication

What are the major types of topoisomerases?

type 1 and type 2

Describe Type 1 topoisomerase

makes a transient cut in one DNA strand

Describe type 2 topoisomerase

makes a transient cut in 2 DNA strands;

What is the type 1 topoisomerase mechanism?

Tyrosine reside attacks phosphate and cuts one strand; forms new bond to DNA strand, enzyme changes to an open conformation, unbroken DNA strand passes through the break in the first strand, enzyme in closed conformation, liberated OH attacks the linkage to re-ligate the cleaved DNA strand

What are the main eukaryotic topoisomerases?

Topo 1, 2alpha, 2beta, 3

What eukaryotic topoisomerases are type 1

Topo 1 and Topo 3

What are the two subfamilies of type 2 topoisomerases?

2a and 2b; can relax both positive and negative supercoils

What is the mechanism of eukaryotic type 2a topoisomerase?

Two tyrosines attack double stranded DNA, Second segment of the same DNA molecule (double stranded) passes through break, breaks are re-ligated via two ATP molecules

What are coumarins (novobiocin, coumermycin A1)?

drug that inhibits bacterial type 2 topoisomerases from binding ATP

What are quinolones(nalidixic acid, ciprofloxacin)?

inhibit the last step of topoisomerase, which is resealing the DNA strand breaks, wide-spectrum and mostly selective for bacterial enzymes (antibiotics)

How are topoisomerases used as chemotherapy agents?

target cancer because most rapidly growing cells (tumors, others) express topoisomerases

How do eukaryotic type 1 topoisomerase inhibitors work?

trap the enzyme-DNA complex in its cleaved state

What is chromatin?

fibers of DNA and protein where DNA associates tightly with proteins called histones

What are histones?

small proteins with lots of basic (Lys, Arg) residues (often positively charged)

What are nucleosomes?

DNA and protein packed into discrete units

What does wrapping of DNA around the histone core require?

the removal of one helical turn

When under-winding occurs without a strand break, what forms?

a compensatory positive supercoil

How is the positive supercoil relaxed?

By a topoisomerase, leaving DNA with a net negative supercoil

Where does histone binding occur more often?

AT rich regions, staggering at 10bp intervals that facilitate its binding around the histone core

What are some roles of nucleic acids?

cellular energetics, messengers (within the cell/mRNA from nucleus) and from outside the cell (in response to hormones), molecular repositories of information

How are nucleic acids involved in biotechnological processes?

genetic testing, vaccine development, drug development, nutraceuticals, metabolic engineering, etc

Nucleic acids have what properties?

ordinal and informative

What is a nucleotide?

nitrogenous base, pentose, and phosphate

What is a nucleoside?

nitrogenous base and pentose

What is a nucleobase?

only nitrogenous abse

What is the phosphate group charge at neutral pH?

negatively charged, in nucleotides at 5' position

What pentose sugar is in RNA?

beta-D-ribofuranose

What pentose sugar is in DNA?

B-2'-deoxy-ribofuranose

Identify adenine

Identify guanine

What are the purines?

adenine and guanine

Identify cytosine

Identify thymine

Identify uracil

What are the pyrimidines?

cytosine, thymine, and uracil

Where do you find cytosine?

in both DNA and RNA

Where do you find thymine?

only in DNA

Where do you find Uracil?

only in RNA

What are some common characteristics of pyrimidine bases?

all are good H-bond donors and acceptors

Pyrimidine bases are neutral molecules at what pH?

7

Where are adenine and guanine found?

in both RNA and DNA

What are some characteristics of purine bases?

good H-bond donors and acceptors

Purine bases are neutral molecules at what pH?

7

How are pentose rings attached to nucleobases?

via N-glycosidic bonds

Where are N-glycosidic bonds formed?

formed to the anomeric carbon of the sugar in the b conformation

In pyrimidines, where is the N-glycosidic bond formed?

position N1

In purines, where is the N-glycosidic bond formed?

position N9

Are N-glycosidic bonds stable toward hydrolysis?

Yes, especially in pyrimidines

What is the rotation like for N-glycosidic bonds in free nucleotides?

free rotation

Identify deoxyadenylate

Identify deoxyguanylate

Identify deoxythymidylate

Identify deoxycytidylate

Identify adenylate

Identify guanylate

Identify uridylate

Identify cytidylate

What is 5-Methylcytidine?

common minor nucleoside in DNA found in eukaryotes and bacteria; is an epigenetic marker

What is an epigenetic marker?

way to mark which genes should be active

What turns genes off from being expressed?

methylation