DNA - Exam 2

Exam 2

What is DNA made up of ?

nucleotides

What are the 3 parts to a nucleotide ?

phosphate group (1-3), deoxyribose sugar, nitrogenous base

Which type of base has a double ring structure ?

purines

Which type of base has a single ring structure ?

pyrimidines

What are the 5 nitrogenous bases and which is found in DNA or RNA?

adenine, thymine (DNA), guanine, cytosine, uracil (RNA)

What make deoxygenated-ATP different from THE ATP?

missing OH group on sugar

How many phosphate groups can be attatched to a DNA nucleotide?

1-3

What is the difference in deoxyribose sugar (DNA) and ribose sugar (RNA)?

deoxyribose has H on 2 carbon spot, ribose has OH on 2 carbon spot

Which nitrogenous bases are purines?

adenine and guanine

Which nitrogenous bases are pyrimidines?

thymine, uracil, cytosine

What makes thymine different from uracil?

thymine has methyl group (CH3)

What type of bond links nucleotides?

phosphodiester bonds

Is the linkage of nucleotide (phosphodiester linkage) energetically favorable?

unfavorable because of condensation rxn (covalent bond)

1’ =

nitrogenous base

3’ =

hydroxyl group

5’ =

phosphate group

What is considered the “top” end of DNA and what is always dangling off it?

5’ end; phosphate group always dangling off

What is considered the “bottom” end of DNA and what is the always dangling off it?

3’ end; hydroxyl group always dangling off (OH)

Number such as 5’ and 3’ refer to ?

carbon atoms in sugar ring

What are the two sources of nucleotides?

de novo synthesis and salvage pathway

What is the de novo synthesis?

cutting and pasting from acid or carbohydrate pieces

What and where are nucleotides synthesized?

synthesized by enzymes in cytoplasm and transport to nucleus

What is the salvage pathway?

old nucleotides are fixed up

Which process of making nucleotides is preferred?

salvage pathway (conserves energy)

What happens to nucleotides that cannot be used in salvage pathway?

nucleotide is broken down into uric acid; eliminated

What is leech-nyan syndrome?

X-linked disorder caused by mutation in HGPRT gene (deficiency in HGPRT gene)

What does HGPRT gene do?

makes enzyme needed to recycle purine nucleotides

What happens in the lesch-nyhan syndrome when there is no HGPRT gene?

uric acid is overproduced; causing arthritis, mental disability, hypotonia (weak muscles)

Does a patient of lesch-nyhan have enough DNA?

yes, symptoms are a result of uric acid accumulated in tissues

What causes Alzheimer’s disease?

tau protein hyper-phosphorylation

What do tau protein do to neuronal cells?

stabilize the microtubules (skeletons of neuronal cells)

What does hyperphosphorylation do to tau proteins?

tau drops off and forms tangles, destabilizing the microtubules

Phosphorylated tau also causes ?

chronic traumatic encephalopathy (CTE)

How does phosphorylated tau cause CTE?

repeated blows to head, brain remembers everytime hit

? is important in dephosphorylating proteins

alkaline phosphatase

When there is a phosphatase deficiency, ? occurs

hypophosphatasia, where bones and teeth are not mineralized (soft bones)

When a protein becomes denatured, ? begin to break and unfolds

H bonds

What are the 4 causes of denaturation?

heat, changes in pH, salt concentration, solvent

Denaturation is not always ?, it depends on method and what denaturatued

permanent

What are the two reasons for cooking?

denature bacterial/fungal proteins and break food molecules down to conserve energy

How else can food be denatured besides cooking?

prolonged exposure to acid in lemon, lime, or tequila (usually fish)

Normal pH of vagina is ?

3.8-4.2

How does sperm survive acidic vaginal environment?

sperm contains buffers that protect it from the acidity of vagina

Are A-T bonds stronger, weaker or the same strength as G-C bonds?

G-C bonds are stronger with 3 H-bonds

Why is DNA double stranded?

A-T and C-G pair via H-bonds

DNA is ? as a single strand

unstable

The two strands in DNA are ? meaning ?

antiparallel, running in opposite directions

When calculating percentages of A,T,G, and C in DNA…

A=T and G=C

What is the percentage of uracil in DNA strand?

0%

Complementary base pairing forms what shape?

double helix

The major grooves are ? and the minor grooves are ? in a double helix structure

major=wider, minor=narrow

DNA is ? and the distance between sugar phosphates differ

asymmetrical

What is the double helix structure most similar to?

staircase, proteins able to grip nitrogenous bases easier

How many bases are in each turn?

10.4

What is an ester bond?

C-O

Where do most protein contact interactions occur?

major groove

How many H-bonds does it take to stabilize G-C pair?

3 bonds

How many H-bond does it take to stablize A-T pair?

2 bonds

What does A-T pair having only 2 H-bonds allow for more easily?

easier to seperate 2 bonds for transcription and replication

Which direction are nucleotide sequences are read?

5’ to 3’ (left to right)

The 5’ end is always ?

top left

The 3’ end is always ?

bottom right

What types of cells have NO cell wall?

animal and fungal cells

Where is DNA kept in a eukaryotic cell?

mitochondria (most DNA HERE) and nucleus

What is DNA packaged as?

chromosomes (linear)

What is a karyotype?

organized profile of all chromosomes

What are the 3 structure needed to make a chromosome in any eukaryotic organisms?

telomere, replication origin, centromere

What is a replication origin?

w/o this cannot pass on from mother to daughter cell, usually several

What is a centromere?

where mitotic spindle attaches, usually 1

What is a telomere?

caps at the ends of chromosomes, usually 2

Are eukaryotic chromosomes haploid or diploid?

diploid (2 copies of each)

What are homologous chromosomes?

same length, bonding pattern, gene order, but sequence of DNA is not identical

Which human chromsomes are not (always) homologous?

X and Y (sex chromosomes)

What are human chromosomes of males?

XY (Y is smaller)

What are the human chromosomes of females?

XX

What does the SRY gene do in the Y chromosome?

stimulate testes development and testerone production

What humans’ sex during the first stages of development?

female

What is swyer syndrome?

XY individuals who have defects in their testosterone production, have uterus, vagina, no ovaries

What are the 3 possible defects of testosterone production?

SRY gene damaged; has SRY gene, but not producing testosterone; produce testosterone, but cannot recept it

How can individuals with swyer syndrome become pregnant?

hormone therapy or donor embryo implantation

What is the zygote that they believed Foekje Dillema had and what did divide into?

XXY and divided into a mosaic of XX and YY cells

What is a mosaic?

when a person has more than 1 genotype

What is XXY ?

Kleinfelter’s condition, usually in men that have feminized features, smaller size, more body fat (inital 47 chromosomes)

What does intersex mean?

having characteristics of human male and female phenotypes

What is the average length of DNA in the human cell?

2 meters

What is the average diameter of DNA?

10 µmeters

DNA cannot be ? or ? when condensing into nucleus

broken or tangled

What are the 3 parts of chromatin?

DNA, histones, nonhistone binding protein

Is there more DNA or protein in the chromosome?

protein (2x much)

What is the difference between the nucleosome and chromatin?

chromatin includes non-histone proteins

What are the 2 parts of a nucleosome?

DNA and histone

Nucleosomes are sometimes called?

beads on a string

How many times does DNA wrap around cylindrical shaped histone?

1.7

How many proteins are in 1 histone and how many of each?

8 proteins (octamers), 2 of H2A, H2B, H3, H4

Why do histone “tails” (N-terminal ends) stick out?

targets for modification and interactions with other proteins

What are three important things to notice about histone protein structure?

forms cylindrical shape, histones stick out, DNA wraps tightly around histones

Do you think DNA binds to the histone by covalent or noncovalent bonds and why?

noncovalent bonds (weak), must be unwrapped all the time for replication and transcription

Why do you think a large percentage of histone amino acids are positively charged?

DNA is very negatively charged; helps anchor DNA to histone

What are the advantages of G-C bonds on the TOP of histone?

3 bonds more stable

What are the advantages of A-T bonds at the BOTTOM of histone?

2 A-T bonds easier to push together