LECTURE 5: Molecular Basis of Heredity Flashcards by Fiara Arnaldo

A eukaryotic cell would contain how many molecules of DNA + why?

how about for prokaryotic organisms and viruses? + their genetic material are either… or….?

more than 1 molecules

bc each chromosome has 1 long molecule of DNA

one long molecule of DNA that are either naked or associated with proteins

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What is the genetic material of all organisms

DNA

but for some viruses, it’s RNA

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Uncoiled DNA of a human chromosome has an average length of?

size of human nucleus?

5 cm

5 x 10^-4 cm

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2 compositions of chromosome

Lipids
Proteins (both histone and non-histone)

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basic repeating unit of the chromatin

+ its composition

nucleosome (only for eukaryotes)

protein core of 8 histone molecules
molecule of DNA wound around the protein core

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Histone molecules contain what histones (4) + how many

+ other term for histone molecules due to its number of histones

each contains 2 of H2A, H2B, and H3, and H4

“octamer”

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One nucleosome is connected to another nucleosome by a?

that gives results to what with what kind of appearance?

linker DNA

chromatin fiber = “beads on a string”

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length of chromatin fiber

10 nm in diameter

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Nucleosomes have a _____ function

packaging

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The winding of DNA around the nucleosome core results to a???

6-10 fold reduction in length

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How is chromatin folded exactly?

histone molecule H1 connects with copies of itself

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What histone molecule is found to be associated with the LINKER DNA

+ its other function

H1 (secures DNA to the histone complex)

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How is chromatin further shortened and packaged?

via successive higher orders of chromatin fiber coiling through the formation of the 30 nm solenoid

once solenoid is formed, the chromatin fiber is packaged along a protein scaffold

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DNA and RNA are____, meaning?

polynucleotides: made of repeating units of nucleotides

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NUCLEOTIDES

composition (3)

phosphate group
pentose sugar
nitrogen base

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PENTOSE SUGAR of:

+ structure
+ difference

DNA: 2-deoxy-D-ribose
RNA: D-ribose

Cyclopentane (house formation) with O atom at the roof

Carbons 1 - 4 are numbered clockwise

DIFFERENCE:
DNA
- C1 and 3 has 1 OH, and 1 H attached
- C2 has 2 H attached
- C4 has 1 H, and 1 HOCH2 attached

RNA
- C1, 2, 3 has 1 OH and 1 H attached
- C4 has 1 H, and 1 HOCH2 attached

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NITROGEN BASES for:

DNA: adenine, guanine, cytosine, and thymine

RNA: adenine, guanine, cytosine, and uracil

PURINE vs PYRIMIDINE

in terms of nitrogen bases

PURINE: adenine and guanine

PYRIMIDINE: cytosine, thymine, and uracil

PURINE vs PYRIMIDINE

in terms of structure

PURINE: double ring structure (purine ring + 5-membered imidazole ring)

PYRIMIDINE: single ring structure (pyrimidine ring)

3 TYPES of covalent bonds in NUCLEIC ACIDS

+ where formed

β-N-glycosidic bonds (nucleosides: pentose sugar + nitrogen base)
phosphoester bonds (nucleotide: nucleoside + PO4 group)
phosphodiester bonds (polynucleotides between adjacent nucleotides)

REMEMBER: when drawing phosphodiester bonds, 2 yon lagi: #1 and #2

How does the Carbon (in pentose sugar) bond with the nitrogen base and the phosphate group?

to form a polynucleotide, what bonds to the next nucleotide and where?

Carbon 1 in sugar attaches to nitrogen base
Carbon 4 in sugar attaches to Carbon 5 which attaches to the phosphate group
3’ OH attaches to 5’ PO4 of the NEXT nucleotide

How are the ff named?

nucleoside
nucleotide

NUCLEOSIDE
- depends on nitrogen base present
- purine: (deoxy)-adenosine or (deoxy)-guanosine
- pyrimidine: (deoxy)-cytidine, (deoxy)-thymidine, or uridine

NUCLEOTIDE
- nucleoside + number of phosphate groups attached

Most common example of nucleotide?

adenosine triphosphate

Strands of DNA are?
- how?
- held together by what bond?

antiparallel
- left strand: 5’ PO4 (upper) and 3’ OH (lower)
- right strand: 3’ OH (upper) and 5’ PO4 (lower)

*orientation of sugar molecule and nitrogen base is also opposite/upsidedown

HYDROGEN BONDS between paired bases

CHARGAFF'S RULE - definition - importance (2) - conclusion

- a rule that states how nitrogen bases are paired together (A:T and G:C) 1. accurate replication of DNA 2. complementary of the antiparallel strands of DNA Therefore, the ratio of purines (A+G) and pyrimidines (C+T) is 1:1 in DOUBLE STRANDED DNA

What is the main characteristic of a DNA molecule?

the arrangement/sequence of the nitrogen bases

the longer the DNA, the ? and enables it to?

the more complex and varied its base sequence is enables it to store huge amounts and diverse kinds of biological information

does base sequences vary among different DNA molecules?

yes

FACTORS contributing to stability of genetic material (3)

1. Covalent Bonds (phosphodiester bonds and N-glycosidic bond) 2. Hydrogen Bonds 3. Base Stacking (hydrophobic interactions build up among stacked bases)

Who proposed the double strand 3D DNA structure? + date + model name + likened to what structure?

James Watson and Francis Crick (1953) DNA Double Helix spiral staircase

PARTS of the DNA double helix model

1. rails: antiparallel sugar-phosphate backbone 2. bars: nitrogen base pairs

the DNA is a _____ (direction) helix wherein a ____ (degrees) turn covers a distance of _______ and _____ (number) base pairs thus, the base pairs are separated by a distance of ______ the diameter of the molecule is ___

- right-handed (clockwise, going down) - 360 - 34 angstroms / 3.4 nm - 10 base pairs - 3.4 angstroms - 20 angstroms

HISTONE and DNA charge + relevance

histone is + charge DNA is - charge due to PO4 grp in its backbone thus, DNA is able to wrap tightly around the protein core and contribute to packaging

DNA: 2-deoxy-D-ribose RNA: D-ribose WHAT is the meaning behind their names?

2-deoxy (no O atom in carbon 2) D-ribose (naturally occurring form of ribose)

NITROGEN BASES - carries _____ _____ information that determines _____ between organisms - derivatives (or galing sa...) of ______ and ____ - OTHER TERM + reason

- genetic sequence - variety - purine and pyrimidine - heterocyclic aromatic ring (alternating C and N atoms)

NUCLEIC ACIDS - 2 types - storage of _____ information - other term? + reason - pairing of nitrogen bases - number of bonds in between pairs^^ - which pair is stronger?

1. DNA 2. RNA - biological - polynucleotides (polymer of nucleotides) A = T/U (double bond) C ≡ G (triple bond) - stronger *kaya ganto yung pairing, kasi A and T & C and G can only form 2 and 3 bonds respectively INDIVIDUALLY if A + G bonds or T + C bonds, hindi ma-mamaximize yung bonds in between

PURINE vs PYRIMIDINE in terms of attachment site of sugar + BOND NAME changes in nucleoside

PURINE: 9th nitrogen in the nitrogen base (β-N-9-glycosidic bond) PYRIMIDINE: 1st nitrogen in the nitrogen base (β-N-1-glycosidic bond)

3 UNIVERSAL CHARACTERISTICS of DNA

1. double stranded 2. anti-parallel 3. complementary

DIMENSIONS OF DNA - 3 conformations - which is the most common ^^ - which was proposed by Watson & Crick ^

A-DNA C-DNA B-DNA (most common, proposed)

CONVERT THE FF: 1 um = __ A 1 um = ___ nm 1 A = __ nm 10 bp = ___ A

1 um = 10 000 A 1 um = 1 000 nm 1 A = 0.1 nm 34 A = 10 bp