DOUMA LECTURE 1

Adenine

make aromatic ring, add amino group, strair case N on both sides

Guanine

1. draw benzene

2. add ncn to the left

3. stair case N

4. c=0 on top

5. Amino group in middle of N so u get triple N still.

6. also triple n in adenine too!

Cytosine

amino group is on top, just like adenine. all pyrimidines have c=0

Uracil

Thymine

Nitrogenous Bases in DNA and RNA

Adenine, Guanine, Cytosine, and Thymine (DNA); Uracil replaces Thymine in RNA. Purines (A, G) have double rings; Pyrimidines (C, T, U) have single rings.

Repeating Units of DNA

2'-deoxyribonucleoside 5'-monophosphates (dNMPs) are the monomers of DNA.

Structure of a Nucleotide

Each nucleotide has a sugar, phosphate group, and nitrogenous base.

Directionality of DNA and RNA

Sequences are written 5' to 3', from the free 5' phosphate to the 3' hydroxyl.

DNA Backbone

Alternating sugar and phosphate groups forming the outer structure of the DNA helix.

Hydrogen Bonding and Base Pairing

A pairs with T via 2 H-bonds; G pairs with C via 3 H-bonds, allowing strand separation.

Base Stacking

Hydrophobic interactions between bases that stabilize the DNA helix.

Melting Temperature (Tm)

The temperature at which DNA is 50% denatured; higher in GC-rich sequences.

Denaturing and Annealing DNA

Denaturing separates strands by breaking H-bonds; annealing reforms them if complementary.

Main Characteristics of B-DNA

Right-handed helix; 10.5 base pairs per turn; major and minor grooves; bases stacked inside.

Major Groove vs Minor Groove

Major groove exposes bases for protein binding; minor groove is narrower.

Definition of DNA

Deoxyribonucleic acid; a double-stranded polymer carrying the genetic blueprint.

Central Dogma of Molecular Biology

Describes flow of information: DNA replication, transcription into RNA, and translation into protein.

Purpose of DNA Replication

To duplicate DNA for inheritance by daughter cells.

Purpose of Transcription

To produce RNA as a temporary working copy of genetic information.

Purpose of Translation

To synthesize proteins using information carried by mRNA.

Reverse Transcription

Synthesis of DNA from an RNA template by specific enzymes.

Key Features of Prokaryotic Cells

DNA located in cytoplasm; no nucleus.

Key Features of Eukaryotic Cells

DNA housed inside the nucleus.

Bacterial Transformation

Uptake of external DNA by a bacterial cell, changing its characteristics.

Streptococcus pneumoniae

Bacteria used in Avery's experiment to identify DNA as genetic material.

Smooth Cells (S cells) vs Rough Cells (R cells)

S cells have a protective capsule (polysaccharides) (virulent); R cells lack it (non-virulent).

Cell-free Extract

Lysed cell contents used in transformation experiments.

Purpose and Findings of Avery's Experiment

DNA was identified as the genetic material because DNase destroyed transformation ability.

Polynucleotide

A polymer of many nucleotides linked by phosphodiester bonds.

dont mix up with polynucleotide

Nucleotides and nucleosides are fundamental components of nucleic acids (DNA/RNA), differing primarily by a phosphate group.

A nucleoside contains only a nitrogenous base and a sugar.

A nucleotide consists of a nucleoside plus one or more phosphate groups, making them the active, structural monomers of DNA/RNA and carriers of cellular energy (e.g., ATP).

Phosphodiester Bond

Covalent bond between the 3' OH of one nucleotide and the 5' phosphate of another.

Chargaff's Rules

1. A=T, G=C

2. Base comp. varies between species

3. Base comp. is the same in different cell types

4. Base comp. does not change with age or environment

Significance of Rosalind Franklin's Photo 51

Provided key evidence of DNA's double helical structure and periodicity.

Antiparallel Orientation of DNA Strands

Two DNA strands run in opposite directions (5'->3' and 3'->5'). DNA is antiparallel (one strand 5'→3', the other 3'→5') primarily to maximize stability through hydrogen bonding between base pairs and to allow enzymes to replicate and transcribe it efficiently.

Definition of Gene

DNA sequence encoding a functional RNA or protein with regulatory elements.

Definition of Genome

Complete set of genetic material in an organism (e.g., 46 chromosomes in humans).

Central Dogma

DNA-transcription-RNA-translation-protein

where is DNA stored in prokaryotes?

cytoplasm/nucleoid

where is DNA stored in eukaryotes?

nucleus

role of smooth streptococcus pneumoniae cells:

produce a polysaccharide capsule

what differentiates rough cells of streptococcus pneumoniae from smooth cells?

they do not produce a polysaccharide capsule (because they lack the genetic info to make it)

which strain of streptococcus pneumoniae causes pneumonia in humans & why?

smooth cells because they produce a polysaccharide capsule that protects it from the immune response of the host

define bacterial transformation:

external DNA is taken up by a bacterial cell

which two types of cell characteristics can bacterial transformation change?

morphology & physiology (structure + function)

define cell-free extract:

the mixture of the contents of a dead cell that open into the environment surrounding the dead cell

Avery's Bacterial Transformation Experiment

Oswald Avery heated smooth streptococcus pneumoniae (S) cells to kill them, causing them to release cell-free extract that was then mixed with rough streptococcus pneumoniae cells (R) which took up the S cell-free extract transforming them into S cells

what were the results of adding an enzyme that degrades one type of macromolecule to the S cell-free extract in Avery's Bacterial Transformation experiment? describe results for:

1. proteinase

2. RNase (ribonuclease)

3. DNase (deoxyribonuclease)

1. R cell transformed into S cell

2. R cell transformed into S cell

3. R cell did not transform into S cell

what were the implications of the results of Avery's Bacterial Cell Transformation Experiment?

suggested that DNA is the genetic info of the cell

what are the 5 bases seen in DNA & RNA? which are purines and which are pyrimidines?

1. adenine - purine

2. guanine - purine

3. cytosine - pyrimidine

4. uracil - pyrimidine

5. thymine - pyrimidine

pyrimidines = CUT

structure of adenine

purine with one NH2 substituent; lacks carbonyl substituent unlike the other purine in DNA & RNA, guanine

structure of guanine

purine with one carbonyl substituent and one carbonyl substituent

structure of cytosine

pyrimidine with one carbonyl substituent & one NH2 substituent; only pyrimidine seen in DNA & RNA with two double bonds within its ring (NH 2 ON TOP LIKE ADENINE)

structure of uracil

pyrimidine with two carbonyl substituents

structure of thymine

pyrimidine with two carbonyl substituents & a methyl group substituent; looks the same as uracil but with a methyl substituent & is only base with a methyl substituent

what are the 3 structural components of a nucleotide?

1. nitrogenous base (1)

2. pentose (1)

3. phosphate (1 or more)

what is the name of a nucleoside + one or more phosphate(s)?

nucleotide

what are the structural components of a nucleoside?

a nitrogenous base & pentose

what kind of bond connects pentose to a nitrogenous base?

glycosidic (covalent) bond

what are Erwin Chargaff's 4 rules?

1. DNA has equal concentrations of A=T & of G=C

2. base composition (%) varies between species

3. base composition is the same in all cells of an individual organism

4. base composition does not change with age, nutrition, or environment

what is the significance of Rosalind Franklin's Photo 51?

showed that DNA is helical with a consistent diameter from an X-ray diffracted image of a hydrated DNA molecule allowing Watson & Crick to determine the structure of DNA

what is the repeating unit of DNA?

2'-deoxyribonucleoside 5'-monophosphates (dNMP)

describe the orientation of the two unbranched chains that make up the DNA double helix?

chains run antiparallel

what kind of bond connects each nucleotide within a single chain (vertical)?

phosphodiester linkage (phosphodiester linkages form all bonds in DNA/RNA involving sugar; such as between pentose & phosphate, and pentose & nitrogen bases)

what kind of bonds link nitrogen bases/DNA chains in a double helix? what is this bonding also referred to as?

hydrogen bonds, "Watson-Crick-Franklin" base pairing

1. how many hydrogen bonds form between A & T?

2. how many hydrogen bonds form between G & C?

3. what does this tell us about the stability of the base pair interactions?

1. A & T = 2 bonds

2. G & C = 3 bonds

3. therefore, the interactions between G & C are stronger than the interactions between A & T

how do we read DNA & RNA sequences?

from 5'→3' along each strand Two different contexts: 1. 🧬 What enzymes do (mechanism)

• DNA polymerase → reads template 3′ → 5′

• RNA polymerase → reads template 3′ → 5′

• New strand made 5′ → 3′

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2. 📖 How humans write/read sequences

• We always write DNA sequences 5′ → 3′

• The coding strand is written 5′ → 3′ and matches RNA (T → U)

what is the difference between ribose sugars and deoxyribose sugars?

ribose sugars have a 2' hydroxyl group (OH) whereas deoxyribose sugars have a 2' hydrogen group (H)

nucleotides making up each strand of DNA are connected through what type of interactions?

covalent interactions

from exterior to interior, what is the sequence of subunits making up DNA chains?

phosphate → deoxyribose → nitrogenous base

what does denaturing DNA do?

separates strands (usually done in lab by heating)

what does it mean for DNA to anneal?

complementary single strands come together via base pairing (can occur in lab after denaturing if solution is cooled to standard temperature)

what drives DNA annealing?

nothing; no energy or catalyst is required, hydrogen bonds will form between base pairs under standard conditions

>99% of DNA in living cells exists in what conformation? what kind of helix is this form?

B-DNA (hydrated form); right-handed helix

base pairs are exposed in B-DNA in which structural characteristic(s)?

major & minor grooves

how do base pairs lay in B-DNA?

flat & perpendicular to the axis/backbone (planar)

are the hydrophobic portions of bases in B-DNA found on the interior or exterior?

interior (because B-DNA is surrounded by water)

which conformation of DNA is the best structural model of double-stranded RNA & RNA-DNA hybrid molecules?

A-DNA (dehydrated)

what is the name of the dehydrated DNA conformation?

A-DNA

what is unique about the structure of Z-DNA? why is it called Z-DNA?

it is a left-handed helix and the letter Z refers to its "zigzagging" sugar-phosphate backbone

what is the composition of the backbone of DNA?

deoxyribose sugar and phosphate

Z-DNA is found in <1% of cellular DNA; in what regions is it most likely to be found and why?

regions with high G-C content because the extra hydrogen bonding allows the conformation to exist

what are 2 ways in which RNA differs structurally from DNA?

1. ribose sugar-phosphate backbone (still on 2' sugar like in DNA)

2. thymine (T) is replaced with uracil (U)

what kind of interactions allow RNA to form a helical structure?

base-stacking interactions

because of its helical structure, RNA can base pair with complementary regions of which two molecules?

DNA or RNA

under what conditions is G-U base pairing allowed to occur?

when RNA pairs to itself or to another RNA molecule

how are complex secondary & tertiary structures formed from RNA?

by internal base pairing within an RNA strand

what kind of RNA structure can function as an enzyme?

tertiary

what do genes contain?

DNA encoding an fRNA (functional RNA) or protein & regulatory elements that control its expression

regardless of the structure or shape of a species' genome, what is always true regarding the position of its genes?

genes are always in a fixed position relative to one another in all organisms of a species (unless there is a mutation)

define chromatin:

chromosomal material in a cell consisting of DNA & (in eukaryotes) the proteins bound to the DNA

what is the repeating unit in chromatin called?

nucleosome

what is the most abundant protein in eukaryotic chromatin?

histones