BIOS 1700

Scientific method: observations

curiosity, detailed attention, clear description

Scientific method: hypothesis

possible answers to explain what is behind what you observed. Hypotheses must be testable and objective.

Scientific method: predictions

what would happen if the hypothesis is correct?

Scientific method: experiment

test of the hypothesis. Repeatable. If the results are not consistent, reject or revise the hypothesis. If they are consistent over many experiments, the hypothesis becomes a theory

Scientific method: theory

a general explanation for what's gong on. Supported by a large body of experiments and observations.

Control group

-same conditions

-no introduced variable

Test group

-same conditions

-one difference (variable)

Central Dogma of Molecular Biology

Prokaryotic cell:

-single celled organisms

-enclosed in plasma membrane

-has cytoplasm

-DNA in multiple locations

Eukaryotic cell:

-can be single celled or multicellular organisms

-enclosed in plasma membrane

-has cytoplasm

-has a nucleus (DNA)

-has more organelles

Element:

pure substance that can't be simplified

Atom:

smallest amount of an element

Molecule:

2 or more atoms that are chemically joined together

Compound:

a molecule that contains more than one element

Atomic number:

number of protons

Atomic mass:

number of protons + neurons

Isotopes:

different numbers of neutrons

Further distance from nucleus

-more energy

-more electron shells = more energy

Covalent bond:

sharing valence electrons (co-valent)

Ionic bond:

chemical bond formed between two ions with opposite charges. Lose or gain electrons. Metal and non-metal

Hydrogen bonds

form between a hydrogen with a partial positive charge and a more electronegative atom

ex. DNA, H2O

Van Der Waal forces

-Constant electron movement leads to regions of partial + / - which can attract / repel neighboring molecules

-Weaker than h-bonds

-Need to be close together

Nonpolar covalent bond

bonding electrons shared equally between two atoms. No charges on atoms. Ex. Cl & Cl

Polar covalent bond

bonding electrons shared unequally between two atoms. Partial charges on atoms. Ex. H & Cl

Electronegativity

the power of protons to attract (or pull) electrons

What would happen when two atoms on the opposite side in the periodic table forms covalent bonds?

polar covalent bonds happen

Example of a polar molecule

H2O

Hydrophilic

-water loving

-charged or polar

Hydrophobic

-water fearing

-nonpolar

Is HCl hydrophilic or hydrophobic?

hydrophilic/polar

pH

-indicates how many protons (H+) molecules are in water

-pH= -log(H+)

0 pH

-acidic

-more H+

14 pH

-basic

-less H+

Carbon

life's chemical backbone- can make 4 covalent bonds with other atoms to become a stable configuration.

-tetrahedron

-free rotation of each single bond

Isomer:

molecules with the same chemical formula but with different structures

Proteins:

-amino acids

-enzymes that help chemical reactions

-hydrophilic

-peptide bonds

Nucleic acids:

-nucleotides

-stores genetic information

-hydrophilic

-phosphodiester bond

Carbohydrates:

-simple sugars (monosaccharides)

-energy/cell wall

-hydrophilic

-glycocidic

Polymers:

long chain of repeated subunits

Monomer:

repeated subunit

Making a polymer

-monomer in

-water out

Breaking a monomer

-monomer out

-water in (hydrolysis)

What connects 2 amino acids together?

-polypeptide bond

amino acid monomer

N-terminus

beginning of an amino acid (amino group)

G-terminus

ending of an amino acid (carboxyl group)

nucleotide (monomer)

nucleotides:

5-carbon sugar + nitrogenous base + phosphate group

DNA vs. RNA

-DNA: has a free H+, thymine, deoxyribose

-RNA: has an OH group, uracil, ribose

Pyrimidine bases:

-thymine, cytosine, uracil

-has one 6 ring

Purine bases:

-adenine, guanine

-have two 6 rings

Nucleic acids

-long chain of nucleotides connected by phosphodiester bonds (sugar + phosphate backbone)

-5' phosphate group (free)

-3' hydroxyl group

DNA structure:

2 strands: 2 sugar phosphate backbone

Adenine and thymine

2 hydrogen bonds

Guanine and cytosine

-3 hydrogen bonds

-more stable than A-T pairing

simple sugar monomer

simple sugars (monosaccharides)

-have 5 or 6 carbons

-6 carbons have the same chemical formula but different structural formulas (isomers)

-become polysaccharides by 1-4 glycosidic bonds

end of carbohydrate polymer

-location of OH (hydroxyl group)

polymer of glucose in plants

starch

polymer of glucose in animals

glycogen

Lipids:

-triaclyglycerol, phospholipids, steroids-> all fatty acids.

-hydrocarbon chain + carboxyl group

Saturated fatty acids (palmitic)

have all potential hydrogens

Unsaturated fatty acids (palmitoleic)

can have more hydrogens, so it's more flexible

Triaclyglycerol

1 glycerol + 3 fatty acids

(3 h2o molecules out)

Stability of fatty acids (melting temp) depend on:

-length of hydrocarbon chain

-number of double bonds

How do fatty acids stack together?

fatty acids stack together via van Der Waals forces

Steroids:

-hydrophobic

-cholesterol (precursor for many hormones- testosterone, estrogens, etc.)

Why are organic molecules so diverse?

-the carbon molecules in an organic compound can make 4 bonds

Dehydration synthesis

The monomers combine with each other via covalent bonds to form larger molecules known as polymers. In doing so, monomers release water molecules as byproducts.

(put together, release water)

Hydrolysis reactions

a chemical process in which a molecule of water is added to a substance. Sometimes this addition causes both substance and water molecule to split into two parts. In such reactions, one fragment of the target molecule (or parent molecule) gains a hydrogen ion.

(break apart, add water)

What substance or molecule transformed nonvirulent bacteria?

DNA

Nucleotide vs. nucleoside

-nucleotide: sugar + base + +phosphate group (1-3)

-nucleoside: sugar + base (no phosphate group- mono, di, try phosphate) ex. adenosine triphosphate (ATP)

Structure of DNA:

-a polymer of nucleotides

-double helix with antiparallel configuration

-sugar/phosphate backbone

5' end of a nucleotide

-phosphate group

-negatively charged

3' end of a nucleotide

-hydroxyl group (OH)

What is the bond between a phosphate group and a hydroxyl group between nucleotides?

-phosphodiester bond

Stabilization of the DNA double helix

-Hydrogen bonding between base pairs on opposite DNA strands (2 for AT, 3 for GC)

-hydrophobic interactions between base pairs on the same DNA strand help to stabilize on

Complementary base pairing:

-Adenine + Thymine (Uracil in RNA)

-Guanine + Cytosine

5' TGCAGT 3'

3' ACGTCA 5'

Semiconservative replication

-DNA replication, in which the two strands of the DNA helix separate and free nucleotides pair with the exposed bases on the single chains to form two new DNA molecules, each containing one original and one newly synthesized strand of DNA.

-parental strands serve as the templates for the daughter strands

Prokaryotic genomic DNA:

-supercoiled

-gets twisted and packed together

for DNA replication/transcription to occur DNA must be unpacked or loosened

Eukaryotic DNA:

-linear and protected by histones forming chromatin (condensed form of DNA)

Transcription

-the first step of gene expression, in which a particular segment of DNA is copied into RNA (especially mRNA) by the enzyme RNA polymerase

-this is because DNA can't leave the nucleus, but mRNA can

Translation

-the final step on the way from DNA to protein

-synthesis of proteins directed by a mRNA template

-the information contained in the nucleotide sequence of the mRNA is read as three letter words (triplets), called codons. Each word stands for one amino acid.

Where does central dogma occur in eukaryotes?

-nucleus

Where does central dogma occur in prokaryotes?

-cytoplasm

Transcription: recognition of a polymer (starting transcription)

eukaryote: lots of proteins

prokaryote: sigma factor

Transcription: elongation (adding ribonucleotides)

-happens in both types of cells

Transcription: RNA processing (altering the RNA copy- transcript)

-eukaryote: lots (3)

-prokaryote: none

RNA vs. DNA

-RNA: ribose has a hydroxyl (OH) group. Uracil has a hydrogen group for bonding.

-DNA: deoxyribose has a free hydrogen (H) Thymine has a methyl (CH3) group for bonding.

Transfer of information from DNA to RNA

-only one strand will be read (template strand)

-the RNA transcript is antiparallel to template strand

Transcription is facilitated by:

RNA Polymerase Complex (Pol II)

1. Ribonucleotides are accepted if they correctly base pair with template DNA

2. The 3' OH of the growing strand bonds with the phosphate group of the incoming ribonucleotide

3. 2 phosphates of the incoming ribonucleotide are released

What does RNA polymerase II do?

-makes an RNA strand from a DNA strand in eukaryotes

Where does transcription start?

-promotor (5')

-many promoters contain the TATA box for RNA polymerase II to bind

Where does transcription end?

-terminator (3')

TATA box

-a DNA sequence that indicates where a genetic sequence can be read and decoded.

Why is one end of DNA or RNA called the 5' end?

-each end of the DNA molecule has an open group

-5'= phosphate attached to the 5' carbon of deoxyribose sugar

Promoter recognition in prokaryotes:

-a sigma factor binds to the TATA box in promotor to recruit RNA polymerase

Sigma factor

-a protein needed only for initiation of transcription

-helps RNA polymerase bind to gene promoters

Promoter recognition in eukaryotes: (1)

-very complex (promoters and enhancers)

-general transcription factors bind to the promoter, and transcriptional activator proteins bind to enhancers