Molecules Flashcards
what is organic chemistry
Organic Chemistry includes carbon containing molecules. they are essential to life. The properties of a carbon-containing molecules depend on the arrangement of its carbon skeleton and on its chemical groups.
why is carbon important for life, and how do different organisms get it
Carbon is the backbone of life
→ all molecules of living organisms are composed of carbon
→ carbon enters living organisms via the process of photosynthesis, the it is passed from plant to animal, then animal to animal, all through consumption.
what kinds of molecules are organic
Organic chemistry contains molecules of carbon and hydrogen, things like $CO_2$ are inorganic.
how did organic chemistry start
in 1953 Stanley Miller showed that an early atmosphere containing $H_2O, CH_4,NH_3,H_2$ when exposed to electricity then condensed could produce organic molecules that would fall in the rain.
So organic molecules could be abiotically synthesized on early earth.
what are the important atoms in organic chemistry, and how many bonds can they form
Carbon has four valence electrons, and so can form 4 different bonds with other atoms, including other carbon atoms.
Other important atoms include:
Hydrogen, which can form 1 bond (valence = 1)
Oxygen, which can form 2 bond (valence = 2)
Nitrogen which can form 3 bonds (valence = 3)
what is important for the function of a molecule
Molecules have three dimensional shape, which is very important for the function of the molecule.
What are hydrocarbons
Since carbon can bond to other carbons, they can link in chains of infinite variety.
Hydrocarbons are formed from chains of carbon with the empty bonds filled with hydrogen.
They can vary in:
- Length
- Branching
- Presence and Position of Double/Triple bonds
- Presence of rings
what are isomers
Isomers are molecules with the same number of each atom, but different structure. There are three types:
what are structural isomers
Structural Isomers: have the same formula, but are otherwise different
what are geometric isomers
Cis-trans (geometric) isomers: Alkenes can either be cis or trans depending on if their chain continues on the same (cis) side or opposite (trans) side
what are Enantiomers
- Enantiomers: non super imposable mirror images. exist when a carbon atom is bonded to 4 different groups/atoms.Enantiomers are important for pharmaceuticals, a mix up of enantiomers can lead to adverse affects, like leading to still births instead of preventing morning sickness.
What is the Hydroxyl group
-OH, found in Alcohols
What is the Carbonyl group
-C=O -R, in ketons (R=R) or aldehydes (R=H)
What is the carboxyl group
-C=O -OH, found in carboxylic acid
What is the Amino group
-NH2, found in Amines
What is the Sulfhyryl group
-SH, found in Thiols
What are Phosphate groups
-PO4, in organic phosphates
what is the methyl group
-CH3, found in Methylated compounds
What is ATP
Adenosine triophosphate
What is ADP
Adenosine Diphosphate
What is the ATP reaction
PO4-PO4-PO4-Adenosine -> PO4-PO4-Adenosine + PO4 + Energy
what are the building blocks of life
- Lipids
- Proteins
- Carbohydrates
- Nucleic Acids
what are lipids
3 groups: no polymers/macromolecules
- fats
- phospholipids
- steroids
All hydrophobic
what are fats
Glycerol + 3 fatty acids,
linked by ester linkages: -OH + HO- —> —O— + H2O
Used for energy storage mainly:
Plants use polysaccharides (a starch), but animals use fat
what are Saturated fatty acids
Saturated fatty acids have no double bonds, fats made from them have the max amount of Hydrogen atoms, are solid at higher temperatures. Typically animal fats like butter
what are unsaturated fatty acids
Unsaturated fatty acids have at least one double or triple bond. Fats made from one or more of them have a bent shape, are harder to pack close to each other, and so melt at lower temperatures. Plants fats are usually like this, such as olive oil.
what are phospholipids
2 fatty acids + Glycerol + phosphate + molecule (R)
Building blocks of cellular membranes, assemble into bilayers
The hydrophilic head is made from the glycerol, phosphate, and molecule (R)
The hydrophobic tails are the two fatty acids
why do Phospholipids only have 2 fatty acids
Phospholipids only have 2 fatty acids since 1 of the glycerol’s 3 bonding sites is being used by the phosphate
what are Steroids
4 fused rings
Part of membranes, main sex hormones
ex: cholesterol, testosterone
what are Monomers and Macromolecules
Monomers: have their own function but can build polymers
Macromolecules: polymers built from many covalently bonded monomers
what is the Dehydration Synthesis reaction
Dehydration Synthesize:
HO-1-2-3-H + HO-4-H → HO-1-2-3-4-H + $H_2O$
dehydration removes a water molecule, forming a new bond
What are Monosaccharides
multiples of the unit $CH_2O$
→ 3-7 carbons
→ carbonyl group (aldose/ketose): one, hydroxyl groups: multiple
→ Major nutrient: glucose breaks down during cell respiration, C skeleton raw material for amino acids, lipids
what are Trioses
Trioses: 3-carbon sugars, C3H6O3
Glyceraldehyde
Dihydroxyacetone
what are Pentoses
Pentoses: 5-carbon sugars, C5H10O5
Ribose
Ribulose
What are Hexoses
Hexoses: 6-carbon sugars (C6H12O6)
Glucose
Galactose
Fructose
what shape can monosaccharides become
Monosaccharides like glucose can form rings where an H from an OH group moves over to the =O and forms an -OH group
what are Disaccharides and the three most common
form from two monosaccharides
Glucose + Glucose → Maltose
Glucose + Fructose → Sucrose
Glucose + Galactose → Lactase
form from this reaction:
-OH + HO- → —O— + H2O
What are Polysaccharides
Long chains of monosaccharide monomers
What Polysaccharide do plants use for storage
Plants use starch for storage, formed from a series of glucose monomers
1-4 linkage = unbranched Amylose
1-6 linkage = somewhat branched Amylopectin
What Polysaccharide do animals use for storage
Animals use glycogen for short term storage of energy, while fat is used for long term
Use glucose monomers, much more branched so their are more ends/access points to break down for energy
What is Cellulose
Cellulose: $10^1 $$^4$ Kg are produced per year by plants. Polymers of glucose with 1-4 glycosidic linkage. Long strands run parallel, held together by hydrogen bonds. While most animals can’t digest cellulose, it is important for gut health (it is fiber)
Describe the Isomers of Glucose and how they affect Cellulose and Starch
Alpha glucose: OH groups of both carbons 1 and 2 face the same direction
Beta glucose: OH groups of carbons 1 and 2 face opposite directions
*Carbons in glucose rings are numbered from first carbon after oxygen moving clockwise.
Cellulose is made of beta glucose, allowing it to run straight
Starch is made of alpha glucose, making it helical
what is Chitin
Chitin: exoskeleton of arthropods, cell walls of fungi. Beta glucose, linkage by 1-4 carbons, with N attachment
-NH-C=O -CH3
What are Proteins
Enzymes, structure, storage, cell signaling
Made of amino acids linked to peptide bonds, unbranched
H2N-HCR-COOH (R = side chain)
Amino group: H-N-H, N2H
Acid group: C=O -OH, COOH
20 amino acids are used for protein synthesis
which Amino acids have non polar side chains
- Glycine
- Alanine
- Valine
- Leucine
- Isoleucine
- Methionine
- Phenylalanine
- Tryptophan
- Proline
What amino acids have a polar side group
- Serine
- Threonine
- Crysteine
- Tyrosine
- Asparagine
- Glutamine
Which amino acids have an ionically charged side group
- Aspartic acid
- Glutamic acid
- Lysine
- Arginine
- Histidine
describe polypeptides
never branched on linear
Connected by peptide bond: OH from COOH group, and H from NH2 group become water, and a bond is formed between carbon and nitrogen
Amino acid end = N-terminus
Carboxyl end = C terminus
describe the four parts of protein structure
- primary structure: chain of different Amino acids
- Secondary structure: hydrogen bonds form the strand into an alpha helix or beta pleated sheet
- Tertiary structure: H-bonds, disulphide brides, ionic bonds, hydrophobic interactions, or van der waals interactions further mold the protein into a complex 3D shape
- Quaternary Structure: alpha and beta subunits make up a bigger structure from multiple (often 4) polypeptides
what is protein denaturing
Changing conditions can cause a protein to lose its shape becoming denatured. This alters or prevents the function of the protein
High temperatures can cause this, including fevers
Some proteins can renature, but not all
What group is Glycine
Non polar
What group is Alanine
Non polar
What group is Valine
Non polar
What group is Leucine
Non polar
What group is ISO leucine
Non polar
What group is Methionine
Non pilar
What group is Phenyl alanine
Non polar
What group is Tryptophan
Non polar
What group is Proline
Non polar
What group is Serine
Polar
What group is Threonine
Polar
What group is Crysteine
Polar
What group is Tyrosine
Polar
What group is Asparagine
Polar
What group is Glutamine
Polar
What group is Aspartic acid
Electrically charged
What group is Glutamic acid
Electrically charged
What group is Lysine
Electrically charged
What group is Arginine
Electrically charged
What group is Histidine
Electrically charged
what does Nucleic Acid do
Nucleic Acids store, transmit, and express hereditary information.
what is the pathway from DNA to proteins
DNA undergoes transcription leading to the synthesis of mRNA.
The mRNA moves into the cytoplasm and to a ribosome.
The ribosome performs translation to synthesize proteins.
what are Nucleotidesqa`
Nucleotides are made from a nitrogenous base + a 5 carbon sugar + a phosphate group
They form a chain by phosphodiester linkages between the phosphate and sugars. This makes the back bone of DNA, RNA, etc
The order of bases in the chain determines the amino acid sequence in a protein.
what are Pyrimidines
Pyrimidines are a 6 carbon ring
Cytosine (C)
Thymine (T, which is in DNA)
Uracil (U, which is in RNA)
how do bases match up in DNA
A pyrimidine always matches with a purine (so the space between each back bone is always roughly the same)
Adenine matches with Thymine or Uracil
Cytosine matches with Guanine
What are Purines
Purines are a 6 carbon ring along with a 5 carbon ring
Adenine (A)
Guanine (G)
what are the sugars in DNA/RNA
Nucleotides include a 5 carbon sugar
In DNA this is Deoxyribose
In RNA this is Ribose
what is one reason DNA is more stable
DNA is way more stable due to the Hydrogen group instead of the -OH group. RNA degrades very easily since they have the extra OH group.
RNA only needs to last for a short time in the cell, while DNA stays for a long time.
describe the structure of DNA vs RNA
DNA runs anti parallel, one side is upside down (5’ C down), and the other is right side up (5’ C up)
RNA is only single sided, but can fold back on itself and form hydrogen bonds where the complimentary bases line up
G and C join with 3 hydrogen bonds. While A, T, and U join with 2 hydrogen bonds.
DNA has deoxyribose, Thymine, and is double stranded
RNA has ribose, uracil, and is single stranded
DNA can bind with proteins (enzymes) which help during DNA replication
describe the history of Genomics
1953: Structure of DNA was uncovered
1970: DNA was sequenced
2001: First draft of human genome was sequenced.
DNA sequences got cheaper and faster
→ lots of application in evolution, paleontology, medical science, conservative biology, and species interactions.
Genomics is working with all the genes in a genome.
While proteomics looks at the proteins and their sequence, it is harder than genomics are currently.
