Chapters 1-5 Flashcards
Systems biology
Exploration of a biological system by analyzing the interactions
Controlled experiment
Experiment that compares an experimental group to a controlled group
Trace element
Required by an organism in minute quantities
ex: boron, copper, zinc
Difference between hypotheses and theories
Hypothesis are narrow
Theories are broad
Emergent properties vs. Reductionism
Emergent: small - large
Reduce: large - small
In a water molecule, electrons…
Oxygen is more electronegative than hydrogen, so the electrons of the covalent bonds spend more time closer to oxygen to hydrogen, creating polar covalent bonds
Polar molecule
Overall charge is unevenly distributed
Nonpolar molecule
Overall charge is evenly distributed
Oxygen
Partially negative
Hydrogen
Partially positive
Total thermal energy
Depends on the matter’s volume
Ex: swimming pool as more thermal energy than a hot teapot
Specific heat
Amount of heat that must be lost or absorbed for 1 g of that substance to change its temperature by 1°C
Polar covalent bonds
Electrons of the polar covalent bond spend more time near the oxygen than the hydrogen
Polarity allows water molecules to form hydrogen bonds with each other
Water’s pH is 7 (neutral) because
Concentrations of H and OH are equal
pH greater than 7
Base
pH less than 7
Acid
For water to vaporize, which bonds have to be broken?
Hydrogen bonds
In a single water molecule, two hydrogen atoms are bonded to a single oxygen atom by
Polar covalent bonds
How many hydrogen bonds can a single water molecule form?
4
What is hydrogen bonding?
The slightly positive H of one molecule is attracted to the slightly negative O of a nearby molecule
Cohesion
Particles of the same substance stick together
Adhesion
One substance clings to another
What does water’s High specific heat mean?
It means it takes a lot of heat for water to get hot
How does hydrogen bonding contribute to water’s high specific heat?
The heat is used to disrupt hydrogen bonds before the water molecules can begin moving faster
Why does ice float?
Because water expands and becomes less dense as a solid than as a liquid
Solvent
The substance by dissolving
Solution
Homogenous mixture of two or more substances
Solute
Substance that is dissolved
Why is water a good solvent?
Water created a hydrogen shell - sphere of water molecules around each dissolved ion
Molarity
Number of moles of solute per liter of solution
Acid
A substance that increases the hydrogen ion concentration of a solution
Base
A substance that decreases the hydrogen ion concentration of a solution
How many bonds can carbon form? How many valence electrons does carbon have? What type of bonds does carbon form?
4
Single or double covalent
How can carbon skeletons differ?
Length, straight, branched, arranged in close rings, doubles bonds that vary in number and location, and other atoms can be bonded
What is a hydrocarbon?
Organic molecules consisting of only hydrogen and carbon
Nonpolar
Extremely hydroPHOBIC
Isomer
Compounds that have the same # of atoms in elements, but different structures, causing different functions
Isotope
Same atom with different number of neutrons
Functional group
Chemical groups that are directly involved in chemical reactions
The 7 groups are across the board and can be on any carbon skeleton
Hydroxyl (-OH)
Polar, due to electronegative oxygen, forms hydrogen bonds with water
Carbonyl (>C=O)
Double bond w/ O
Sugars w/ ketone groups are called ketoses; those with aldehydes are called aldehydes
Carboxyl (-COOH)
Acts as an ACID
More polar, sticks to H2O because H2O is polar!
Like likes like!
Amino Group (-NH2)
Acts as a BASE
Takes out hydrogen from solution
Sulfhydryl (-SH or HS-)
Sulfur will always be attached
Two -SH groups can react, forming a “cross-link” that helps stabilize protein structure
Phosphate (-OPO3 2-)
Contributes negative charge
When attached, confers on a molecule the ability to react w/ water, releasing energy
ATP
Methyl Group (-CH3)
Affects the expression of genes
Affects the shape and function of sex hormones
Carbon mainly forms…
Covalent bonds
Polar and nonpolar
Hydrocarbons are…
Extremely hydrophobic
Saturated
Holding as much as it can
Solid at room temperature
Unsaturated
Means that there’s a double bond because it’s not holding as much as it can
Liquid at room temperature
“Big players”
CHON
Enzyme
Specialized macromolecules that speed up chemical reactions
Carbohydrates
Includes sugars and polymers of sugars
Simplest carbs. are monosaccharides
Glucose is a
MONOSACCHARIDE
Disaccharide
Two monomers joined by a glycosidic linkage, a covalent bond formed between 2 monomers
Formed when a dehydration reaction joins two monosaccharides
Lipids are insoluble!
Mix poorly, if at all, with water
HydroPHOBIC because they consist mostly of hydrocarbons, which form nonpolar covalent bonds
Cell membranes, fats, energy storage
Lipids are made of
Fatty acids
Carbohydrates are made of
Monosaccharides
Nucleic acids are made of
Nucleotides
Proteins are made of
Amino acids
Purines
Adenine
Guanine
5 membered ring
Small word big structure (double rings)
Pyrimidines
Cytosine Thymine (in DNA) Uracil (in RNA) U replaced T in RNA 6 membered ring Big word, small structure (single rings)
Sugars in DNA & RNA
Deoxyribose (DNA)
Ribose (RNA)
Nucleotides use which type of sugar?
Pentose
How many different transfer RNAs are there?
20, because there are 20 different types of amino acids
Genome
All genes that you are made up of
Denature
Disrupting protein structure
Chaperonins
Protein molecules that assist the proper folding of other proteins
Types of proteins
Enzymatic Defensive Storage Transport Hormonal Receptor Contractile + Motor Structural
Enzymatic (catalyst)
Selective acceleration of chemical reactions
Ex: digestive enzymes catalyst the hydrolysis of bonds in food molecules
Defensive
Protection against disease
Ex: Antibodies inactive and help destroy viruses and bacteria
Storage
Storage of amino acids
Ex: casein, protein of milk, is the main source of amino acids
Transport
Transport of substances across the membrane
Ex: hemoglobin transports oxygen
Hormonal
Coordination of an organism’s activities
Receptor
Response of cell to chemical
Contractile and motor
Movement
Structural
Support
All enzymes are __ but not all proteins are __
Catalytic
Enzymes
Polypeptide
polymer of amino acids
Protein
Molecule that consists of on or more polypeptides
Carbohydrates include
Monosaccharides (monomer)
Polysaccharide (polymer)
Disaccharide
Saturated fats
Only single covalent bonds
Unsaturated fats
Double or triple bonds
Cis
Trans
Fish have
Unsaturated has kinks: helps when it gets cold, because they want to go together and the molecules slow down, but the kinks help them stay apart
Phospholipids
Head is polar (hydrophilic)
Tail is nonpolar (hydrophobic)
Protein is
Chains of amino acids linked by peptide bonds
Primary structure
Specific arrangement of amino acids
Amino acids consist of
An amino group Carboxyl group A hydrogen An R group Central Carbon (NCC BACKBONE)
There are 20 different monomers for amino acids
5 different monomers for nucleic acids
Difference between deoxyribose and ribose
Deoxyribose lacks an oxygen
DEOXYribose
Transfer RNA
Brings amino acids to the ribosome during the synthesis of a protein
Peptide bond
A covalent bond joining amino acids together to form a polypeptide
Fats have 2 kinds of small molecules
Glycerol + fatty acids
Nonpolar C-H bonds in hydrocarbon chains of fatty acids are the reason fats are hydroPHOBIC
Unsaturated have what type of double bonds?
Cis double bonds
(“X” is on both sides)
Nearly all the bonds in fatty acids
Trans double bonds
“X” is on different sides
Peptide bond is between
Amino acids
Dehydration reaction
Removes one water molecule + joins two monomers
Hydrolysis
Adds a water molecule and breaks apart polymers
Hydrophobic molecules are
Uncharged, repel water
Hydrophilic molecules are
Slightly charged and attracted to the slightly charged of water
Glycogen
Storage polysaccharide in animals
Stored in:
Liver and muscle cells
Starch
Storage polysaccharide of plant, consists entirely of glucose monomers
What do maltose, sucrose, and lactose have in common?
All disaccharides
Cellulose
Polysaccharide, major component of the rough wall of plant cells
Chitin
Structural polysaccharide (exoskeleton in bugs)
Cis double bond causes
Bending/kinks
The type of monomer is most important in
Lipids//diversity
Fats (lipids)
Energy storage
Adipose tissue
Cushions vital organs + insulates body
There is no phosphorous in
Proteins
Amino acids only differ in their
R groups
Secondary structure
Hydrogen bonding
Alpha helix-where it twists
B pleated sheet-where it folds
Tertiary structure
Polar forces, ionic bonds, covalent bonds Interactions of R groups Hydrophobic interactions Van Der Waals interactions Disulfide bridge
Quaternary structure
Chains interacting with each other
Denaturing
Disrupts protein structure
Chaperonins
Protein molecules that assist the proper folding of other proteins
DNA -> RNA
Transcription
RNA -> Protein
Translation
Peptides are
Chains of amino acids
What is ATP’s importance in the cell?
ATP stores the potential to react with water
Thereby removing a phosphate group and releasing energy for cellular processes
CO2 is considered
Inorganic because organic carbon always has a hydrogen atom covalently attached to it
Hydrogen bond
Attraction between a hydrogen and an electronegative atom
Van der Waals interactions
Individually weak and occur only when atoms and molecules are very close together
Ever changing regions of positive and negative charge that enable all atoms and molecules to stick to one another
Chemical equilibrium
Reached when the forward and reverse reaction rates are equal
Van der Waals interactions occur between
Positive and negative regions of molecules
Mass number
Proteins and neutrons
Atomic mass
Protons
Valence shell
Outer shell
Covalent bonds
Electrons are shared
Cohesion
Hydrogen bonds hold the substance together
Adhesion
Clinging of one substance to another
Glycosidic linkage
Covalent bonds that links monosaccharides
Peptide bond links
Amino acids (covalent bond)
Water’s high specific heat means what
It takes a lot of heat for water to get hot
Specific heat
The amount of heat that must be absorbed or lost for 1g of that substance to change its temperature by 1°C
How does water’s high specific heat contribute to the moderation of temperature?
The specific heat stabilizes ocean temperatures, keeps temperature fluctuations on earth within the limits that permit life, and organisms are able to resist changes in their own temperature
Polymer
Long molecule consisting of many similar or identical building blocks linked by covalent bonds
Monomer
The building blocks that are repeated, smaller molecules
Large macromolecules fall into 4 main classes
Carbohydrates
Lipids
Proteins
Nucleic acids
Macromolecules are
Huge molecules that are polymers
Monomers are connected in what type of reaction?
Dehydration reaction - two molecules covalently bonded to each other, with the loss of a water molecule
Polymers are converted to monomers in what type of reaction?
Hydrolysis - reverse of the dehydration reaction. The bond between monomers is broken by the addition of a water molecule
Amino acid
Has an amino group and a carbonyl group
Peptide bond is created by
Dehydration synthesis
Disulfide bridges
Covalent bonds
Structural isomers
Differ in covalent arrangements
Cis-trans isomer
Have covalent bonds to same atoms, but these atoms differ in their arrangements
Enantiomers
Mirror images