Biochemistry Flashcards
Atomic Number
the number of protons and electrons
Atomic Mass
weight of protons and neutrons
Oxidization Number
the number of bonds valence shell will make
Electronegativity
atom’s ability to attract electron in bond
Ionic Bonding
Intramolecular force - transfer of electrons, forms a crystal lattice
Covalent Bonding
Intermolecular force - both nuclei pull on atom, sharing of electrons - since electrons are in constant motion there are temporary dipoles
Polar Bonds
Intermolecular force - weak partial charges on molecule - due to electronegativity difference - electrons are unequally shares
Hydrogen Bonding
Strongest Intermolecular force - weak connections between partial charges
Hydrophilic
water loving, polar
Hydrophobic
afraid of water, non polar
Acid
high concentration of H+ ions, proton donor (pH less than 7)
Base
high concentration of OH- ions, proton acceptor (pH greater than 7)
Buffers
- acts as a proton donor as solution becomes more basic - acts as a proton acceptor as solution becomes more acidic - moderates change in pH
Carbonic acid
A common buffer - carbonic acid (basic) when solution is more acidic - H+ and bicarbonate (acidic) when solution is more basic
Special Properties of Water
- Solvent (medium for chemical reactions)
- Adhesion (for non polar) / Cohesion (for polar)
- Less dense at 0 than at
- less dense as solid 4. High Specific Heat
Mole
unit of amount of substance
Molar Mass
mass of given substance/mol
Molarity
mol/L…molar concentration
Hypertonic
solution with a higher concentration of solute
Isotonic
maintained balance solution
Hypotonic
solution with a lower concentration of solute
Condensation synthesis
is a chemical reaction in which two molecules or moieties, often functional groups, combine to form a larger molecule, together with the loss of a small molecule. (forms water with OH and H from each molecule)
Hydrolysis
reaction that breaks down polymers
Skeletal formula
representation of molecules bonding and geometry
Structural formula
shows how atoms of molecule are chemically bonded
Molecular formula
shows number of each type of atom in the compound
Name: Hydroxyl
Shortform: OH
Molecule Type: Alcohol
Ending: -ol
Properties/Polarity: polar and soluble
Found in: carbohydrates, lipids, proteins, and nucleic acids
Name: Carboxyl
Shortform: COOH or HOOC
Molecule Type: Organic Acid
Ending: -ic acid, -ate
Properties/Polarity: weakly ionic, acidic, soluble
Found in: proteins and lipids
Name: Ketone Carbonyl
Shortform: CO
Molecule Type: Ketone
Ending: -one
Properties/Polarity: weakly polar, somewhat soluble, strong smelling
Found in: carbohydrates and nucleic acids
Name: Aldehyde Carbonyl
Shortform: CHO
Molecule Type: Aldehyde
Ending: -al
Properties/Polarity: weakly polar, somewhat soluble, strong smelling
Found in: carbohydrates and nucleic acids
Name: Amino
Shortform: NH2 or NH or N
Molecule Type: amine, secondary amine, tertiary amine
Ending: -ine
Properties/Polarity: basic, soluble
Found in: proteins and nucleic acids
Name: Sulfhydryl
Shortform: SH
Molecule Type: thiol
Ending: thio
Properties/Polarity: non polar, not soluble, smelly
Found in: proteins
Name: Phosphate
Shortform: P
Molecule Type: phosphate
Ending: phospho
Properties/Polarity: strongly ionic, very soluble, acidic
Found in: nucleic acids
monomer
simple unit molecules from which lareger molecules are built
dimer
2 monomers covalently bonded
polymer
many molecules/units
oligiomer
3-20 monomer chain
What makes polymers?
Carbohydrates, Proteins and Nucleic Acids. Lipids do not make polymers but instead glycerides, because they are non polar.
Carbohydrates
- made up of CHO in a 1:2:1 ratio
- energy storage molecule (short term)
Monosaccharides
- single sugar, relativley small to transport things
- small structure is more soluble as long as there is polarity
- only functional group present is OH
Sterioisomer
have same molecular formula and sequence of bonds, different 3D
Structural Isomer
same chemical formula, different structure
Glucose
aldose
Fructose
ketose
Alpha isomer
when hydroxyl on C#1 faces down
Beta isomer
when hydroxyl on C#1 faces up
Disaccharides
- 2 sugars
- store twice as much energy / moleculer
- less osmotic pressure because concentration is reduced by 1/2, pass through membrane easier
- exisits in alpha isomers
Examples of Disaccharides
Maltose (glucose+glucose)
Sucrose (glucose+fructose)
Lactose (glucose+galactose)
Polysaccharides
- less water can react with chain making it more insoluble
- long term storage
Starches
alpha polysaccharides
Beta Glucose
forms linear chains with the OH and methyl side, can stack closer in this shape (ex. Cellulose)
Alpha Glucose
Alpha Glucose forms chains of heleces held together by hydrogen bonds (ex. amylose, amylopectin, glycogen)
Glycosidic Bond
Chitin
- modified form of beta glucose
- replaces hydrocyl with more polar ‘R’ group
- structurally strong
- chemical reactions stronger because more polar
Lipids
- majority of structure is nonpolar and is hydrophobic
- more energy by less mass
Results of Hydrophobic Nature
- Waterproofing
- Thermal Insulator
- Electrical Insulator
Structure of Lipids
- triglycerides consist of glycerol condensed with 3 fatty acids
Fatty Acid
hydrocarbon chain with carboxyl on one end
Ester bond: formed when hydroxyl on glycerl condense with cabroxyls
(bond between glycerol and carboxyl)
Saturated
all single bonds (solid state- ex. butter)
Unsaturated
double bonds (liquid state- ex. oil)
Monounsaturated
1 double bond
Polyunsaturated
2 or more double bonds
Oleic Acid
most abundant fatty acid on olive oil, kinked shape, less dense
Hydrogenation
adding hydrogens to break double bonds
Phospholipids
- modified triglyceride by replacing fatty acid with phosphate, Na or K
- polar funcitonal group on top
- amphiphilic
Amphiphilic
one end hydrophobic one end hydrophilic
Waxes
- complex organic ester
- long chain hydroxyl +fatty acid (OH on end )
Steroids
- communication molecule
- non polar, derived from cholosterol
Membranes
- slectively permeable membrane made by phospholipids
- amphiphilic nature allows it to form bilayers
- polar face out, non polar face in
Fluid Mosaic Model
-membranes are composed of a Phospholipid Bilayer with various protein molecules floating around within it. The ‘Fluid’ part represents how some parts of the membrane can move around freely, if they are not attached to other parts of the cell.
Phospholipids (membranes)
- impermeable to large soluble and polar molecules
Transmembrane Proteins
(carriers, channels, and receptors)
- transmission of information into cell
Interior Proteins
- determine shape of cells as well as acting as anchor site
Glycoproteins
- self recognition, major histocompatibility complex, made with oligiosaccharides
Glycolipids
- tissue recognition, made with oligiosaccharides
Cholesterol
- membrane fluidity, increase in cholesterol decreases membrane fluidity
Types of membrane transport
- Passive transport - does not require energy
- Active transport - requires energy
Types of passive transport
- Passive diffusion
- Facilitated diffusion
- Osmosis
Passive diffusion
- natural process for nonpolar molecules pass across membrane
- net movement from an area of high concentration to low concentration
- based on random and molecular motion of particles
Facilitated diffusion
- a protein facilitates/helps atom get through channel
- Carrier or channel proteins
- larger or polar molecules use this
- net movement from an area of high concentration to low concentration
Osmosis
- low concentration and high water potential (pressure)
- movement of water from hypotonic solution into a cell
Types of active transport
- protein carrier
- endocytosis
- exocytosis
Protein carrier
- transfer of molecules against concentration gradient
- requires energy from ATP
Endocytosis
Particles being engulfed into membrane
Exocytosis
Particles being released by membrane
Peptides and proteins
- contain amino and carboxyl group
- R group made of CHNOS
Monomer of protein (amino acid)
Peptide
Polymer of amino acid
Polypeptide chains
R Differ in
- size
- shape
- polarity
- ionization (acidic and basic)
- special editions (funcitonal groups, sulfur)
Primary structure
- sequence of amino acids, determined by DNA
Secondary structure
- involve the bond angles that are produced by particular sequences of amino acids
- twisting of the chain due to R-groups and C=O and NH groups
- alpha helix and beta pleated sheet held together by hydrogen bonds
Tertiary folding
- the globule folding of the molecule as a result of attractions and repulsion between different parts of the chain based on electrical charges, attraction to water, size and shape restrictions
Structures 1-4
1-3 found in all peptides
Quaternary structure
- the folding together of multiple chains to produce a more complex protein
Nucleic acids
- Carrie coded information about primary structure
- linear polymers
Monomers in nucleic acid
nucleotide
What is a nucleotide made of?
- a phosphate group, pentose monosaccharide, and a purine or pyrimidine nitrogen base
Purine
- double ring structure
- adenine and guanine
Pyrimidine
- single ring structure
- cytosine, thymine and uracil
RNA
- ribose sugar (OH at C#2)
- adenine, guanine, cytosine, and uracil
- single-stranded polymer
DNA
- deoxyribose sugar (H at C#2)
- adenine, guanine, cytosine, and thymine
- double-stranded polymer
Peptide bond
Bonding of 2 nucleotides happens between C#__ and C#__
Bonding of 2 nucleotides happens between C#3 and C#5
What types of purine and pyrimidine match up?
AT GC
AU GC
Phosphodiester linkage
What are enzymes?
- Proteins that act as catalysts within living cells
- Can facilitate same chemical reactions over and over again
- Lower activation energy
What are enzymes made of?
composed of one or more long chains of interconnected amino acids (polypeptides)
What are the two models of enzyme action?
Lock and Key
The substrate simply fits into the active site to form a reaction intermediate.
Induced Fit
when the active site on the enzymes makes contact with the proper substrate, the enzyme molds itself to the shape of the molecule
What variables can affect enzyme action (rate of reaction)?/ What is the effect of each variable?
- pH (H+ and OH- ions)
- When you change pH to more acidic greater concentration of H+ ions there would be ionic bonds with the amino or change O to carboxyl group, will repel the amino acid and bonds the folded enzyme will unravel, changing the shape so the substrate will not fit in it.
- optimum point is balance of OH- and H+ that allow enzyme to remain/ maintain perfect shape, stabilize
more acidic then more unfolded called denaturing
more basic then more unfolding denaturing
- OH- will attract amino group but does not attract O+ so no carboxyl, depends on how many OH, concentration dependent
2. Temperature - As temp increases the rate of reaction increases because more frequent collisions
- enzyme has flexibility to bond that is more rigid at low temp and very high at high temp
- at optimal temp range, there is the most collisions being able to reduce fit without compromising the shape
- the rate goes down afterwards because you can break H bonds (which hold up tertiary structure) and the enzyme will unfold
3. Concentration of substrates - at a certain point the speed in which a reaction occurs the rate does not change
- if you have more substrates than enzymes, the number of bonds is limited, called saturation
Concentration of enzyme
- More enzymes more probability of binding
Salt concentration (same as why pH affects)
- Salt is ionic compound so one +ve and –ve ion
Regulation (promote or inhibit certain chemical reactions)
Explain one way that an enzyme can be regulated.
- An inhibitor may bind to an enzyme and block binding of the substrate, for example, by attaching to the active site. This is called competitive inhibition, because the inhibitor “competes” with the substrate for the enzyme.
- In noncompetitive inhibition, the inhibitor doesn’t block the substrate from binding to the active site. Instead, it attaches at another site and blocks the enzyme from doing its job. This inhibition is said to be “noncompetitive” because the inhibitor and substrate can both be bound at the same time.
- Cooperativity: the substrate itself can serve as an allosteric activator (bind to locations on an enzyme other than the active site, causing an increase in the function of the active site): when it binds to one active site, the activity of the other active sites goes up.
- Feedback inhibition works by deactivating an enzyme using the product of the reaction the enzyme catalyzes. Enzymes bind to molecules with active sites that are specifically designed to fit with the molecule undergoing the reaction. These enzymes have a second active site for the reaction product to bind to. This causes the enzyme to spatially re-arrange so it can no longer bind to the initial reagent and the reaction stops. Many mechanisms, such as bile acid synthesis in the liver and cellular respiration, use feedback inhibition on a regular basis.
- A zymogen requires a biochemical change (such as a hydrolysis reaction revealing the active site, or changing the configuration to reveal the active site) for it to become an active enzyme (converted into an enzyme when activated by another enzyme). … Enzymes like pepsin are created in the form of pepsinogen, an inactive zymogen.
Explain the reasons why carbon is an ideal element for life
- forms 4 bonds
- a large variety
- large stable molecules can form because of a decreased potential energy
- low energy levels, greater ENC
- small input of energy to break the bonds
Compare lipids and carbohydrates as energy sources
- lipids more energy/mass, more long term storage
- carbs more short term storage
Compare and contrast passive and active membrane transport
- both allow cell to maintian homeostasis
- both use ion channels to move ions across
- active requires energy, passive doesn’t
- passive moves molecules with concentration gradient, active moves against concentration gradient
Explain how cells transport bulk materials across the cell membrane.
endo anc exocytosis
