Module 2: Chemistry And Biochemistry Flashcards
3 types of mixtures
Solutions, colloid, suspensions
Solutions
Solute particles are very tiny, do not settle out or scatter light. Tends to not have any color to it.
e.g., mineral water
Colloid
Solute particles are larger than in a solution and scatter light; do not settle out (proteins). Do have color to it.
e.g., jello-o
Suspension
Solute particles are very large, settle out, and may scatter light e.g. Blood
What are the ways we can note the concentrations of a solution?
% (D5 = 5% dextrose solution) *IV fluid
mg/dL or mg/L
molarity (mmol/L)
1 mol =
of grams of an element/compound equal to atomic weight of that substance
– this gives equal number of particles in the solution
avogadro’s number
Molarity
1 mole dissolved in enough solvent to give IL volume
Molarity (M) of a solution is expressed in
Moles of solute/liters of solution
Molality (m) is expressed in
Moles of solute I mass of solvent (kg)
Molality
I mole dissolved in IL of solvent
Biological solutions are - solutions
Molal
Bonding occurs between
Electrons in the valence shell
How many electrons do most elements want
8
How many elections does hydrogen want
2
How can we make a complete shell
In order to make a complete shell, we can either lose extra electrons to go down to the next shell, or we can add electrons to the outer shell to make it complete
Types of chemical bonds
Ionic
–Anion vs cation
–Salts
Covalent
–Nonpolar
–Polar
–Hydrogen bonds
What happens in ionic bonding
Electrons are transferred from one element to another
Causes them to have a charge (either +/-) depending if they lost or gained an electron
What happens in covalent bonding
Electrons are shared
What happens in covalent bonding
Electrons are shared
Example of ionic bond
Sodium Chloride (NaCl)
Sodium has 1 extra electron in its outer shell, so it loses it and drops it down to a full outer shell at the next level
Chlorine has 7 shell electrons in its outer shell, it wants to gain another electron to make its outer shell 8 and complete
Sodium becomes + chlorine -
Example of ionic bond
Sodium Chloride (NaCl)
Sodium has 1 extra electron in its outer shell, so it loses it and drops it down to a full outer shell at the next level
Chlorine has 7 shell electrons in its outer shell, it wants to gain another electron to make its outer shell 8 and complete
Sodium becomes + chlorine -
Example of a covalent bond
Methane CH4
Nonpolar covalent bonds have_______sharing
Equal e.g. Co2
Polar covalent bonds have______ sharing
Unequal
Nonpolar vs. Polar examples
Nonpolar: CO2, methane
Polar: water, ammonia
Polar things like to group together, non polar things like to group together… Why does this cause issues?
Causes issues when it comes to things in the bloodstream
This is because polar molecules tend to form slight bonds between each other
What does hydrogen bonding do in H20?
It helps give water its surface tension, it also helps form grouping.
Polar vs nonpolar molecules in blood
Nonpolar molecules e.g., fats have to find themselves in a polar environment with water.
***hydrophobic
How to more non polar molecules inthe bloodstream
Carrier proteins
or
Fat soluble (sequester the non polar things away from the water)
Think of oil and vinegar salad dressing
Types of chemical reactions
Synthesis/combination
(anabolic)
endergonic (uses energy)
Decomposition (catabolic)
Exergonic (releases energy)
Exchange/displacement
(combined)
Example of synthesis (anabolic) reaction
Dehydration synthesis
Ex ample of decomposition (catabolic) reaction
Hydrolysis
Example of exchange/displacement reaction
Oxidation-reduction (electron-donor acceptor)
Synthesis (combination) reaction
A reaction in which two or more substances combine to form a new compound
Decomposition reaction
A reaction in which a single compound breaks down to form two or more simpler substances
Exchange (displacement) reaction
Bonds are both made and broken
Rate of reactions is affected by
Body temperature
Concentration
Reactant size
Catalysts (ex: enzymes)
Acids
Acids release H+
e.g., HCl (stomach acid), H2CO3 (found in bloodstream)
Bases
Bases absorb H+
e.g.,HCO3 , NH3 (ammonia)
pH scale
Measurement of H+
concentration in a solution (how acidic or basic a solution is)
Solutions with lower concentrations of hydrogen ions have ______ pHs and are considered _______
Higher, basic
Solutions with higher concentrations of hydrogen ions have ______ pHs and are considered _______
Lower, acidic
Solutions with higher concentrations of hydrogen ions have ______ pHs and are considered _______
Lower, acidic
Negative logarithmic scale
Negative = lower numbers = higher
concentration
Logarithmic = each unit =10-fold change
(pH 6 is 10X higher concentration than pH
7)
Arterial pH
7.35- 7.45
Denaturation
Changes in pH can cause
disruption in protein
structure by disrupting
hydrogen bonding
What happens W denaturation
Denature hydrogen bonding, so it can denature our proteins and render them nonfunctional. Causing our enzymes, hormones, etc to stop working.
Eventually will die if too basic or too acidic.
Buffers
prevent significant/rapid pH changes
a buffer will absorb the extra acid and neutralize it. if you do not have enough acid, that same compound can dissociate and form acid.
What serves as buffers intracellularly?
phosphates, hemoglobins, other proteins. resist pH changes inside the cells.
What serves as buffers extracellularly
HCO3, plasma
What server as a buffer for both Intra/extracellular
Amino acids
What server as a buffer for both Intra/extracellular
Amino acids
Carbohydrates function
Energy source (it’s all about those hydrogens) ***the hydrogen are used by the mitochondria to flow through ATP synthase enzyme and form ATP. All about getting the hydrogens off of the carbohydrates and moving them over to the mitochondria.
Cell-cell interactions, on surface of cell membrane
-Glycosylated (proteins with sugars attached) molecules on cell surfaces
-form signaling molecules that help signal to other cells
Structure of carbohydrates
C,H,O in a 1:2:1 ratio
(CH20)n
“Hydrated carbon” (water +carbon)
monosaccharides
Monomers of carbohydrates (5 or 6 sided ring of carbon with an oxygen in the last position)
hexose or pentose sugars
simple sugars (glucose, fructose, galactose, deoxyribose, ribose)
Disaccharides
Consist of two linked monosaccharides
Sucrose, maltose, lactose
Polysaccharides
Long chains (polymers) of linked monosaccharides
Glycogen
Carbohydrates are added to many molecules for ____
Cell communication
Carbohydrates are added to the surface of cells for recognition of ___
Self
Outer cell membrane ofcarbohydrates
Glycocalyx
Glycoplipids, glycophingolipids, glycoproteins
Glycocalyx
sticky/sugary coating surrounding the cell made up of carbohydrate proteins and sugars
Glyco means
Sugar
How is it indicated that disruption of the glycocalyx is involved in disease processes?
The disruption of this in chronic inflammation can make it easier for viruses to invade cells, due to the glycocalyx being disrupted.
How is it indicated that disruption of the glycocalyx is involved in disease processes?
The disruption of this in chronic inflammation can make it easier for viruses to invade cells, due to the glycocalyx being disrupted.
What are lipids
Lipids are macromolecules made of fatty acid monomers
Lipids
Longer chains/rings of hydrocarbons (ch)
nonpolar
Main types of lipids
Triglycerides
Phospholipids
Steroids and waxes
Lipids are
Hydrophobic, non-polar
Functions of lipids (triglycerides)
Long term energy storage
Protection of organs
Insulation
Functions of lipids (phospholipids, steroids)
Cell membrane
Functions of lipids (steroids)
Nonpolar hormones
Functions of lipids (glycolipids, eicosanoids)
Cell-cell interactions
Functions of lipids (lipoproteins)
Transport of nonpolar substances
Triglycerides
1 glycerol + 3 fatty acids
Types of triglycerides
Saturated and unsaturated
Saturated triglycerides
All singe bonds
solid (i.e. butter)
Very straight chain, easier to pack molecules close together.
Unsaturated triglyceride
One or more double bonds
liquid (i.e. oil)
Puts a kink in the chains, harder to pack molecules together
What are omega-3 and omega-6 fats?
Omega-n refers to the number (n) of the carbon atom with the first double bond from the methyl end
What are omega-3 and omega-6 fatty important with?
Cardiovascular health
Can help prevent acrosclerosis, help regulate level of triglycerides in bloodstream
e.g., prescriptions
Phospholipids
1 glycerol + 2 fatty acids + 1 phosphate
One polar portion and one non polar portion
What happens to phospholipids in a polar environment?
In a polar environment, phospholipids line up and form a semi-permeable membrane. This is how we form the cell membranes.
Membranes (phospholipids)
Outer cell membrane
Inner organelle membranes
Phospholipid structure
Hydrophilic head and hydrophobic tail (helps form a non polar membrane)
What happens to phospholipids in a watery environment?
In a watery environment, phospholipids automatically line up with their heads facing the water on either side, and their hydrophobic tails “hiding” away from the water
Steroids
Derived from cholesterol (4 rings)
Non polar
Need transport in bloodstream (hormones)
How are steroid hormones formed
Different steroids have different groups attached to the 4-ring backbone.
***cholesterol is the basis for all steroids formed in the body
Ex of steroid hormones
Testosterone, estrogen, progesterone, cortisol, aldosterone, vitamin D
Steroid uses
Hormones
Membrane structure (esp cholesterol. embedded in bipolar layer to give fluidity to cell membrane)
Bile salts (made by liver, stored in gallbladder, released into small intestine. takes fats and foods we eat and sequester it into lipid droplets. makes it easier to digest and transport in the body)
Vitamins
Eicosanoids
==Derived from arachidonic acid
e.g., prostaglandins
==Involved in inflammation, tissue damage response
What do prostaglandin do
Mediates inflammation
A lot of the hormones we find in the body are:
Non polar steroid hormones
So they require some sort of transport in the blood, but then move very easily through the membrane into the cells. Therefore can affect all cells in the body.
Proteins are
Chains of AA
Proteins are
Chains of AA
Basic AA #?
20
AA structure
A central carbon, a hydrogen, carboxyl group, amino group, and r group
What causes amino acids to be different?
R group
What are post - translational changes
Addition of chemical groups
Addition of larger molecules
Changes of amino acid structure
Post translational changes info
Amino acids can undergo post-translational changes. These changes occur on the R-group and form a completely new amino acid.
***
Arginine is an example, sometimes changes into citrulline
Primary structure
The sequence of amino acids forms the polypeptide chain. R groups are on opposite sides of each other.
Secondary structure
The primary chain forms spirals (alpha-helices) and sheets (beta-sheets).
Secondary structure
The primary chain forms spirals (alpha-helices) and sheets (beta-sheets).
Tertiary structure
Superimposed on secondary structure, alpha helices and/or beta sheets are folded up to form a compact globular molecule held together by intermolecular bonds.
a three-dimensional combination of α-helices and β-sheets
Tertiary structure
Superimposed on secondary structure, alpha helices and/or beta sheets are folded up to form a compact globular molecule held together by intermolecular bonds.
a three-dimensional combination of α-helices and β-sheets
Quaternary structure
Two or more polypeptide chains, each with its own tertiary structure, combine to form a functional protein.
e.g., hemoglobin
Function of structural proteins
Mechanical support
example: collagen, found in all connective tissue, is the single most abundant protein in the body. It is responsible for the tensile strength of bones, tendons, and ligaments. Collagen basically helps form shape.
Function of enzyme proteins
Catalysts. Protein enzymes are essential for virtually every biochemical reaction in the body.
example: disaccharidases hydrolyze disaccharides, proteases hydrolyze proteins, and oxidases oxide food fuels.
What did older enzymes end in?
- in
What do newer enzymes end in
-ase
What does the naming of enzymes do?
The newer names tell what they do. Older names do not necessarily tell you (renin for example).
e.g., alcohol dehydrogenase. It takes away an hydrogen from alcohol.
What are proenzymes
Inactive enzymes
The enzyme is premade and has a “inactive cap” on its active cite. When the enzyme is needed another enzyme cleaves off the cap and the enzyme is not inactive and can be used.
Competitive inhibition
Substance that resembles the normal substrate competes with the substrate for the active site. Blocking the substrate from binding. Reversible.
Noncompetitive inhibition
Inhibitor binds elsewhere on the enzyme; alters active site so that the substrate cannot bind.
Induces an irreversible shape change to the active site. Becomes completely nonfunctional.
Transport proteins
Moving substances
membrane transporters or sebum transports across the plasma membrane
example: hemoglobin transports oxygen in blood. Some plasma membrane proteins transport substance (such as ions) across the plasma membrane
Contraction/movement proteins
Movement
example: actin and myosin cause muscles cell contraction and function in cell division in all cell types.
Communication proteins
Transmitting signals between cells. Can act as chemical messengers or as receptors in the plasma membrane
example: insulin (a protein) acts as its receptor to regulate blood sugar levels.
Communication proteins
Transmitting signals between cells. Can act as chemical messengers or as receptors in the plasma membrane
example: insulin (a protein) acts as its receptor to regulate blood sugar levels.
Types of communication proteins
Peptide hormones
Membrane receptors
Neurotransmitters
Energy of activation (EA)
The amount of energy that reactants must absorb before a chemical reaction will start
Immune/defense proteins
Prevent and protect against pathogen attack/disease
example: antibodies released by certain immune cells are specialized proteins that bind and inactive foreign substances (e.g., bacteria, toxins, viruses).
What are immune proteins
Antibodies - made against a specific virus/bacteria.
Complement - nonspecific, does not matter what invader is in.
Nucleic acids are
Largest molecules in the body
What are nucleic acids made of
Nucleotides
What are nucleic acids involved in
Protein synthesis
Names of nucleotides
Adenine
Thymine
Cytosine
Guanine
Uracil
What is DNA
Deoxyribonucleic Acid
Genetic code that gives the sequence of information on how to make the proteins.
Replicates and stores genetic information
RNA
Ribonucleic acid. Translates the code from DNA into the protein. Carry out instructions encoded in DNA.
Encodes amino acid sequence of all proteins
Strands held together by hydrogen bonds
RNA
Ribonucleic acid. Translates the code from DNA into the protein. Carry out instructions encoded in DNA.
Encodes amino acid sequence of all proteins
Strands held together by hydrogen bonds
What is RNA
Copy of a gene used to make protein
1 Strand
What is RNA
Copy of a gene used to make protein
1 Strand
Parts of a nucleotide
Sugar, phosphate, nitrogen base
ATP
adenosine + phosphate
adenosine triphosphate
what we use to speed up reactions
ATP → ADP + Pi
Releases energy
==”spring”
Energy transfer to enzyme-substrate complex to help complete the reaction
Describe the fundamental composition of matter.
The atom
Solids, liquids, gases
4 most abundant elements in the body
Oxygen, carbon, hydrogen, nitrogen
Distinguish between ionic bonds, covalent bonds, and hydrogen bonds.
ionic bond attraction between an anion and a cation
covalent bond chemical bond in which two atoms share electrons, thereby completing their valence shells
hydrogen bond dipole-dipole bond in which a hydrogen atom covalently bonded to an electronegative atom is weakly
attracted to a second electronegative atom
Explain how energy is invested, stored, and released via chemical reactions, particularly those reactions that are critical to life.
In the human body, potential energy is stored in the bonds between atoms and molecules. Chemical energy is the form of potential energy in which energy is stored in chemical bonds. When those bonds are formed, chemical energy is invested, and when they break, chemical energy is released. Notice that chemical energy, like all energy, is neither created nor destroyed; rather, it is converted from one form to another.
Chemical reactions that release more energy than they absorb are characterized as exergonic. The catabolism of the foods in your energy bar is an example. Some of the chemical energy stored in the bar is absorbed into molecules your body uses for fuel, but some of it is released-for example, as heat. In contrast, chemical reactions that absorb more energy than they release are endergonic.
