Unit 1- biochemistry Flashcards
what are the two kinds of chemical bonding?
- Intramolecular: the force that holds atoms together within a molecule (super strong)- sew and needle
- intermolecular: the force that holds the two molecules together( super weak) - velcro
ionic bonds
- complete transfer of electrons
- generates two oppositely charged ions
- metal loses electrons (becomes positively charged) and non-metal gains electrons (becomes negatively charged)
Covalent bond
a bond formed between atoms with similar electronegativities- affinity or desire for electron
- they share electrons to obtain octet configuration.
- have two different subbonds
Non- polar covalent bonds
- formed between the same atoms or ones that have VERY similar electronegativities
Cl — Cl –> n.p
0.5> elec negativity
Polar covalent
- formed between atoms with slightly different elect negativity
- 0.5< x ≤ 1.9
strongest type of intermolecular molecules.
- dipole-dipole: occurs when partially positive interacts with partially negative of the neighboring molecule
- in order to exist it needs partially charged ions
Hydrogen bonding:
- a special kind of dipole to dipole
- occurs between hydrogen atoms bonded to H, N, O,
- the positive end of hydrogen is attracted to the charged negative end of O, F, N.
Condensation: aka dehydration
-ANABOLISM: assembly of a polymer
-as two monomers are joined together to make a polymer chain– h20 is removed
hydrolysis:
- Catabolism: disassembly of large polymers back into monomers
- one hydrogen is added into the hydroxyl group and the other to the other monomer
categories of biological molecules:
- carbohydrates
- lipids
- proteins
- nucleic acids
hydroxyl group
O-H
Carbonyl (aldehydes)
C=O
|
H
Carbonyl (ketones)
C=O
|
R
Carboxyl
COOH
or
O
||
C
||
OH
amino
– NH2
H
||
N
||
H
Phosphate group
PO4^2
or
+
Cohesion
- only polar causes cohesion since it is polar
- the ability for water to bond with itself
- gives rise to surface tension
Adhesive
- only polar causes adhesion because water is polar
- the ability for water to bond to other polar or ionic substances. - meniscus and hydrophilic interactions.
Macromolecules
- large complex organic molecules
- ” form fits function”
Monomer
small molecules chemically joined to form larger, more complex biological molecules called polymers
polymers
long chains of monomer joined chemically.
metabolism
the breaking down and building up of metabolic processes.
Monosaccharide
single sugar molecules AKA “simple sugars”
isomer
monosaccharides that have the same chemical formula, but different shapes and arrangements.
Disaccharides
- two monosaccharides joined together by the condensation/ dehydration reaction
3 examples of disaccharides
- sucrose (qlucose+ fructose)
- lactose ( glucose +galactose)
- maltose ( glucose+ glucose)
3 examples of monosacrides
-Glucose
-fructose
- galactose
what is a glycosidic linkage
the covalent bonds formed between two monosaccharide monomers
ex- alpha glucose.
4 examples of polysacchrides
- Starch
- cellulose
- glycogen
- chitin
alpha form
- when the ring closes, the hydroxyl group on c-1 is locked below the plane of rings
vvvvvvv
beta form
- when the ring closes, the hydroxyl group on c-1 is locked above the plane of rings
- unable to break
- ^ v ^ v- every other glucose is turned “upside down”
alpha form examples
- startch
- glycogen
quick energy sugarrs
disaccharides
fast and short term energy
monosaccharides
what are polysaccharides
- complex carbohydrates
-the polymers - 4 main groups
1st example of a polysaccharide
- plant startches :
-long branches of glucose monomers - storages of energy for plants
2 types: - amylose: ( 1 chain of monomers)
- amylopectin (2 chains of monomers)
2nd example of a polysaccharide
- animal starches:
- storage of energy in the liver and skeletal muscles.
- highly branched chains of glucose monomers
- glycogen (3 chains)
what is the polarity of alpha glucose??
- alpha glucose is polar
what happens if polysaccharides are too big
water will not be able to surround them and they will not be able to be dissolved.
third example of a polysaccharide:
cellulose: AKA fiber
- found in the cell wall
- structure component
- most abundant
- undigestable due to its beta form
difference between alpha and beta forms:
- alpha is when the bonds occur all in the carbon 6 same row below the plane and an example would be starch.
- beta is when carbon 6 causes every other glucose to turn upside down. an example is cellulose. -
the fourth example of polypeptide?
- chitin ( insects, crabs, lobsters, shrimp)
- a structural component
- glucose monomers with nitrogen
- contains side chains on c-2 instead of hydroxyl group
what two polysaccharides are for storage? what is their glycogen linkage form? are they digestible?
- starch and glycogen
- alpha glycogenic linkage
- can be digestible
what two polysaccharides are for structure? what is their glycogen linkage form? are they digestible?
- cellulose and chitin
- beta glycogenic linkage
- can not be digestible
what are the general characteristics of lipids?
- three large and diverse groups of molecules
- lipids are not polymers
- the lipid groups differ structurally
- all lipids are non-polar
and since water is polar they do not attract each other - they have high C-H content
what are the three groups of lipids?
- fats/ oils
- phospholipids
- steroids
what do you know about the first sub- group of lipids
- fats and oils
- energy reserves for animals
- used for insulation
- non- polar
- only contains oxygen ( not much), hydrogen, and carbon
- basic structure is triglyceride
what is the basic structure of triglyceride?
- one glycerol (3 carbon alcohol)
- three fatty acids ( long hydrocarbon chains, carboxylic acid attached on one end, always have even number of carbon atoms in the chain)
what are two types of fats?
- saturated: (solids)– full, can not hold anymore. more animal fats
((( no double bonds))) - unsaturated (liquids) – “unfull” can still hold more. more plant fats
((( active double bonds)))
why are unsaturated fats liquid?
- because they double bond creates angles in the carbon skeleton of the fatty acid that prevents them from packing together and solidifying at room temperature
why do we need fats in our diet?
- a source of many essential fatty acids needed for hair and skin
- needed for phospholipids in all the membranes of the cell
- essential for the absorption of all fat-soluble vitamins, such as vitamins A,D, E
- also for long-term energy once the body runs out of short-term energy
what do you know about the second sub- group of lipids?
- phospholipids:
- phospholipids have a partial exception to the hydrophobic lipid rule.
- have both a polar and a non polar region on each molecule.
meaning of amphilic
one part is water-loving, and one part hates water.
what part of a phospholipid loves water/ soluble
- hydrophilic head
- polar “head” glycerol and phosphate group
- because it contains a charged phosphate function group that replaces the 3rd fatty acids.
what part of a phospholipid hates water/ insoluble
- hydrophobic tail
- two non- polar fatty acid “tails”
what is phospholipids a major component of?
forms a double layer in all cell membrane
what does the double membrane of a phospholipid looks like?
- the polar heads are oriented towards the aqueous areas
- the non-polar fatty acids form a non-polar lipid barrier between the inside and outside of the cells.
what is the main function of phospholipids?
covers all cells, is the membrane of all cells
what do you know about the third sub-group of lipids?
- steroids:
- different structure than fats and phospholipids
what is the characteristic structure od steriods?
- 4 fused rings aka (sterol backbone)
- the steroid backbone is found in all steroid backbone
- what attaches to the backbone determines what type of steroid it is.
examples of steroid
- cholestrol
- sex hormones
what are steroids used for?
give 5 examples…
- sex hormones ( testosterone in males, and estrogen and progesterone in females)
- vitamin D
- important parts of the cell membrane
- bile salts
- corticosteroids from adrenals
what is the third group of biological molecules?
- proteins
list some functions of proteins
- structural proteins (skeletal and muscles)
- enzymes
- defense
- hormones
- cell movement
- toxins
what is the difference between tendon and ligament?
a tendon attaches muscles and bones while ligaments attaches bone and bone.
what is a monomer of protein?
amino acids
what is the basic structure of all amino acids
- central carbons with FOUR functional groups
- amino group
- carboxyl group
- hydrogen
- and an amino acid (R)
what does the R group determine?
- idenity of amino acids
- physical properties of amino acids( size and shape)
- chemical properties of amino acids( polarity and [H+]
what are the three categories of amino acids?
- non- polar
- uncharges polar
- charged polar ( negatively- acid or positively- basic )
what is the polymer of amino acids called?
- polypeptide chain/ linear chain
what is removed everytime two amino acids are chemically bonded?
molecule of water is removed.
what is the bond that forms between the amino acids? what is it called?
the bond between amino acids is a covalent bond called “ peptide bond”
how many levels of structure are in proteins? what are they?
- there are four levels of protein structure”
- primary level
- secondary level
- tertiary levels
- quaternary level
what is the primary level of a protein?
- the specific sequence of amino acids that join the polypeptide chain
- when peptide bonds form they produce a long chain with a carboxylic acid group on one end and an amino acid on the other.
what determines the primary structure of the polypeptide chain?
the gene in the dna coding for the protein
what is the secondary level of proteins?
- the way the polypeptide chain is coiled up and folded UPON ITSELF.
- there are two types of secondary structures:
there are two types of secondary structures, what are they?
alpha helix: in hair and horn
- peptide chain in coiled, hydrogen bonds are between every fourth
beta pleated sheet: spider silk and silkworm
- chain is folded back with regions of chain parallel to itself
- hydrogen bonds hold it together.
tertiary level of proteins.
- the overall 3- D conformation
- the hydrophobic “R” groups are oriented in the middle of the molecule.
- interactions between the “R” groups of the amino acids.
how many forces hold the tertiary conformation? what are they?
four forces are all intermolecular
- hydrogen bonds
- hydrophobic bonds
- ionic bonding
- disulfide bonds
what are disulfide bonds?
- are strong covalent bonds formed between two amino acids containing sulfhydryl groups in the “R” groups of amino acids
- amino acids cysteine
Quatenary levels of proteins.
-founds only in proteins composed of two or more polypeptide chain
- examples: collagen, hemoglobin,
what is the denaturing of proteins?
- the unfolding of secondary and tertiary structures.
- not reversible, and will lose function
- the hydrogen bonds are broken
- if the primary structure is destroyed the whole protein is destroyed.
three things proteins are sensitive two
- high temp (fever)
- extreme pH
- high salt concentration
what is the fourth group of biological molecules?
nucleic acids
what is the longest polymer in the body?
nucleic acids.
what is the monomer of nucleic acids?
nucleotide
what is the basic structure of a nucleotide?
- a 5- carbons sugar
- phosphate group
- nitrogen base
what are the two types of nitrogen bases? how are they different? and list examples…
- purine: double rings
(adenine, guanine) - pyrimidines: single rings
(thymine, cytosine, uracil)
what type of base is found in all nucleic acids? DNA? and RNA?
- all nucleic acids: A, G, C
- DNA: T
- RNA: U
what sugar is DNA, RNA?
DNA: deoxyribose( missing hydroxyl group on C2)
RNA: ribose
what happens during the condensation of amino acids?
what is it called?
- the two nucleotides are joined together by a phosphate group of one nucleotide and the sugar on the other nucleotide.
- called the “sugar-phosphate” backbone
what is an active site?
the binding site for the substrate
what is a substrate?
- any molecule that is recognized by an enzyme.
- substrate must have a similar shape
induced fit model
- describes how an enzyme changes shape to better accommodate a substrate
activation energy:
the energy required to start a reaction
what do enzymes do to the activation energy,
they lower it to make it more readily
what are co enzymes-
an organic molecule that acts as a co-factor
organic meaning contains carbon
cofactor-
a non-protein atom or molecule that binds to an enzyme and is essential for catalytic activity
- examples of cofactors: are iron, magnesium, potassium, and zinc.
enzyme inhibitors-
enzyme inhibitors-
