Ch. 12 Biochemistry Flashcards
molecules that are the building blocks of living organisms
biomolecules
biomolecules fall into about four categories:
- carbohydrates
- amino acids and proteins
- lipids
- nucleic acids
Carbohydrates or sugars were originally believed to be
“hydrates of carbon”
Carbohydrates are now known as
polyhydroxy aldehydes or ketones
Monosaccharides are
simple sugars
Monosaccharides are not broken down by _____ ____ into simpler sugars
aqueous acid
Monosaccharides are the fundamental building blocks of
sugars
the fundamental building blocks of sugars are:
Monosaccharides
Disaccharides are composed of two _______.
Joined by an ______ or ______ linkage.
Monosaccharides .
joined by an ACETAL or
KETAL linkage
Polysaccharides are composed of many:
Monosaccharides joined by acetal or ketal linkages
Classification of sugars is by the number of
C atoms
Trioses are sugars that contain
3 carbon atoms
Tetrosese are sugars that contain
4 carbon atoms
Pentoses are sugars that contain
5 carbon atoms
Hexoses are sugars that contain
6 carbon atoms
sugars that contain an aldehyde functional group are called
aldoses
sugars that contain a ketone functional group are called
ketoses
Chirality is a property of an object if it is different from its
mirror image
The Greek word for “handed” is
Chiros
a chiral molecule needs at least one
stereocenter
a carbon is a _____ when it has _____ different groups
stereocenter
4 different groups
a cool property of chiral molecules is
optical activity
shining polarized light through one isomer rotates light to the ___.
this is the _____ isomer.
right
-this is the (+) or dextrorotatory isomer
the isomer that rotates polarized light to the left is the
(-) or levorotatory isomer
carbohydrates and amino acids are grouped into optical families:
D family and the L family
L-threose
D-threose
the two most important sugars are
glucose and fructose
glucose and fructose are both naturally occurring and belong in what family of sugars?
D family
the old name for glucose was
dextrose
*b/c glucose rotates plane polarized light to the RIGHT (D-glucose is dextrorotatory)
the old name for fructose was
levulose
*b/c fructose rotates plane polarized light to the LEFT (D-Fructose is levorotatory)
D-glucose is
dextrorotatory
D-Fructose is
levorotatory
the most important sugar is
glucose
*occurs so frequently in nature
sugars exists primarily as what type of structures?
cyclic structures
sugars usually have a ____ or ____ membered ring
six- or five-membered ring
these molecules share a common physical property - they’re all soluble in organic solvents (i.e. ether)
Lipids
The purpose of lipids:
- energy storage
- sending chemical signals (both w/in an individual and between individuals)
fatty acids are long-chained
carboxylic acids
naturally occurring fatty acids always have an even number of:
carbon atoms
saturated fatty acids have all:
carbon-carbon single bonds in the chain
unsaturated fatty acids have one or more
double bonds in the chain
*these are called cis
name some saturated fatty acids (4):
- Lauric acid
- Myristic acid
- Palmitic acid
- Stearic acid
Oleic acid (18:1) is a:
monounsaturated fatty acid
Linoleic acid (18:2) is a :
polyunsaturated fatty acid
Triglycerides are
tri-esters of glycerol and 3 fatty acids
examples of triglycerides:
- Tristearin
- Triolein
Tristearin is a typical saturated fat molecule. Where would you find this type of triglyceride?
-butter or animal fat
Triolein is a typical unsaturated triglyceride. where would you find this type of triglyceride?
veg oil, olive oil
a fat is a ____ triglyceride at room temperature
SOLID
fats tend to come from
animal sources
fats tend to have a greater percentage of
saturated fatty acids
an oil is a ____ triglyceride at room temperature
LIQUID
oils tend to come from
vegetable sources
oils tend to have a greater percentage of
unsaturated fatty acids
fats and oils are triglycerides, but differ in their
fatty acid composition
since triglycerides are esters, they undergo the same kinds of reactions as other esters. one important reaction is:
hydrolysis by base
*remember basic hydrolysis is called saponification, which means “soap forming”
hydrolysis of a triglyceride (with NaOH) gives:
glycerin and three fatty acids (As they are sodium salts)
All soaps have a _____ tail and a _____ head
non-polar tail
polar head
when the sodium salt of a fatty acid is placed into water, they hydrophobic tails tend to:
This leads to formation of a:
- cluster and dissolve in each other
- forming a MICELLE
a roughly spherical agglomeration of soap molecules in which the greasy tails are hidden away from the polar aqueous environment on the inside of the sphere is a:
micelle
detergents are synthetic
“soaps”
like soaps, detergents have a long,
polar tail and a polar head
the polar head of a detergent can be
anionic, cationic, or neutral
many detergents are derived from
triglyceride sources
sodium dodecylsulfate (SDS) is a
typical anionic detergent
SDS is also known as
sodium laurylsulfate
SDS has several advantages over soap; can you name them (2)?
- it does not form insoluble percipitates w/hard water ions ===> forms soap scum
- since sulfuric acid is a strong acid, SDS is a weak base and is pH neutral
quaternary ammonium salts are common
cationic detergents
the 16-carbon chain of cationic detergents is call a
cetyl group
steroids are characterized by a
ring system
the steroid ring system they’re characterized by is called the :
“perhydrocyclopentanophenanthrene” ring system
is one of the male sex hormones
testosterone
this is a synthetic steroid that is used as one component of an oral contraceptive
ethynyl estradiol
powerful hormones in mammalian systems are:
prostaglandins
prostaglandins have a 5-membered ring with a 7-carbon side chain (often ending in a carboyxlic acid group) adjacent to an
8-carbon chain
these are relatively simple organic molecules that are strung together into chains called proteins:
amino acids
all living organisms are chemical factories, and virtually every chemical reaction that occurs in a living system is catalyzed by special proteins called:
enzymes
amino acids have three components:
- a carboxylic functional group
- an amino group on the carbon alpha to the carboxyl group
- a side chain group on the carbon alpha to the caboxyl group
there are about how many naturally occurring amino acids?
20
each amino acid has a
1- and 3- letter abbreviation
the identity of the amino acids is determined by the various
side chains
Hydrocarbon side chains 1:
- Glycine
- Alanine
- Valine
Gly or G
The side chain on _____.
Glycine.
*the side chain on clycine is a Hydrogen.
Hydrocarbon side chains 1
the only non-chiral amino acid is:
Gly
Ala or A
The side chain on
alanine
*is a methyl group
Hydrocarbon side chains 1
Val or V
The side chain on:
Valine
*is an isopropyl group
Hydrocarbon side chains 1
Hydrocarbon side chains 2:
- Leucine
2. Isoleucine
Leu or L
The side chain on:
Leucine
*is an isobutyl group
Ile or I
The side chain on:
Isoleucine
*is a sec butyl group
Aromatic side chains 1 (examples):
- Phenylalaine
2. Tyrosine
Phe or F
the side chain is a
Phenylalaine
benzyl group
*Phe is an alaine with a phenyl group
Tyr or Y
Tyr is
Tyrosine
Tyr is Phe with a para hydroxyl group
example of aromatic side chains 2:
Tryptophan
Trp or W
*has a heteroaromatic ring sys in the side chain called an indole group
Name the acidic side chains:
- Aspartic acid
2. Glutamic acid
Aspartic Acid
Asp or D
The side chain in Asp is an acetic acid chain
Notice both start with “a”
Glutamic acid
Glu or E
The side chain of Glu has more methylene than Asp
Amide side chain examples (2)
- Asparagine
2. glutamine
Asparagine :
Asn or N
Asn is the ammonia amide of aspartic acid
Glutamine:
Gln or Q
Gln is the ammonia amide of glutamic acid
Essential amino acids must be obtained through
diet
you cannot synthesize these
the essential amino acids are:
“A HILL Make People Think To Vomit”
A - Arginine H - Histidine I - Isoleucine L- Leucine L- Lysine M- Methionine P-Pheynylalanine T- Threonine T-Tryptophan V- Valine
This is arguably the most important analytical tool in a biochemist’s repertoire:
electrophoresis
electrophoresis is used to
separate and/or identify:
- amino acids
- proteins
- nucleic acids
electrophoresis uses an electric field to separate amino acids (proteins or n. acids) based on:
electrical charge and molecular weight
- more highly charged species move faster
- heavier species move more slowly
The amino group of one amino acid can form an amide bond to the carboxyl group of another amino acid
this is a peptide bond
this is how amino acids are strung together into proteins:
peptide bonds
peptide bonds in living systems is a reaction accomplished by an enzyme:
petidyl transferase
when two amino acids are joined together the product is a
dipeptide
when three amino acids are joined together the product is a
tripeptide
polypeptides are
when many amino acids are joined together
polymers of amino acids, joined by amide (or peptide) bonds are:
proteins
all proteins have a primary structure and some have :
higher levels of structure
amino acid sequence:
in r/t structural levels of proteins
Primary structure
alpha helices or beta pleated sheets:
in r/t structural levels of proteins
Secondary structure
superimposed folding of secondary structures:
in r/t structural levels of proteins
tertiary structure
polypeptide chains linked together in a specific manner
(in r/t structural levels of proteins
quaternary
Reversible unfolding of proteins d/t drops in pH and/or increased temperature is
protein denaturation
Irreversible protein denaturation - when proteins cannot refold and are formed by:
extreme pH or temperature changes
Nucleic Acids are composed of
carbon oxygen hydrogen nitrogen phosphorus
Two major classes of nucleic acids are:
DNA and RNA
The structural unit, the nucleotide, is composed of (3):
- N-containing base
- a pentose sugar
- a phosphate group
Five nitrogen bases contribute to nucleotide structure:
Adenine (A) Guanine (G) Cytosine (C) Thymine (T) Uracil (U)
DNA =
deoxyribonucleic acid
DNA is a double stranded helical molecule found in the
nucleus of the cell
This replicates itself before the cell divides , ensuring genetic continuity:
DNA
DNA provides instructions for
protein synthesis
RNA =
ribonucleic acid (RNA)
RNA is a single-stranded molecule Found in
both the nucleus and cytoplasm of a cell
RNA uses this nitrogenous base instead of tymine
uracil
Three varieties of RNA:
messenger RNA
transfer RNA
ribosomal RNA
Purines are:
how many rings?
Adenine, Guanine have TWO rings
PURe As Gold
Pyrimidines are:
How many rings?
Cytosine, Thymine, Uracil have ONE ring
**CUT the PY[pie]ramididnes
Uracil is found in
RNA
Thymine is found in
DNA
4 steps of DNA replication:
- dna duplicates itself
- nucleotides are always added to the 3’ end
- “new” DNA is proofread by DNA polymerase
- Repairs are made by DNA ligase
“new” DNA is proofread by
DNA polymerase
Repairs are made by
DNA ligase
multiple ribosomes can simultaneously translate a single
mRNA
This type of RNA carries genetic code from nucleus to cytoplasm
mRNA
mRNA are long single stranded molecules containing:
condons
*code triplets for amino acids
each codon “codes” for
one amino acid
this is the START Codon:
AUG
“AUG inAUGurates protein synthesis”
these are STOP codons:
UAA
UAG
UGA
this type of rna acts as a carrier to transport amino acids to ribosomes:
transfer RNA
this RNA is present in ribosomes and synthesize proteins (translation)
Ribosomal RNA
the formation of mRNA is called
transcription
transcription is controlled by
RNA polymerase
mRNA moves to the cytoplasm and dictates the formation of proteins; this is called:
translation
protein synthesis occurs in
ribosomes (protein factories)
this attaches the amino acid to mRNA
tRNA
peptide bonds are formed b/w amino acids by
peptidyl transferase
Agent | Effect:
Aminoglycosides, Tetracycline
bind to 30S subunit of bacterial ribosome inhibiting protein synthesis
Agent | Effect:
Chloramphenicol, Erythromycine, Lincomycin, cLindamycin
bind to the 50S subunit of bacterail ribosome inhibiting protein synthesis
“buy AT 30….
CELL at 50”
bind to 30S subunit of bacterial ribosome inhibiting protein synthesis
Aminoglycosides, Tetracycline
bind to the 50S subunit of bacterail ribosome inhibiting protein synthesis
Chloramphenicol, Erythromycine, Lincomycin, cLindamycin
Agent | Effect:
Sulfonamide
inhibit bacterial synthesis of folic acid
Agent | Effect:
Quinolones (ciprofloxacin, nalidixic acid)
inhibit bacterial DNA gyrase
Toposiomerase II
Agent | Effect:
Rifampin
blocks bacterial mRna synthesis
R’s** Rifampin=mRNA**
Agent | Effect:
Penicillin, cephalosporin, vancomycin
interfere with bacterial cell wall synthesis
Agent | Effect:
polymyxin
disrupt permeability of bacterial cell membrane –> leakage of cell contents
“S” of 30S or 50S =
savedburg unit
inhibit bacterial synthesis of folic acid
Sulfonamide
inhibit bacterial DNA gyrase
Quinolones (ciprofloxacin, nalidixic acid)
blocks bacterial mRna synthesis
R’s** Rifampin=mRNA**
interfere with bacterial cell wall synthesis
Penicillin, cephalosporin, vancomycin
disrupt permeability of bacterial cell membrane –> leakage of cell contents
polymyxin
inhibition of tetrahydrofolate synthesis by
trimethoprin-sulfamethoxazole
