Chapter 1 Flashcards
what is biochem?
the interface of biology and chemistry
what are the 4 main small biomolecules?
- amino acids
- nucleotides
- simple sugars
- fatty acids
where is biochem often studied? what does this mean?
in vitro, or outside a living cell
what are catalysts?
biomolecules that increase the rate (catalyze) of reactions dramatically
what are catalysts essential for?
all living cells
give 5 of the many processes that catalysts are responsible for
- digestion
- fermentation
- metabolism
- apoptosis
- biofuel production
list and describe 2 examples of catalysts
- enzymes: proteins that catalyze reactions
- ribozymes: catalytic RNA
how do catalysts increase the rate of reactions?
by lowering the activation energy
how is biochem an applied science?
used to create methods that exploit cellular processes and enzymatic reactions
what are the 3 categories of the building blocks of life?
- main elements
- trace elements
- essential ions
what are main elements?
the elements that make up most of organisms
what 4 (plus an additional sometimes 5th) elements are super important in amino acids?
carbon, nitrogen, oxygen, hydrogen, sometimes sulfur
what are trace elements?
make up less than 1% of living things
how do trace elements work/are used?
used as cofactors, work with main elements for better and proper functioning
what are essential ions?
charged elements
what are essential ions involved in?
- signaling
- neurochemistry
give 5 examples of essential ions
- Ca2+
- Cl-
- Mg3+
- K+
- Na+
describe bare bones what a chemical bond is
atoms share electrons
how many times can carbon bond before filling it octet? what geometry is this?
4 times; if all four bonds used is called tetrahedral geometry
describe rotation around a sigma (single) bond and give an analogy
is easy, like sticking a board to a wall with one nail, can rotate easily
describe rotation around a pi (double) bond
impossible, like trying to rotate a board stuck in a wall with two nails
see flashcards for functional groups!!
go see them!!
what is the main function of amino acids?
build proteins
list 3 additional amino acid functions other than building proteins
- neurotransmission
- nitrogen metabolism
- energu conversion (BUT NOT A MAIN ENERGY SOURCE, INEFFICIENT)
what is the main function of nucleotides?
build nucleic acids (DNA and RNA)
list 3 additional functions of nucleotides other than building nucleic acids
- energy conversion
- signal transduction
- enzyme catalysis
what is the main function of simple sugars (CHOs)?
energy conversion
list 3 additional functions of simple sugars other than energy conversion
- cell wall structure
- cell recognition
- nucleotide structure
what is the main function of fatty acids?
linking noncovalently to form cell membranes both around and within cells
what do amino acids, nucleotides, and simple sugars all have in common?
they are monomers that link covalently to form polymers
what determines the identity of an amino acid?
the side chain; is the only variable part
how are amino acids linked?
covalently by peptide bonds
what do amino acids link covalently through peptide bonds to form?
peptides
what are large polypeptides called?
proteins
what is another name for simple sugars?
carbohydrates
what 3 atoms do carbohydrates contain?
C, H, O
what is the ratio of hydrogen atoms to oxygen atoms in carbohydrates?
2:1; 2 hydrogens for every oxygen
how are carbohydrates linked? what do they form when they link?
covalently through glycosidic bonds; form polysaccharides
what is a monosaccharide?
1 simple sugar
what a disaccharide?
two simple sugars linked
what type of molecules are fatty acids? what does this mean?
amphipathic; have a hydrophilic polar head group attached to a hydrophobic hydrocarbon chain
how do fatty acids assemble? what does this form?
via noncovalent interactions to form membranes
what do fatty acids act as?
a storage form of energy
list 2 ways to describe macromolecules
- large molecules; functional units
- polymers: many units of monomers covalently linked together
what are polymers?
many units of monomers covalently linked together
what are 3 types of polymers and what are they made of?
- proteins: amino acid polymers
- nucleic acids: nucleotide polymers
- polysaccharides: sugar polymers
what is the reaction that forms the peptide bonds that link amino acids to form proteins?
condensation (dehydration synthesis)
how do you read amino acids?
from N-terminus to C-terminus
where are new amino acids added?
to the C terminus
what 3 atoms are the cue to recognize a full amino acid?
NCC
what are the 2 ways to describe macromolecules?
- as large molecules; functional units
- as polymers; many unites of monomers covalently linked together
what macromolecules are considered the workhorses of life that perform most biological functions?
proteins
what is very important to the function of a protein?
the structure!
give 3 examples of proteins performing biological functions
- enzymes like lipase metabolize fat
- antibodies like immunoglobulins kill bacteria and viruses
- transport proteins like hemoglobin deliver oxygen to cells
define nucleic acids as macromolecules
genetic material that determines everything about an organism
contrast the shape of DNA and RNA
DNA is double helix and RNA is single helix
contrast the ribose sugar in DNA and RNA
DNA has deoxyribose sugar (hydrogen at 2’ carbon) and RNA has oxyribose sugar (OH at 2’ carbon)
how are polymers of nucleotides (DNA and RNA) formed?
by covalently linked nucleotides via phosphodiester bonds from the 5’ to 3’ end
during transcription, where are nucleotides added?
to the 3’ end, NEVER the 5’ end
what are polysaccharides?
complex carbohydrates
list and describe the 3 functions of polysaccharides
- structure: gliding motion in joints
- biomarkers: sugar flags for blood typing and virus detection
- energy: glycogen degradation
how are simple sugars linked to form polysaccharides?
via variable glycosidic bonds
what is key to the identification and chemical properties of a polysaccharide? (2)
orientation and position of the glycosidic bond
give 2 types of glycosidic bonds
a-1,4 and a-1,6 linkages
what is always the same about a glycosidic bond?
2 carbons (one from each ring) are connected via an oxygen outside the ring
what are metabolites?
small biomolecules that serve as both reactants and products in biochemical reactions within cells
what is metabolic flux?
the rate at which reactants and products are interconverted in a metabolic pathway
what is influx?
the entry of metabolites into a pathway
what it efflux?
the flow of metabolites out of a pathway
what are the 3 types of metabolic pathways?
- linear
- forked
- cyclic
how is cellular communication accomplished? (main actors)
proteins mostly
give the general process of cellular communication
- a ligan binds to an extracellular receptor and causes a conformational change in the receptor protein to an active state
- once active, the receptor protein does its thang
- since the ligand is bound reversibly to the receptor protein, it detaches and causes another conformation change of that receptor protein back to inactive state
what are the two types of nitrogenous base pairs?
purines and pyrimidines
what are the 2 purines of DNA?
adenine and guanine
what are the two pyrimidines of DNA?
cytosine and thymine
which purines pair with which pyrimidines in DNA?
guanine with cytosine and
adenine with thymine pyrimidine
what are the 2 purines of RNA
same as DNA, adenine and guanine
what are the two pyrimidines of RNA?
cytosine and uracil
what purines pair with which pyrimidines in RNA?
guanine with cytosine and
adenine with uracil
which purine-pyrimidine bond is stronger and why?
G-C pair is stronger than A-T because there are 3 bonds between G-C and only 2 bonds between A-T or A-U
which way do you read DNA?
5’ to 3’
what is a gene?
a stretch of DNA that will eventually code for a protein
what is a nucleosome?
a string of negatively charged DNA wrapped tightly around a postively charged histone; tightly packed to prevent damage
what is chromatin?
multiple nucleosomes tightly packed together
what is a chromosome?
tightlt packed chromatin
what is a nucleus?
tightly packed chromosomes with a protective membrane
give the levels of genetic structure from smallest to largest (5)
- gene
- nucleosome
- chromatin
- chromosome
- nucleus
give the central dogma
DNA is transcribed into mRNA that is translated into proteins that do jobs
will noncoding DNA ever become a protein?
no!
what makes a codon?
3 nucleotide bases
what are the 2 types of mutations?
- germ-line cell
- somatic cell
describe germ-line cell mutations (2)
- passed from parents to offspring
- can result in inherited genetic diseases (ex. sickle cell anemia)
describe somatic cell mutations (3)
- not inherited by offspring
- limited to individual organism
- can result in developed diseases (ex. cancer)
what is the danger of mutation?
mutations can change the sequence and moleculer structure of proteins, which can affect function (could be real bad)
what is an advantage of mutation?
evolution! could make organisms more fit for the environment
how are phylogenetic trees created?
using bioinformatics
describe how similar human DNA is to chimpanzee DNA (2)
- 98% is identical
30% of proteins have the exact same sequence
what are orthologous genes?
- similar genes in different species
- conserved sequence and function
- likely from common ancestral gene
give an example of an orthologous gene
G6P dehydrogenase
what are paralogous genes?
similar genes in the SAME species
how are paralogous genes created?
through gene duplication, as there are only 3 possible outcomes for a codon
give an example of a paralogous gene
nuclear receptors
what is a genome?
a collection of all an organism’s genes
what is a transcriptome?
a collection of all DNA transcripts (RNA products) generated by DNA transcription
what is a proteome?
collection of all proteins produced by mRNA translation
describe the determination of biomolecular structure and function
sequence determines structure determines function
