Chapter 3 Flashcards
nucleic acids
polymers that store, transmit, and express heredity information
DNA
deoxyribonucleic acid, stores and transmits genetic information
RNA
specify the amino acid sequences of proteins
nucleotides
the monomers of nucleic acids consisting of three components: nitrogen-containing base, pentose sugar, one to three phosphate groups
nucleosides
consists of pentose sugar and a base, but no phosphate group
pyrimidine
six-membered single-ring structure of the base
purine
fused double-ring structure of the base
What is the difference between deoxyribose and ribose?
Ribose has one more oxygen atom
phosphodiester bond
linkage between the pentose sugar of one nucleotide and the phosphate of another nucleotide after a condensation reaction
oligonucleotides
RNA: begin duplication of DNA, regulate gene expression
DNA: amplifying and analysing other nucleotide sequences
polynucleotides
DNA
most RNA
What are the bases found in DNA?
adenine
cytosine
guanine
thymine
What are the bases found in RNA?
adenine
cytosine
guanine
uracil
What are the complementary base pairs for DNA?
A-T
C-G
What are the complementary base pairs for RNA?
A-U
C-G
What intermolecular force holds together base pairs?
hydrogen bonds
Describe the structure of RNA
usually single-stranded, but it can fold on itself to attain a three dimensional structure
Describe the structure of DNA
two separate polynucleotide strands which are antiparallel, twists into a double helix, typically a right handed molecule
DNA replication
precise reproduction through polymerization using an existing strand as a base-pairing template
tnanscription
Information coded in the sequence of nucleotide bases in DNA is passed to a sequence of nucleotide bases in RNA
translation
Information in RNA is passed to polypeptides, but never the reverse
genes
sequences of DNA that encode specific proteins and are transcribed into RNA
genome
complete set of DNA in a living organism
enzymes
catalytic molecules that speed up biochemical reactions, typically proteins
defensive proteins
recognize and respond to substance of particles that invade the organism from the environment
hormonal and regulatory proteins
control physiological processes
receptor proteins
receive and respond to molecular signals
storage proteins
store chemical building blocks for later use
structural proteins
provide physical stability and enable movement
transport proteins
carry substances without the organism
genetic regulatory proteins
transcription factors, regulate when, how, and to what extent a gene is expressed
proteins
polymers made up of amino acids
What are the functional groups found in amino acids?
nitrogen-containing amino group and acidic carboxyl group
R group
also known as side chain, this distinguishes each of the amino acids
disulfide bridge
covalent bond between sulfurs on side chains
oligopeptides
can just be referred to as peptides, these are short polymers of 20 or fewer amino acids
polypeptides
longer polymers with unique sequences of amino acids
peptide bond
between the amino group of one amino acid and the carboxyl group of another after a condensation reaction occurs
primary structure
precise sequence of amino acids in a polypeptide chain
secondary structure
consists of regular, repeated patterns in different regions along the polypeptide chain
~alpha helix
~beta pleated sheet
alpha helix
right-handed coil, as a result of hydrogen bonds between N-H group and C=O group
beta pleated sheet
sequences of amino acids that are extended and aligned, can form between different polypeptide chains or a single chain folded on itself
tertiary structure
results in the polypeptide’s three-dimensional shape, as a result of interactions between R groups
denatured
secondary and tertiary structures break down due to heating
quarternary structure
results from the ways in which the subunits bind together and interact
What is the effect of temperature increases on protein structure?
cause more rapid molecular movements and thus can break hydrogen bonds and hydrophobic interactions
What is the effect of pH changes on protein structure?
can change the patterns of ionization of the exposed carboxyl and amino groups. This can disrupt the patterns of ionic attractions and repulsions
What is the effect of high concentrations of polar substances on protein structure?
disrupt the hydrogen bonding that is crucial to protein structure
What is the effect of nonpolar substances on protein structure?
may also denature a protein in cases where hydrophobic groups are essential for maintaining the protein’s structure
catalyst
speeds up the reaction without altering it by lowering the activation energy, can be reused
DOES NOT CAUSE THE REACTION TO OCCUR
enzymes
biological catalysts (mostly proteins, but some are RNA)
free energy (G)
amount of energy in a system that is available to do work, released by an exergonic reaction
transition state
reactive mode after an input of energy (peak of graph)
activation energy
energy input to reach the transition state
substrates
the reactants in an enzyme-catalyzed reaction
active site
particular site on the enzyme where catalysis takes place
What contributes to the specificity of an enzyme?
The exact three dimensional shape, or conformation, and chemical properties of the active site make it so that only substrates with certain shapes, functional groups, and chemical properties can bind to the enzyme.
Enzyme-Substrate Complex
binding of a substrate to the active site of an enzyme
What is the general form of an enzyme-substrate reaction?
E + S –> ES –> E + P
inducing strain
enzyme causes bonds in the substrate to stretch, putting it in an unstable state
substrate orientation
brings together specific atoms so that bonds can form
adding chemical groups
R groups of an enzyme may be directly involved in the reaction
What are the roles of the rest of the enzyme macromolecule?
~provides a framework so the amino acids of the active site are properly positioned in relation to the substrate
~participates in the changes in protein shape and structure that result in induced fit
~provides binding sites for regulatory molecules
cofactors
ions or other molecules that certain enzymes need in order to function
What are the three categories of cofactors?
~metal ions
~coenzymes
~prosthetic groups
metal ions
bind to certain enzymes and participate in the enzyme-catalyzed reactions
coenzyme
a relatively small, carbon-containing molecule required for the action of one or more enzymes. It binds to the active site of the enzyme, adds or removes a chemical group from the substrate, and then separates from the enzyme to participate in other reactions
prosthetic groups
organic molecules that are permanently bound to their enzymes
metabolic pathways
product of one reaction is the substrate for the next
systems biology
scientists describe mathematically the components of metabolic systems
Why do cells need to regulate their metabolic pathways?
so that they can respond to changes either within the organism or in its environment
How could a cell regulate metabolism?
~control the amount of an enzyme
~regulate the activity of enzymes
competitive inhibitor
competes with the natural substrate for the active site, it is reversible
noncompetitive inhibitor
binds to an enzyme at a site distinct from the active site, it is reversible
allosteric regulation
non-substrate molecule binds or modifies a site other than the active site of an enzyme
noncovalent binding (allosteric regulation)
causes the enzyme to change shape, is reversible, may result in the inactivation of an enzyme
covalent bonding (allosteric regulation)
when a molecule or chemical group binds to an allosteric site
feedback inhibition
when the end product is present at a high concentration, some of it binds to a site (active or allosteric) on the commitment step enzyme, causing it to become inactive
What is the effect of temperature on a chemical reaction?
Generally increases the rate of the reaction, can result in protein denaturing at high temperatures
irreversible inhibition
occurs when an inhibitor covalently binds to an amino acid side chain at the active site of an enzyme, so the enzyme is permanently inactivated
