exam 1 info Flashcards
what functions do proteins carry out
catalyze reactions form cellular structures transmit signals carry oxygen repair damaged DNA
why are enzymes used
to speed up reactions
“ase” means what
enzyme
what is the the cytoskeleton and its purpose
network of filaments and helps regulate a cell’s shape
what is the primary level of structure
linear sequence of amino acids joined covalent peptide bonds. Disordered and folded string
what is the second level of structure
hydrogen bonds of nearby amino acids
what is the tertiary level of structure
entire 3D structure of a protein. non-covalent bonds
what is the quaternary level of structure
multiple smaller proteins interacting to form one large protein
how does the identity change by the varying structure levels
- straight chain
- beta sheet
- jumbled protein
- several proteins jumbled
what are the components of an amino acid structure
amino group
alpha carbon
carboxyl group
r group/ side chain
why does the acidity of proteins matter?
many proteins act as enzymes
what is pepsin
stomach enzyme that is very acidic
what is salivary amylase
saliva, neutral, slightly acidic
what is alkaline phosphatase
bones, very basic
what is the primary protein structure
linear sequence of amino acids, joined by covalent peptide bonds
what is the secondary protein structure
local interactions between nearby amino acids with non-covalent hydrogen bonds
what is the tertiary protein structure
the entire 3D structure of a protein, generally mediated by non-covalent bonds
what is quaternary protein structure
interaction of multiple smaller proteins, to form one large protein
how are covalent peptides formed
energy-requiring condensation (aka dehydration reaction), that produces water
what characterizes the alpha-helix
rod like structure. looks like a spring, right handed.
stiff due to hydrogen bonds of the carboxyl and amino groups
what characterizes the beta-strand
segment of 5-20 amino acids that make up the peptide background
what characterizes the beta-sheet
segment of 2-6 beta strands running parallel to one another. held together by hydrogen bonds
what are the amino acids that have high helix-forming potential
(MALEK) Methionine, alanine, leucine, glutamic acid, lysine
what amino acids disrupt helices
proline (bc easily breaks) and glycine (bc energy costly)
what is the coiled coil
structure formed by the interaction of 2+ a-helices, found in proteins
coiled coil characteristics
very strong
found in proteins that need the strength, such as muscles, hair, and blood clot fibrin
beta sheet parallel vs antiparallel
parallel– sequence matches from left to right
anti-parallel– sequence turns in opposite direction every other strand
the parallel beta sheet is often finds what amino acids
proline
what are the super-secondary structures
hairpin turn
helix-loop-helix
beta-alpha-beta unit
greek key
whats the hydrophobic collapse
pulls a string of hydrophobic molecules together when in water. hydrophilic molecules shift the strand to surround the hydrophobic molecules on the inside
purpose of myoglobin
carries oxygen to the muscles
how does a protein embed itself into a lipid bilayer, with regards to water sustainability
the potions of hydrophilic and hydrophobic amino strands correspond to their most comfortable locations in the bilayer
what are van der waals forces and their characteristics
weak interactions, created from slight fluctuations on electron densities around atoms, that are effective in large groups. The bonds are used to hold small short distance proteins together
what bonds are the strongest and can hold over a long distance range
covalent
the oxidation of 2 cysteines creates what?
a cystine
what are discrete protein domains
part of a given protein sequence that exist and function independently from the rest of the protein strand.
how are protein domains created
they are added, restricted, or part of it is duplicated
domains are a part of what part of the protein structure?
tertiary
what is the x-ray crystallography used for
to determine protein identity
what is the quaternary protein structure
arrangement of multiple subunits into a larger protein complex
how is the quaternary protein structure stabilized
hydrogen bonds ionic bonds van der waals forces hydrophobic interactions (sometimes by covalent disulfide bonds
what form of protein structure does hemoglobin example?
quaternary bc it is composed of proteins
electrophoresis purpose/ procedure
determines protein size
- proteins are run through gel
- electrical field migrates charged proteins
- smaller they are, the further they fall into the gel
- separated by size bc of molecular weight
what is the solution used in electrophoresis and it’s properties?
sodium dodecyl sulfate. negatively charged
has hydrophobic side and hydrophilic side
what is western blotting
technique to identify and locate specific individual proteins in a sample of membrane
what is the central dogma of molecular biology
DNA copies itself through replication transcription translation polypeptide is formed\
DNA-> RNA -> protein
what are the purines
adenine and guanine
what are the pyrimidine
thymine and cytosine
what is a deoxyribonucleoside
base plus a sugar molecule
what is a deoxyribonucleotide
deoxyribonucleoside plus 1-3 phosphate groups
called mono, di, or triphosphate
what direction does DNA go?
5’ to 3’ direction
what is a phosphodiester bond
nucleosides joined together by a common phosphate group
what is a prerequisite to adding onto the DNA strand
3’ end has to be free to add anything on to the strand
What is the tetranucleotide hypothesis
levene discovering the 4 bases, deoxyribose, and phosphate. Believed DNA was composed of equal amounts of A, C, G, T in repetition
explain the transforming principle experiment
- living s cells are injected and mouse dies of pneumonia
- living r cells are injected and mouse is healthy
- heat killed s cells are injected and mouse is healthy
- living r cells and heat killed s cells are injected and mouse dies of pneumonia
what was the outcome of the transforming principle? what did it tell us?
the live r strain converted into the s strain. Something must allow the transfer of material to occur, causing sickness. The transforming principle is the DNA
what supports DNA as the transforming principle
treatment of s cells with deoxyribonuclease eliminated transforming activity
whats the purpose of bacteriophage infection
it’s on form of replication
explain the process of lytic bacteriophage infection
1) attachment of phage to cell
2) entry of phage and degradation of host DNA
3) synthesis of viral genome
4) assembly of phage replication
5) release of phages
what did the hershey-chase experiment study?
studied if proteins or DNA were the genetic material
method of hershey-chase experiment
injected sulfur labeled proteins vs injected phosphorus labeled DNA
what was the outcome of the hershey-chase experiment
experiment supported DNA as the hereditary genetic material
what did chargaff discover while studying DNA
DNA has varying molar amounts, countering tetranucleotide hypothesis of all 4 bases being equal
what is chargaffs rule
double stranded DNA must have equal A-T concentrations and G-C concentrations
in what direction does the two strands of DNA twist?
right handed twist, antiparallel
one goes 3’-5’ and other goes 5’-3’
how many hydrogen bonds do the bases have
A and T have 2 H bonds
G and C have 3 H bonds
what make up the backbone of the helix?
phosphate and deoxyribose
what is the helix diameter
2.0 nanometers
the structure repeats itself after how many base pairs
about 10.5
which ends of the DNA strands have a phosphate group and an OH
5’ has phosphate
3’ has OH
the watson crick form of DNA is referred to as what?
B-DNA
what is the most compact form of DNA
A-DNA
what is the dominant form of DNA
B-DNA
what is the major difference between B-DNA and A-DNA
A-DNA is NOT perpendicular to the helix axis while B-DNA IS
which form of DNA is left handed
Z-DNA
which has the least and most base pairs per helical turn
least- B-DNA
most Z-DNA
which is more functional, DNA or RNA
RNA
what does mRNA do?
product of transcription, encodes proteins
what does rRNA do?
structural and enzymatic component, translation machine
what does tRNA do?
loads amino acids into the ribosome
how is the second DNA sequence strand written
it is complementary to the original, the 5’ and 3’ are written in the opposite direction
What is the most common form of RNA structure
stem loop
what forms of RNA are involved in protein synthesis
tRNA and rRNA
what causes nucleic acid strands to separate (denature)
heat and alkani
what are helicases
use energy to pry apart DNA strands to access the genetic info
what is hybridization of nucleic acids
complementary single-strand can reform double stranded molecules
what is the job of DNA polymerase
makes new strands by adding free nucleotides to the 3’ daughter strand (dsDNA, not ssDNA)
molecular cloning
isolation of a DNA sequence and its insertion into a vector for propagation
what are plasmid vectors
small DNA circles that are physically separated from chromosomal DNA and can replicate independently
how does temperature fluctuate based on percentage of G-C
the temp rises as percentage of C-G increased
what are restriction enzymes
bacterial enzymes found in bacteria, that protect from bacterial viruses called phages
how do restriction enzymes work
recognize, blind to, and cut short specific sequences, that are palindromic (can be read the same forward or backward)
what is an isoschizomer
new restriction enzyme that that cuts the same sequence as a known restriction enzyme
why doesn’t bacterial DNA get degraded by restriction enzymes
bacteria produced and add methyl groups to the sequence, preventing digestion by the restriction enzyme
by what are digested restriction enzymes catalyzed
DNA ligase
how do sticky ends play a role in the RE catalyzation
overhang of complementary single stranded sticky ends
explain plasmids transformation and selection processes
- ligation products are placed into bacteria
- heat shock
- some bacteria then takes up the plasmid (some don’t)
- place bacteria on antibiotic plate
- bacteria with a plasmid are capable of making a colony
explain blue-white screening
blue color can be detected of the colonies with a x-gal chemical
what is a genome
genetic material of an organism (DNA in all organisms)
which chromosomes are linear and which are circular
prokaryotic = similar eukaryotic = linear
explain genome coding
regions that encode m/t/rRNA
explain genome functional non-coding
regions that regulate gene expression, do not encode protein sequences
explain nonfunctional genome coding
transposable elements–DNA sequence that can change its position in the genome
describe the relationship between genome size/ gene number and organism complexity and EXPLAIN
there is no relationship between the two. A majority of DNA in large eukaryotic genomes is not protein coding
non-protein coding DNA encodes
tRNA, rRNA, and regulatory RNA
whats a promoter
binding sites for general transcription factors
whats an enhancer
binding site for sequence-specific transcription factors
how does the enhancer find the promoter
DNA looping
whats an insulator
site that forms a boundary between different chromatic structures or enhancers
whats a silencer
denies gene expression
what are centromeres
part of chromosome thats responsible for cells ability to properly segregate sister chromatids during cell division
what are telomeres
the ends of eukaryotic linear chromosomes that contain repeated DNA sequences
ribosome function
synthesize proteins in the cell
what percent of RNA is rRNA
80-90 percent in a cell
a single copy of a human genome has about how many rDNA genes
200 ish
what are nucleolar organizer regions
genome regions that contain clusters of rDNA genes
what is a transposable element
“jumping gene” that can change its genomic location
what are the 2 classes of TEs
class 1: copy and paste class 2: cut and paste
TEs make up about what percentage of the human genome
44 percent
how were TEs discovered
found insertions that could change the color of maize kernels, but “crossing” genetics
what happens to the kernel color gene when Ds is involved
it becomes inactivated
what connection did McClintock find between kernel color and element movement
kernel color correlated with Ds element movement by specific breaks in chromosomes
what comprises the majority of non-protein coding DNA in most eukaryotes
transposable elements
what 2 chromosomal sites were required to observe jumping behavior of TEs
dissociation element Ds
Activator element Ac
what energizes the Ds to make it move
The Ac element supplies transposase
describe class 1 TE
DNA is copied into a RNA intermediate and placed back into genome at a new site
describe class 2 TE
DNA is cut out, with NO intermediate and placed back into the genome at a new site
what is the human genome project
sequenced the entire human genome within 15 yrs with billions of dollars
what is the most abundant TE in the human genome
Alu, about 10.7 percent
most bacteria TEs use what class mechanism
cut and paste (class 2)
what is a mutagen
something that causes mutations
TEs can cause mutations by
jumping into a gene, causing the it to become nonfunctional
improper repair of DNA gaps, cause by its leaving
what are real life example of diseases that TEs can cause
cystic fibrosis, cancer, hemophilia etc
pseudogenes
relatives of functional genes that lost expression/ ability to encode proteins
what are the 3 types of pseudogenes
processed
unprocessed
unitary
what was the first significant part of the human genome to be sequences
mitochondria DNA
why are organelle genomes circular
endsymbiotic theory, resembling bacterial genomes
explain processed pseudogenes
created by reverse transcription, which integrated back into genome without mutation sequences, therefore are dead on arrival
how are non-processed pseudogenes created
gene duplication
how were unitary pseudogenes created
bu disabling mutations in a gene, not involving reverse transcription or duplication
what shape does mitochondria and plastids take on
circular
human mtDNA encodes how many genes
37
