Term
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Definition
most proteins
Compact shape (ball/sphere) with irregular surfaces
Enzymes |
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Term
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Definition
Usually span long distance in the cell
3D structure; usually long, rod-shaped
Ex: hair |
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Term
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Definition
Makes about 15 percent of the cell
Performs many cell functions:
Enzymes
Structural support
Transport
Motor
Storage
Signaling |
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Term
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Definition
| Amino acids linked by peptide bonds |
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Term
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Definition
Repeating sequence of NCC
R group not included |
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Term
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Definition
| amino acid sequence of proteins |
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Term
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Definition
H bonds among atoms in peptide chain backbone (alpha helices and beta sheets)
the 2 folding patterns are due to h-bonding between N-H and C=O in the peptide backbone |
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Term
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Definition
Full 3D structure
Non covalent interactions between R groups within protein |
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Term
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Definition
Multiple subunits
Interaction between 2 or more polypeptide chains |
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Term
| What allows for rotation in proteins? |
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Definition
peptide bond
allows protein to fold |
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Term
| What can hold protein in functional shape? |
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Definition
Non-covalent interactions
though weak, many are available to hold 3D shape |
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Term
| h-bonds can form between... |
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Definition
1. atoms involved in the peptide bond (secondary structure)
2. peptide bond atoms and R groups (tertiary and quartenary structures)
3. R groups (tertiary and quaternary structures) |
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Term
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Definition
protein held in a spiral
impt to fibrous proteins (hair, nails, horns)
also found in globular proteins
formed by H-bond between every 4th peptide bond (C=O to N-H)
usually in proteins that span a membrane
can coil to right or left
can coil around each either for structure |
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Term
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Definition
individual chains held by H-bonds
impt to globular proteins
core of many proteins
form rigid structures with H-bonding
2 types: anti-parallel and parallel |
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Term
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Definition
conformation determined by primary structure (sequence of amino acids)
generally fold into lowest free energy conformation |
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Term
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Definition
special proteins
help protein fold into correct conformation |
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Term
| globular protein conformation determined by... |
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Definition
| side chains (in aqueous solutions) |
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Term
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Definition
| each polypeptide chain of a large protein |
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Term
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Definition
| region where proteins interact with one another through non-covalent bonds |
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Term
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Definition
| protein made of 2 subunits (can be same or different subunits) |
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Term
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Definition
has 2 alpha globin subunits and 2 beta globin subunits
both subunits contain heme group |
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Term
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Definition
protein can form long chains if the protein has 2 binding sites (link together as a ring)
actin fibers in muscles and cytoskeleton are made from thousands of actin molecules as a helical fiber |
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Term
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Definition
disulfide bonds form between adjacent cysteine-SH groups
can be between 2 cys within a single protein chain, or between 2 subunits making up the protein
disulfide bond often forms in ER for extracellular proteins |
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Term
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Definition
basic structural unit of a protein
distinct from conformations
part of protein that can independently fold into a stable structure
different domains can impart different functions to proteins
proteins can have one or many domains (depends on protein size) |
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Term
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Definition
similar in amino acid sequence and 3D structure
have similar functions |
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Term
| intermediate filaments of cytoskeleton |
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Definition
structural scaffold inside cell
forms keratin in hair, horns, and nails |
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Term
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Definition
binds cells together into tissues
secreted from cells, assemble in long fibers (collagen and elastin) |
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Term
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Definition
| long triple helix with glycine every third amino acid |
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Term
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Definition
unstructured polypeptides cross-linked
tissue an elastic characteristic |
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Term
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Definition
| molecule a protein can bind to |
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Term
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Definition
part of protein that interacts with ligand
cavity formed by specific arrangement of amino acids |
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Term
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Definition
example of protein family dependent on binding sites
can be created by specific cells of immune system to match with almost any molecule
also called immunoglobulins
made in response to foreign molecules (antigens)
bind to antigens tightly to inactivate them/mark them for destruction
Y shaped molecules with 2 identical binding sites at upper ends on each arm
loops of polypeptides on end form binding site where antigen binds
changes in aa sequence or in length of loops = diversity of antigen binding sites (allows for many highly specific antibodies) |
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Term
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Definition
proteins that bind to particular substrates and convert them into products
can make or break covalent bonds
active site = cavity/binding site
can be grouped depending on function |
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Term
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Definition
enzyme example
important in protecting body from bacteria
breaks bacterial cell walls making it a natural antibiotic
hydrolyzes glycosidic bond in cell wall
holds polysaccharide in position to allow water to break glycosidic bond (transition state)
non covalent bonds hold polysaccharide in enzyme active site for efficient reaction |
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Term
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Definition
sometimes a protein's atoms aren't sufficient for a specific function so it requires a non-protein molecule to enhance function
example: hemoglobin requires heme to carry oxygen
required by some enzymes
if the group is an organic molecule it is called a co-enzyme (vitamins)
if it is a metal ion, it's called a cofactor (trace metals)
may be either covalently or non-covalently linked to proteins |
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Term
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Definition
can occur at many levels
types: regulating genes, confining enzymes, possessing regulatory site |
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Term
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Definition
| end product of pathway regulates enzyme early in pathway |
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Term
| negative feedback regulation |
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Definition
pathway inhibited by accumulation of final product
prevents enzyme from working |
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Term
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Definition
regulatory molecule stimulates enzyme activity, usually between 2 pathways
example= high ADP activates glycolysis which forms more ATP |
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Term
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Definition
some proteins have 2 binding sites that communicate (an active site for substrate binding and a regulatory site for regulatory molecule binding)
protein undergoes conformational change (allosteric transition) when regulatory molecule binds; called an allosteric protein |
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Term
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Definition
used by other proteins besides enzymes (receptors, structural, and motor proteins)
example: ADP activates sugar metabolism allosterically |
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Term
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Definition
some proteins are regulated by addition of phosphate group
negative charges on phosphate can attract positively-charged side chains which creates a conformational change
reversible protein phosphorylations regulate many eukaryotic cell functions by turning functional proteins on and off
protein kinases add phosphates
protein phosphatases remove phosphate |
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Term
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Definition
each has an alcohol group
serine, threonine, and tyrosine |
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Term
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Definition
GTP-binding proteins
important to molecular switches
GTP binds tightly to protein which activates protein by transferring phosphate
hydrolysis (GTP to GDP): occurs by GTPase enzyme, GDP dissociates, deactivates protein
usually involved in cell signaling |
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Term
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Definition
proteins can move in the cell but with very little uniformity (conformational change not sufficient to regulate this process)
hydrolysis of ATP can direct movement and makes it unidirectional |
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Term
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Definition
complexes of 10 or more proteins that work together
ex: DNA replication, RNA or protein synthesis, transmembrane signaling
usually driven by ATP or GTP hydrolysis |
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Term
| ways of identifying proteins |
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Definition
| affinity chromatography, SDS-page, mass spectrometry |
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Term
| importance of DNA as genetic instructor |
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Definition
life depends on the ability of cells to store, retrieve, and translate genetic instructions
hereditary info passed from cell to cell, generation to generation |
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Term
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Definition
began in the beginning of the 20th century
1940s- scientists realized that genetic info consists primarily of instructions for making proteins |
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Term
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Definition
become visisble as cells prepare to divide
identified in the 19th century
made of nucleic acid and proteins |
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Term
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Definition
become visisble as cells prepare to divide
identified in the 19th century
made of nucleic acid and proteins |
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Term
| griffith's experiment showed... |
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Definition
| that heat-killed bacteria can transform living cells |
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Term
| hershey and chase showed... |
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Definition
| definitively that genes are made of DNA |
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Definition
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Term
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Definition
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Term
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Definition
within DNA
each code for peptide
some sequences are different for function
only portions of gene may code for amino acids
ex: human beta-globin gene |
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Term
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Definition
| will be connected with mRNA processing |
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Term
| length of human DNA in one cell |
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Definition
| about 6 ft long but packaged to fit in the nucleus |
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Term
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Definition
made of DNA + protein
wound together in chromosomes |
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Term
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Definition
| where rRNA genes cluster and replicate |
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Term
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Definition
| chromosomes extended until DNA replication |
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Term
| 3 important sequences for chromosome pairing |
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Definition
replication origin (many along eukaryote DNA)
centromere (attaches to spindle, important to pull apart pairs)
telomere (important for end replication) |
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Term
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Definition
site where replication will begin
allows DNA to open so DNA replication machinery can get in and accomplish DNA synthesis |
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Term
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Definition
series of repeated nucleotides
allows DNA replication machinery access to entire genomic sequence without losing important info |
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Term
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Definition
where microtubules attach
separates chromosomes to new daughter cells |
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Term
| interphase chromosome vs. mitotic chromosome |
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Definition
interphase chromosome is less compact
chromatin in tangle in nucleus when not replicating
DNA is in condensed form only during cell division (discourages transcription) |
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Term
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Definition
where chromosome organization starts
first level of packing
like beads on a string
string = DNA (includes linker DNA)
beads = core particles (protein core, DNA wound around core) |
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Term
| protein core in nucleosomes |
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Definition
made of 8 histone molecules
has DNA wound around it
called histone proteins (octamer)
postively charged (so they attract sugar-phosphate backbone)
equivalent mass as DNA
has 146 base pairs wrapped around histone core
linker 50 base pairs (3x compaction) |
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Term
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Definition
30 nm fibers form loops
loops form rosettes
rosettes form chromosomes
chromosomes for protein scaffolds |
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Term
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Definition
not replicating
cell "living", synthesizing proteins, metabolizing
varied amounts of packing (must unfold at regions of trasncription)
most condensed = heterochromatin (about 10% of the interphase chromosome, mostly in centromere end regions, inactive transcriptionally)
euchromatin- remainder of chromatin |
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Term
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Definition
active chromatin
varied packed states (about 10% actively transcribed or available for transcription)
least condensed
in nucleosomes, some in 30 nm fibers |
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Term
| loosening chromosome organization --> exposing DNA bases |
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Definition
must occur rapidly
chromatin-remodeling complexes
protein machines
energy from ATP hydrolysis
changes position of DNA on nucleosomes to decondensation of DNA
inactivated during mitosis |
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Term
| histones' role in exposing DNA bases |
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Definition
histone core proteins can be reversilby modified (acetylated, phosphorylated, methylated)
enzymes are found in their nucleus
apparently affect stability of 30 nm fibers and above
different patterns of modification yield different proteins associated with DNA which yield different decondensation and condensation events |
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Term
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Definition
| cell passes along info about histone modification to daughter cells |
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Term
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Definition
females have 2, males have 1
one becomes inactive and highly condensed, now called Barr body
some cells have paternal X inactive and some have the maternal X inactive (happens during early development, once inactive all cell that arise from that cell will have that chromosome inactive) |
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