Exam 1 Flashcards
what 3 amino acids can be phosphorylated?
serine, threonine, and tyrosine
what is an allosteric interaction?
when molecules bind at alternative sites rather than the active sites, still allows them to control the protein and influence it
what happens if you change the pH of a cell?
it drastically changes the molecular shape & alters the chemistry of the entire region (area) of the cell
What are the different types of cells?
(unicellular) bacteria & yeast
(multicellular) animal & plant
gametes (sex cells)
Are viruses considered to be a living cell? why or why not?
no, they’re not considered to be a living cell. this is because viruses have to have a host in order to live and reproduce, whereas animal or plant cells are self replicating and don’t need the DNA of a host to multiply.
What instructions do genes provide?
form, function, and behavior of cells and organisms
describe a catalyst.
a molecule that can facilitate a chemical reaction without being consumed or changed
what is the reason for cells varying forms and functions?
all cells have different jobs within the body, and those different jobs (functions) require a variety of forms. for example, a neuron is used to send out electrical signals to the body and it has a cell body with dendrites protruding from the sides, whereas a skin cell is used as a layer of protection and balance for your body and is a pretty uniform “square” shape
explain central dogma.
theory that states that genetic information can only flow one way, and that way is DNA, RNA, and then proteins, or just directly from RNA to proteins
what are the 4 amino acids?
adenosine, thymine, guanine, cytosine
what induces the internalization of the COVID-19 virus?
the spike proteins binding with ACE2 receptors
animal and plant DNA is located within the nucleus, where is the DNA material in bacteria cells located?
it is incorporated within the cytoplasm of the cell
what advancements did the light microscope help to make happen?
the discovery of cells and the idea that cell come from other preexisting cells
what cell components did the light microscope reveal?
nuclei, cytoplasm, organelles, sub cellular structures, cell ultrastructure, specific molecular locations
chromatic dyes
presence of nuclei
interference contrast
nuclei, cytoplasm, organelles, sub cellular structures
electron microscope
cell ultrastructure
fluorescence microscopy
specific molecular locations, subunits composed of fiber, molecules as components of vesicles
why do you have to “embalm”, or remove the water, from cells in electron microscopy and interference contrast?
if there is water in the cell the light will refract off of it and wouldn’t allow us to see into the cell
what is resolution?
the ability to distinguish between two points
conventional light microscopy
allows us to magnify cells up to 1000x and resolve details as small as 200 nm
fluorescence microscopy
cells are stained with fluorescent dyes, similar to light microscope except light is passing through two filters (yellow). first filter filters the light, second filter blocks out the light and only allows wavelengths that excite the particular fluorescent dye to reach the specimen, uses “reflective” light and mirror to control wavelength
transmitted light microscopy
uses laser light that is transmitted THROUGH the specimen
what kind of cell has a singular circular chromosome?
prokaryotic cells
prokaryotic cell features
no nuclei
very few compartments
most diverse & numerous cells on Earth
divided into 2 domains: bacteria & archaea
eukaryotic cell components
nucleus, mitochondria, chloroplast, internal membrane, cytosol, cytoskeleton
nucleus
stores information
mitochondria
generates useable energy from food molecules
chloroplast
capture energy from sunlight
internal membrane
creates intracellular compartments all with different functions
cytosol
concentrated aqueous gel that contains large and small molecules, highly dynamic (not static)
cytoskeleton
responsible for directed cell movement
what is chromatin and where is it located within the cell?
DNA & associated structural proteins, it is located in the nucleus
what are the two types of chromatin and what are their characteristics?
heterochromatin: condensed, packed, genes less available for expression
euchromatin: dispersed, open form, open for gene expression
what are the prokaryotic qualities of the mitochondria?
has independent genetic system
contains circular DNA
contains ribosomes that are more similar to prokaryotic ribosomes than eukaryotic
why does the mitochondria have a convoluted inner membrane?
it contains proteins for energy production, the convoluted inner membrane gives the cell more surface area for energy production
smooth endoplasmic reticulum function
stores lipids and proteins, not decorated with ribosomes
rough endoplasmic reticulum function
site of protein synthesis for proteins destined for secretion or membrane proteins, studded with ribosomes
symbiosis theory: the origin of the mitochondria
suggests that mitochondria are descended from specialized bacteria that somehow survived endocytosis by another species of prokaryote or some other cell type and became incorporated into the cytoplasm
Golgi apparatus functions
site of molecular sorting
packaging and modifying proteins & lipids destined for specialized regions of the cell
site of glycosylation
what is glycosylation?
carbohydrate modification of of proteins and lipids
cytoskeleton function and structure
composed of three major filament systems
required for structural maintenance of compartments: ER, Golgi, etc
responsible for directed movements, cell shape, and cell motility
what are the 3 different types of cytoskeleton filaments?
actin, microtubules, and intermediate filaments
microtubule function
reorganized to form mitotic spindles to segregate chromosomes in a dividing animal cell
what particle tells us atomic number?
protons
what part of a fatty acid chain carries the charge?
the carboxylic head carries the charge
why are all amino acids different
they all have different R groups
what are nucleotides made up of?
5 carbon sugar, base, and ribonucleic acid (RNA) or deoxyribonucleic acid (DNA)
what kind of impact do bonds have one molecules?
they impact how they bond with water and the shape of the molecule
can regional affects happen without any significant changes?
yes
how are macromolecules formed?
polymer formed from small molecules, like monomers, that are linked together by covalent bonds
what gives you the primary structure of macromolecules?
polymerization of the molecular subunits
will upping the charge in a cell disassemble a hydrophobic tail?
no, because hydrophobic regions run from charge in a cell
what kind of interaction can mediate between a macromolecule and a small molecule?
non covalent bonds
what does a longer half life mean for non covalent reactions?
it means they will take longer to dissociate
what competes water off of proteins and why?
things like glycerol will compete water off of proteins, this will allow the protein to have a higher chance of polymerization
can molecules with a lot of charge groups & polarity interact with water without their cells polymerizing?
yes
What do hydrocarbons associate with?
they don’t interact with water, they associate with other like non polar, hydrophobic molecules and will ultimately be displaced (oil slick on top of water)
what drives hydrophobic reactions within cells?
the collision energy of water
what kind of interactions give you a bilayer membrane?
tail to tail interactions
what do polysaccharides do for a cell?
there are a place of major storage and a structural entity used by all cells
what is glycogen?
storage form of energy in the liver of animals, is a long chain of sugars regulated by insulin
why are polysaccharides important for cells?
cell cell recognition, communication, and how cells interact with the outside environment, blood groups, etc.
What makes different isomers?
the distribution of hydroxyl and charge groups
What are oligosaccharides important for?
structure, energy storage, and molecule signaling// defines blood type
How is mobility limited in a polysaccharide?
tail to tail interactions limit mobility, and allow mobility
What is a macromolecule?
polymer formed from monomers or subunits that are linked together through covalent bonding
What does a double bond in the tail of a triglyceride mean?
that it’s unsaturated
How are bilayer membranes possible?
When there is a bubble of hydrophobic tails
Isoprenes form what basic subunit that forms the backbone of cholesterol?
isoprenoids
Why don’t cholesterol molecules spin?
they’re shape is extremely planar
Are glycolipids phospholipids? Why or why not?
They are not because they don’t have phosphate groups
What is the formula for amino acids?
Carbon, amino group, carboxyl group, r side group chain
What kind of isomers are proteins formed through?
L isomers
Does electron density restrict rotation?
Yes
What are the pyrimidines?
uracil (only found in RNA), cytosine, and thymine
What are the purines?
adenine and guanine
What part of the base-sugar linkage distinguishes DNA from RNA?
the 2’ carbon
What kind of proteins control where and when certain proteins are expressed?
receptor proteins
What will depolymerize a microtubule?
extreme cold
What are the two most common properties of protein folding?
alpha helix and beta pleated sheets
Is a proteins function disrupted if it’s not folded correctly?
Yes
What can abnormal folding lead to?
extreme conditions and disease states
What does every protein have?
amino terminal and carboxy terminal
Can you denature and renature (unfold and refold) in certain environments?
yes
Primary structure
amino acid sequence
Secondary structure
charge charge interaction, R group interactions
tertiary structure
water contributes to this structure
What gives a protein its shape?
R group interactions
Low energy equals…
less flexibility
Does the R group side chain also determine properties of the proteins along with shape?
yes
what kinds of disorders have been linked to the misfolding of proteins?
neurodegenerative disorders/ alzheimers, dementia, etc
A cell experiences more dysfunction when…
the aggregates get bigger
What do lysozymes do?
breakdown carbohydrates
What are 80% of medications?
natural products such as plants, microbes, etc
can you have multiple domains within the same protein? if yes can they perform different things?
yes, they can perform different things
hemoglobin has 4 subunits to the molecule, what are they?
2 alpha helixes and 2 beta pleated sheets
what is a homodimer?
2 proteins interacting with a single identical binding site
what is a homotetramer?
4 different subunits acting at different sights
is every subunit composed of the same number of amino acid sequences?
yes
explain the structural reasons for sickle cell anemia.
a single amino acid difference alters the structure to where it is still functional, however leads to a shape change of the red blood cell
is tubulin a heterodimer or a homodimer?
heterodimer
since elastin isn’t very rigid and can react, what does it allow?
it allows the tissue to stretch
After elastin stretches it…
goes back to same structure just with different folding patterns
are all r groups charged at active sites?
yes, allows them to have interactive capabilities
What happens when an antigen binding site is hit?
it starts making as many antibodies as they can as quick as they can
What happens when a substrate gets into enzyme state?
lowers the activation energy
What do hydrolysis reactions do?
break down molecules
Why do we prefer to use organic and natural things for modern medicine?
It is easier for us to deduce and synthesize ourselves
How do cells obtain energy through respiration?
they obtain energy by the oxidation of organic molecules
What do photosynthetic organisms use to synthesize organic molecules?
sunlight
What subunits do cells obtain most of their energy from?
mitochondria and chloroplast inner membranes
water is the original electron donor in…
photosynthesis
oxygen is the final electron acceptor in…
respiration
What generates ATP from ADP & phosphate?
the flow of hydrogen and protons through an ATP-synthase enzyme
What features do mitochondria and chloroplasts share?
contain own DNA & ribosomes, translate some of their own proteins, inner membranes contain protein complexes for ATP synthesis
In what way do chemical reactions proceed?
in the direction that causes a loss of free energy
Do all reactions, cellular or not, require activation energy to get them started?
yes
What do enzymes do?
convert substrates into products while remaining unchanged themselves
Are enzymes consumed during reactions?
no
Enzyme catalyzed reactions depend on…
rapid molecular collisions
What kind of interactions allow enzymes to bind specific molecules at the enzyme active site?
non covalent interactions
What is the most used activated carrier?
ATP
what is the only way to get rid of a covalent linkage?
breaking those covalent bonds
tyrosine phosphorylation is very closely related to…
cell growth, cell multiplication, cancer, etc
name the enzyme that can take away phosphate groups.
phosphatase
what are the 2 groups of protein kinases?
tyrosine & serine/threonine
what do G proteins do?
they regulate and signal the cells
what subunit allows GDP to bind to it?
the alpha subunit
describe scaffolds
structures that can serve as binding sites to recruit some interacting proteins depending on their functions
Are scaffold proteins membrane bound?
no, they are transient proteins
Are scaffold proteins membrane bound?
no, they are transient proteins
when does phase transition occur?
from protein protein interactions
