Unit 1 Flashcards
What are proteins made of
Amino acids
How are proteins joined together by
Peptide bonds
What are the functions of proteins in cell
Speed up the rate of chemical reactions, & move cells
How many different type of amino acids are there
20 types
What are fatty acids made up of
Long chains of carbon bonded to one another & to hydrogen atoms
What are triglycerides
Have 3 fatty acid chains attached to a glycerol molecule
What are phospholipids
a lipid containing a phosphate group in its molecule
What are carbohydrates made up of
Monosaccharides
What do carbohydrates do
Act as energy storing molecules in many organisms
What are monosaccharides
simple sugars
What are complex carbohydrates
Monosaccharides bonded together
What are the macromolecules
Sugars, fatty acids, amino acids, & nucleotides
Small organic building blocks (sugar, fatty acids, etc.) build what
Large organic molecules of the cell such as polysaccharides glycogen & starch in plants, fats & membrane lipids, proteins & nucleic acids
What is the central dogma; & what is the steps
DNA to protein
DNA to RNA to protein
What is a gene
Portion of DNA that encodes info needed to synthesize a specific protein
Transcribed
Changed into to
Transcription
The first step of gene expression in which RNA is made
Translation
Specific protein is synthesized from a code of the RNA transcript
Having a codon, means having what
3 nucleotides
Having 3 nucleotides means
Having a codon
What does RNA have
Info to build a protein
What is the RNA transcript divided into
3 base codons
Where does the translation start
Start codon
where does translation stop
Stop codon
What is the promoter & what does it do
The promoter is the Dna being ready to make the transcription happen but NOT the start codon
What does upstream mean
Before
What does downstream mean
After
What is RNA polymerase?
Transcription
What is the terminator
The stop site or stops the process of transcription
-ASE
Deals with enzymes
What do transcription factors do
Bind to protein & regulates DNA to mRNA
what are transcription factor binding sites
Proteins with DNA binding activity that are involved in the regulation of transcription
what does template strand mean?
The DNA sequence that can duplicate itself during mRNA synthesis
what does consensus sequence mean
A consensus sequence is a sequence of DNA, RNA, or protein that represents aligned, related sequences
What does it mean when a Transcription factors can be master regulators
a gene at the top of a gene regulation hierarchy, particularly in regulatory pathways related to cell fate and differentiation.
What are exons
Regions of the transcript that contain codons that code for protein
What are Intron
a segment of a DNA or RNA molecule which does not code for proteins and interrupts the sequence of genes.
BACTERIAS DONT HAVE WHAT
INTRONS BECAUSE THEY ARE GENES
What can be selectively removed & retained to increase the diversity of transcripts & what is the offical name for it
Introns
Alternative splicing
What is the start codon
AUG
If the mRNA transcript codons are shifted by one letter what would happen
Change the sequence & will go back to the original on the third shift
What are the stop codons
UAA, UAG, UGA
What does degrading protein mean
Remove protein cell
What can an inactive protein do
Change how a pathway is working
Protein are made of what
Amino acids
What binds amino acids
Peptide bond
N terminus
Beginning of polypeptide chain
C-terminus
End of polypeptide chain
What determines how the protein folds
R group
What is van deer walls attraction
Interaction between hydrophobic amino acids
What helps assist with protein folding
Chaperons
What are chaperones
Proteins that assist in protein folding
What are the two common protein folding pattern
Alpha Felix and beta sheet
When folding what does it contain
Alpha and beta patterns because of hydrogen bonding
How many steps are there in the protein structure
4
What are the 4 main protein structure; out of all of these which one is where a lot of important stuff happens
Primary protein
Secondary protein
Tertiary protein (Important, and chaperones are here)
Quaternary protein
-ase
Enzymes
What do enzyme do
Help speed or start chemical reaction
Where do enzymes bind
Substrate and active site
Kinase
Enzyme that transfers a phosphate group from atp to another protein, changes the protein structure, turns it on or off, protein count stays the same and RNA as well
Competitive inhibition
Competiting to bind and prevents reactions
Non-competitive inhibition
Inhibitor binds to an allsteric site altering the protein conformation, use to activate or deactivate
what determine which protein is selected for degradation?
Ubiquities-protea some system
Ubiquities-protea some system
This enzyme puts on a protein that states that this needs to be degraded; it then goes to the trash so not all of them are taken out
proteasome
The trash can that proteins are disassembled
Glucose is used for what
ATP
What is a oligosaccharides
2-10 monosaccharides units
What are polysaccharides
Form hundreds or thousand of monosaccharides
Condensation reaction
One unit of OH and another react to each other
What is hydrolysis
Carbohydrate polymers can be broken
Condensation and hydrolysis are reversable? T or F
True
What happens in condensation
H2O is expelled and makes a chain
What happens in hydrolysis
Water is consumed and it breaks down chain
Glycosidic bond
Unit of glucose
Is hydrophilic head region reactive
Yes
Is hydrophobic tail region reactive
No
Saturated
Double bond
Unsaturated
Single bond
What do phospholipids make up
2 Cell membrane
What caused bending in the hydrophobic tail
Saturated bond
What does ATP stand for
Adenosine TriPhosphate
What do phosphoanhydride bonds produce
Lots of energy
How many parts is ATP divided into & what are they
Adenine, ribose, & phosphate
ATP hydrolysis yields?
ADP
ADP hydrolysis yields
AMP
What is the process of getting glycolysis & at the end what do you get
Polysaccharides -> simple sugars -> glucose -> GLYCOLYSIS -> pyruvate
Where does glycolysis occur
Cytoplasm
Result of glycolysis produces and what is the net gain?
2 ATP/ Pyrite
What happens when too much atp is produced
Negative feedback occurs & inhibits Hexokinase, Phosphofructokinase(PFK) & pyruvate kinase
What does PFK mean
Phosphofructokinase
What happens when too little ATP happens
Glycolytic enzymes active PFK & pyruvate kinase
PFK is dual regulated? T or F
True
What does allosterically mean?
Hydrophobic and Hydrophilic
What does the allosteric activator & inhibitor do
Repress & boost its
Once pyruvate gets converted to Acetyl-CoA and enters the mitochondria what is it called
Citric Acid cycle
what does NADH & FADH_2 do
Donate electrons
What does carnitine acyltransferase do
Modifies fatty acid (Oxidation)/ transfer channel
What is Beta- oxidation
Fatty acids to Acetyl CoA
After the fatty acid is modified it goes through a transporter channel called what
Carnitine acyltransferase 1 & 2
Where are the matrix, inner membrane, outer membrane, & intermembrane space located int he mitochondria
Matrix- gray space? open space :)
inner membrane- in between inner & outer membrane
outer- outside wall
inner- inside wall
What does dynamic mean
Changing
where is there high production of ATP
Intermembrane of mitochondria
Oxidative phosphorylation
Electron passing through
what does OXPHOS mean
Oxidative Phosphorylation
purpose of OXPHOS
Electron flow across complexes
Two stages to OXPHOS
1) Energy of electron transport is used to pump protons across membrane
2) ENERGY IN THE PROTON GRADIENT IS HARNESSED BY ATP SYNTHASE TO MAKE ATP
How many complexes are there
4 for atp synthesis, they pass the electron over to the next till its to the goal or ATP
What is the endosymbiosis theory
Agent cells engulf a cell & became a mitochondria
What is hydrolyze ATP
reverse synthase & pump protons back into the intermembrane space
Compare & contrast Carbohydrates & Lipid (SODAS)
C- short term storage L- Long term storage
C- More readily digested L- Less easily digested
C- Stores half as much ATP L- Stores twice as much ATP
What is autophagy & how many membrane?
Self recycling of cellular material & compose of a double membrane
What is the largest organelle in the cell
Endoplasmic reticulum
Endoplasmic reticulum
Network of membrane enclosed tubules & sacs
Rough ER function
synthesis protein
Smooth ER function
Detoxify & lipid metabolism
Order of secretory pathway
ER -> Golgi apparatus -> secretory vesicles ->outside of cell(Secreation)
Do ER protein use a common set of ribosomes? T or F
True
Contranslational
Transportation to compartment as its getting translated
Order of docking the ribosome to the ER membrane
Er protein synthesis -> Er signal sequence(Info stored) -> Signal recognition particle (SRP) (NONMEMBRANE) -> SRP receptors (receives) -> Protein translator (Last step)
What does SRP
Signal recognition particle
Peptidase
PEPTIDE ENZYME
What does the signal peptidase do
Chopped off signal peptide because it is hydrophobic
endocytosis
Removal of plasma membrane components to be delieverd to internal structure
Exocytosis
Secretory pathways delivers protein, carbohydrates, or lipids to plasma
Lumen
Opening or Hole
What does it mean when a pathway has directionality
Vesicles have direction or go one way
Coated vesicles
Protein coat vesicles to give direction
What are the fuctions of coated vesicles
Concentrates the cargo protein inside the vesicles (Concentrate/Max cargo protein)
Provides the shape to the vesicle by bending the membrane around (Give shape)
What are the three different coated vesicles
Clathrin-coated: Golgi -> Plasma membrane
COP1 coated vesicles: Golgi -> ER
COP2 coated vesicles: Er -> Golgi
How do coated proteins get added on or removed
Proteins called GTPases
What are GTPases
Enzymes that are for cell signaling (On or Off)
What happens when GTPases binds to GTP
hydrolyzes it & becomes GDP Nd is considered off
What happens when GTPases is bind to GDP
GDP make it turn off
What does GTPases regulate two proteins
GAP (GTPases activating Protein)
GEF ( Guanine Exchange Factor)
GAP binds to GTPase
Makes hydrolyzation happen to GDP, & GAP turns off GTPases
What does GEF do
It exchange the GDP of GTPases for GTP, turning on GTPases
What are the two main group
ARF GTPase & Sar1 GTPase
ARF GTPase
Regulates COP1 & clathrin coat assembly
SAR1 GTPase
Regulate COP2 coat assembly
COP2 vesicles bud from where & do what
ER membrane & regulated by the Sar1 GTPase
What is Sar1 GTPase involved in
Disassembling the COP2 vesciles & hydroluyes GTP to GDP
What is the area being curved in a membrane bending protein called
BAR domain
What is Dynamin
A type of GTPase & a lipid binding domain
How does the cell maintain?
Specific protein mediate this; teather needs to have a specific protein?????
