Biology 1107 Exam Review - Fill in the Blank Flashcards

Flashcards in the FILL_IN_THE_BLANK style based on Biology 1107 lecture notes.

A __ bond is the strongest of the IMFs and is driven by polarity and electronegativity.

Hydrogen

__ forces are weak individually, very strong collectively, and involve brief electron interactions between molecules.

Van Der Waals

__ lipids are for energy storage and consist of Glycerol+3 Fatty acids.

Neutral

__ lipids make up membranes and are covalently bound to a PO4.

Phospholipids

__ are lipid molecules found in membranes or on their own as signaling molecules, having a skeletal base structure of 3 6-carbon rings and 1 5-carbon ring.

Steroids

The amino group is

and positively charged, the carboxylic acid group is
and negatively charged at pH 7.4.

basic, acidic

With proteins, __ DETERMINES function!!

Form

__ Structure of a protein is the actual sequence of Amino acids that a peptide is made up of.

Primary

__ Structure of a protein is caused by hydrogen bonding between the N and C termini of individual AAs in the peptide back bone.

Secondary

__ Structure of a protein is where R groups start to play.

Tertiary

__ Structure of a protein ONLY comes into play when we have multiple “subunits” in our polypeptide protein situation.

Quaternary

__ is used to note the carbon of the ribose sugar ring something is attached to.

Prime notation

The end with an exposed 5’ phosphate is called the __ end.

5’

The end with an exposed 3’ hydroxyl is the __ end.

3’

__ contains the “master copy” of all of an organisms genetic information.

DNA

__is transcribed or copied from DNA and carries the specific gene you want to make a protein from.

mRNA

Overall: A process that takes existing double stranded DNA (dsDNA) and replicates it to form 2 identical copies of dsDNA is called __.

DNA replication

__: each resultant copy contains one “parent” strand and one newly replicated strand.

Semiconservative

__ breaks apart dsDNA so that bases are no longer H-bonding to each other, causes the replication fork

DNA helicase

__ actually polymerizes a new complementary strand of DNA, READS existing parent DNA in the 3’→ 5’ direction, SYNTHESIZES an antiparallel daughter strand in the 5’→3’ direction ALWAYS, and Requires a free 3’ hydroxyl to synthesize dna, hence the predefined direction.

DNA polymerase

__ makes a primer made of RNA that DNA polymerise requires to get started

RNA primase

__ relieves tension that is a result of supercoiling of the DNA around itself, prevents it from breaking apart downstream od the replication form

Topoisomerase

__ bind to the newly separated strands of DNA to prevent them from coming back together

Single stranded binding proteins

__ catalyzes phosphodiester bond formation between fragments of DNA that are part of the same strand

DNA ligase

__ are fragmented pieces of DNA that were created during replication.

Okazaki fragments

The process that transcribes or copies information in one form, DNA, into another form, RNA is called __.

Transcription

__ reads the DNA in a 3→5 direction and writes new, complimentary RNA in a 5→3 direction.

RNA polymerase

Translating the code of RNA into actual proteins that the body can use is called __.

Translation

__ is read by the ribosome in sets of 3 nucleotides.

RNA

__- transfer RNA, Can be charged with a specific amino acid by an enzyme called aminoacyl tRNA synthetase, and Contains an anticodon, a 3 base pair sequence that is complementary to the codon.

tRNA

After association with a ribosome, the ribosome scans the RNA for the __ – AUG (adenine, uracil, guanine), which codes for the amino acid methionine.

start codon

__- cuts the bond between the AA/peptide bound to P site tRNA and transfers it on top of the new AA bound to the A site tRNA.

Peptidyl transferase

There are 3 __ codons: UAA, UGA, UAG. After the stop codon is read by the ribosome, GTP and release factors release the newly synthesized polypeptide from the attached tRNA

stop

Cell membranes are __ layered.

DOUBLE

__- contain a sugar group, usually involved in immune recognition

Glycoproteins

__- channels, pumps, carriers, that let things that normally cannot pass through the membrane in or out

Transport proteins

__- involved in cell signaling

Receptor proteins

Small,

molecules can sneak past the smaller
heads and ALSO survive the nonpolar membrane interior for free entrance/exit

Nonpolar, hydrophobic

__ Transport- requires no external source of energy for transport. Uses solely energy found in a molecule’s electrochemical gradient to push itself

Passive

__ Diffusion- DOWN an electrochemical gradient, Goes through lipid bilayer ALONE. NO protein help

Simple

__ Diffusion- DOWN an electrochemical gradient, Requires a transport protein to give it a path through the membrane, REQUIRES a transport protein

Facilitated

__ active- Involves use of an energy carrying molecule ATP, GTP, etc to active give a protein energy to PUMP a molecule or ion AGAINST its concentration gradient

Primary

__ active- Uses an EXISTING concentration gradient. Allows one thing to go in its gradient direction to provide energy to push another molecule against its concentration gradient

Secondary

__- the Michaelis constant, the substrate concentration at which we have reached HALF of the maximum velocity

Km

__- the maximum rate of reaction we can achieve with a given amount of enzyme

Vmax

__- Bind at the active site to prevent substrate binding. Increase Km, no affect Vmax

Competitive

__- Bind at the allosteric site to either prevent substrate binding OR any reaction with a bound substrate. No effect on Km, decreased Vmax

Non competitive

A __ is a protein capable of binding a GTP/GDP molecule and is Generally found anchored to cell membrane interior.

G protein

__ is an effector enzyme that turns ATP into cyclic AMP (cAMP).

Adenylyl cyclase

__ an effector enzyme that cleaves a membrane lipid PIP2 into two products: DAG- Diacylglycerol, and IP3- Inositol Triphosphate

Phospholipase C

__ - Generally, cause changes in gene expression, are Transmembrane proteins with extracellular and intracellular regions, Ligand binds extracellularly, and Dimerize (2 subunits come together) upon ligand binding.

Receptor Tyrosine Kinases

Individual reactions within metabolic pathways CAN be __.

nonspontaneous

__ reactions= Reduction-oxidation reactions. Reactions in which chemicals and molecules gain or lose electrons.

Redox

__ is losing (electrons).

Oxidation

__ is gaining (electrons)

Reduction

__- Series of redox reactions that oxidize Acetyl CoA into CO2, transferring electrons to NADH and FADH2.

Krebs Cycle/Citric Acid Cycle

__- Transfer of electrons from NADH and FADH2 through protein complexes, releasing energy that later allows for the phosphorylation of TONS of ADP into ATP.

Oxidative phosphorylation

__- the oxidation of glucose into pyruvate

Glycolysis

__- the oxidation of pyruvate into Acetyl CoA

Pyruvate oxidation

__- This is where we cash in all of our NADH and FADH to make tons of ATP during oxidative phosphorylation

Oxidative Phosphorylation

__Used by humans, Glucose →2 Pyruvate → 2 Lactate

Lactic Acid Fermentation

__Does not occur in humans, Pyruvate → Acetaldehyde→reduced to Ethanol

Ethanol Fermentation

What is a Hydrogen bond in the context of intermolecular forces (IMFs)?

A hydrogen bond is the strongest type of intermolecular force and is driven by polarity and electronegativity.

What are Van Der Waals forces?

Van Der Waals forces are weak individually, very strong collectively, and involve brief electron interactions between molecules.

What is the purpose of Neutral lipids?

Neutral lipids are for energy storage and consist of Glycerol and 3 Fatty acids.

What are Phospholipids?

Phospholipids make up cell membranes and are covalently bound to a phosphate group (PO4).

What are Steroids?

Steroids are lipid molecules found in membranes or on their own as signaling molecules, characterized by a skeletal base structure of 3 six-carbon rings and 1 five-carbon ring.

What charge does the amino group carry at physiological pH?

The amino group is basic and positively charged at pH 7.4.

What charge does the carboxylic acid group carry at physiological pH?

The carboxylic acid group is acidic and negatively charged at pH 7.4.

How does the form of proteins impact their function?

In proteins, form determines function.

What is the Primary structure of a protein?

The primary structure of a protein is the actual sequence of amino acids that a peptide is made up of.

What defines the Secondary structure of a protein?

The secondary structure of a protein is caused by hydrogen bonding between the N and C termini of individual amino acids in the peptide backbone.

What is the Tertiary structure of a protein?

The tertiary structure of a protein is where side chains (R groups) start to interact and influence the overall shape of the protein.

What is the Quaternary structure of a protein?

The quaternary structure of a protein is the arrangement and interaction of multiple polypeptide subunits.

What is Prime notation in biochemistry?

Prime notation is used to note the carbon of the ribose sugar ring to which something is attached.

What is the 5’ end of a nucleic acid?

The end with an exposed 5’ phosphate is referred to as the 5’ end.

What is the 3’ end of a nucleic acid?

The end with an exposed 3’ hydroxyl is referred to as the 3’ end.

What does DNA contain?

DNA contains the 'master copy' of all of an organism's genetic information.

What is mRNA?

mRNA is a form of RNA that is transcribed or copied from DNA and carries the specific gene used to make proteins.

What is DNA replication?

DNA replication is the process that takes existing double-stranded DNA (dsDNA) and replicates it to form two identical copies of dsDNA.

What does 'Semiconservative' mean in the context of DNA replication?

Semiconservative replication means that each resultant copy contains one 'parent' strand and one newly replicated strand.

What is the role of DNA helicase in DNA replication?

DNA helicase breaks apart dsDNA so that bases are no longer hydrogen-bonded to each other, creating the replication fork.

What is the function of DNA polymerase?

DNA polymerase polymerizes a new complementary strand of DNA, reads existing parent DNA in the 3’->5’ direction, synthesizes an antiparallel daughter strand in the 5’->3’ direction, and requires a free 3’ hydroxyl to synthesize DNA.

What is RNA primase?

RNA primase makes a primer made of RNA that DNA polymerase needs to start DNA synthesis.

What is the function of Topoisomerase?

Topoisomerase relieves tension resulting from supercoiling of the DNA, preventing it from breaking apart downstream of the replication fork.

What do Single stranded binding proteins do?

Single stranded binding proteins bind to the newly separated strands of DNA to prevent them from re-annealing.

What is the role of DNA ligase?

DNA ligase catalyzes phosphodiester bond formation between fragments of DNA that are part of the same strand.

What are Okazaki fragments?

Okazaki fragments are fragmented pieces of DNA that were created during replication.

What is Transcription in molecular biology?

Transcription is the process that transcribes or copies information from DNA into RNA.

What is the role of RNA polymerase?

RNA polymerase reads the DNA in a 3’->5’ direction and writes new, complementary RNA in a 5’->3’ direction.

What is Translation in the context of genetic expression?

Translation is the process of translating the code of RNA into actual proteins that the body can use.

How is RNA read during Translation?

RNA is read by the ribosome in sets of 3 nucleotides.

What is tRNA?

tRNA (transfer RNA) can be charged with a specific amino acid by an enzyme called aminoacyl tRNA synthetase and contains an anticodon that is complementary to the codon in mRNA.

What is the start codon in mRNA?

The start codon is the sequence AUG (adenine, uracil, guanine) that codes for the amino acid methionine.

What is the function of Peptidyl transferase?

Peptidyl transferase cuts the bond between the amino acid/peptide bound to the P site tRNA and transfers it on top of the new amino acid bound to the A site tRNA.

What are stop codons?

There are 3 stop codons: UAA, UGA, UAG, which signal the termination of protein synthesis when read by the ribosome.

What is the structure of cell membranes?

Cell membranes are double-layered.

What are Glycoproteins?

Glycoproteins are proteins with a sugar group attached, usually involved in immune recognition.

What are Transport proteins?

Transport proteins include channels, pumps, and carriers that allow substances that normally cannot pass through the membrane to enter or exit.

What are Receptor proteins?

Receptor proteins are involved in cell signaling.