Biology Exam 2

Mutation Type: Frameshift Change in amino acid sequence/codon Impact on Protein

- All codons after insertion or deletion of mRNA base are changed. - Huge differences in amino acid sequence and protein structure and function.

Mutation Type: Missense-Conservative Change in amino acid sequence/codon Impact on Protein

- Codon changes and amino acid also changes. However, new amino acid has same molecular characteristic. - Could have no impact or slight impact depending on the protein, the substitution and degree of change to protein structure.

Mutation Type: Missense Non-conservative Change in amino acid sequence/codon Impact on Protein

- Codon changes and amino acid also changes. New amino acid has different molecular characteristic. - Typically a large difference in protein structure and function. Since new amino acid has different molecular characteristic, bonds that are usually formed are not form, and new bonds can be made giving a different 3-D structure. Could also have slight impact, again depending on the protein and the substitution.

Mutation Type: Silent Change in amino acid sequence/codon Impact on Protein

- Codon changes but amino acids does not because of the redundant/degenerate property of the genetic language - No impact, primary to tertiary structure of protein is unchanged thus function is maintained.

Mutation Type: Nonsense Change in amino acid sequence/codon Impact on Protein

- Codon changes to a stop codon, ending translation early. - Truncated (short) protein. Could have huge impact if new stop codon is early in the mRNA transcript. Could have slight impact if new stop codon is later in the transcript.

Activate a transcription factor to change gene expression. Nonpolar Hormone

passes through cell membrane, binds to transcription factor in cytoplasm causing a conformation change so the transcription factor can pass into the nucleus

What are the components of blood?

plasma, white blood cells, platelets, red blood cells

What two main things need to happen before a cell can use the resources from a cheeseburger?

1. Breakdown of molecules 2. Absorption of monomers (carbs/sugars & proteins/amino acids) or smaller molecules (fats)

initiation (transcription)

4 things need to occur in order to initiate transcription: 1. Open chromatin arrangement 2. Gene-specific transcription factors bind DNA in activating orientation: activators bound & repressor removed 3. General transcription factors bind DNA & make a beacon 4. RNA polymerase locates beacon & binds DNA

A cell lining a gland in your skin that secretes sweat is likely a(n) A. epithelial cell B. component of the extracellular matrix C. muscle cell D. neuron

A

In a differentiated cell, if a gene region of DNA is in an open-looped chromatin structure (euchromatin) it.... A. codes for a protein that needs to be made for proper cell function B. codes for a protein that does not need to be expressed in this type of cell C. either A or B could be correct because all genes are in open chromatin structure regardless of whether they are expressed in a certain cell type

A

In a human with sickle cell anemia, a point mutation in the gene encoding hemoglobin causes a hydrophobic valine to replace a negatively charged glutamic acid. What type of point mutation is this? A. Non-conservative B. Conservative C. Nonsense D. Silent

A

RNA polymerase A. creates mRNA transcripts using DNA as a template B. creates proteins from mRNA transcripts

A

The chemical breakdown of which macromolecules begins in the mouth? A. Carbohydrates B. Proteins C. Fats D. Nucleic Acids E. All of the above begin breaking down chemically in the mouth

A

mRNA is synthesized in this direction by RNA polymerase A. 5' to 3' B. 3' to 5' C. Either direction

A

Transcription factor - nonsense mutation

A nonsense mutation early in the gene thus mRNA transcript will truncate the protein and make it very short. It will not be able to bind to the sequence of DNA that it recognizes. If it is a TF that activates a gene, the target gene will not be transcribed.

Primase

Adds RNA primer to DNA so DNA pol III can bind and start

Describe the path of blood flow from the small intestine to a cell in your toe

After absorbing monomers from the digestive system in the small intestine, blood travels via the hepatic portal vein to the liver where blood content is monitored. Blood then enters the inferior vena cava and travels to the right side of the heart. There it is pumped through the pulmonary circuit, first to the lungs, then back to the left side of the heart. Next it is pumped into the system circuit eventually taking a path of arteries to your toe.

Describe the 'problem' with lagging strand synthesis (use vocab words like primase, Okazaki fragment, DNA polymerase, and strand polarity and directionality of enzymes). How do telomeres protect chromosomes against this problem? How does telomerase protect against this problem?

After helicase opens up a replication fork ready for DNA replication, primase creates RNA primers on regions of DNA using the DNA as a template. This DNA/RNA helix creates a double strand for DNA polymerase to bind. DNA polymerase can only bind to a double-stranded nucleic acid. These gaps of RNA in the DNA double helix are eventually filled in with DNA nucleotides by DNA polymerase. Two main things create the 'problem' the lagging strand synthesis: (1) The strands of the DNA double helix are antiparallel (one goes in the 3' 5' direction and the other in the 5' 3' direction (review DNA structure, nucleotide constituents, and bonds if this does not make sense). (2) DNA polymerase can only read DNA in the 3' 5' direction and synthesize DNA in the 5' 3' direction. As the lagging strand is synthesized, short fragments (Okazaki fragments) of double stranded DNA are made as the DNA polymerase moves away from the direction helicase is opening the DNA. At the end of a strand of DNA, once the RNA nucleotides are removed from the RNA/DNA helix created by primase there is no double strand available for DNA polymerase to bind. This single helix at the end of the chromosome is cleaved to the last base where is a DNA double helix on the chromosome. Every time a cell replicates, the chromosome is shortened, the extent to which depends on the cell. Telomeres are regions of repetitive sequences of DNA that do not code for proteins. Therefore, as these regions disappear during DNA replication, it does not impact the function of a cell because no information that codes for a protein is lost. After these regions get too small the cell will not divide because it cannot pass cell cycle checkpoints for DNA damage.

How does differential gene expression lead to cell differentiation?

As cells acquire specific gene expression patterns, they make proteins that give them, as a cell, unique functions compared to the stem cell progenitor and other cells with different jobs. Proteins made to function of cell.

DNA is read in this direction by RNA polymerase A. 5' to 3' B. 3' to 5' C. Either direction

B

What role do histones play in gene expression? A. Non, they are involved in tight pack DNA into chromosomes B. They hold information to decondense DNA into an open arrangement when a gene needs to be expressed C. They are transcription factors that bind upstream of genes to regulate their expression

B

Where do transcription factors come from? A. They are part of the structure of the nucleus B. They are transcribed and translated like any protein that functions in the cell C. They are specific regions of DNA near a gene - transcription factors bind to specific regions of a gene - but they themselves are proteins whose recipe comes from DNA.

B

Which of the following best describes the major purpose of the digestive system? A. It delivers nutrients to all parts of the body B. It breaks down and absorbs molecules from food C. It transfers energy by burning the calories found in food D. It produces energy by burning the calories found in food E. It transfers the oxygen, found in food, to all cells of the body

B

Which of the following is an appropriate description of mechanical digestion in the digestive system? A. The reduction of macromolecules into monomers and molecules B. The physical reduction of food into smaller and smaller pieces C. The reduction of food particles by acids in the stomach D. The breakdown of food molecules by bacteria in the gut E. The transfer of energy out of food by physically extracting it

B

Both chemical and mechanical digestion in the first part of the digestive system (mouth to stomach) are trying to achieve greater surface area of food molecules, why is this useful once we get to the duodenum?

By increasing the surface area of food particles and molecules, enzymes that disassemble the molecules (or break them down) have more places to access the molecules. This ensures they are broken down completely and faster.

How do white blood cells get to tissue/cells where they are needed? A. They are endocytosed by epithelial cells of capillaries. B. They undergo active transport by cells of capillaries. C. They are able to squeeze through the gaps between epithelial cells in capillaries.

C

What is the function of tRNA? A. Join amino acids together B. Read DNA C. Bring amino acids to the building polypeptide (protein) D. A and B E. A and C

C

Which blood vessel types is bordered by a single layer of epithelial cells that are specialized for diffusion? A. Arteries B. Arterioles C. Capillaries D. Venules E. Veins

C

This type of cell secretes the proteins that make up the extracellular matrix (ECM) A. Neuron B. Fat Cell C. Fibroblast D. Smooth Muscle Cell

C Remember extracellular matrix (ECM) is extracellular - outside of cell. Fibroblasts express genes that code for these proteins, then exocytose them out of the cell and the ECM proteins arrange themselves into a lattice structure based on which proteins are present.

What are the 2 main ways epithelial cells arrange in epithelial tissue? What is similar about them? How does their different structure lead to differences in their roles in the human body?

Cells in epithelial tissue arrange in single-layers and multi-layers. In both types of arrangements, cells are tightly packed and act as barriers. Single layered - specialized for diffusion of nutrients, gases, toxins, water, ions, etc. Multilayered - specialized for protection and barrier function.

How do cells inherit gene expression patterns separate from the information coded in DNA?

Chromatin patterns - histones & DNA methylation tags - determine if a gene can be accessed by transcription protein machinery in order to be expressed/made into a protein.

What 2 main factors determine which genes are expressed in a cell?

Chromatin structure + Transcription factors

The digestive tract has 4 layers of tissue. The function of the outermost layer is A. A mucous membrane layer that has many folds for expansion B. to provide resources to the inner lining via blood vessels C. to conduct peristaltic contractions to move and pulverize food D. Secrete fluid to keep outer surface slippery E. None of the above

D

The purpose of cell cycle checkpoints is to A. Make sure DNA is not damaged before a cell divides B. Keep cells that may have damage from creating more damaged copies of themselves C. Double check the environment can support more cells D. All of the above You Answered E. A and B only

D

elongation (transcription)

RNA polymerase unwinds DNA, reads DNA, & synthesizes mRNA. mRNA sequence is determined by complementary base pairing between the template DNA strand and corresponding RNA bases.

What is being checked in the cell checkpoints? Why are these checkpoints important?

DNA damage, resource availability and cell size to support more cells, growth cues from other cells, correctly replicated DNA, chromosome spindle attachment so both cells get the same DNA.

S phase

DNA replication

Which of the following determine differential gene expression patterns that lead to cell differentiation? A. Transcription factors B. Chromatin arrangement C. The Phospholipid Bilar D. All of the above E. A and B Only

E

What is the function of nervous tissue?

Rapidly send and receive signals throughout the body. Sense environment, tell muscles to move, integrate information into a response.

The extracellular matrix (ECM) is an important part of multicellular organisms. Describe where it is located, what the function is, and the general arrangement of proteins. Where do these proteins come from?

ECM is located all over the body connecting tissue to other tissue and acting as a scaffold for cells of an organ. The function is to create a scaffold for organs and tissues to organize and facilitate cell signaling and nutrient distribution. Different types of proteins connect in web-like structures. The rigidity/flexibility of these structures depends on the proteins that are part of the web. Fibroblasts are cells of the ECM that excrete proteins that make up ECM tissues.

Draw a hierarchy of cells in terms of their 'potency', indicate which type of cells they can become: Embryonic stem cells, adult stem cells, somatic cells.

Embryonic Stem Cells are Totipotent, could become any time of cell in the human body Adult Stem Cells are Multipotent, could become a small subset of cells in the human body (less than the pluripotent germ cells layer stem cells) Somatic cells are Not potent, they are differentiated cells that have a specific function/cell identity.

True or False: After a gene is transcribed, the mRNA transcript does not need any processing before it is translated.

False

Interphase (Mitosis)

G1, S, G2

Describe the problem with undigested sugars: why are they not absorbed by the small intestine? Why can they cause diarrhea as they pass through the large intestine?

If sugars are not digested down to their monomer form, then they cannot be absorbed by the small intestine and moved into the blood. Once they reach the large intestine, the presence of sugar causes water to move INTO the large intestine which results in diarrhea. Water moves into the intestine because of osmosis Think back to the question you had on exam 1.

Enzyme - conservative mutation in active site

If there is a conservative mutation in the active site of an enzyme, folding (thus shape) could be only slightly different than what the protein should normally look like. Still, the substrate that fits in that enzyme will probably not fit as well, causing the enzyme to catalyze less of the biochemical reaction than it should.

white blood cells (leukocytes)

Immune system cells. Rides around in the blood/blood vessels surveilling all the cells in the body to see if any need repairing or help with defense against pathogens (bad bacteria and viruses).

Why does it make sense that DNA is replicated in a semi-conservative manner?

It would take too many resources to split the 'old' template strand and new strand that was made using that strand as a template (because of breaking the hydrogen bonds). It would also take a lot of carefully monitored mechanisms to re-attach the two 'old' strands back together and attach the two 'new' strands to each other after they were made.

The pancreas releases both digestive enzymes and hormones. Describe what these different types of molecules do.

Lipase - breaks down fats into small fatty acids and glycerol Amylase - breaks down carbohydrates into sugar monomers Protease - breaks down proteins into amino acid monomers Insulin - triggers the liver to store glucose in the blood in large carbohydrate molecules called glycogen Glucagon - triggers the liver to release glucose from glycogen into the blood

After a cell divides, where did the parent cell go? Would you say that it died?

No it does not die. The original parent cells makes a copy of itself and after copying itself is still a cell that functions in the body.

Channel protein for sucrose - non-conservative mutation in hydrophobic region

Non-conservative mutation in a channel protein in the hydrophobic region of a protein will change the way that it folds, creating new bonds between the new amino acid and other hydrophilic amino acids in the protein. This will impact if it can embed in the membrane or impact the channel part of the protein. This will cause sucrose to not be transport through the channel protein.

What are 3 reasons for cell death?

Physical damage, viral infections, radiation, DNA damage, senescence. Getting rid of these cells prevents further DNA damage that could lead to mutations that promote cancer and reduced function of an organ or tissue.

What is translation?

RNA (ribosome) and tRNA build a protein by reading the genetic code of the mRNA strand in the cytoplasm. Codons in the mRNA represent amino acids.

How does chemical digestion and absorption of fats differ from carbohydrates and proteins? Why is it different in terms of the chemical properties of the molecules?

Since fats are hydrophobic, they do not mix with the aqueous liquid in our digestive system well. They first must be emulsified or broken down by bile salts in bile that is make in the liver and stored in the gall bladder. Bile salts are both hydrophobic and hydrophilic, so they are able to break down fats and mix with aqueous digestive juice. This makes them small enough for lipase to then start to disassemble them into smaller molecules. Once broken down into smaller pieces, they are moved across the intestinal epithelia first by diffusion across the membrane, they by exocytosis into lymphatic capillaries. Amino acids and sugars are broken down by enzymes into their monomer form. They move across the intestinal epithelia into the blood first by active transport, then by facilitated and simple diffusion.

Why do you think older animals die of cancer at higher rates than younger animals?

Since they have been around longer, they have been exposed to more mutagens, and their cells have had time to acquire more DNA mutations. The more DNA mutations in a cell, the higher likelihood those mutations can activate genes that enable cells to grow and divide without regard the organism that it resides in.

Since DNA polymerase can only move in one direction, _______________________ at the end of our chromosomes protect protein coding regions of DNA as chromosomes are shortened progessively during each round of cell division because of the way the lagging strand must be copied. Okazaki Fragments Telomere Regions RNA primase Replication Fork

Telomere Regions

elongation (translation)

The E, P, and A sites on the ribosome guide the tRNAs as they read the mRNA. There are 3 mRNA base pairs in each of the 3 sites representing 1 codon in each site. The rRNA catalyzes the bonds between amino acids before the tRNAs leave through the E site.

punctuated code

The same start codon AUG is at the beginning of EVERY transcript in EVERY live organism. Similarly, 3 stop codons are at the end of EVERY transcript in EVERY live organism.

How are mesoderm cells distinct from the endoderm and ectoderm.

They can migrate - are not tied to another cell in a sheet. They 'fill in' the gap left between the endoderm and ectoderm as the embryo starts to take shape and make the tube within the tube.

termination (translation)

When a stop codon is reached. No tRNA comes to bind to it, and the rRNA disassemble and releases the protein.

What are the reasons to have an RNA intermediate?

To keep the DNA protected in the nucleus. So you can make many transcripts of 1 gene to amply expression RNA is transient (it degrades), so you can change which genes are made into proteins

Which of the following molecules discussed in class can dictate what proteins are made in a cell by binding DNA and regulating transcription? ATP Carbohydrates Phospholipids Transcription factors Lysosomes

Transcription factors

What is transcription?

Transcription is the process by which a gene region of DNA is read 3' to 5' by RNA polymerase II while it synthesizes an mRNA transcript 5' to 3'.

True or False. A muscle cell and an immune cell contain the same DNA.

True

True or False. Transcription factors are a critical part of regulating differential gene expression.

True

True or False: Chromatic structure (DNA + Histone = nucleosome) is also replicated during DNA replication

True

What does voluntary vs involuntary mean? Which types of muscle cells are voluntary, which are involuntary?

Voluntary are muscles you move by thinking about it - Skeletal Involuntary are muscles that move without thought, and that cannot be controlled directly by thought - smooth and cardiac

How does the nervous system and other hormones (not secreted by pancreas) coordinate the release of digestive juices/enzymes and movement of food through the digestive system?

When protein is detected in the stomach, and stretch receptors are triggered by the stomach filling with food gastrin is released to trigger the release of gastric juices (pepsin, HCl, bicarbonate, mucus) When stomach acid is sensed in the duodenum (small intestine) secretin is released and stimulates pancreas to release bicarbonate (neutralizes acid (Tums)). When fat and protein is sensed in the duodenum (small intestine) Cholecystokinin is released which triggers the gall bladder to release bile and the pancreas to release digestive enzymes.

Embryonic Stem Cells

can divide and become any type of cell

Activate a transcription factor to change gene expression. Polar Molecule

binds to carrier protein on cell membrane to enter the cell, binds to transcription factor in the cytoplasm, enter the nucleus

red blood cells (erythrocytes)

carry oxygen and carbon dioxide with the help of hemoglobin proteins. Markers on cells surface determine blood type. Do not have nucleus after maturation to make more room for more hemoglobin proteins increasing gas-carrying capacity.

Platelets (thrombocytes)

cell fragments. Help with clotting if there is a rupture of a blood vessel. Bind fibrin/fibrinogen to create mesh network around wound.

M phase

cell, along with DNA, splits into identical daughter cells

triplet code

codons are in sets of 3 RNA base pairs.

DNA ligase

connects okazaki fragments

DNA polymerase II

creates new strand of DNA using existing strand as template

unambiguous code

each codon is always translated into 1 amino acid

True or False. A muscle cell and an immune cell express the same set of genes.

false

True or False. In adult humans, most cells continue to divide throughout their lifetime

false

true or false: The cells in your body contain different DNA in the nucleus depending on the type of cell

false As we learned from mitosis - when cells divide to create the human body, the resulting daughter cells have the same genomic information. Therefore, even if cells in your body look different and act different, they have the same DNA in the nucleus.

true or false: A majority of cells in your body are constantly dividing during the span of their cell lives

false In an adult human, most of the cells in your body exit the cell cycle at G0 and just exist - these are somatic cells that are differentiated and do a specific function in the body/tissue. The cells in your body that are constantly dividing as an adult are stem cells. Your adult stem cells replace old or damaged cells in most tissue. There are specific adult stem cells that replenish cells in specific tissue, because adult stem cells are multipotent, thus able to become a smaller set of stem cells that embryonic or germ layer stem cells.

true or false: The cells in your body express all the same proteins

false Although all cells have the same DNA, they express different genes and make different proteins (differential gene expression). There are some 'housekeeping' genes or proteins that they make in common, but by no means do they express all the same proteins.

Plasma

fluid all the blood cells move around in. Mainly water. Holds proteins, salts/ions, O2/CO2, glucose, amino acids, wastes, and hormones. Take these components to where they are needed for cell growth, signaling, and waste removal.

Which type of DNA mutations tend to cause the most drastic changes in the structure, therefore function, of a protein? CHOOSE ALL THAT APPLY. Frameshift Mutation Silent Conservative Nonconservative Nonsense

frameshift Nonconservative Nonsense

G1 phase

growth and normal metabolic processes

G2 phase

growth and preparation for mitosis

the 3 types of RNAs we talked about today, and what are their roles in the central dogma

mRNA - a copy of a DNA protein coding region that is used to make proteins by tRNA and rRNA tRNA - reads mRNA by matching anticodon region in tRNA to codons of mRNA. tRNAs are 'charged' with amino acids, and drop off the corresponding amino acid according to the codon in the mRNA transcript. rRNA - ribosome - facilitates the reading and binding of tRNA to mRNA. Catalyzes the bond between the protein being made and the amino acids brought over by the tRNA.

non-overlapping code

mRNA bases are read only once in sets of 3. So, 9 mRNA bases consist of 3 codons and code for 3 amino acids.

degenerate code

multiple different codons can be translated to the same amino acid.

initiation (translation)

tRNA binds to the start codon (AUG) on the mRNA and this triggers the assembly of the rRNA on the mRNA transcript.

termination (translation)

termination sequence in DNA causes RNA polymerase to detach from DNA, mRNA then detaches from RNA polymerase.

universal code

the same codons translate to the same amino acids in EVERY live organism

During [ Select ] , a(n) [ Select ] is made using nitrogenous bases in a strand of DNA as a template. This process is carried out by [ Select ]. (x2)

transcription, mRNA, RNA polymerase translation, protein, ribosomes and tRNA

True or False. A single nucleotide change in DNA can have drastic effects on protein function.

true

True or False: One function of the mRNA intermediate in the central dogma is to amplify the amount of a gene that is expressed

true

True or False: mRNA from any live cell can be translated by any other live cell regardless of the branch of life

true

True or false: There is a tRNA for each codon

true

Transcript factors give cells the ability to change gene expression patterns based on which of the following? CHOOSE ALL THAT APPLY. Type of cell or tissue cell is part of Age of human Time of day Response to stress

type of cell or tissue cell is part of Age of human Time of day Response to stress

helicase

unwinds DNA

What is absorbed in the large intestine?

water and ions (salts)