Biology final part 1

Question 1

Exocytosis (active)

Answer 1

Substances produced inside the cell are processed and packaged in vesicles, which will fuse with the cell membrane and release their contents to the extracellular space (requires ATP)

Examples of exocytosis: insulin (hormone) secreted from pancreatic cells; neurotransmitters secreted from neurons into synapse

Question 2

Endocytosis (active)

Answer 2

The fluidity of the membrane allows it to change shape so parts of it can be “pinched off” to form vesicles around larger molecules/ fluids/ structures to move them into the cell
When a vesicle enters a cell, the ends of the membrane that are left reattach due to the presence of water and the properties of the phospholipids

Question 3

Active Transport:

Answer 3

Active (against concentration gradient, ATP is required):
Substances move from areas of low concentration to areas of high concentration through protein pumps

Examples: glucose reabsorption in kidney, glucose absorption in small intestine (ileum)

Question 4

Simple Diffusion (passive)

Answer 4

Substances move from areas of high concentration/ high osmolarity (hypertonic solution) to areas of low concentration (hypotonic solution) to balance them out = move toward equilibrium – DOWN a concentration gradient

Question 5

Facilitated Diffusion

Answer 5

Diffusion of large molecules/ ions through highly specific protein carriers/ channels (proteins change shape to “facilitate” this – rate of transport levels off with saturation of proteins)

Question 6

Osmosis (passive)

Answer 6

Osmosis (H2Osmosis!): Diffusion of water across membrane (through special protein channels called aquaporins); often to balance out solute concentrations (water moves from areas of low (hypotonic) solute concentration (high water) to areas of high (hypertonic) solute concentration (low water) to balance the solutes out)

Question 7

Passive transport mechanisms
Include examples of each and be able to describe concentration gradients (hypertonic, isotonic, hypotonic).

Answer 7

Passive (along concentration gradient, no ATP expenditure):

concentration gradients:
Hypertonic: High solute concentration (gains water)
* Hypotonic: Low solute concentration (loses water) * Isotonic:Samesoluteconcentration(nonetflow)

Question 8

What occurs during interphase of the cell cycle?

Answer 8

• DNA is uncondensed (chromatin)
• DNA is replicated (S phase) to form
  genetically identical sister chromatids
• Cell grows in size and organelles are
  duplicated (G1 and G2)

Question 9

What occurs during metaphase of the cell cycle?

Answer 9

• Centrosomespindlefibresattachto the centromere of each chromosome
• Spindle fibres contract and move the chromosomes towards the cell centre
• Chromosomes form a line along the equator (middle) of the cell

Question 10

What occurs during anaphase of the cell cycle?

Answer 10

• Spindlefibrescontinuetocontract
• Sister chromatids separate and move
  to opposite sides of the cell
• Sister chromatids are now regarded as two separate chromosomes

Question 11

What occurs during cytokinesis of the cell cycle?

Answer 11

• Cytoplasmic division occurs to divide
  the cell into two daughter cells
• Each daughter cell contains one copy of each identical sister chromatid
• Daughter cells are genetically identical

Question 12

What occurs during prophase of the cell cycle?

Answer 12

During prophase the centrosome divides into two centrosomes
Each of the two centrosomes move to opposite ends of the cell as they make microtubules (the mitotic spindle), which will grow out of them
Chromatin (DNA and protein in the nucleus) condenses, forming visible chromosomes (made up of sister chromatids connected together at the centromere, as they have already been duplicated)
The nucleolus disappears and the nuclear membrane breaks down/ disappears

Question 13

Be able to outline the stages of the cell cycle (in order) and be able to describe what happens in each.

Answer 13

The cell cycle (whether being used for asexual reproduction or somatic (body) cell production) consists of two phases:
Interphase
Cells spend MOST of their “lives” in this phase
Growth, protein production, ATP production, and copying of chromosomes – DNA replication – in preparation for division
Mitotic (M) Phase (mitosis and cytokinesis)
Mitosis = division of the nucleus
Cytokinesis = division of the cytoplasm

Question 14

Describe controls of the cell cycle

Answer 14

A cell cycle contains numerous checkpoints that ensure the fidelity and viability of continued cell divisions
G1 checkpoint
* Monitors potential growth conditions (nutrients, etc.)
* Assesses level of DNA damage (from UV, etc.)
G2 checkpoint
* Monitors state of pre-mitotic cell (suitable size, etc.)
* Identifies and repairs any DNA replication errors
Metaphase checkpoint
* Ensures proper alignment (prevents aneuploidy)

How cyclins control cell cycle:
Cyclins (protein) bind to cyclin-dependent protein kinases (CDK’s) to activate them
CDK’s are enzymes (end in “-ase”) that control chemical reactions that allow a cell to move into the next phase
Cyclin/ CDK complexes bind to target proteins and activate them via phosphorylation to cause an “event” that moves the cell into the next phase of the cell cycle
Cyclins are degraded after “event” and CDK’s become inactive again
Different cyclins are produced at different times and bind to specific CDK’s to ensure cell cycle occurs in proper sequence/ at normal rate – cyclins are ONLY in high amounts when their target protein is needed for function/ progression in cell cycle (they are highly regulated)
Some cells “pause” after G1 and do NOT enter S-phase and enter G0 (non-growing/ amitotic) instead.
Damaged cells/ DNA
Muscle cells, nerve cells

Question 15

Know what a nucleosome is (and its structure) and understand that nucleosomes are the fundamental unit of DNA packaging in eukaryotic cells (also important in gene expression/ transcription regulation)

Answer 15

DNA (deoxyribonucleic acid) is a type of organic molecule called a nucleic acid
Nucleic acids are made up of subunits (monomers) called nucleotides

Each nucleotide is made up of three parts:
1. A phosphate group covalently (phosphodiester bond) bonded to
2. A sugar (pentose) molecule covalently bonded to
3. A nitrogenous (nitrogen-containing) base

Nucleotides are linked together to form macromolecules (polymers) called nucleic acids. The nucleic acids in living systems are:
1. DNA (Deoxyribonucleic Acid) – genetic information
2. RNA (Ribonucleic Acid) – genetic information
3. ATP (Adenosine Triphosphate) – energy

The first structure involved in DNA packaging/ coiling is the nucleosome
In a nucleosome:
8 histone proteins (+ charged) make a core
A DNA strand (- charged) wraps around the core twice
A 9th histone protein (H1) attaches to hold the
DNA in place around the core

Many nucleosomes form along a single molecule of DNA, and resemble “beads on a string”
Single “strings” of DNA between nucleosomes are called “linker DNA” (because they “link” one nucleosome to the next)

Question 16

Know and describe the central dogma of molecular biology (all the steps- from DNA all the way to protein)

Answer 16

Transcription – making mRNA (messenger RNA) from DNA
Translation – making a polypeptide chain – a protein - (putting amino acids together) from mRNA
Amino acids are put together using the genetic code – universal to ALL life (uses mRNA bases in sets of 3, called codons)!

Question 17

Know the steps of transcription (including the direction and difference between the sense/ antisense DNA strands)

Answer 17

Transcription (making mRNA from DNA) happens in a 5’ to 3’ direction, and it happens in three stages:
1. Initiation
2. Elongation
3. Termination

Transcription is the process of synthesizing mRNA identical to the coding (sense) strand of DNA (except uracil will be present instead of thymine)
The antisense strand acts as the template strand
DNA will be unzipped, RNA nucleotides will be added → creating an mRNA strand
mRNA will be processed before moving to the ribosome for translation

Initiation:
RNA Polymerase binds to a gene in DNA at a region/ sequence called the promoter (“start here”)

Enlogation:
RNA Polymerase unwinds the DNA double helix (breaking hydrogen bonds between bases)
This exposes DNA bases for pairing with RNA nucleotides
RNA Polymerase reads the DNA sequence of the gene (on the antisense/ template strand)
Uses it to add free RNA nucleotides together (5’ to 3’) to make a molecule of mRNA (complementary to the antisense/template strand of DNA; adenine and uracil, cytosine and guanine)
Hydrogen bonds form between A&U and C&G
Note: Free RNA nucleotides exist as nucleoside triphosphates (2 extra phosphate groups to provide energy for bonding), and they temporarily base pair to DNA during transcription.

Termination:
RNA polymerase continues until it reads a terminator sequence
mRNA molecule detaches from DNA (and DNA winds back together)
RNA polymerase detaches from DNA
This happens right at the terminator sequence in prokaryotes, but in eukaryotes the RNA polymerase continues for 10-35 bases beyond the terminator before it stops and detaches
Note: Many RNA polymerases can follow each other to transcribe the same gene multiple times in a row
This will make many copies of the same mRNA molecule, which allows the cell to make large amounts of the same protein (when needed)

Question 18

Explain RNA processing in eukaryotic cells (including one gene = many polypeptides)

Answer 18

one gene = many polypeptides
mRNA molecules made during transcription in eukaryotic cells are called “pre-mRNA” because they must be modified (by enzymes) before they can exit the nucleus and be used by ribosomes to make a protein
1. A 5’ cap (of modified guanine) is added
Protects mRNA from hydrolytic enzymes in the cytoplasm (that want to break it down)
Functions as an “attach here” signal for ribosomes (for translation)
2. A poly-A tail is added (to the 3’ end)
Protects mRNA from hydrolytic enzymes in cytoplasm
Facilitates export of mRNA from the nucleus and ribosome attachment

Question 19

Explain the epigenetic control of gene expression

Answer 19

Gene expression in a cell is affected by an organism’s epigenome:
Epi = above, genome = entire collection of DNA sequences (“above the genome”)
Epigenome = a collection of all the factors that modify/ impact the activity/ expression of genes without altering DNA sequences
Nucleosomes
More nucleosomes = DNA packaged more tightly together/ genes less accessible to RNA polymerase (less transcription/ less mRNA/ less protein from those genes, if any at all)
Methylation
Methyl groups (CH3) bind to DNA, causing it to wrap more tightly around histones
More methylation = less transcription/ less protein from those genes (if any)
Highly methylated genes are usually not expressed at all, and methylation of DNA is maintained through cell division and even from parent to offspring!
Proteins/ Hormones
Transcription factors – aid in RNA polymerase binding to DNA
Transcription activators/ transcription repressors
Hormones – turn certain genes on or off at different times/ stages of development
The Environment
Can change methylation patterns and/ or affect proteins involved in regulating gene expression/ mRNA splicing (wrong genes on or off, incorrectly spliced mRNA etc.)
Chemicals (cigarette smoke, preservatives, pollutants, topical medications/ creams etc.)
Infectious agents (bacteria, viruses, prions)

Question 20

Know the steps of translation (including the direction)

Answer 20

Following transcription (DNA → mRNA), translation (the second stage of protein synthesis) occurs (mRNA → Protein)
During translation, blocks of three nucleotides called codons/ triplets (mRNA), are decoded (by ribosomes and tRNA molecules) into a sequence of amino acids that are attached together by peptide bonds (primary structure of a protein).

Initiation (aka “making the sandwich”):
Small subunit of ribosome binds to mRNA at start codon (AUG) at 5’ end of mRNA molecule
tRNA (with complementary anticodon UAC) binds to mRNA at start codon AUG (complementary base pairing - temporary)
tRNA carrying amino acid MET
Large subunit binds (with 1st tRNA in P site)
Requires energy of GTP (guanosine triphosphate- like ATP)

Enlogation:
2nd tRNA comes into A site (complementary base pairing with mRNA codon)
Ribosome facilitates formation of peptide bond between amino acids of two tRNA molecules (one in P site and one in A site – once peptide bond forms, polypeptide chain transferred to tRNA in A site)
1st tRNA moves (translocates) into E (exit) site and detaches/ leaves ribosome (goes back to cytoplasm to get another amino acid)
2nd tRNA moves (translocates) into P (polypeptide) site
Ribosome moves along mRNA in 5’ to 3’ direction (one codon at a time)
3rd tRNA comes into A site
Peptide bond forms between amino acids of two tRNA molecules (one in P site and one in A site)
The three steps of elongation (A-P-E) continue, codon by codon, to add amino acids together until the polypeptide chain is completed.

Termination:
Stop codon (on mRNA) reached (A site)
“Release factor” binds to stop codon on mRNA
“Release factor” hydrolyzes bond between polypeptide chain and tRNA in P site
Polypeptide released from tRNA in P site
Ribosome disassembles

Question 21

Describe the genetic code (and be able to use it to determine amino acid sequences)

Answer 21

Translation occurs following the genetic code
mRNA molecules contain codons (series of 3 – triplet – bases)
Each codon specifies ONE amino acid (61 of 64)
Start codon (AUG) specifies amino amid: MET
Stop codons (3 of them -do not code for amino acids – end translation)

Question 22

Describe the structure of ribosomes

Answer 22

Made of protein and rRNA (ribosomal RNA) → most abundant type of RNA in cells (made in the nucleolus in eukaryotes)
Has a tertiary structure and globular shape
Two subunits
Small subunit (has mRNA binding site)
Large subunit (has tRNA binding sites (A site, P site, E site)
Small and large subunits only join together during translation
Two tRNA molecules can bind at the same time
Form polysomes (many ribosomes translating same mRNA at the same time)- to make lots of one type of protein
Ribosomes are 70S in prokaryotes and 80s in eukaryotes

Question 23

Describe the structure of tRNA, its role in translation, and how it becomes “activated”

Answer 23

Structure and function:
tRNA facilitates translation
tRNA molecules are transcribed from DNA template in nucleus
20 different tRNA molecules (one for each amino acid)
All contain anticodons (3 bases – complementary to codons on mRNA – will base pair/ hydrogen bond to mRNA during translation)
Each made up of one chain of RNA nucleotides (single-stranded) that loops/ folds/ hydrogen bonds to itself to form a 3D clover leaf shape
Each tRNA binds with its amino acid at the 3’ end of the molecule (at the sequence CCA)

Role in translation:
Enzymes join each tRNA molecule to the correct amino acid (aminoacyl-tRNA synthetases/ tRNA activating enzymes)
20 different synthetases (20 different amino acids)
Each has active sites for only a specific tRNA and amino acid combination.
The synthetase catalyzes a covalent bond between tRNA and amino acid (utilizing ATP to do so).

Activation:Once tRNA molecules reach the cytoplasm, each tRNA is used repeatedly to:
1. Pick up its specific amino acid (which binds to the 3’ end of the molecule at a sequence of bases – CCA). Once attached to its amino acid, the tRNA is “activated”
2. Bring/ deposit the amino acid at the ribosome
3. Return to the cytoplasm to pick up another copy of its amino acid

Question 24

Compare protein synthesis in prokaryotes and eukaryotes

Answer 24

RNA polymerases are different
Eukaryotic cells require transcription factors
Transcription is terminated differently.
Their ribosomes are different (70S/ 80S).
Their chromosomes are different
Prokaryotes can transcribe and translate the same gene simultaneously.
Nucleus separates transcription from translation in eukaryotes
Extensive RNA processing occurs after transcription and before translation in eukaryotic cells

Question 25

Be able to explain the significance of complementary base pairing

Answer 25

To prevent mutations